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Sample records for 1-4-alkyloxybenzyl-3-methyl-1h-imidazol-3-ium organic backbone

  1. Side-Chain-Induced Rigid Backbone Organization of Polymer Semiconductors through Semifluoroalkyl Side Chains.

    Science.gov (United States)

    Kang, Boseok; Kim, Ran; Lee, Seon Baek; Kwon, Soon-Ki; Kim, Yun-Hi; Cho, Kilwon

    2016-03-23

    While high-mobility p-type conjugated polymers have been widely reported, high-mobility n-type conjugated polymers are still rare. In the present work, we designed semifluorinated alkyl side chains and introduced them into naphthalene diimide-based polymers (PNDIF-T2 and PNDIF-TVT). We found that the strong self-organization of these side chains induced a high degree of order in the attached polymer backbones by forming a superstructure composed of "backbone crystals" and "side-chain crystals". This phenomenon was shown to greatly enhance the ordering along the backbone direction, and the resulting polymers thus exhibited unipolar n-channel transport in field-effect transistors with remarkably high electron mobility values of up to 6.50 cm(2) V(-1) s(-1) and with a high on-off current ratio of 10(5).

  2. Impact of Backbone Fluorination on π-Conjugated Polymers in Organic Photovoltaic Devices: A Review

    Directory of Open Access Journals (Sweden)

    Nicolas Leclerc

    2016-01-01

    Full Text Available Solution-processed bulk heterojunction solar cells have experienced a remarkable acceleration in performances in the last two decades, reaching power conversion efficiencies above 10%. This impressive progress is the outcome of a simultaneous development of more advanced device architectures and of optimized semiconducting polymers. Several chemical approaches have been developed to fine-tune the optoelectronics and structural polymer parameters required to reach high efficiencies. Fluorination of the conjugated polymer backbone has appeared recently to be an especially promising approach for the development of efficient semiconducting polymers. As a matter of fact, most currently best-performing semiconducting polymers are using fluorine atoms in their conjugated backbone. In this review, we attempt to give an up-to-date overview of the latest results achieved on fluorinated polymers for solar cells and to highlight general polymer properties’ evolution trends related to the fluorination of their conjugated backbone.

  3. The Construction of Metal-Organic Framework with Active Backbones by the Utilization of Reticular Chemistry

    Science.gov (United States)

    Choi, Eunwoo

    With the principles of reticular chemistry, metal-organic frameworks with ultra-high porosity, chiral-recognition unit as a chiral stationary phase, metalloporhyrins for enhanced hydrogen adsorption and an intrinsic conductivity to form porous conductors, have been prepared. This dissertation presents how the principles of reticular chemistry were utilized to achieve in the preparations of metal-organic frameworks with a large surface area and active backbones. Through the simple isoreticular (having the same framework topology) expansion from MOF-177 composed with 1,3,5-tris(4'-carboxyphenyl-)benzene (BTB3-) as the strut; MOF-200 was prepared with 4,4',4"-(benzene-1,3,5-triyl-tris(benzene-4,1-diy1))tribenzoic acid an extension from BTB3- by a phenylene unit to yield one of the most porous MOFs with a Langmuir surface area of 10,400 m2. and the lowest density of 0.22 cm3.g-1. A successful thermal polymerization reaction at 325 °C inside of the pores of highly porous MOF, MOF-177, was performed and verified the integrity of the MOF structure even after the thermal reaction. 1,4-Diphenylbutadiyne that is known to polymerize upon heating to form a conjugated backbone was impregnated via solution-diffusion into MOF-177 and then subsequently polymerized by heat to form polymer impregnated MOF-177. Characterization was carried out using powder X-ray diffraction and volumetric sorption analyzer. MOF-1020 with a linear quaterphenyl dicarboxylate-based strut was designed to contain a chiral bisbinaphthyl crown-ether moiety for alkyl ammonium resolution was precisely placed into a Zn4O(CO2)6-based cubic MOF structure. Unfortunately, the chiral resolution was not achieved due to the sensitivity and the pore environment of MOF-1020. However, an interesting phenomenon was observed, where the loss of crystallinity occurs upon solvent removal while the crystallites remain shiny and crystalline, but it readily is restored upon re-solvation of the crystallites. This rare

  4. Testing Backbone.js

    CERN Document Server

    Roemer, Ryan

    2013-01-01

    This book is packed with the step by step tutorial and instructions in recipe format helping you setup test infrastructure and gradually advance your skills to plan, develop, and test your backbone applications.If you are a JavaScript developer looking for recipes to create and implement test support for your backbone application, then this book is ideal for you.

  5. Gas transport in metal organic framework–polyetherimide mixed matrix membranes: The role of the polyetherimide backbone structure

    NARCIS (Netherlands)

    Hegde, Maruti; Shahid, Salman; Norder, Ben; Dingemans, Theo J.; Nijmeijer, Kitty

    2015-01-01

    We report on how the morphology of the polymer matrix, i.e. amorphous vs. semi-crystalline, affects the gas transport properties in a series of mixed matrix membranes (MMMs) using Cu3(BTC)2 as the metal organic framework (MOF) filler. The aim of our work is to demonstrate how incorporation of Cu3(BT

  6. Constructing backbone network by using tinker algorithm

    Science.gov (United States)

    He, Zhiwei; Zhan, Meng; Wang, Jianxiong; Yao, Chenggui

    2017-01-01

    Revealing how a biological network is organized to realize its function is one of the main topics in systems biology. The functional backbone network, defined as the primary structure of the biological network, is of great importance in maintaining the main function of the biological network. We propose a new algorithm, the tinker algorithm, to determine this core structure and apply it in the cell-cycle system. With this algorithm, the backbone network of the cell-cycle network can be determined accurately and efficiently in various models such as the Boolean model, stochastic model, and ordinary differential equation model. Results show that our algorithm is more efficient than that used in the previous research. We hope this method can be put into practical use in relevant future studies.

  7. Backbone topology, access, and the commercial Internet, 1997 - 2000

    OpenAIRE

    Morton E O'Kelly; Grubesic, Tony H.

    2002-01-01

    As the Internet grows in popularity, telecommunications infrastructure in the United States continues to increase in capacity and geographic reach to meet market demand. Important components of this infrastructure include the commercial fiber-optic backbones used to transport digital information between locations. The spatial organization of commercial Internet backbones reflects an increasingly competitive privatized market for service provision, in which certain locations are more accessibl...

  8. Future High Capacity Backbone Networks

    DEFF Research Database (Denmark)

    Wang, Jiayuan

    This thesis - Future High Capacity Backbone Networks - deals with the energy efficiency problems associated with the development of future optical networks. In the first half of the thesis, novel approaches for using multiple/single alternative energy sources for improving energy efficiency...... the context of the integrated control plane structure. Results show improvements of energy efficiency over three types of traffic, while still keeping acceptable QoS levels for high priority traffic....

  9. Exercise: The Backbone of Spine Treatment

    Medline Plus

    Full Text Available Exercise: The Backbone of Spine Treatment | View Video Back About Video Struggling with Low Back Pain? Many people are surprised to learn that carefully selected exercise can actually reduce back pain. Some exercises can ...

  10. Green Network Planning Model for Optical Backbones

    DEFF Research Database (Denmark)

    Gutierrez Lopez, Jose Manuel; Riaz, M. Tahir; Jensen, Michael

    2010-01-01

    Communication networks are becoming more essential for our daily lives and critically important for industry and governments. The intense growth in the backbone traffic implies an increment of the power demands of the transmission systems. This power usage might have a significant negative effect...... on the environment in general. In network planning there are existing planning models focused on QoS provisioning, investment minimization or combinations of both and other parameters. But there is a lack of a model for designing green optical backbones. This paper presents novel ideas to be able to define...

  11. Microsoft Operations Framework implementation for The Backbone

    NARCIS (Netherlands)

    Kienhuis, G.H.

    2007-01-01

    Doel The Backbone ontwerpt, implementeert en beheert IT infrastructuren voor bedrijven en instellingen. Beheer wordt proactief uitgevoerd met behulp van Microsoft Operation Manager (MOM) 2005. MOM is een applicatie die de status en gebeurtenissen van systemen zichtbaar maakt vanuit één locatie. Om

  12. Orientation-dependent backbone-only residue pair scoring functions for fixed backbone protein design

    Directory of Open Access Journals (Sweden)

    Bordner Andrew J

    2010-04-01

    Full Text Available Abstract Background Empirical scoring functions have proven useful in protein structure modeling. Most such scoring functions depend on protein side chain conformations. However, backbone-only scoring functions do not require computationally intensive structure optimization and so are well suited to protein design, which requires fast score evaluation. Furthermore, scoring functions that account for the distinctive relative position and orientation preferences of residue pairs are expected to be more accurate than those that depend only on the separation distance. Results Residue pair scoring functions for fixed backbone protein design were derived using only backbone geometry. Unlike previous studies that used spherical harmonics to fit 2D angular distributions, Gaussian Mixture Models were used to fit the full 3D (position only and 6D (position and orientation distributions of residue pairs. The performance of the 1D (residue separation only, 3D, and 6D scoring functions were compared by their ability to identify correct threading solutions for a non-redundant benchmark set of protein backbone structures. The threading accuracy was found to steadily increase with increasing dimension, with the 6D scoring function achieving the highest accuracy. Furthermore, the 3D and 6D scoring functions were shown to outperform side chain-dependent empirical potentials from three other studies. Next, two computational methods that take advantage of the speed and pairwise form of these new backbone-only scoring functions were investigated. The first is a procedure that exploits available sequence data by averaging scores over threading solutions for homologs. This was evaluated by applying it to the challenging problem of identifying interacting transmembrane alpha-helices and found to further improve prediction accuracy. The second is a protein design method for determining the optimal sequence for a backbone structure by applying Belief Propagation

  13. Porous solid backbone impregnation for electrochemical energy conversion systems

    KAUST Repository

    Boulfrad, Samir

    2013-09-19

    An apparatus and method for impregnating a porous solid backbone. The apparatus may include a platform for holding a porous solid backbone, an ink jet nozzle configured to dispense a liquid solution onto the porous solid backbone, a positioning mechanism configured to position the ink jet nozzle proximate to a plurality of locations of the porous solid backbone, and a control unit configured to control the positioning mechanism to position the ink jet nozzle proximate to the plurality of locations and cause the ink jet nozzle to dispense the liquid solution onto the porous solid backbone.

  14. Process-based network decomposition reveals backbone motif structure.

    Science.gov (United States)

    Wang, Guanyu; Du, Chenghang; Chen, Hao; Simha, Rahul; Rong, Yongwu; Xiao, Yi; Zeng, Chen

    2010-06-08

    A central challenge in systems biology today is to understand the network of interactions among biomolecules and, especially, the organizing principles underlying such networks. Recent analysis of known networks has identified small motifs that occur ubiquitously, suggesting that larger networks might be constructed in the manner of electronic circuits by assembling groups of these smaller modules. Using a unique process-based approach to analyzing such networks, we show for two cell-cycle networks that each of these networks contains a giant backbone motif spanning all the network nodes that provides the main functional response. The backbone is in fact the smallest network capable of providing the desired functionality. Furthermore, the remaining edges in the network form smaller motifs whose role is to confer stability properties rather than provide function. The process-based approach used in the above analysis has additional benefits: It is scalable, analytic (resulting in a single analyzable expression that describes the behavior), and computationally efficient (all possible minimal networks for a biological process can be identified and enumerated).

  15. Peptoid-Peptide hybrid backbone architectures

    DEFF Research Database (Denmark)

    Olsen, Christian Adam

    2010-01-01

    -amino acids (alpha/beta-peptides) have been investigated in some detail as well. The present Minireview is a survey of the literature concerning hybrid structures of alpha-amino acids and peptoids, including beta-peptoids (N-alkyl-beta-alanine oligomers), and is intended to give an overview of this area......Peptidomimetic oligomers and foldamers have received considerable attention for over a decade, with beta-peptides and the so-called peptoids (N-alkylglycine oligomers) representing prominent examples of such architectures. Lately, hybrid or mixed backbones consisting of both alpha- and beta...

  16. Instant Backbone.js application development

    CERN Document Server

    Hunter, Thomas

    2013-01-01

    Get to grips with a new technology, understand what it is and what it can do for you, and then get to work with the most important features and tasks. This book is a practical, step-by-step tutorial that will teach you to build Backbone.js applications quickly and efficiently.This book is targeted towards developers. It is assumed that you have at least a basic understanding of JavaScript and jQuery selectors. If you are interested in building dynamic Single Page Applications that interact heavily with a backend server, then this is the book for you.

  17. Extracting the information backbone in online system

    CERN Document Server

    Zhang, Qian-Ming; Shang, Ming-Sheng

    2013-01-01

    Information overload is a serious problem in modern society and many solutions such as recommender system have been proposed to filter out irrelevant information. In the literature, researchers mainly dedicated to improve the recommendation performance (accuracy and diversity) of the algorithms while overlooked the influence of topology of the online user-object bipartite networks. In this paper, we find that some information provided by the bipartite networks is not only redundant but also misleading. With such "less can be more" feature, we design some algorithms to improve the recommendation performance by eliminating some links from the original networks. Moreover, we propose a hybrid method combining the time-aware and topology-aware link removal algorithms to extract the backbone which contains the essential information for the recommender systems. From the practical point of view, our method can improve the performance and reduce the computational time of the recommendation system, thus improve both of...

  18. Sofosbuvir as backbone of interferon free treatments.

    Science.gov (United States)

    Bourlière, Marc; Oules, Valèrie; Ansaldi, Christelle; Adhoute, Xavier; Castellani, Paul

    2014-12-15

    Sofosbuvir is the first-in-class NS5B nucleotide analogues to be launched for hepatitis C virus (HCV) treatment. Its viral potency, pangenotypic activity and high barrier to resistance make it the ideal candidate to become a backbone for several IFN-free regimens. Recent data demonstrated that sofosbuvir either with ribavirin alone or in combination with other direct-acting antivirals (DAAs) as daclatasvir, ledipasvir or simeprevir are able to cure HCV in at least 90% or over of patients. Treatment experienced genotype 3 population may remain the most difficult to treat population, but ongoing DAA combination studies will help to fill this gap. Safety profile of sofosbuvir or combination with other DAAs is good. Resistance to sofosbuvir did not appear as a significant issue. The rationale for using this class of drug and the available clinical data are reviewed.

  19. Extracting the information backbone in online system.

    Science.gov (United States)

    Zhang, Qian-Ming; Zeng, An; Shang, Ming-Sheng

    2013-01-01

    Information overload is a serious problem in modern society and many solutions such as recommender system have been proposed to filter out irrelevant information. In the literature, researchers have been mainly dedicated to improving the recommendation performance (accuracy and diversity) of the algorithms while they have overlooked the influence of topology of the online user-object bipartite networks. In this paper, we find that some information provided by the bipartite networks is not only redundant but also misleading. With such "less can be more" feature, we design some algorithms to improve the recommendation performance by eliminating some links from the original networks. Moreover, we propose a hybrid method combining the time-aware and topology-aware link removal algorithms to extract the backbone which contains the essential information for the recommender systems. From the practical point of view, our method can improve the performance and reduce the computational time of the recommendation system, thus improving both of their effectiveness and efficiency.

  20. Backbone analysis and algorithm design for the quadratic assignment problem

    Institute of Scientific and Technical Information of China (English)

    JIANG He; ZHANG XianChao; CHEN GuoLiang; LI MingChu

    2008-01-01

    As the hot line in NP-hard problems research in recent years, backbone analysis is crucial for phase transition, hardness, and algorithm design. Whereas theoretical analysis of backbone and its applications in algorithm design are still at a begin-ning state yet, this paper took the quadratic assignment problem (QAP) as a case study and proved by theoretical analysis that it is NP-hard to find the backbone, l.e., no algorithm exists to obtain the backbone of a QAP in polynomial time. Results of this paper showed that it is reasonable to acquire approximate backbone by inter-section of local optimal solutions. Furthermore, with the method of constructing biased instances, this paper proposed a new meta-heuristic - biased instance based approximate backbone (BI-AB), whose basic idea is as follows: firstly, con-struct a new biased instance for every QAP instance (the optimal solution of the new instance is also optimal for the original one); secondly, the approximate backbone is obtained by intersection of multiple local optimal solutions computed by some existing algorithm; finally, search for the optimal solutions in the reduced space by fixing the approximate backbone. Work of the paper enhanced the re-search area of theoretical analysis of backbone. The meta-heuristic proposed in this paper provided a new way for general algorithm design of NP-hard problems as well.

  1. NHC Backbone Configuration in Ruthenium-Catalyzed Olefin Metathesis

    Directory of Open Access Journals (Sweden)

    Veronica Paradiso

    2016-01-01

    Full Text Available The catalytic properties of olefin metathesis ruthenium complexes bearing N-heterocyclic carbene ligands with stereogenic centers on the backbone are described. Differences in catalytic behavior depending on the backbone configurations of symmetrical and unsymmetrical NHCs are discussed. In addition, an overview on asymmetric olefin metathesis promoted by chiral catalysts bearing C2-symmetric and C1-symmetric NHCs is provided.

  2. NHC Backbone Configuration in Ruthenium-Catalyzed Olefin Metathesis.

    Science.gov (United States)

    Paradiso, Veronica; Costabile, Chiara; Grisi, Fabia

    2016-01-20

    The catalytic properties of olefin metathesis ruthenium complexes bearing N-heterocyclic carbene ligands with stereogenic centers on the backbone are described. Differences in catalytic behavior depending on the backbone configurations of symmetrical and unsymmetrical NHCs are discussed. In addition, an overview on asymmetric olefin metathesis promoted by chiral catalysts bearing C₂-symmetric and C₁-symmetric NHCs is provided.

  3. The Backbone of the Climate Networks

    Science.gov (United States)

    Zou, Y.; Donges, J. F.; Marwan, N.; Kurths, J.

    2009-12-01

    We propose a method to reconstruct and analyze a complex network from data generated by a spatio-temporal dynamical system, relying on the nonlinear mutual information of time series analysis and betweenness centrality of complex network theory. We show, that this approach reveals a rich internal structure in complex climate networks constructed from reanalysis and model surface air temperature data. Our novel method uncovers peculiar wave-like structures of high energy flow, that we relate to global surface ocean currents. This points to a major role of the oceanic surface circulation in coupling and stabilizing the global temperature field in the long term mean (140 years for the model run and 60 years for reanalysis data). We find that these results cannot be obtained using classical linear methods of multivariate data analysis. Furthermore, we introduce significance tests to quantify the robustness of measured network properties to uncertainties. References: [1] J.F. Donges, Y. Zou, N. Marwan, and J. Kurths. Complex networks in climate dynamics -- -- Comparing linear and nonlinear network construction methods. European Physical Journal -- Special Topics, 174, 157-179, 2009. [2] J.F. Donges, Y. Zou, N. Marwan, and J. Kurths. Backbone of the climate network. Europhysics Letters, in press, 2009.

  4. Extracting the information backbone in online system.

    Directory of Open Access Journals (Sweden)

    Qian-Ming Zhang

    Full Text Available Information overload is a serious problem in modern society and many solutions such as recommender system have been proposed to filter out irrelevant information. In the literature, researchers have been mainly dedicated to improving the recommendation performance (accuracy and diversity of the algorithms while they have overlooked the influence of topology of the online user-object bipartite networks. In this paper, we find that some information provided by the bipartite networks is not only redundant but also misleading. With such "less can be more" feature, we design some algorithms to improve the recommendation performance by eliminating some links from the original networks. Moreover, we propose a hybrid method combining the time-aware and topology-aware link removal algorithms to extract the backbone which contains the essential information for the recommender systems. From the practical point of view, our method can improve the performance and reduce the computational time of the recommendation system, thus improving both of their effectiveness and efficiency.

  5. NET amyloidogenic backbone in human activated neutrophils.

    Science.gov (United States)

    Pulze, L; Bassani, B; Gini, E; D'Antona, P; Grimaldi, A; Luini, A; Marino, F; Noonan, D M; Tettamanti, G; Valvassori, R; de Eguileor, M

    2016-03-01

    Activated human neutrophils produce a fibrillar DNA network [neutrophil extracellular traps (NETs)] for entrapping and killing bacteria, fungi, protozoa and viruses. Our results suggest that the neutrophil extracellular traps show a resistant amyloidogenic backbone utilized for addressing reputed proteins and DNA against the non-self. The formation of amyloid fibrils in neutrophils is regulated by the imbalance of reactive oxygen species (ROS) in the cytoplasm. The intensity and source of the ROS signal is determinant for promoting stress-associated responses such as amyloidogenesis and closely related events: autophagy, exosome release, activation of the adrenocorticotrophin hormone/α-melanocyte-stimulating hormone (ACTH/α-MSH) loop and synthesis of specific cytokines. These interconnected responses in human activated neutrophils, that have been evaluated from a morphofunctional and quantitative viewpoint, represent primitive, but potent, innate defence mechanisms. In invertebrates, circulating phagocytic immune cells, when activated, show responses similar to those described previously for activated human neutrophils. Invertebrate cells within endoplasmic reticulum cisternae produce a fibrillar material which is then assembled into an amyloidogenic scaffold utilized to convey melanin close to the invader. These findings, in consideration to the critical role played by NET in the development of several pathologies, could explain the structural resistance of these scaffolds and could provide the basis for developing new diagnostic and therapeutic approaches in immunomediated diseases in which the innate branch of the immune system has a pivotal role.

  6. High Speed Fibre Optic Backbone LAN

    Science.gov (United States)

    Tanimoto, Masaaki; Hara, Shingo; Kajita, Yuji; Kashu, Fumitoshi; Ikeuchi, Masaru; Hagihara, Satoshi; Tsuzuki, Shinji

    1987-09-01

    Our firm has developed the SUMINET-4100 series, a fibre optic local area network (LAN), to serve the communications system trunk line needs for facilities, such as steel refineries, automobile plants and university campuses, that require large transmission capacity, and for the backbone networks used in intelligent building systems. The SUMINET-4100 series is already in service in various fields of application. Of the networks available in this series, the SUMINET-4150 has a trunk line speed of 128 Mbps and the multiplexer used for time division multiplexing (TDM) was enabled by designing an ECL-TTL gate array (3000 gates) based custom LSI. The synchronous, full-duplex V.24 and V.3.5 interfaces (SUMINET-2100) are provided for use with general purpose lines. And the IBM token ring network, the SUMINET-3200, designed for heterogeneous PCs and the Ethernet can all be connected to sub loops. Further, the IBM 3270 TCA and 5080 CADAM can be connected in the local mode. Interfaces are also provided for the NTT high-speed digital service, the digital PBX systems, and the Video CODEC system. The built-in loop monitor (LM) and network supervisory processor (NSP) provide management of loop utilization and send loop status signals to the host CPU's network configuration and control facility (NCCF). These built-in functions allow both the computer system and LAN to be managed from a single source at the host. This paper outlines features of the SUMINET-4150 and provides an example of its installation.

  7. High Performance Infiltrated Backbones for Cathode-Supported SOFC's

    DEFF Research Database (Denmark)

    Gil, Vanesa; Kammer Hansen, Kent

    2014-01-01

    The concept of using highly ionic conducting backbones with subsequent infiltration of electronically conducting particles has widely been used to develop alternative anode-supported SOFC's. In this work, the idea was to develop infiltrated backbones as an alternative design based on cathode......-supported SOFC. The cathodes are obtained by infiltrating LSM into a sintered either thick (300 μm) yttria stabilized zirconia (YSZ) backbone or a thin YSZ backbone (10-15 μm) integrated onto a thick (300 μm) porous strontium substituted lanthanum manganite (LSM) and YSZ composite. Fabrication challenges...... printed symmetrical cells. Samples with LSM/YSZ composite and YSZ backbones made with graphite+PMMA as pore formers exhibited comparable Rp values to the screen printed LSM/YSZ cathode. This route was chosen as the best to fabricate the cathode supported cells. SEM micrograph of a cathode supported cell...

  8. High Performance Infiltrated Backbones for Cathode-Supported SOFC's

    DEFF Research Database (Denmark)

    Gil, Vanesa; Kammer Hansen, Kent

    2014-01-01

    A four-step infiltration method has been developed to infiltrate La0.75Sr0.25MnO3+δ (LSM25) nanoparticles into porous structures (YSZ or LSM-YSZ backbones). The pore size distribution in the backbones is obtained either by using PMMA and/or graphites as pore formers or by leaching treatment of sa...... of samples with Ni remained in the YSZ structure at high temperatures. All impregnated backbones, presented Rs comparable to a standard screen printed cathode, which proves that LSM nanoparticles forms a pathway for electron conduction....

  9. A backbone lever-arm effect enhances polymer mechanochemistry

    Science.gov (United States)

    Klukovich, Hope M.; Kouznetsova, Tatiana B.; Kean, Zachary S.; Lenhardt, Jeremy M.; Craig, Stephen L.

    2013-02-01

    Mechanical forces along a polymer backbone can be used to bring about remarkable reactivity in embedded mechanically active functional groups, but little attention has been paid to how a given polymer backbone delivers that force to the reactant. Here, single-molecule force spectroscopy was used to directly quantify and compare the forces associated with the ring opening of gem-dibromo and gem-dichlorocyclopropanes affixed along the backbone of cis-polynorbornene and cis-polybutadiene. The critical force for isomerization drops by about one-third in the polynorbornene scaffold relative to polybutadiene. The root of the effect lies in more efficient chemomechanical coupling through the polynorbornene backbone, which acts as a phenomenological lever with greater mechanical advantage than polybutadiene. The experimental results are supported computationally and provide the foundation for a new strategy by which to engineer mechanochemical reactivity.

  10. LOAD AWARE ADAPTIVE BACKBONE SYNTHESIS IN WIRELESS MESH NETWORKS

    Institute of Scientific and Technical Information of China (English)

    Yuan Yuan; Zheng Baoyu

    2009-01-01

    Wireless Mesh Networks (WMNs) are envisioned to support the wired backbone with a wireless Backbone Networks (BNet) for providing internet connectivity to large-scale areas.With a wide range of internet-oriented applications with different Quality of Service (QoS) requirement,the large-scale WMNs should have good scalability and large bandwidth.In this paper,a Load Aware Adaptive Backbone Synthesis (LAABS) algorithm is proposed to automatically balance the traffic flow in the WMNs.The BNet will dynamically split into smaller size or merge into bigger one according to statistic load information of Backbone Nodes (BNs).Simulation results show LAABS generates moderate BNet size and converges quickly,thus providing scalable and stable BNet to facilitate traffic flow.

  11. On Backbone Structure for a Future Multipurpose Network

    DEFF Research Database (Denmark)

    Gutierrez Lopez, Jose Manuel; Cuevas, Ruben; Riaz, M. Tahir

    2008-01-01

    Telecommunications are evolving towards the unification of services and infrastructures. This unification must be achieved at the highest hierarchical level for a complete synergy of services. Therefore, one of the requirements is a multipurpose backbone network capable of supporting all the curr......Telecommunications are evolving towards the unification of services and infrastructures. This unification must be achieved at the highest hierarchical level for a complete synergy of services. Therefore, one of the requirements is a multipurpose backbone network capable of supporting all...

  12. Triazine-Based Sequence-Defined Polymers with Side-Chain Diversity and Backbone-Backbone Interaction Motifs.

    Science.gov (United States)

    Grate, Jay W; Mo, Kai-For; Daily, Michael D

    2016-03-14

    Sequence control in polymers, well-known in nature, encodes structure and functionality. Here we introduce a new architecture, based on the nucleophilic aromatic substitution chemistry of cyanuric chloride, that creates a new class of sequence-defined polymers dubbed TZPs. Proof of concept is demonstrated with two synthesized hexamers, having neutral and ionizable side chains. Molecular dynamics simulations show backbone-backbone interactions, including H-bonding motifs and pi-pi interactions. This architecture is arguably biomimetic while differing from sequence-defined polymers having peptide bonds. The synthetic methodology supports the structural diversity of side chains known in peptides, as well as backbone-backbone hydrogen-bonding motifs, and will thus enable new macromolecules and materials with useful functions.

  13. Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops

    Directory of Open Access Journals (Sweden)

    Gendrault-Jacquemard A

    2005-07-01

    Full Text Available Abstract Background Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related genomes. Recent analyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strain-specific sequences called loops. Results Here, we generalize this approach and propose a strategy that allows systematic and non-biased genome segmentation based on multiple genome alignments. Segmentation analyses, as applied to 13 different bacterial species, confirmed the feasibility of our approach to discern the 'mosaic' organization of bacterial genomes. Segmentation results are available through a Web interface permitting functional analysis, extraction and visualization of the backbone/loops structure of documented genomes. To illustrate the potential of this approach, we performed a precise analysis of the mosaic organization of three E. coli strains and functional characterization of the loops. Conclusion The segmentation results including the backbone/loops structure of 13 bacterial species genomes are new and available for use by the scientific community at the URL: http://genome.jouy.inra.fr/mosaic.

  14. Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design.

    Directory of Open Access Journals (Sweden)

    Kevin Drew

    Full Text Available Peptidomimetics are classes of molecules that mimic structural and functional attributes of polypeptides. Peptidomimetic oligomers can frequently be synthesized using efficient solid phase synthesis procedures similar to peptide synthesis. Conformationally ordered peptidomimetic oligomers are finding broad applications for molecular recognition and for inhibiting protein-protein interactions. One critical limitation is the limited set of design tools for identifying oligomer sequences that can adopt desired conformations. Here, we present expansions to the ROSETTA platform that enable structure prediction and design of five non-peptidic oligomer scaffolds (noncanonical backbones, oligooxopiperazines, oligo-peptoids, [Formula: see text]-peptides, hydrogen bond surrogate helices and oligosaccharides. This work is complementary to prior additions to model noncanonical protein side chains in ROSETTA. The main purpose of our manuscript is to give a detailed description to current and future developers of how each of these noncanonical backbones was implemented. Furthermore, we provide a general outline for implementation of new backbone types not discussed here. To illustrate the utility of this approach, we describe the first tests of the ROSETTA molecular mechanics energy function in the context of oligooxopiperazines, using quantum mechanical calculations as comparison points, scanning through backbone and side chain torsion angles for a model peptidomimetic. Finally, as an example of a novel design application, we describe the automated design of an oligooxopiperazine that inhibits the p53-MDM2 protein-protein interaction. For the general biological and bioengineering community, several noncanonical backbones have been incorporated into web applications that allow users to freely and rapidly test the presented protocols (http://rosie.rosettacommons.org. This work helps address the peptidomimetic community's need for an automated and expandable

  15. APPECT: An Approximate Backbone-Based Clustering Algorithm for Tags

    DEFF Research Database (Denmark)

    Zong, Yu; Xu, Guandong; Jin, Pin

    2011-01-01

    algorithm for Tags (APPECT). The main steps of APPECT are: (1) we execute the K-means algorithm on a tag similarity matrix for M times and collect a set of tag clustering results Z={C1,C2,…,Cm}; (2) we form the approximate backbone of Z by executing a greedy search; (3) we fix the approximate backbone...... resulting from the severe difficulty of ambiguity, redundancy and less semantic nature of tags. Clustering method is a useful tool to address the aforementioned difficulties. Most of the researches on tag clustering are directly using traditional clustering algorithms such as K-means or Hierarchical...

  16. Optimal sink placement in backbone assisted wireless sensor networks

    Directory of Open Access Journals (Sweden)

    I. Snigdh

    2016-07-01

    Full Text Available This article proposes a scheme for selecting the best site for sink placement in WSN applications employing backbone assisted communications. By placing the sink at a specific position, energy scavenging and delay constraints can effectively be controlled. In contrast to the conventional scheme for base station placement at the geographical centre or random placement at the end of the region of interest, the proposed scheme places the base station at either the graph theoretical centre or centroid of the backbone connecting nodes in the region of interest. This strategy shows a considerable reduction in the total number of hops that each packet needs to travel to reach the sink. The proposed scheme is applied on all the families of graphs prevalent in backbone assisted sensor networks to confirm the performance consistency and improvement in network parameters of the communication backbone measured in terms of delay, the carried load and the total energy consumption, eventually affected by the average number of hops for the message to reach the sink.

  17. The Graphical Representation of the Digital Astronaut Physiology Backbone

    Science.gov (United States)

    Briers, Demarcus

    2010-01-01

    This report summarizes my internship project with the NASA Digital Astronaut Project to analyze the Digital Astronaut (DA) physiology backbone model. The Digital Astronaut Project (DAP) applies integrated physiology models to support space biomedical operations, and to assist NASA researchers in closing knowledge gaps related to human physiologic responses to space flight. The DA physiology backbone is a set of integrated physiological equations and functions that model the interacting systems of the human body. The current release of the model is HumMod (Human Model) version 1.5 and was developed over forty years at the University of Mississippi Medical Center (UMMC). The physiology equations and functions are scripted in an XML schema specifically designed for physiology modeling by Dr. Thomas G. Coleman at UMMC. Currently it is difficult to examine the physiology backbone without being knowledgeable of the XML schema. While investigating and documenting the tags and algorithms used in the XML schema, I proposed a standard methodology for a graphical representation. This standard methodology may be used to transcribe graphical representations from the DA physiology backbone. In turn, the graphical representations can allow examination of the physiological functions and equations without the need to be familiar with the computer programming languages or markup languages used by DA modeling software.

  18. Identification of systems containing nonlinear stiffnesses using backbone curves

    Science.gov (United States)

    Londoño, Julián M.; Cooper, Jonathan E.; Neild, Simon A.

    2017-02-01

    This paper presents a method for the dynamic identification of structures containing discrete nonlinear stiffnesses. The approach requires the structure to be excited at a single resonant frequency, enabling measurements to be made in regimes of large displacements where nonlinearities are more likely to be significant. Measured resonant decay data is used to estimate the system backbone curves. Linear natural frequencies and nonlinear parameters are identified using these backbone curves assuming a form for the nonlinear behaviour. Numerical and experimental examples, inspired by an aerospace industry test case study, are considered to illustrate how the method can be applied. Results from these models demonstrate that the method can successfully deliver nonlinear models able to predict the response of the test structure nonlinear dynamics.

  19. Variation of protein backbone amide resonance by electrostatic field

    OpenAIRE

    Sharley, John N.

    2015-01-01

    Amide resonance is found to be sensitive to electrostatic field with component parallel or antiparallel the amide C-N bond. This effect is linear and without threshold in the biologically plausible electrostatic field range -0.005 to 0.005 au. Variation of amide resonance varies Resonance-Assisted Hydrogen Bonding such as occurs in the hydrogen bonded chains of backbone amides of protein secondary structures such as beta sheet and alpha helix, varying the stability of the secondary structure....

  20. Backbone decomposition for continuous-state branching processes with immigration

    CERN Document Server

    Ren, A E Kyprianou Y-X

    2011-01-01

    In the spirit of Duqesne and Winkel (2007) and Berestycki et al. (2011) we show that supercritical continuous-state branching process with a general branching mechanism and general immigration mechanism is equal in law to a continuous-time Galton Watson process with immigration with Poissonian dressing. The result also characterises the limiting backbone decomposition which is predictable from the work on consistent growth of Galton-Watson trees with immigration in Cao and Winkel (2010).

  1. Control of polymer-packing orientation in thin films through synthetic tailoring of backbone coplanarity

    KAUST Repository

    Chen, Mark S.

    2013-10-22

    Controlling solid-state order of π-conjugated polymers through macromolecular design is essential for achieving high electronic device performance; yet, it remains a challenge, especially with respect to polymer-packing orientation. Our work investigates the influence of backbone coplanarity on a polymer\\'s preference to pack face-on or edge-on relative to the substrate. Isoindigo-based polymers were synthesized with increasing planarity by systematically substituting thiophenes for phenyl rings in the acceptor comonomer. This increasing backbone coplanarity, supported by density functional theory (DFT) calculations of representative trimers, leads to the narrowing of polymer band gaps as characterized by ultraviolet-visible-near infrared (UV-vis-NIR) spectroscopy and cyclic voltammetry. Among the polymers studied, regiosymmetric II and TII polymers exhibited the highest hole mobilities in organic field-effect transistors (OFETs), while in organic photovoltaics (OPVs), TBII polymers that display intermediate levels of planarity provided the highest power conversion efficiencies. Upon thin-film analysis by atomic force microscropy (AFM) and grazing-incidence X-ray diffraction (GIXD), we discovered that polymer-packing orientation could be controlled by tuning polymer planarity and solubility. Highly soluble, planar polymers favor face-on orientation in thin films while the less soluble, nonplanar polymers favor an edge-on orientation. This study advances our fundamental understanding of how polymer structure influences nanostructural order and reveals a new synthetic strategy for the design of semiconducting materials with rationally engineered solid-state properties. © 2013 American Chemical Society.

  2. Extracting the multiscale backbone of complex weighted networks

    Science.gov (United States)

    Serrano, M. Ángeles; Boguñá, Marián; Vespignani, Alessandro

    2009-01-01

    A large number of complex systems find a natural abstraction in the form of weighted networks whose nodes represent the elements of the system and the weighted edges identify the presence of an interaction and its relative strength. In recent years, the study of an increasing number of large-scale networks has highlighted the statistical heterogeneity of their interaction pattern, with degree and weight distributions that vary over many orders of magnitude. These features, along with the large number of elements and links, make the extraction of the truly relevant connections forming the network's backbone a very challenging problem. More specifically, coarse-graining approaches and filtering techniques come into conflict with the multiscale nature of large-scale systems. Here, we define a filtering method that offers a practical procedure to extract the relevant connection backbone in complex multiscale networks, preserving the edges that represent statistically significant deviations with respect to a null model for the local assignment of weights to edges. An important aspect of the method is that it does not belittle small-scale interactions and operates at all scales defined by the weight distribution. We apply our method to real-world network instances and compare the obtained results with alternative backbone extraction techniques. PMID:19357301

  3. Design of an IPTV Multicast System for Internet Backbone Networks

    OpenAIRE

    T. H. Szymanski; Gilbert, D

    2010-01-01

    The design of an IPTV multicast system for the Internet backbone network is presented and explored through extensive simulations. In the proposed system, a resource reservation algorithm such as RSVP, IntServ, or DiffServ is used to reserve resources (i.e., bandwidth and buffer space) in each router in an IP multicast tree. Each router uses an Input-Queued, Output-Queued, or Crosspoint-Queued switch architecture with unity speedup. A recently proposed Recursive Fair Stochastic Matrix Decompos...

  4. Application of Multicast-based Video Conference on CERNET Backbone

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Multicast-based video conference is a representative application in advanced network. In multi-point video conference using multicast can get better efficiency facilitated by inner-group broadcast mechanism. In the application, the multicast-based network resources assignment, management and security should be considered together. This paper presents a framework model of multicast-based video conferencing application with three layers. And a practical multicast-based video conferencing is implemented in CERNET(China Education and Research Network) backbone. The practice is valuable for the development of multicast-based video conferencing application in China.

  5. Resistance of Feynman diagrams and the percolation backbone dimension.

    Science.gov (United States)

    Janssen, H K; Stenull, O; Oerding, K

    1999-06-01

    We present an alternative view of Feynman diagrams for the field theory of random resistor networks, in which the diagrams are interpreted as being resistor networks themselves. This simplifies the field theory considerably as we demonstrate by calculating the fractal dimension D(B) of the percolation backbone to three loop order. Using renormalization group methods we obtain D(B)=2+epsilon/21-172epsilon(2)/9261+2epsilon(3)[-74 639+22 680zeta(3)]/4 084 101, where epsilon=6-d with d being the spatial dimension and zeta(3)=1.202 057... .

  6. Unique optimal solution instance and computational complexity of backbone in the graph bi-partitioning problem

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    As an important tool for heuristic design of NP-hard problems, backbone analysis has become a hot spot in theoretical computer science in recent years. Due to the difficulty in the research on computational complexity of the backbone, many researchers analyzed the backbone by statistic ways. Aiming to increase the backbone size which is usually very small by the existing methods, the unique optimal solution instance construction (UOSIC) is proposed for the graph bi-partitioning problem (GBP). Also, we prove by using the UOSIC that it is NP-hard to obtain the backbone, i.e. no algorithm exists to obtain the backbone of a GBP in polynomial time under the assumption that P ( NP. Our work expands the research area of computational complexity of the backbone. And the UOSIC provides a new way for heuristic design of NP-hard problems.

  7. Characterizing Aciniform Silk Repetitive Domain Backbone Dynamics and Hydrodynamic Modularity

    Directory of Open Access Journals (Sweden)

    Marie-Laurence Tremblay

    2016-08-01

    Full Text Available Spider aciniform (wrapping silk is a remarkable fibrillar biomaterial with outstanding mechanical properties. It is a modular protein consisting, in Argiope trifasciata, of a core repetitive domain of 200 amino acid units (W units. In solution, the W units comprise a globular folded core, with five α-helices, and disordered tails that are linked to form a ~63-residue intrinsically disordered linker in concatemers. Herein, we present nuclear magnetic resonance (NMR spectroscopy-based 15N spin relaxation analysis, allowing characterization of backbone dynamics as a function of residue on the ps–ns timescale in the context of the single W unit (W1 and the two unit concatemer (W2. Unambiguous mapping of backbone dynamics throughout W2 was made possible by segmental NMR active isotope-enrichment through split intein-mediated trans-splicing. Spectral density mapping for W1 and W2 reveals a striking disparity in dynamics between the folded core and the disordered linker and tail regions. These data are also consistent with rotational diffusion behaviour where each globular domain tumbles almost independently of its neighbour. At a localized level, helix 5 exhibits elevated high frequency dynamics relative to the proximal helix 4, supporting a model of fibrillogenesis where this helix unfolds as part of the transition to a mixed α-helix/β-sheet fibre.

  8. Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates.

    Science.gov (United States)

    Gront, Dominik; Kmiecik, Sebastian; Kolinski, Andrzej

    2007-07-15

    In this contribution, we present an algorithm for protein backbone reconstruction that comprises very high computational efficiency with high accuracy. Reconstruction of the main chain atomic coordinates from the alpha carbon trace is a common task in protein modeling, including de novo structure prediction, comparative modeling, and processing experimental data. The method employed in this work follows the main idea of some earlier approaches to the problem. The details and careful design of the present approach are new and lead to the algorithm that outperforms all commonly used earlier applications. BBQ (Backbone Building from Quadrilaterals) program has been extensively tested both on native structures as well as on near-native decoy models and compared with the different available existing methods. Obtained results provide a comprehensive benchmark of existing tools and evaluate their applicability to a large scale modeling using a reduced representation of protein conformational space. The BBQ package is available for downloading from our website at http://biocomp.chem.uw.edu.pl/services/BBQ/. This webpage also provides a user manual that describes BBQ functions in detail.

  9. Icosahedral medium-range orders and backbone formation in an amorphous alloy

    Science.gov (United States)

    Lee, Mirim; Kim, Hong-Kyu; Lee, Jae-Chul

    2010-12-01

    Analyses of metallic amorphous solids constructed using molecular dynamics (MD) simulations have demonstrated that individual short-range orders (SROs) are linked with neighboring SROs and form various medium-range orders (MROs). These MROs have been observed to have different structural stability depending on their linking patterns. On the basis of the assessment of the structural stability of various MROs, we propose new types of structural organization, namely, icosahedral medium-range orders (I-MROs) and their extended-range order that forms the backbone of amorphous solids. We also discuss why the atomic-scale structure of an amorphous alloy can be more appropriately described in terms of I-MROs, rather than by the degree of short-range ordering as characterized by the fractions of SROs.

  10. Essential roles of four-carbon backbone chemicals in the control of metabolism

    Institute of Scientific and Technical Information of China (English)

    Sabrina; Chriett; Luciano; Pirola

    2015-01-01

    The increasing incidence of obesity worldwide and its related cardiometabolic complications is an urgent public health problem. While weight gain results from a negative balance between the energy expenditure and calorie intake, recent research has demonstrated that several small organic molecules containing a four-carbon backbone can modulate this balance by favoring energy expenditure, and alleviating endoplasmic reticulum stress and oxidative stress. Such small molecules include the bacterially produced short chain fatty acid butyric acid, its chemically produced derivative 4-phenylbutyric acid, the main ketone body D-β-hydroxybutyrate- synthesized by the liver- and the recently discovered myokine β-aminoisobutyric acid. Conversely, another butyraterelated molecule, α-hydroxybutyrate, has been found to be an early predictor of insulin resistance and glucose intolerance. In this minireview, we summarize recent advances in the understanding of the mechanism of action of these molecules, and discuss their use as therapeutics to improve metabolic homeostasis or their detection as early biomarkers of incipient insulin resistance.

  11. Changing the topology of protein backbone: the effect of backbone cyclization on the structure and dynamics of a SH3 domain

    Directory of Open Access Journals (Sweden)

    Frank H Schumann

    2015-04-01

    Full Text Available Understanding of the effects of the backbone cyclization on the structure and dynamics of a protein is essential for using protein topology engineering to alter protein stability and function. Here we have determined, for the first time, the structure and dynamics of the linear and various circular constructs of the N-SH3 domain from protein c-Crk. These constructs differ in the length and amino acid composition of the cyclization region. The backbone cyclization was carried out using intein-mediated intramolecular chemical ligation between the juxtaposed N- and the C-termini. The structure and backbone dynamics studies were performed using solution NMR. Our data suggest that the backbone cyclization has little effect on the overall three-dimensional structure of the SH3 domain: besides the termini, only minor structural changes were found in the proximity of the cyclization region. In contrast to the structure, backbone dynamics are significantly affected by the cyclization. On the subnanosecond time scale, the backbone of all circular constructs on average appears more rigid than that of the linear SH3 domain; this effect is observed over the entire backbone and is not limited to the cyclization site. The backbone mobility of the circular constructs becomes less restricted with increasing length of the circularization loop. In addition, significant conformational exchange motions (on the sub-millisecond time scale were found in the N-Src loop and in the adjacent β-strands in all circular constructs studied in this work. These effects of backbone cyclization on protein dynamics have potential implications for the stability of the protein fold and for ligand binding.

  12. Variation of protein backbone amide resonance by electrostatic field

    CERN Document Server

    Sharley, John N

    2015-01-01

    Amide resonance is found to be sensitive to electrostatic field with component parallel or antiparallel the amide C-N bond. This effect is linear and without threshold in the biologically plausible electrostatic field range -0.005 to 0.005 au. Variation of amide resonance varies Resonance Assisted Hydrogen Bonding such as occurs in the hydrogen bonded chains of backbone amides of protein secondary structures such as beta sheet and non-polyproline helix such as alpha helix, varying the stability of the secondary structure. The electrostatic properties including permittivity of amino acid residue sidegroups influence the electrostatic field component parallel or antiparallel the C-N bond of each amide. The significance of this factor relative to other factors in protein folding depends on the magnitude of electrostatic field component parallel or antiparallel the C-N bond of each amide, and preliminary protein-scale calculations of the magnitude of these components suggest this factor warrants investigation in ...

  13. Backbones of evolutionary history test biodiversity theory for microbes.

    Science.gov (United States)

    O'Dwyer, James P; Kembel, Steven W; Sharpton, Thomas J

    2015-07-07

    Identifying the ecological and evolutionary mechanisms that determine biological diversity is a central question in ecology. In microbial ecology, phylogenetic diversity is an increasingly common and relevant means of quantifying community diversity, particularly given the challenges in defining unambiguous species units from environmental sequence data. We explore patterns of phylogenetic diversity across multiple bacterial communities drawn from different habitats and compare these data to evolutionary trees generated using theoretical models of biodiversity. We have two central findings. First, although on finer scales the empirical trees are highly idiosyncratic, on coarse scales the backbone of these trees is simple and robust, consistent across habitats, and displays bursts of diversification dotted throughout. Second, we find that these data demonstrate a clear departure from the predictions of standard neutral theories of biodiversity and that an alternative family of generalized models provides a qualitatively better description. Together, these results lay the groundwork for a theoretical framework to connect ecological mechanisms to observed phylogenetic patterns in microbial communities.

  14. Transforming plastic surfaces with electrophilic backbones from hydrophobic to hydrophilic.

    Science.gov (United States)

    Kim, Samuel; Bowen, Raffick A R; Zare, Richard N

    2015-01-28

    We demonstrate a simple nonaqueous reaction scheme for transforming the surface of plastics from hydrophobic to hydrophilic. The chemical modification is achieved by base-catalyzed trans-esterification with polyols. It is permanent, does not release contaminants, and causes no optical or mechanical distortion of the plastic. We present contact angle measurements to show successful modification of several types of plastics including poly(ethylene terephthalate) (PET) and polycarbonate (PC). Its applicability to blood analysis is explored using chemically modified PET blood collection tubes and found to be quite satisfactory. We expect this approach will reduce the cost of manufacturing plastic devices with optimized wettability and can be generalized to other types of plastic materials having an electrophilic linkage as its backbone.

  15. Phase Transitions and Backbones of the Asymmetric Traveling Salesman Problem

    CERN Document Server

    Zhang, W

    2011-01-01

    In recent years, there has been much interest in phase transitions of combinatorial problems. Phase transitions have been successfully used to analyze combinatorial optimization problems, characterize their typical-case features and locate the hardest problem instances. In this paper, we study phase transitions of the asymmetric Traveling Salesman Problem (ATSP), an NP-hard combinatorial optimization problem that has many real-world applications. Using random instances of up to 1,500 cities in which intercity distances are uniformly distributed, we empirically show that many properties of the problem, including the optimal tour cost and backbone size, experience sharp transitions as the precision of intercity distances increases across a critical value. Our experimental results on the costs of the ATSP tours and assignment problem agree with the theoretical result that the asymptotic cost of assignment problem is pi ^2 /6 the number of cities goes to infinity. In addition, we show that the average computation...

  16. Bioactivities of fish protein hydrolysates from defatted salmon backbones

    Directory of Open Access Journals (Sweden)

    Rasa Slizyte

    2016-09-01

    Full Text Available Bioactivities of bulk fish protein hydrolysates (FPH from defatted salmon backbones obtained with eight different commercial enzymes and their combinations were tested. All FPH showed antioxidative activity in vitro. DPPH scavenging activity increased, while iron chelating ability decreased with increasing time of hydrolysis. All FPH showed ACE inhibiting effect which depended on type of enzyme and increased with time of hydrolysis. The highest effect was found for FPH produced with Trypsin. Bromelain + Papain hydrolysates reduced the uptake of radiolabelled glucose into CaCo-2 cells, a model of human enterocytes, indicating a potential antidiabetic effect of FPH. FPH obtained by Trypsin, Bromelain + Papain and Protamex showed the highest ACE inhibitory, cellular glucose transporter (GLUT/SGLT inhibitory and in vitro antioxidative activities, respectively. Correlation was observed between the measured bioactivities, degree of hydrolysis and molecular weight profiles, supporting prolonged hydrolysis to obtain high bioactivities.

  17. Design of an IPTV Multicast System for Internet Backbone Networks

    Directory of Open Access Journals (Sweden)

    T. H. Szymanski

    2010-01-01

    Full Text Available The design of an IPTV multicast system for the Internet backbone network is presented and explored through extensive simulations. In the proposed system, a resource reservation algorithm such as RSVP, IntServ, or DiffServ is used to reserve resources (i.e., bandwidth and buffer space in each router in an IP multicast tree. Each router uses an Input-Queued, Output-Queued, or Crosspoint-Queued switch architecture with unity speedup. A recently proposed Recursive Fair Stochastic Matrix Decomposition algorithm used to compute near-perfect transmission schedules for each IP router. The IPTV traffic is shaped at the sources using Application-Specific Token Bucker Traffic Shapers, to limit the burstiness of incoming network traffic. The IPTV traffic is shaped at the destinations using Application-Specific Playback Queues, to remove residual network jitter and reconstruct the original bursty IPTV video streams at each destination. All IPTV traffic flows are regenerated at the destinations with essentially zero delay jitter and essentially-perfect QoS. The destination nodes deliver the IPTV streams to the ultimate end users using the same IPTV multicast system over a regional Metropolitan Area Network. It is shown that all IPTV traffic is delivered with essentially-perfect end-to-end QoS, with deterministic bounds on the maximum delay and jitter on each video frame. Detailed simulations of an IPTV distribution system, multicasting several hundred high-definition IPTV video streams over several essentially saturated IP backbone networks are presented.

  18. Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments

    OpenAIRE

    Lies Baeten; Joke Reumers; Vicente Tur; François Stricher; Tom Lenaerts; Luis Serrano; Frederic Rousseau; Joost Schymkowitz

    2008-01-01

    As modeling of changes in backbone conformation still lacks a computationally efficient solution, we developed a discretisation of the conformational states accessible to the protein backbone similar to the successful rotamer approach in side chains. The BriX fragment database, consisting of fragments from 4 to 14 residues long, was realized through identification of recurrent backbone fragments from a non-redundant set of high-resolution protein structures. BriX contains an alphabet of more ...

  19. Thin Films Formed from Conjugated Polymers with Ionic, Water-Soluble Backbones.

    Science.gov (United States)

    Voortman, Thomas P; Chiechi, Ryan C

    2015-12-30

    This paper compares the morphologies of films of conjugated polymers in which the backbone (main chain) and pendant groups are varied between ionic/hydrophilic and aliphatic/hydrophobic. We observe that conjugated polymers in which the pendant groups and backbone are matched, either ionic-ionic or hydrophobic-hydrophobic, form smooth, structured, homogeneous films from water (ionic) or tetrahydrofuran (hydrophobic). Mismatched conjugated polymers, by contrast, form inhomogeneous films with rough topologies. The polymers with ionic backbone chains are conjugated polyions (conjugated polymers with closed-shell charges in the backbone), which are semiconducting materials with tunable bad-gaps, not unlike uncharged conjugated polymers.

  20. A hierarchical virtual backbone construction protocol for mobile ad hoc networks

    Directory of Open Access Journals (Sweden)

    Bharti Sharma

    2016-07-01

    Full Text Available We propose a hierarchical backbone construction protocol for mobile ad hoc networks. Our protocol is based on the idea of using an efficient extrema finding method to create clusters comprising the nodes that are within certain prespecified wireless hop distance. Afterward, we apply our ‘diameter’ algorithm among clusters to identify the dominating nodes that are, finally, connected via multi-hop virtual links to construct the backbone. We present the analytic as well as simulation study of our algorithm and also a method for the dynamic maintenance of constructed backbone. In the end, we illustrate the use of the virtual backbone with the help of an interesting application.

  1. Controlled Conjugated Backbone Twisting for an Increased Open-Circuit Voltage while Having a High Short-Circuit Current in Poly(hexylthiophene) Derivatives

    KAUST Repository

    Ko, Sangwon

    2012-03-21

    Conjugated polymers with nearly planar backbones have been the most commonly investigated materials for organic-based electronic devices. More twisted polymer backbones have been shown to achieve larger open-circuit voltages in solar cells, though with decreased short-circuit current densities. We systematically impose twists within a family of poly(hexylthiophene)s and examine their influence on the performance of polymer:fullerene bulk heterojunction (BHJ) solar cells. A simple chemical modification concerning the number and placement of alkyl side chains along the conjugated backbone is used to control the degree of backbone twisting. Density functional theory calculations were carried out on a series of oligothiophene structures to provide insights on how the sterically induced twisting influences the geometric, electronic, and optical properties. Grazing incidence X-ray scattering measurements were performed to investigate how the thin-film packing structure was affected. The open-circuit voltage and charge-transfer state energy of the polymer:fullerene BHJ solar cells increased substantially with the degree of twist induced within the conjugated backbone-due to an increase in the polymer ionization potential-while the short-circuit current decreased as a result of a larger optical gap and lower hole mobility. A controlled, moderate degree of twist along the poly(3,4-dihexyl-2,2′:5′,2′′- terthiophene) (PDHTT) conjugated backbone led to a 19% enhancement in the open-circuit voltage (0.735 V) vs poly(3-hexylthiophene)-based devices, while similar short-circuit current densities, fill factors, and hole-carrier mobilities were maintained. These factors resulted in a power conversion efficiency of 4.2% for a PDHTT:[6,6]-phenyl-C 71-butyric acid methyl ester (PC 71BM) blend solar cell without thermal annealing. This simple approach reveals a molecular design avenue to increase open-circuit voltage while retaining the short-circuit current. © 2012 American

  2. Navigating the massive world of reddit: using backbone networks to map user interests in social media

    Directory of Open Access Journals (Sweden)

    Randal S. Olson

    2015-05-01

    Full Text Available In the massive online worlds of social media, users frequently rely on organizing themselves around specific topics of interest to find and engage with like-minded people. However, navigating these massive worlds and finding topics of specific interest often proves difficult because the worlds are mostly organized haphazardly, leaving users to find relevant interests by word of mouth or using a basic search feature. Here, we report on a method using the backbone of a network to create a map of the primary topics of interest in any social network. To demonstrate the method, we build an interest map for the social news web site reddit and show how such a map could be used to navigate a social media world. Moreover, we analyze the network properties of the reddit social network and find that it has a scale-free, small-world, and modular community structure, much like other online social networks such as Facebook and Twitter. We suggest that the integration of interest maps into popular social media platforms will assist users in organizing themselves into more specific interest groups, which will help alleviate the overcrowding effect often observed in large online communities.

  3. Thin Films Formed from Conjugated Polymers with Ionic, Water-Soluble Backbones

    NARCIS (Netherlands)

    Voortman, Thomas P; Chiechi, Ryan C

    2015-01-01

    This paper compares the morphologies of films of conjugated polymers in which the backbone (main chain) and pendant groups are varied between ionic/hydrophilic and aliphatic/hydrophobic. We observe that conjugated polymers in which the pendant groups and backbone are matched, either ionic-ionic or h

  4. Backbone Assignment of the MALT1 Paracaspase by Solution NMR.

    Science.gov (United States)

    Unnerståle, Sofia; Nowakowski, Michal; Baraznenok, Vera; Stenberg, Gun; Lindberg, Jimmy; Mayzel, Maxim; Orekhov, Vladislav; Agback, Tatiana

    2016-01-01

    Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) is a unique paracaspase protein whose protease activity mediates oncogenic NF-κB signalling in activated B cell-like diffuse large B cell lymphomas (ABC-DLBCLs). ABC-DLBCLs are aggressive lymphomas with high resistance to current chemotherapies. Low survival rate among patients emphasizes the urgent need for alternative treatment options. The characterization of the MALT1 will be an essential tool for developing new target-directed drugs against MALT1 dependent disorders. As the first step in the atomic-level NMR studies of the system, here we report, the (15)N/(13)C/(1)H backbone assignment of the apo form of the MALT1 paracaspase region together with the third immunoglobulin-like (Ig3) domain, 44 kDa, by high resolution NMR. In addition, the non-uniform sampling (NUS) based targeted acquisition procedure is evaluated as a mean of decreasing acquisition and analysis time for larger proteins.

  5. Backbone Assignment of the MALT1 Paracaspase by Solution NMR.

    Directory of Open Access Journals (Sweden)

    Sofia Unnerståle

    Full Text Available Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1 is a unique paracaspase protein whose protease activity mediates oncogenic NF-κB signalling in activated B cell-like diffuse large B cell lymphomas (ABC-DLBCLs. ABC-DLBCLs are aggressive lymphomas with high resistance to current chemotherapies. Low survival rate among patients emphasizes the urgent need for alternative treatment options. The characterization of the MALT1 will be an essential tool for developing new target-directed drugs against MALT1 dependent disorders. As the first step in the atomic-level NMR studies of the system, here we report, the (15N/(13C/(1H backbone assignment of the apo form of the MALT1 paracaspase region together with the third immunoglobulin-like (Ig3 domain, 44 kDa, by high resolution NMR. In addition, the non-uniform sampling (NUS based targeted acquisition procedure is evaluated as a mean of decreasing acquisition and analysis time for larger proteins.

  6. Data acquisition backbone core DABC release v1.0

    Energy Technology Data Exchange (ETDEWEB)

    Adamczewski-Musch, Joern; Essel, Hans G.; Kurz, Nikolaus; Linev, S. [GSI Helmholtzzentrum fuer Schwerionenforschung, Darmstadt (Germany)

    2010-07-01

    The new experiments at FAIR require new concepts of data acquisition systems for the distribution of self-triggered, time stamped data streams over high performance networks for event building. The Data Acquisition Backbone Core (DABC) is a general purpose software framework developed for the implementation of such data acquisition systems. A DABC application consists of functional components like data input, combiner, scheduler, event builder, filter, analysis and storage which can be configured at runtime. Application specific code including the support of all kinds of data channels (front-end systems) is implemented by C++ program plug-ins. DABC is also well suited as environment for various detector and readout components test beds. A set of DABC plug-ins has been developed for the FAIR experiment CBM (Compressed Baryonic Matter) at GSI. This DABC application is used as DAQ system for test beamtimes. Front-end boards equipped with n-XYTER ASICs and ADCs are connected to read-out controller boards (ROC). From there the data is sent over Ethernet (UDP), or over optics and PCIe interface cards into Linux PCs. DABC does the controlling, event building, archiving and data serving. The first release of DABC was published in 2009 and is available under GPL license.

  7. Backbone of complex networks of corporations: The flow of control

    Science.gov (United States)

    Glattfelder, J. B.; Battiston, S.

    2009-09-01

    We present a methodology to extract the backbone of complex networks based on the weight and direction of links, as well as on nontopological properties of nodes. We show how the methodology can be applied in general to networks in which mass or energy is flowing along the links. In particular, the procedure enables us to address important questions in economics, namely, how control and wealth are structured and concentrated across national markets. We report on the first cross-country investigation of ownership networks, focusing on the stock markets of 48 countries around the world. On the one hand, our analysis confirms results expected on the basis of the literature on corporate control, namely, that in Anglo-Saxon countries control tends to be dispersed among numerous shareholders. On the other hand, it also reveals that in the same countries, control is found to be highly concentrated at the global level, namely, lying in the hands of very few important shareholders. Interestingly, the exact opposite is observed for European countries. These results have previously not been reported as they are not observable without the kind of network analysis developed here.

  8. Backbone of complex networks of corporations: the flow of control.

    Science.gov (United States)

    Glattfelder, J B; Battiston, S

    2009-09-01

    We present a methodology to extract the backbone of complex networks based on the weight and direction of links, as well as on nontopological properties of nodes. We show how the methodology can be applied in general to networks in which mass or energy is flowing along the links. In particular, the procedure enables us to address important questions in economics, namely, how control and wealth are structured and concentrated across national markets. We report on the first cross-country investigation of ownership networks, focusing on the stock markets of 48 countries around the world. On the one hand, our analysis confirms results expected on the basis of the literature on corporate control, namely, that in Anglo-Saxon countries control tends to be dispersed among numerous shareholders. On the other hand, it also reveals that in the same countries, control is found to be highly concentrated at the global level, namely, lying in the hands of very few important shareholders. Interestingly, the exact opposite is observed for European countries. These results have previously not been reported as they are not observable without the kind of network analysis developed here.

  9. Peptide Backbone Sampling Convergence with the Adaptive Biasing Force Algorithm

    Science.gov (United States)

    Faller, Christina E.; Reilly, Kyle A.; Hills, Ronald D.; Guvench, Olgun

    2013-01-01

    Complete Boltzmann sampling of reaction coordinates in biomolecular systems continues to be a challenge for unbiased molecular dynamics simulations. A growing number of methods have been developed for applying biases to biomolecular systems to enhance sampling while enabling recovery of the unbiased (Boltzmann) distribution of states. The Adaptive Biasing Force (ABF) algorithm is one such method, and works by canceling out the average force along the desired reaction coordinate(s) using an estimate of this force progressively accumulated during the simulation. Upon completion of the simulation, the potential of mean force, and therefore Boltzmann distribution of states, is obtained by integrating this average force. In an effort to characterize the expected performance in applications such as protein loop sampling, ABF was applied to the full ranges of the Ramachandran ϕ/ψ backbone dihedral reaction coordinates for dipeptides of the 20 amino acids using all-atom explicit-water molecular dynamics simulations. Approximately half of the dipeptides exhibited robust and rapid convergence of the potential of mean force as a function of ϕ/ψ in triplicate 50-ns simulations, while the remainder exhibited varying degrees of less complete convergence. The greatest difficulties in achieving converged ABF sampling were seen in the branched-sidechain amino acids threonine and valine, as well as the special case of proline. Proline dipeptide sampling was further complicated by trans-to-cis peptide bond isomerization not observed in unbiased control molecular dynamics simulations. Overall, the ABF method was found to be a robust means of sampling the entire ϕ/ψ reaction coordinate for the 20 amino acids, including high free-energy regions typically inaccessible in standard molecular dynamics simulations. PMID:23215032

  10. MCBT: Multi-Hop Cluster Based Stable Backbone Trees for Data Collection and Dissemination in WSNs.

    Science.gov (United States)

    Shin, Inyoung; Kim, Moonseong; Mutka, Matt W; Choo, Hyunseung; Lee, Tae-Jin

    2009-01-01

    We propose a stable backbone tree construction algorithm using multi-hop clusters for wireless sensor networks (WSNs). The hierarchical cluster structure has advantages in data fusion and aggregation. Energy consumption can be decreased by managing nodes with cluster heads. Backbone nodes, which are responsible for performing and managing multi-hop communication, can reduce the communication overhead such as control traffic and minimize the number of active nodes. Previous backbone construction algorithms, such as Hierarchical Cluster-based Data Dissemination (HCDD) and Multicluster, Mobile, Multimedia radio network (MMM), consume energy quickly. They are designed without regard to appropriate factors such as residual energy and degree (the number of connections or edges to other nodes) of a node for WSNs. Thus, the network is quickly disconnected or has to reconstruct a backbone. We propose a distributed algorithm to create a stable backbone by selecting the nodes with higher energy or degree as the cluster heads. This increases the overall network lifetime. Moreover, the proposed method balances energy consumption by distributing the traffic load among nodes around the cluster head. In the simulation, the proposed scheme outperforms previous clustering schemes in terms of the average and the standard deviation of residual energy or degree of backbone nodes, the average residual energy of backbone nodes after disseminating the sensed data, and the network lifetime.

  11. Ruthenium-catalyzed olefin metathesis accelerated by the steric effect of the backbone substituent in cyclic (alkyl)(amino) carbenes.

    Science.gov (United States)

    Zhang, Jun; Song, Shangfei; Wang, Xiao; Jiao, Jiajun; Shi, Min

    2013-10-21

    Three ruthenium complexes bearing backbone-monosubstituted CAACs were prepared and displayed dramatic improvement in catalytic efficiency not only in RCM reaction but also in the ethenolysis of methyl oleate, compared to those bearing backbone-disubstituted CAACs.

  12. Pseudo 5D HN(C)N Experiment to Facilitate the Assignment of Backbone Resonances in Proteins Exhibiting High Backbone Shift Degeneracy

    CERN Document Server

    Kumar, Dinesh; Shukla, Vaibhav Kumar; Pandey, Himanshu; Arora, Ashish; Guleria, Anupam

    2014-01-01

    Assignment of protein backbone resonances is most routinely carried out using triple resonance three dimensional NMR experiments involving amide 1H and 15N resonances. However for intrinsically unstructured proteins, alpha-helical proteins or proteins containing several disordered fragments, the assignment becomes problematic because of high degree of backbone shift degeneracy. In this backdrop, a novel reduced dimensionality (RD) experiment -(5,3)D-hNCO-CANH- is presented to facilitate (and/or to validate) the sequential backbone resonance assignment in such proteins. The proposed 3D NMR experiment makes use of the modulated amide 15N chemical shifts (resulting from the joint sampling along both its indirect dimensions) to resolve the ambiguity involved in connecting the neighboring amide resonances (i.e. HiNi and Hi-1Ni-1) for overlapping amide NH peaks. The experiment -encoding 5D spectral information- leads to a conventional 3D spectrum with significantly reduced spectral crowding and complexity. The impr...

  13. Chemistry and applications of inorganic-organic polymers : organically modified silicates

    OpenAIRE

    Schmidt, Helmut K.; Seiferling, Bernhard

    1986-01-01

    The conbination of inorganic polymeric networks with organic components leads ot inorganic-organic polymers. A convenient method for the introduction of organic radials into an inorganic backbone is the use of aorganosubstituted silico esters in a polycondensation process. This leads to ≡Si-O-Si≡ network containing materials, so-called organically modified silicates (ORMOSILs). For the synthesis of the inorganic backbone, in opposition to the high temperature preparation of non-me...

  14. Dependence of crystallite formation and preferential backbone orientations on the side chain pattern in PBDTTPD polymers

    KAUST Repository

    El Labban, Abdulrahman

    2014-11-26

    (Figure Presented) Alkyl substituents appended to the π-conjugated main chain account for the solution-processability and film-forming properties of most π-conjugated polymers for organic electronic device applications, including field-effect transistors (FETs) and bulk-heterojunction (BHJ) solar cells. Beyond film-forming properties, recent work has emphasized the determining role that side-chain substituents play on polymer self-assembly and thin-film nanostructural order, and, in turn, on device performance. However, the factors that determine polymer crystallite orientation in thin-films, implying preferential backbone orientation relative to the device substrate, are a matter of some debate, and these structural changes remain difficult to anticipate. In this report, we show how systematic changes in the side-chain pattern of poly(benzo[1,2-b:4,5-b′]dithiophene-alt-thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymers can (i) influence the propensity of the polymer to order in the π-stacking direction, and (ii) direct the preferential orientation of the polymer crystallites in thin films (e.g., "face-on" vs "edge-on"). Oriented crystallites, specifically crystallites that are well-ordered in the π-stacking direction, are believed to be a key contributor to improved thin-film device performance in both FETs and BHJ solar cells.

  15. Dependence of crystallite formation and preferential backbone orientations on the side chain pattern in PBDTTPD polymers.

    Science.gov (United States)

    El Labban, Abdulrahman; Warnan, Julien; Cabanetos, Clément; Ratel, Olivier; Tassone, Christopher; Toney, Michael F; Beaujuge, Pierre M

    2014-11-26

    Alkyl substituents appended to the π-conjugated main chain account for the solution-processability and film-forming properties of most π-conjugated polymers for organic electronic device applications, including field-effect transistors (FETs) and bulk-heterojunction (BHJ) solar cells. Beyond film-forming properties, recent work has emphasized the determining role that side-chain substituents play on polymer self-assembly and thin-film nanostructural order, and, in turn, on device performance. However, the factors that determine polymer crystallite orientation in thin-films, implying preferential backbone orientation relative to the device substrate, are a matter of some debate, and these structural changes remain difficult to anticipate. In this report, we show how systematic changes in the side-chain pattern of poly(benzo[1,2-b:4,5-b']dithiophene-alt-thieno[3,4-c]pyrrole-4,6-dione) (PBDTTPD) polymers can (i) influence the propensity of the polymer to order in the π-stacking direction, and (ii) direct the preferential orientation of the polymer crystallites in thin films (e.g., "face-on" vs "edge-on"). Oriented crystallites, specifically crystallites that are well-ordered in the π-stacking direction, are believed to be a key contributor to improved thin-film device performance in both FETs and BHJ solar cells.

  16. Influence of backbone rigidness on single chain conformation of thiophene-based conjugated polymers.

    Science.gov (United States)

    Hu, Zhongjian; Liu, Jianhua; Simón-Bower, Lauren; Zhai, Lei; Gesquiere, Andre J

    2013-04-25

    Structural order of conjugated polymers at different length scales directs the optoelectronic properties of the corresponding materials; thus it is of critical importance to understand and control conjugated polymer morphology for successful application of these materials in organic optoelectronics. Herein, with the aim of probing the dependence of single chain folding properties on the chemical structure and rigidness of the polymer backbones, single molecule fluorescence spectroscopy was applied to four thiophene-based conjugated polymers. These include regioregular poly(3-hexylthiophene) (RR-P3HT), poly(2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT-14), poly(2,5-bis(3-tetradecylthiophen-2-yl)thiophene-2-yl)thiophen-2-ylthiazolo[5,4-d]thiazole) (PTzQT-12), and poly(3,3-didodecylquaterthiophene)] (PQT-12). Our previous work has shown that RR-P3HT and PBTTT-14 polymer chains fold in their nanostructures, whereas PQT-12 and PTzQT-12 do not fold in their nanostructures. At the single molecule level, it was found that RR-P3HT single chains almost exclusively fold into loosely and strongly aggregated conformations, analogous to the folding properties in nanostructures. PQT-12 displays significant chain folding as well, but only into loosely aggregated conformations, showing an absence of strongly aggregated polymer chains. PBTTT-14 exhibits a significant fraction of rigid polymer chain. The findings made for single molecules of PQT-12 and PBTTT-14 are thus in contrast with the observations made in their corresponding nanostructures. PTzQT-12 appears to be the most rigid and planar conjugated polymer of these four polymers. However, although the presumably nonfolding polymers PQT-12 and PTzQT-12 exhibit less folding than RR-P3HT, there is still a significant occurrence of chain folding for these polymers at the single molecule level. These results suggest that the folding properties of conjugated polymers can be influenced by the architecture of the

  17. A Distributed Virtual Backbone Formation for Wireless Ad Hoc and Sensor Networks

    Institute of Scientific and Technical Information of China (English)

    CAO Yong-tao; HE Chen; JIANG Ling-ge

    2007-01-01

    The virtual backbone is an approach for solving routing problems in wireless ad hoc and sensor networks. A connected dominating set (CDS) was proposed as a virtual backbone to improve the performance of wireless networks. The quality of a virtual backbone is measured not only by approximation factor, which is the ratio of its size to that of minimum CDS, but also time complexity and message complexity. In this paper, a distributed algorithm is presented to construct a minimum CDS for ad hoc and sensor networks. By destroying triangular loops in the virtual backbone, the proposed algorithm can effectively construct a CDS with smaller size. Moreover, our algorithm, which is fully localized, has a constant approximation ratio, linear message and time complexity, and low implementation complexity. The simulation results and theoretical analysis show that our algorithm has better efficiency and performance than conventional approaches.

  18. Conjugated polyions : Polymers with ionic, water-soluble backbones

    NARCIS (Netherlands)

    Voortman, Thomas Pieter

    2016-01-01

    Organic photovoltaics (OPV) is an emerging solar power technology in which the active layer consists of molecules that are built-up mostly from carbon and hydrogen. However, OPV technologies still face major scientific challenges: high performance materials with good synthetic accessibility must be

  19. Gender features of functional condition of backbone of teenagers with scoliotic posture

    Directory of Open Access Journals (Sweden)

    Sergiy Afanasiev

    2016-10-01

    Full Text Available Purpose: to study mobility of backbone, endurance of muscles of a trunk and to define gender features of functional condition of backbone at children of the middle school age with scoliotic posture depending on the direction of the top of arch of curvature of spine. Material & Methods: 40 girls and 40 boys, including 18 girls and 18 boys with the right-side deformation of backbone in the thoracic department, the left-side – 22 girls and 22 boys are examined. Results: features of changes of indicators, depending on sex of children and frontage of the top of arch of curvature of spine column, are revealed when studying the level of flexibility of backbone and endurance of muscles of a trunk at children of the middle school age with scoliotic posture. Conclusions: it is established that the level of decrease in flexibility of backbone is higher at boys, than at girls, whereas indicators of contractile ability and tone of muscles of "muscular corset" are higher at boys.

  20. Poly(meta-phenylene) Derivative with Rigid Twisted Biphenyl Units in Backbone: Synthesis, Structural Characterization,Photophysical Properties and Electroluminescence

    Institute of Scientific and Technical Information of China (English)

    ZHENG Yan; YANG Bing; ZHANG Hai-quan; LU Ping; SHEN Fang-zhong; LIU Lin-lin; XU Hai; YANG Guang-di; MA Yu-guang

    2007-01-01

    A soluble poly(meta-phenylene) derivative with rigid twisted biphenyl unit was synthesized by the Yamamoto coupling reaction. The polymer is soluble in common organic solvents, and the number-average molecular weight is about 6500. The UV-Vis and quantum chemical calculation indicate that the different conformation segments named "conformers" exist in the polymer backbones; it was also further confirmed by the single crystal X-ray diffraction study of the dimeric model compound. The π-π* transition of biphenyl segments of twisted and planar conformations made the polymer exhibit a strong absorption around 256 nm and a weak absorption at about 300 nm. Furthermore,the polymer exhibits a strong UV photoluminescence at 372 nm when the excitation wavelengths are longer than 300 nm. The ultraviolet-emitting electroluminescence(EL) device with the single layer structure shows EL λmax of the derivative at 370 nm.

  1. INFLUENCE OF BACKBONE RIGIDITY ON THE LIQUID CRYSTALLINITY OF MESOGEN-CONTAINING POLYACETYLENES

    Institute of Scientific and Technical Information of China (English)

    1998-01-01

    Two acetylene polymers containing cyanobiphenyl-based mesogens,poly{10-[((4'-cyano-4-biphenylyl)oxy)carbonyl]-1-decyne} (PA8CN), which has a relatively flexible polyalkyne backbone, and poly {[4-(((12-((4'-cyano-4-biphenylyl)oxy)dodecyl)oxy)carbonyl) phenyl]-acetylene} (PB12CN), which has a fairly rigid poly(phenylacetylene)backbone, were synthesized using respectively WCl6 and [Rh(nbd)Cl]2 as the catalysts.PA8CN exhibits enantiotropic interdigitated smectic A phase (SAd) over a temperature range as wide as ca. 100℃, whereas PB12CN is non-mesomorphic, demonstrating that the backbone rigidity plays an important role in determining the liquid crystallinity of the polyacetylenes.

  2. Wetting of nonconserved residue-backbones: A feature indicative of aggregation associated regions of proteins.

    Science.gov (United States)

    Pradhan, Mohan R; Pal, Arumay; Hu, Zhongqiao; Kannan, Srinivasaraghavan; Chee Keong, Kwoh; Lane, David P; Verma, Chandra S

    2016-02-01

    Aggregation is an irreversible form of protein complexation and often toxic to cells. The process entails partial or major unfolding that is largely driven by hydration. We model the role of hydration in aggregation using "Dehydrons." "Dehydrons" are unsatisfied backbone hydrogen bonds in proteins that seek shielding from water molecules by associating with ligands or proteins. We find that the residues at aggregation interfaces have hydrated backbones, and in contrast to other forms of protein-protein interactions, are under less evolutionary pressure to be conserved. Combining evolutionary conservation of residues and extent of backbone hydration allows us to distinguish regions on proteins associated with aggregation (non-conserved dehydron-residues) from other interaction interfaces (conserved dehydron-residues). This novel feature can complement the existing strategies used to investigate protein aggregation/complexation.

  3. No-Enclave Percolation Corresponds to Holes in the Cluster Backbone

    Science.gov (United States)

    Hu, Hao; Ziff, Robert M.; Deng, Youjin

    2016-10-01

    The no-enclave percolation (NEP) model introduced recently by Sheinman et al. can be mapped to a problem of holes within a standard percolation backbone, and numerical measurements of such holes give the same size-distribution exponent τ =1.82 (1 ) as found for the NEP model. An argument is given that τ =1 +dB/2 ≈1.822 for backbone holes, where dB is the backbone dimension. On the other hand, a model of simple holes within a percolation cluster yields τ =1 +df/2 =187 /96 ≈1.948 , where df is the fractal dimension of the cluster, and this value is consistent with the experimental results of gel collapse of Sheinman et al., which give τ =1.91 (6 ). This suggests that the gel clusters are of the universality class of percolation cluster holes. Both models give a discontinuous maximum hole size at pc, signifying explosive percolation behavior.

  4. Mnn10 Maintains Pathogenicity in Candida albicans by Extending α-1,6-Mannose Backbone to Evade Host Dectin-1 Mediated Antifungal Immunity.

    Directory of Open Access Journals (Sweden)

    Shi Qun Zhang

    2016-05-01

    Full Text Available The cell wall is a dynamic structure that is important for the pathogenicity of Candida albicans. Mannan, which is located in the outermost layer of the cell wall, has been shown to contribute to the pathogenesis of C. albicans, however, the molecular mechanism by which this occurs remains unclear. Here we identified a novel α-1,6-mannosyltransferase encoded by MNN10 in C. albicans. We found that Mnn10 is required for cell wall α-1,6-mannose backbone biosynthesis and polysaccharides organization. Deletion of MNN10 resulted in significant attenuation of the pathogenesis of C. albicans in a murine systemic candidiasis model. Inhibition of α-1,6-mannose backbone extension did not, however, impact the invasive ability of C. albicans in vitro. Notably, mnn10 mutant restored the invasive capacity in athymic nude mice, which further supports the notion of an enhanced host antifungal defense related to this backbone change. Mnn10 mutant induced enhanced Th1 and Th17 cell mediated antifungal immunity, and resulted in enhanced recruitment of neutrophils and monocytes for pathogen clearance in vivo. We also demonstrated that MNN10 could unmask the surface β-(1,3-glucan, a crucial pathogen-associated molecular pattern (PAMP of C. albicans recognized by host Dectin-1. Our results demonstrate that mnn10 mutant could stimulate an enhanced Dectin-1 dependent immune response of macrophages in vitro, including the activation of nuclear factor-κB, mitogen-activated protein kinase pathways, and secretion of specific cytokines such as TNF-α, IL-6, IL-1β and IL-12p40. In summary, our study indicated that α-1,6-mannose backbone is critical for the pathogenesis of C. albicans via shielding β-glucan from recognition by host Dectin-1 mediated immune recognition. Moreover, our work suggests that inhibition of α-1,6-mannose extension by Mnn10 may represent a novel modality to reduce the pathogenicity of C. albicans.

  5. Using Excel To Study The Relation Between Protein Dihedral Angle Omega And Backbone Length

    Science.gov (United States)

    Shew, Christopher; Evans, Samari; Tao, Xiuping

    How to involve the uninitiated undergraduate students in computational biophysics research? We made use of Microsoft Excel to carry out calculations of bond lengths, bond angles and dihedral angles of proteins. Specifically, we studied protein backbone dihedral angle omega by examining how its distribution varies with the length of the backbone length. It turns out Excel is a respectable tool for this task. An ordinary current-day desktop or laptop can handle the calculations for midsized proteins in just seconds. Care has to be taken to enter the formulas for the spreadsheet column after column to minimize the computing load. Supported in part by NSF Grant #1238795.

  6. Organizations

    DEFF Research Database (Denmark)

    Hatch, Mary Jo

    Most of us recognize that organizations are everywhere. You meet them on every street corner in the form of families and shops, study in them, work for them, buy from them, pay taxes to them. But have you given much thought to where they came from, what they are today, and what they might become...... and considers many more. Mary Jo Hatch introduces the concept of organizations by presenting definitions and ideas drawn from the a variety of subject areas including the physical sciences, economics, sociology, psychology, anthropology, literature, and the visual and performing arts. Drawing on examples from...... prehistory and everyday life, from the animal kingdom as well as from business, government, and other formal organizations, Hatch provides a lively and thought provoking introduction to the process of organization....

  7. Influence of structures of polymer backbones on cooperative photoreorientation behavior of p-cyanoazobenzene side chains

    DEFF Research Database (Denmark)

    Han, Mina; Kidowaki, Masatoshi; Ichimura, Kunihiro;

    2001-01-01

    Photoinduced orientational behavior of a polymethacrylate (CN6) and a polyester (p6a12) with p-cyanoazobenzene side chains was studied to reveal the structural effect of the liquid crystalline polymer backbones. Irradiation with linearly polarized W light resulted in the reorientation of the azob...

  8. Analysis of components of conserved "backbone sequences" among genomes of Shigella spp. strains

    Institute of Scientific and Technical Information of China (English)

    LIU Hong; PENG Junping; YANG Jian; SUN Lilian; CHEN Shuxia; Jin Qi

    2004-01-01

    Difference in the genomic compositions of prokaryotes is the basis of the diversity in their biological characters. However, besides their flora- or strain-specific genes, those floras with closer relationship in the evolution also have conserved "backbone sequences", which reveal the marks of their origin and evolution, and these "backbone sequences" are just the basis of their elementary living abilities and common biological properties. Shigella is very closely related to E. coli in the origin and evolution, and may turn out to belong to the same genus. In this study, a microarray containing E. coli K-12 whole genome and Sf301 specific ORFs is used to investigate the genomic components of four Shigella strains. The results indicate that 16%-22% K-12 ORFs sequences are not detected in the genome of Shigella strains while the genome of Shigella contains at least 2800 conserved ORFs, which compose the common "backbone sequences". Advanced analysis indicated that the "backbone sequences" are the essential components in maintaining the normal physiological activities of intestinal bacteria. Furthermore, only 20% Sf301-specific ORFs exist in other strains simultaneously, which demonstrate the great genome heterogeneity and the genetic diversity among the strains.

  9. Peptide-functionalized semiconductor surfaces: strong surface electronic effects from minor alterations to backbone composition.

    Science.gov (United States)

    Matmor, Maayan; Lengyel, George A; Horne, W Seth; Ashkenasy, Nurit

    2017-02-22

    The use of non-canonical amino acids is a powerful way to control protein structure. Here, we show that subtle changes to backbone composition affect the ability of a dipeptide to modify solid surface electronic properties. The extreme sensitivity of the interactions to the peptide structure suggests potential applications in improving the performance of electronic devices.

  10. Integrative technology of massage manipulations in physical rehabilitation of students with backbone pathology

    Directory of Open Access Journals (Sweden)

    Kotelevskiy V.I.

    2016-06-01

    Full Text Available Purpose: to analyze effectiveness of massage manipulations’ integrative technology in physical rehabilitation of higher educational establishments’ students with backbone pathology. Material: in the research 195 students of 19-20 years’ age participated. All students had periodical initial neurological symptoms of functional pathology and first stage osteochondrosis in different parts of backbone. We conducted a course of 10 sessions of therapeutic massage. Results: the sense of massage integrative technology is that every specialist shall have certain optimal set of skills and knowledge in technique of manipulation sessions of massage. Integrative technology of massage manipulations consists of psycho-corrective and manipulation parts. It considers psycho-somatic, mechanical and reflex rehabilitation aspects of patho-genesis of backbone functional disorders and vertebral osteochondrosis. Conclusions: depending on pathological process or backbone functional state of every person (peculiarities of his (her psycho-somatic status or, even, his (her bents. Individual approach in choice of strategy, tactic and methodological provisioning of massage session shall be used.

  11. Sequential insertion of three different organometallics into a versatile building block containing a PNA backbone.

    Science.gov (United States)

    Patra, Malay; Gasser, Gilles; Bobukhov, Dmytro; Merz, Klaus; Shtemenko, Alexander V; Metzler-Nolte, Nils

    2010-06-28

    In the view of developing a synthetic route for the controlled insertion of distinct organometallic moieties into peptide nucleic acid (PNA) oligomers, a proof-of-principle study of the chemoselective insertion of three different organometallics into a building block containing both a PNA backbone and an alkyne side-chain is presented in this study.

  12. Treatment Results of Injuries of Thoracic and Lumbar Backbone Departments at Osteoporosis Patients

    Directory of Open Access Journals (Sweden)

    D.Y. Sumin

    2009-06-01

    Full Text Available Information relates to radiologic (computer tomography manifestations providing the visualization of thoracic and lumbar backbone department injuries at osteoporotic patients. Contemporary methods of transcutaneous and trans-pedicle vertebroplasty with bone cement allows to obtain a stable positive healing effect against such pathologies.

  13. Synthesis of a Backbone Hexasaccharide Fragment of the Pectic Polysaccharide Rhamnogalacturonan I

    DEFF Research Database (Denmark)

    Zakharova, Alexandra N.; Madsen, Robert; Clausen, Mads H.

    2013-01-01

    Synthesis of the fully unprotected hexasaccharide backbone of the pectic polysaccharide rhamnogalacturonan I is described. The strategy relies on iterative coupling of a common pentenyl disaccharide glycosyl donor followed by a late-stage oxidation of the C-6 positions of the galactose residues. ...

  14. Interconnection and Competition Among Asymmetric Networks in the Internet Backbone Market

    NARCIS (Netherlands)

    Jahn, E.; Prüfer, J.

    2006-01-01

    We examine the interrelation between interconnection and competition in the internet backbone market.Networks asymmetric in size choose among different interconnection regimes and compete for end-users.We show that a direct interconnection regime, Peering, softens competition compared to indirect in

  15. Solvent-induced differentiation of protein backbone hydrogen bonds in calmodulin.

    Science.gov (United States)

    Juranić, Nenad; Atanasova, Elena; Streiff, John H; Macura, Slobodan; Prendergast, Franklyn G

    2007-07-01

    In apo and holoCaM, almost half of the hydrogen bonds (H-bonds) at the protein backbone expected from the corresponding NMR or X-ray structures were not detected by h3JNC' couplings. The paucity of the h3JNC' couplings was considered in terms of dynamic features of these structures. We examined a set of seven proteins and found that protein-backbone H-bonds form two groups according to the h3JNC' couplings measured in solution. H-bonds that have h3JNC' couplings above the threshold of 0.2 Hz show distance/angle correlation among the H-bond geometrical parameters, and appear to be supported by the backbone dynamics in solution. The other H-bonds have no such correlation; they populate the water-exposed and flexible regions of proteins, including many of the CaM helices. The observed differentiation in a dynamical behavior of backbone H-bonds in apo and holoCaM appears to be related to protein functions.

  16. Graduate Education in Kinesiology: Are We Part of "America's Backbone for Competitiveness and Innovation"?

    Science.gov (United States)

    DePauw, Karen P.

    2008-01-01

    Graduate education in the United States has been identified as being the backbone of American competitiveness and innovation in a recent report by the Council of Graduate Schools. The report provides a framework for examining the role of graduate education in partnership with business and government to advance an action agenda for achieving…

  17. Animals without Backbones: The Invertebrate Story. Grade Level 5-9.

    Science.gov (United States)

    Jerome, Brian; Fuqua, Paul

    This guide, when used in tandem with the videotape "Animals Without Backbones," helps students learn about invertebrates. These materials promote hands-on discovery and learning. The guide is composed of six curriculum-based teaching units: (1) "Getting Started"; (2) "Porifera"; (3) "Cnidarians"; (4) "Worms"; (5) "Mollusks"; (6) "Arthropods"; and…

  18. Semiconductors for organic transistors

    OpenAIRE

    Antonio Facchetti

    2007-01-01

    Organic molecules/polymers with a π-conjugated (hetero)aromatic backbone are capable of transporting charge and interact efficiently with light. Therefore, these systems can act as semiconductors in opto-electronic devices similar to inorganic materials. However, organic chemistry offers tools for tailoring materials' functional properties via modifications of the molecular/monomeric units, opening new possibilities for inexpensive device manufacturing. This article reviews the fundamental as...

  19. Analytical Model based on Green Criteria for Optical Backbone Network Interconnection

    DEFF Research Database (Denmark)

    Gutierrez Lopez, Jose Manuel; Riaz, M. Tahir; Pedersen, Jens Myrup

    2011-01-01

    to the evaluation of the environmental impact of networks from physical interconnection point of view. Networks deployment, usage, and disposal are analyzed as contributing elements to ICT’s (Information and Communications Technology) CO2 emissions. This paper presents an analytical model for evaluating...... and quantifying the CO2 emissions of optical backbone networks during their lifetime. The main goal of this work is to present the model and illustrate how to evaluate the physical interconnection of backbones from an environmental perspective. This model can be applied as a new type of decision support criteria...... for backbone’s interconnection, since minimization of CO2 emissions is becoming an important factor. In addition, two case studies are presented to illustrate the use and application of this model, and the need for de facto and international standards to reduce CO2 emissions through good network planning....

  20. Smart-Grid Backbone Network Real-Time Delay Reduction via Integer Programming.

    Science.gov (United States)

    Pagadrai, Sasikanth; Yilmaz, Muhittin; Valluri, Pratyush

    2016-08-01

    This research investigates an optimal delay-based virtual topology design using integer linear programming (ILP), which is applied to the current backbone networks such as smart-grid real-time communication systems. A network traffic matrix is applied and the corresponding virtual topology problem is solved using the ILP formulations that include a network delay-dependent objective function and lightpath routing, wavelength assignment, wavelength continuity, flow routing, and traffic loss constraints. The proposed optimization approach provides an efficient deterministic integration of intelligent sensing and decision making, and network learning features for superior smart grid operations by adaptively responding the time-varying network traffic data as well as operational constraints to maintain optimal virtual topologies. A representative optical backbone network has been utilized to demonstrate the proposed optimization framework whose simulation results indicate that superior smart-grid network performance can be achieved using commercial networks and integer programming.

  1. Backbone cyclization of a recombinant cystine-knot peptide by engineered Sortase A.

    Science.gov (United States)

    Stanger, Karen; Maurer, Till; Kaluarachchi, Harini; Coons, Mary; Franke, Yvonne; Hannoush, Rami N

    2014-11-28

    Cyclotides belong to the family of cyclic cystine-knot peptides and have shown promise as scaffolds for protein engineering and pharmacological modulation of cellular protein activity. Cyclotides are characterized by a cystine-knotted topology and a head-to-tail cyclic polypeptide backbone. While they are primarily produced in plants, cyclotides have also been obtained by chemical synthesis. However, there is still a need for methods to generate cyclotides in high yields to near homogeneity. Here, we report a biomimetic approach which utilizes an engineered version of the enzyme Sortase A to catalyze amide backbone cyclization of the recombinant cyclotide MCoTI-II, thereby allowing the efficient production of active homogenous species in high yields. Our results provide proof of concept for using engineered Sortase A to produce cyclic MCoTI-II and should be generally applicable to generating other cyclic cystine-knot peptides.

  2. Protein and peptide alkoxyl radicals can give rise to C-terminal decarboxylation and backbone cleavage

    DEFF Research Database (Denmark)

    Davies, Michael Jonathan

    1996-01-01

    when the free amino acid does not, and that hydroperoxides can be formed on both the backbone (at alpha-carbon positions) and the side chain. Decomposition of alpha-carbon hydroperoxides by Fe(II)-EDTA gives initially an alkoxyl radical via a pseudo-Fenton reaction; these radicals fragment rapidly...... with k estimated as > or = 10(7) s(-1). With N-acetyl amino acids and dipeptides beta-scission of an alkoxyl radical at the C-terminal alpha-carbon results in C-terminal decarboxylation, with release of CO2.-; the corresponding amides undergo deamidation with release of .C(O)NH2. Cyclic dipeptides...... undergo analogous reactions with cleavage of the alpha-carbon to carbonyl-carbon bond and formation of .C(O)NHR radicals. With substrates with large aliphatic side chains, radicals from side-chain hydroperoxides are also observed. C-terminal decarboxylation and backbone fragmentation are also observed...

  3. Aromatic Copolyamides with Anthrazoline Units in the Backbone: Synthesis, Characterization, Pervaporation Application

    Directory of Open Access Journals (Sweden)

    Galina A. Polotskaya

    2016-10-01

    Full Text Available Copolyamides with anthrazoline units in the backbone (coPA were synthesized and dense nonporous films were prepared by solvent evaporation. Glass transition temperature, density, and fractional free volume were determined for the dense nonporous films composed of polyamide and two of its copolymers containing 20 and 30 mol % anthrazoline units in the backbone. Transport properties of the polymer films were estimated by sorption and pervaporation tests toward methanol, toluene, and their mixtures. An increase in anthrazoline fragments content leads to an increasing degree of methanol sorption but to a decreasing degree of toluene sorption. Pervaporation of a methanol–toluene mixture was studied over a wide range of feed concentration (10–90 wt % methanol. Maximal separation factor was observed for coPA-20 containing 20 mol % fragments with anthrazoline units; maximal total flux was observed for coPA-30 with the highest fractional free volume.

  4. Energy Efficient Low-Cost Virtual Backbone Construction for Optimal Routing in Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    K. Mohaideen Pitchai

    2014-01-01

    Full Text Available Many prominent applications in wireless sensor networks which require collected information have to be routed to end nodes in an efficient manner. In general, weighted connected dominating Sets (WCDS based routing is a promising approach for enhancing the routing efficiency in sensor networks. Backbone has been used extensively in routing. Here an efficient WCDS algorithm for constructing a virtual backbone with low total cost, hop spanning ratio, and minimum number of dominators is proposed. We report a systematic approach, which has three phases. Initial phase considers the issues of revoking a partial CDS tree from a complete CDS tree. Secondary and final phases make the design of the complete algorithm by considering the determination of dominators using an iteration process. Our findings reveal better performance than the existing algorithms in terms of total cost, hop spanning ratio, and number of dominators.

  5. Synthesis, Characterization and Structure of Chiral Amino Acids and Their Corresponding Amino Alcohols with Camphoric Backbone

    Institute of Scientific and Technical Information of China (English)

    QIAN Hui-Fen; HUANG Wei; LI Hui-Hui; YAO Cheng

    2006-01-01

    Chiral amino acids and their corresponding amino alcohols bearing camphoric backbone were prepared from D-(+)-camphoric imide and characterized by infrared, elemental analysis, ESI-MS, and NMR measurements. Among them, one intermediate (lS,3R)-3-amino-2,2,3-trimethyl cyclopentane-1-carboxylic acid hydrochloride 3 was structurally elucidated by X-ray diffraction techniques. Versatile intermolecular hydrogen bonding interactions observed in its packing structure result in a two-dimensional framework.

  6. Inferential protein structure determination and refinement using fast, electronic structure based backbone amide chemical shift predictions

    CERN Document Server

    Christensen, Anders S

    2015-01-01

    This report covers the development of a new, fast method for calculating the backbone amide proton chemical shifts in proteins. Through quantum chemical calculations, structure-based forudsiglese the chemical shift for amidprotonen in protein has been parameterized. The parameters are then implemented in a computer program called Padawan. The program has since been implemented in protein folding program Phaistos, wherein the method andvendes to de novo folding of the protein structures and to refine the existing protein structures.

  7. Protein backbone dynamics revealed by quasi spectral density function analysis of amide N-15 nuclei.

    Science.gov (United States)

    Ishima, R; Nagayama, K

    1995-03-14

    Spectral density functions J(0), J(omega N), and J(omega H + omega N) of individual amide N-15 nuclei in proteins were approximated by a quasi spectral density function (QSDF). Using this function, the backbone dynamics were analyzed for seven protein systems on which data have been published. We defined J(0; omega N) as the difference between the J(0) and the J(omega N) values, which describes motions slower than 50 (or 60) MHz, and J(omega N; omega H+N) as the difference between the J(omega N) and the J(omega H + omega N) values, which describes motions slower than 450 (or 540) MHz. The QSDF analysis can easily extract the J(0; omega N) of protein backbones, which have often some relation to biologically relevant reactions. Flexible N-terminal regions in eglin c and glucose permease IIA and a loop region in eglin c showed smaller values of both the J(0; omega N) and the J(omega N; omega H+N) as compared with the other regions, indicating increases in motions faster than nanosecond. The values of the J(0; omega N) for the backbone of the FK506 binding protein showed a large variation in the apoprotein but fell in a very narrow range after the binding of FK506. Characteristic increase or decrease in the values of J(0) and J(omega N) was observed in two or three residues located between secondary structures.

  8. NMR backbone dynamics of VEK-30 bound to the human plasminogen kringle 2 domain.

    Science.gov (United States)

    Wang, Min; Prorok, Mary; Castellino, Francis J

    2010-07-07

    To gain insights into the mechanisms for the tight and highly specific interaction of the kringle 2 domain of human plasminogen (K2(Pg)) with a 30-residue internal peptide (VEK-30) from a group A streptococcal M-like protein, the dynamic properties of free and bound K2(Pg) and VEK-30 were investigated using backbone amide (15)N-NMR relaxation measurements. Dynamic parameters, namely the generalized order parameter, S(2), the local correlation time, tau(e), and the conformational exchange contribution, R(ex), were obtained for this complex by Lipari-Szabo model-free analysis. The results show that VEK-30 displays distinctly different dynamic behavior as a consequence of binding to K2(Pg), manifest by decreased backbone flexibility, particularly at the binding region of the peptide. In contrast, the backbone dynamics parameters of K2(Pg) displayed similar patterns in the free and bound forms, but, nonetheless, showed interesting differences. Based on our previous structure-function studies of this interaction, we also made comparisons of the VEK-30/K2(Pg) dynamics results from different kringle modules complexed with small lysine analogs. The differences in dynamics observed for kringles with different ligands provide what we believe to be new insights into the interactions responsible for protein-ligand recognition and a better understanding of the differences in binding affinity and binding specificity of kringle domains with various ligands.

  9. An Analytic Method for the Kinematics and Dynamics of a Multiple-Backbone Continuum Robot

    Directory of Open Access Journals (Sweden)

    Bin He

    2013-01-01

    Full Text Available Continuum robots have been the subject of extensive research due to their potential use in a wide range of applications. In this paper, we propose a new continuum robot with three backbones, and provide a unified analytic method for the kinematics and dynamics of a multiple‐backbone continuum robot. The robot achieves actuation by independently pulling three backbones to carry out a bending motion of two‐degrees‐of‐freedom (DoF. A three‐dimensional CAD model of the robot is built and the kinematical equation is established on the basis of the Euler‐Bernoulli beam. The dynamical model of the continuum robot is constructed by using the Lagrange method. The simulation and the experiment’s validation results show the continuum robot can exactly bend into pre‐set angles in the two‐dimensional space (the maximum error is less than 5% of the robot length and can make a circular motion in three‐dimensional space. The results demonstrate that the proposed analytic method for the kinematics and dynamics of a continuum robot is feasible.

  10. East vergent structure of Backbone Range: Insights from A-Lan-Yi area and sandbox modeling

    Science.gov (United States)

    Lee, C. A.; Lu, C. Y.

    2015-12-01

    Southern Taiwan, including Pingtung peninsula and Taitung, is the incipient oblique collision zone of Eurasian plate and Philippine Sea plate. The Luzon volcanic arc converged toward Taiwan Island and formed Hengchun Ridge south offshore Taiwan. Thus, Taiwan mountain belt developed from north to south as the Backbone Range, so that we can infer the incipient feature structure from the topography and outcrop study of southern Taiwan. Our field survey of this study concentrated at the southeast coastline of Taiwan, also known as A-Lan-Yi Trail. According to previous study, the deformational structures such as faults and folds are consistent with regional kinematic processes, and the preserved transpression structure is the most important evidence of incipient collision. In this study, we use the sedimentary sequences of study area to trace the regional tectonics from north to south. Discovered structures in this area show the similar kinematic history as the eastern flank of Backbone Range, so that we suggest they are at the same series of a tectonic event. To complete the regional structure mapping in this accessible area, besides the field geological data, we also applied the LiDAR-derived DTM which is a 3D visualization technology to improve our topography information. In addition, we use the sandbox modeling to demonstrate the development of structures in the eastern flank of Backbone Range. After combining the results of field observation and regional structure mapping, this study provides a strong evidence of backthrusting and backfolding deformation during the incipient oblique collision stage.

  11. Membrane adsorption and binding, cellular uptake and cytotoxicity of cell-penetrating peptidomimetics with α-peptide/β-peptoid backbone

    DEFF Research Database (Denmark)

    Jing, Xiaona; Yang, Mingjun; Kasimova, Marina Robertovna

    2012-01-01

    Cell-penetrating peptides (CPPs) provide a promising approach for enhancing intracellular delivery of therapeutic biomacromolecules by increasing transport through membrane barriers. Here, proteolytically stable cell-penetrating peptidomimetics with α-peptide/β-peptoid backbone were studied to ev...

  12. Synthesis and Molecular Recognition of Novel Cyclic Pseudopeptides Containing L-Glutamic Acid or L-Aspartic Acid Backbones

    Institute of Scientific and Technical Information of China (English)

    WANG Tao王涛; HUANG Xiao-Yi黄小毅; XIA Chuan-Qin夏传琴; YU Xiao-Qi余孝其; XIE Ru-Gang谢如刚

    2004-01-01

    Novel cyclic pseudopeptides containing L-glutamic acid or L-aspartic acid backbone structures were efficiently synthesized and characterized. Their chiral recognition properties for L- and D-amino acid methyl ester hydrochloride were discussed also.

  13. Oxidation Responsive Polymers with a Triggered Degradation via Arylboronate Self-Immolative Motifs on a Polyphosphazene Backbone

    Science.gov (United States)

    2017-01-01

    Oxidation responsive polymers with triggered degradation pathways have been prepared via attachment of self-immolative moieties onto a hydrolytically unstable polyphosphazene backbone. After controlled main-chain growth, postpolymerization functionalization allows the preparation of hydrolytically stable poly(organo)phosphazenes decorated with a phenylboronic ester caging group. In oxidative environments, triggered cleavage of the caging group is followed by self-immolation, exposing the unstable glycine-substituted polyphosphazene which subsequently undergoes to backbone degradation to low-molecular weight molecules. As well as giving mechanistic insights, detailed GPC and 1H and 31P NMR analysis reveal the polymers to be stable in aqueous solutions, but show a selective, fast degradation upon exposure to hydrogen peroxide containing solutions. Since the post-polymerization functionalization route allows simple access to polymer backbones with a broad range of molecular weights, the approach of using the inorganic backbone as a platform significantly expands the toolbox of polymers capable of stimuli-responsive degradation.

  14. Synthesis of novel cationic lipids with fully or partially non-scissile linkages between the hydrocarbon chains and pseudoglyceryl backbone

    Indian Academy of Sciences (India)

    Santanu Bhattacharya; Saubhik Haldar

    2002-06-01

    Five novel cationic lipids with fully or partially non-scissile linkage regions between the pseudoglyceryl backbone and the hydrocarbon chains have been synthesized. The membrane-forming properties of these new lipids are briefly presented.

  15. Effect of Liquid-Crystalline Epoxy Backbone Structure on Thermal Conductivity of Epoxy-Alumina Composites

    Science.gov (United States)

    Giang, Thanhkieu; Kim, Jinhwan

    2017-01-01

    In a series of papers published recently, we clearly demonstrated that the most important factor governing the thermal conductivity of epoxy-Al2O3 composites is the backbone structure of the epoxy. In this study, three more epoxies based on diglycidyl ester-terminated liquid-crystalline epoxy (LCE) have been synthesized to draw conclusions regarding the effect of the epoxy backbone structure on the thermal conductivity of epoxy-alumina composites. The synthesized structures were characterized by proton nuclear magnetic resonance (1H-NMR) and Fourier-transform infrared (FT-IR) spectroscopy. Differential scanning calorimetry, thermogravimetric analysis, and optical microscopy were also employed to examine the thermal and optical properties of the synthesized LCEs and the cured composites. All three LCE resins exhibited typical liquid-crystalline behaviors: clear solid crystalline state below the melting temperature ( T m), sharp crystalline melting at T m, and transition to nematic phase above T m with consequent isotropic phase above the isotropic temperature ( T i). The LCE resins displayed distinct nematic liquid-crystalline phase over a wide temperature range and retained liquid-crystalline phase after curing, with high thermal conductivity of the resulting composite. The thermal conductivity values ranged from 3.09 W/m-K to 3.89 W/m-K for LCE-Al2O3 composites with 50 vol.% filler loading. The steric effect played a governing role in the difference. The neat epoxy resin thermal conductivity was obtained as 0.35 W/m-K to 0.49 W/m-K based on analysis using the Agari-Uno model. The results clearly support the objective of this study in that the thermal conductivity of the LCE-containing networks strongly depended on the epoxy backbone structure and the degree of ordering in the cured network.

  16. Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design.

    Directory of Open Access Journals (Sweden)

    Colin A Smith

    Full Text Available Predicting the set of sequences that are tolerated by a protein or protein interface, while maintaining a desired function, is useful for characterizing protein interaction specificity and for computationally designing sequence libraries to engineer proteins with new functions. Here we provide a general method, a detailed set of protocols, and several benchmarks and analyses for estimating tolerated sequences using flexible backbone protein design implemented in the Rosetta molecular modeling software suite. The input to the method is at least one experimentally determined three-dimensional protein structure or high-quality model. The starting structure(s are expanded or refined into a conformational ensemble using Monte Carlo simulations consisting of backrub backbone and side chain moves in Rosetta. The method then uses a combination of simulated annealing and genetic algorithm optimization methods to enrich for low-energy sequences for the individual members of the ensemble. To emphasize certain functional requirements (e.g. forming a binding interface, interactions between and within parts of the structure (e.g. domains can be reweighted in the scoring function. Results from each backbone structure are merged together to create a single estimate for the tolerated sequence space. We provide an extensive description of the protocol and its parameters, all source code, example analysis scripts and three tests applying this method to finding sequences predicted to stabilize proteins or protein interfaces. The generality of this method makes many other applications possible, for example stabilizing interactions with small molecules, DNA, or RNA. Through the use of within-domain reweighting and/or multistate design, it may also be possible to use this method to find sequences that stabilize particular protein conformations or binding interactions over others.

  17. ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence

    Directory of Open Access Journals (Sweden)

    Cañizares Joaquin

    2011-06-01

    Full Text Available Abstract Background The possibilities offered by next generation sequencing (NGS platforms are revolutionizing biotechnological laboratories. Moreover, the combination of NGS sequencing and affordable high-throughput genotyping technologies is facilitating the rapid discovery and use of SNPs in non-model species. However, this abundance of sequences and polymorphisms creates new software needs. To fulfill these needs, we have developed a powerful, yet easy-to-use application. Results The ngs_backbone software is a parallel pipeline capable of analyzing Sanger, 454, Illumina and SOLiD (Sequencing by Oligonucleotide Ligation and Detection sequence reads. Its main supported analyses are: read cleaning, transcriptome assembly and annotation, read mapping and single nucleotide polymorphism (SNP calling and selection. In order to build a truly useful tool, the software development was paired with a laboratory experiment. All public tomato Sanger EST reads plus 14.2 million Illumina reads were employed to test the tool and predict polymorphism in tomato. The cleaned reads were mapped to the SGN tomato transcriptome obtaining a coverage of 4.2 for Sanger and 8.5 for Illumina. 23,360 single nucleotide variations (SNVs were predicted. A total of 76 SNVs were experimentally validated, and 85% were found to be real. Conclusions ngs_backbone is a new software package capable of analyzing sequences produced by NGS technologies and predicting SNVs with great accuracy. In our tomato example, we created a highly polymorphic collection of SNVs that will be a useful resource for tomato researchers and breeders. The software developed along with its documentation is freely available under the AGPL license and can be downloaded from http://bioinf.comav.upv.es/ngs_backbone/ or http://github.com/JoseBlanca/franklin.

  18. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit.

    Directory of Open Access Journals (Sweden)

    Daniel A Keedy

    2015-10-01

    Full Text Available Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP to evaluate an extremely large number of combinations of sidechain conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the "flap" regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramatic local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Overall, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems.

  19. Limits on variations in protein backbone dynamics from precise measurements of scalar couplings.

    Science.gov (United States)

    Vögeli, Beat; Ying, Jinfa; Grishaev, Alexander; Bax, Ad

    2007-08-01

    3JHN,Halpha, 3JHN,Cbeta, and 3JHN,C' couplings, all related to the backbone torsion angle phi, were measured for the third immunoglobulin binding domain of protein G, or GB3. Measurements were carried out using both previously published methods and novel sequences based on the multiple-quantum principle, which limit attenuation of experimental couplings caused by finite lifetimes of the spin states of passive spins. High reproducibility between the multiple-quantum and conventional approaches confirms the accuracy of the measurements. With few exceptions, close agreement between 3JHN,Halpha, 3JHN,Cbeta, and 3JHN,C' and values predicted by their respective Karplus equations is observed. For the three types of couplings, up to 20% better agreement is obtained when fitting the experimental couplings to a dynamic ensemble NMR structure, which has a phi angle root-mean-square spread of 9 +/- 4 degrees and was previously calculated on the basis of a very extensive set of residual dipolar couplings, than for any single static NMR structure. Fits of 3J couplings to a 1.1-A X-ray structure, with hydrogens added in idealized positions, are 40-90% worse. Approximately half of the improvement when fitting to the NMR structures relates to the amide proton deviating from its idealized, in-peptide-plane position, indicating that the positioning of hydrogens relative to the backbone atoms is one of the factors limiting the accuracy at which the backbone torsion angle phi can be extracted from 3J couplings. Introducing an additional, residue-specific variable for the amplitude of phi angle fluctuations does not yield a statistically significant improvement when fitting to a set of dynamic Karplus curves, pointing to a homogeneous behavior of these amplitudes.

  20. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit.

    Science.gov (United States)

    Keedy, Daniel A; Fraser, James S; van den Bedem, Henry

    2015-10-01

    Proteins must move between different conformations of their native ensemble to perform their functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this heterogeneity as a spatial and temporal conformational average. Although movement between natively populated alternative conformations can be critical for characterizing molecular mechanisms, it is challenging to identify these conformations within electron density maps. Alternative side chain conformations are generally well separated into distinct rotameric conformations, but alternative backbone conformations can overlap at several atomic positions. Our model building program qFit uses mixed integer quadratic programming (MIQP) to evaluate an extremely large number of combinations of sidechain conformers and backbone fragments to locally explain the electron density. Here, we describe two major modeling enhancements to qFit: peptide flips and alternative glycine conformations. We find that peptide flips fall into four stereotypical clusters and are enriched in glycine residues at the n+1 position. The potential for insights uncovered by new peptide flips and glycine conformations is exemplified by HIV protease, where different inhibitors are associated with peptide flips in the "flap" regions adjacent to the inhibitor binding site. Our results paint a picture of peptide flips as conformational switches, often enabled by glycine flexibility, that result in dramatic local rearrangements. Our results furthermore demonstrate the power of large-scale computational analysis to provide new insights into conformational heterogeneity. Overall, improved modeling of backbone heterogeneity with high-resolution X-ray data will connect dynamics to the structure-function relationship and help drive new design strategies for inhibitors of biomedically important systems.

  1. RosettaRemodel: a generalized framework for flexible backbone protein design.

    Directory of Open Access Journals (Sweden)

    Po-Ssu Huang

    Full Text Available We describe RosettaRemodel, a generalized framework for flexible protein design that provides a versatile and convenient interface to the Rosetta modeling suite. RosettaRemodel employs a unified interface, called a blueprint, which allows detailed control over many aspects of flexible backbone protein design calculations. RosettaRemodel allows the construction and elaboration of customized protocols for a wide range of design problems ranging from loop insertion and deletion, disulfide engineering, domain assembly, loop remodeling, motif grafting, symmetrical units, to de novo structure modeling.

  2. Backbone resonance assignments of the micro-RNA precursor binding region of human TRBP.

    Science.gov (United States)

    Benoit, Matthieu P M H; Plevin, Michael J

    2013-10-01

    TAR-RNA binding protein (TRBP) is a multidomain human protein involved in micro-RNA (miRNA) biogenesis. TRBP is a component of both the Dicer complex, which processes precursor miRNAs, and the RNA-induced silencing complex-loading complex. In addition, TRBP is implicated in the human immunodeficiency virus replication cycle and interferon-protein kinase R activity. TRBP contains 3 double-stranded RNA binding domains the first two of which have been shown to interact with miRNA precursors. Here we present the backbone resonance assignments and secondary structure of residues 19-228 of human TRBP2.

  3. SEVA Linkers: A Versatile and Automatable DNA Backbone Exchange Standard for Synthetic Biology

    DEFF Research Database (Denmark)

    Kim, Se Hyeuk; Cavaleiro, Mafalda; Rennig, Maja

    2016-01-01

    DNA vectors serve to maintain and select recombinant DNA in cell factories, and as design complexity increases, there is a greater need for well-characterized parts and methods for their assembly. Standards in synthetic biology are top priority, but standardizing molecular cloning contrasts...... flexibility, and different researchers prefer and master different molecular technologies. Here, we describe a new, highly versatile and automatable standard “SEVA linkers” for vector exchange. SEVA linkers enable backbone swapping with 20 combinations of classical enzymatic restriction/ligation, Gibson...... to the synthetic biology community....

  4. Sulfation and Cation Effects on the Conformational Properties of the Glycan Backbone of Chondroitin Sulfate Disaccharides

    Science.gov (United States)

    Faller, Christina E.; Guvench, Olgun

    2015-01-01

    Chondroitin sulfate (CS) is one of several glycosaminoglycans that are major components of proteoglycans. A linear polymer consisting of repeats of the disaccharide -4GlcAβ1-3GalNAcβ1-, CS undergoes differential sulfation resulting in five unique sulfation patterns. Because of the dimer repeat, the CS glycosidic “backbone” has two distinct sets of conformational degrees of freedom defined by pairs of dihedral angles: (ϕ1, ψ1) about the β1-3 glycosidic linkage and (ϕ2, ψ2) about the β1-4 glycosidic linkage. Differential sulfation and the possibility of cation binding, combined with the conformational flexibility and biological diversity of CS, complicate experimental efforts to understand CS three-dimensional structures at atomic resolution. Therefore, all-atom explicit-solvent molecular dynamics simulations with Adaptive Biasing Force sampling of the CS backbone were applied to obtain high resolution, high precision free energies of CS disaccharides as a function of all possible backbone geometries. All ten disaccharides (β1-3 vs. β1-4 linkage x five different sulfation patterns) were studied; additionally, ion effects were investigated by considering each disaccharide in the presence of either neutralizing sodium or calcium cations. GlcAβ1-3GalNAc disaccharides have a single, broad, thermodynamically important free-energy minimum whereas GalNAcβ1-4GlcA disaccharides have two such minima. Calcium cations but not sodium cations bind to the disaccharides, and binding is primarily to the GlcA –COO− moiety as opposed to sulfate groups. This binding alters the glycan backbone thermodynamics in instances where a calcium cation bound to –COO− can act to bridge and stabilize an interaction with an adjacent sulfate group, whereas, in the absence of this cation, the proximity of a sulfate group to –COO− results in two like charges being both desolvated and placed adjacent to each other and is found to be destabilizing. In addition to providing

  5. Backbone tuning in indenylidene–ruthenium complexes bearing an unsaturated N-heterocyclic carbene

    Directory of Open Access Journals (Sweden)

    César A. Urbina-Blanco

    2010-11-01

    Full Text Available The steric and electronic influence of backbone substitution in IMes-based (IMes = 1,3-bis(2,4,6-trimethylphenylimidazol-2-ylidene N-heterocyclic carbenes (NHC was probed by synthesizing the [RhCl(CO2(NHC] series of complexes to quantify experimentally the Tolman electronic parameter (electronic and the percent buried volume (%Vbur, steric parameters. The corresponding ruthenium–indenylidene complexes were also synthesized and tested in benchmark metathesis transformations to establish possible correlations between reactivity and NHC electronic and steric parameters.

  6. Synthesis of Aminophosphine Ligands with Binaphthyl Backbones for Silver(I)-catalyzed Enantioselective Allylation of Benzaldehyde

    Institute of Scientific and Technical Information of China (English)

    WANG,Yi(王以); JI,Bao-Ming(吉保明); DING,Kui-Ling(丁奎岭)

    2002-01-01

    A series of aminophosphine ligands was synthesized from 2amino-2′-hydroxy-1,1′-binaphthyl (NOBIN). Their asymmetric induction efficiency was examined for silver(I)catalyzed enantioselective allylation reaction of benzaldehyde with allyltributyltin.Under the optimized reaction conditions,quantitative yield as well as moderate ee value (54.5% ee)of product was achieved by the catalysis with silver(I)/3 complex. The effects of the binaphthyl backbone and the substituted situated at chelating N, Patoms on enantioselectivity of the reaction were also discussed.

  7. Relative specificities of water and ammonia losses from backbone fragments in collision-activated dissociation

    DEFF Research Database (Denmark)

    Savitski, Mikhail M; Kjeldsen, Frank; Nielsen, Michael L

    2007-01-01

    Analysis of a database containing over 20,000 high-resolution collision-activation mass spectra of tryptic peptide dications was employed to study the relative specificity of neutral losses from backbone fragments. The high resolution of the FTMS instrument allowed for the first time the first...... isotope of the water loss and the monoisotope of the ammonia loss to be distinguished. Contrary to a popular belief, water losses from y' ions are not specific enough to rely upon for detecting the presence of amino acids with oxygen in the side chains. At the same time, ammonia loss from b ions...

  8. Redox-controlled backbone dynamics of human cytochrome c revealed by {sup 15}N NMR relaxation measurements

    Energy Technology Data Exchange (ETDEWEB)

    Sakamoto, Koichi [Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810 (Japan); Kamiya, Masakatsu [Graduate School of Life Science, Hokkaido University, Sapporo 060-0810 (Japan); Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810 (Japan); Uchida, Takeshi [Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810 (Japan); Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810 (Japan); Kawano, Keiichi [Graduate School of Life Science, Hokkaido University, Sapporo 060-0810 (Japan); Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810 (Japan); Ishimori, Koichiro, E-mail: koichiro@sci.hokudai.ac.jp [Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810 (Japan); Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810 (Japan)

    2010-07-23

    Research highlights: {yields} The dynamic parameters for the backbone dynamics in Cyt c were determined. {yields} The backbone mobility of Cyt c is highly restricted due to the covalently bound heme. {yields} The backbone mobility of Cyt c is more restricted upon the oxidation of the heme. {yields} The redox-dependent dynamics are shown in the backbone of Cyt c. {yields} The backbone dynamics of Cyt c would regulate the electron transfer from Cyt c. -- Abstract: Redox-controlled backbone dynamics in cytochrome c (Cyt c) were revealed by 2D {sup 15}N NMR relaxation experiments. {sup 15}N T{sub 1} and T{sub 2} values and {sup 1}H-{sup 15}N NOEs of uniformly {sup 15}N-labeled reduced and oxidized Cyt c were measured, and the generalized order parameters (S{sup 2}), the effective correlation time for internal motion ({tau}{sub e}), the {sup 15}N exchange broadening contributions (R{sub ex}) for each residue, and the overall correlation time ({tau}{sub m}) were estimated by model-free dynamics formalism. These dynamic parameters clearly showed that the backbone dynamics of Cyt c are highly restricted due to the covalently bound heme that functions as the stable hydrophobic core. Upon oxidation of the heme iron in Cyt c, the average S{sup 2} value was increased from 0.88 {+-} 0.01 to 0.92 {+-} 0.01, demonstrating that the mobility of the backbone is further restricted in the oxidized form. Such increases in the S{sup 2} values were more prominent in the loop regions, including amino acid residues near the thioether bonds to the heme moiety and positively charged region around Lys87. Both of the regions are supposed to form the interaction site for cytochrome c oxidase (CcO) and the electron pathway from Cyt c to CcO. The redox-dependent mobility of the backbone in the interaction site for the electron transfer to CcO suggests an electron transfer mechanism regulated by the backbone dynamics in the Cyt c-CcO system.

  9. Importance of backbone angles versus amino acid configurations in peptide vibrational Raman optical activity spectra

    Science.gov (United States)

    Herrmann, Carmen; Ruud, Kenneth; Reiher, Markus

    2008-01-01

    In this work, we investigate whether the differential scattering of right- and left-circularly polarized light in peptide Raman optical activity spectra are uniquely dominated by the backbone conformation, or whether the configurations of the individual amino acid also play a significant role. This is achieved by calculating Raman optical activity spectra using density functional theory for four structurally related peptides with a common backbone conformation, but with different sequences of amino acid configurations. Furthermore, the ROA signals of the amide normal modes are decomposed into contributions from groups of individual atoms. It is found that the amino acid configuration has a considerable influence on the ROA peaks in the amide I, II, and III regions, although the local decomposition reveals that the side-chain atoms only contribute to those peaks directly in the case of the amide II vibrations. Furthermore, small changes in the amide normal modes may lead to large and irregular modifications in the ROA intensity differences, making it difficult to establish transferable ROA intensity differences even for structurally similar vibrations.

  10. The structure of the carbohydrate backbone of the lipopolysaccharide of Pectinatus frisingensis strain VTT E-79104.

    Science.gov (United States)

    Vinogradov, Evgeny; Li, Jianjun; Sadovskaya, Irina; Jabbouri, Said; Helander, Ilkka M

    2004-06-22

    The structure of the carbohydrate backbone of the lipopolysaccharide from Pectinatus frisingensis strain VTT E-79104 was analyzed using chemical degradations, NMR spectroscopy, mass spectrometry, and chemical methods. The LPS contains two major structural variants, differing in the presence or absence of an octasaccharide fragment. The largest structure of the carbohydrate backbone of the LPS, that could be deduced from experimental results, consists of 20 monosaccharides arranged in a nonrepetitive sequence: [carbohydrate structure: see text] where R is H or 4-O-Me-alpha-L-Fuc-(1-2)-4-O-Me-beta-Hep-(1-3)-alpha-GlcNAc-(1-2)-beta-Man-(1-3)-beta-ManNAc-(1-4)-alpha-Gal-(1-4)-beta-Hep-(1-3)-beta-GalNAc-(1- where Hep is a residue of D-glycero-D-galacto-heptose; all monosaccharides have the D-configuration except for 4-O-Me-L-Fuc and L-Ara4N. This structure is architecturally similar to the oligosaccharide system reported previously in P. frisingensis VTT E-82164 LPS, but differs from the latter in composition and also in the size of the outer region.

  11. A fusion networking model for smart grid power distribution backbone communication network based on PTN

    Directory of Open Access Journals (Sweden)

    Wang Hao

    2016-01-01

    Full Text Available In current communication network for distribution in Chinese power grid systems, the fiber communication backbone network for distribution and TD-LTE power private wireless backhaul network of power grid are both bearing by the SDH optical transmission network, which also carries the communication network of transformer substation and main electric. As the data traffic of the distribution communication and TD-LTE power private wireless network grow rapidly in recent years, it will have a big impact with the SDH network’s bearing capacity which is mainly used for main electric communication in high security level. This paper presents a fusion networking model which use a multiple-layer PTN network as the unified bearing of the TD-LTE power private wireless backhaul network and fiber communication backbone network for distribution. Network dataflow analysis shows that this model can greatly reduce the capacity pressure of the traditional SDH network as well as ensure the reliability of the transmission of the communication network for distribution and TD-LTE power private wireless network.

  12. Di-Isocyanate Crosslinked Aerogels with 1, 6-Bis (Trimethoxysilyl) Hexane Incorporated in Silica Backbone

    Science.gov (United States)

    Vivod, Stephanie L.; Meador, Mary Ann B.; Nguyen, Baochau N.; Quade, Derek; Randall, Jason; Perry, Renee

    2008-01-01

    Silica aerogels are desirable materials for many applications that take advantage of their light weight and low thermal conductivity. Addition of a conformal polymer coating which bonds with the amine decorated surface of the silica network improves the strength of the aerogels by as much as 200 times. Even with vast improvement in strength they still tend to undergo brittle failure due to the rigid silica backbone. We hope to increase the flexibility and elastic recovery of the silica based aerogel by altering the silica back-bone by incorporation of more flexible hexane links. To this end, we investigated the use of 1,6-bis(trimethoxysilyl)hexane (BTMSH), a polysilsesquioxane precursor3, as an additional co-reactant to prepare silica gels which were subsequently cross-linked with di-isocyanate. Previously, this approach of adding flexibility by BTMSH incorporation was demonstrated with styrene cross-linked aerogels. In our study, we varied silane concentration, mol % of silicon from BTMSH and di-isocyanate concentration by weight percent to attempt to optimize both the flexibility and the strength of the aerogels.

  13. Structure and assembly of group B streptococcus pilus 2b backbone protein.

    Science.gov (United States)

    Cozzi, Roberta; Malito, Enrico; Lazzarin, Maddalena; Nuccitelli, Annalisa; Castagnetti, Andrea; Bottomley, Matthew J; Margarit, Immaculada; Maione, Domenico; Rinaudo, C Daniela

    2015-01-01

    Group B Streptococcus (GBS) is a major cause of invasive disease in infants. Like other Gram-positive bacteria, GBS uses a sortase C-catalyzed transpeptidation mechanism to generate cell surface pili from backbone and ancillary pilin precursor substrates. The three pilus types identified in GBS contain structural subunits that are highly immunogenic and are promising candidates for the development of a broadly-protective vaccine. Here we report the X-ray crystal structure of the backbone protein of pilus 2b (BP-2b) at 1.06Å resolution. The structure reveals a classical IgG-like fold typical of the pilin subunits of other Gram-positive bacteria. The crystallized portion of the protein (residues 185-468) encompasses domains D2 and D3 that together confer high stability to the protein due to the presence of an internal isopeptide bond within each domain. The D2+D3 region, lacking the N-terminal D1 domain, was as potent as the entire protein in conferring protection against GBS challenge in a well-established mouse model. By site-directed mutagenesis and complementation studies in GBS knock-out strains we identified the residues and motives essential for assembly of the BP-2b monomers into high-molecular weight complexes, thus providing new insights into pilus 2b polymerization.

  14. Structure and assembly of group B streptococcus pilus 2b backbone protein.

    Directory of Open Access Journals (Sweden)

    Roberta Cozzi

    Full Text Available Group B Streptococcus (GBS is a major cause of invasive disease in infants. Like other Gram-positive bacteria, GBS uses a sortase C-catalyzed transpeptidation mechanism to generate cell surface pili from backbone and ancillary pilin precursor substrates. The three pilus types identified in GBS contain structural subunits that are highly immunogenic and are promising candidates for the development of a broadly-protective vaccine. Here we report the X-ray crystal structure of the backbone protein of pilus 2b (BP-2b at 1.06Å resolution. The structure reveals a classical IgG-like fold typical of the pilin subunits of other Gram-positive bacteria. The crystallized portion of the protein (residues 185-468 encompasses domains D2 and D3 that together confer high stability to the protein due to the presence of an internal isopeptide bond within each domain. The D2+D3 region, lacking the N-terminal D1 domain, was as potent as the entire protein in conferring protection against GBS challenge in a well-established mouse model. By site-directed mutagenesis and complementation studies in GBS knock-out strains we identified the residues and motives essential for assembly of the BP-2b monomers into high-molecular weight complexes, thus providing new insights into pilus 2b polymerization.

  15. Automatic assignment of protein backbone resonances by direct spectrum inspection in targeted acquisition of NMR data.

    Science.gov (United States)

    Wong, Leo E; Masse, James E; Jaravine, Victor; Orekhov, Vladislav; Pervushin, Konstantin

    2008-10-01

    The necessity to acquire large multidimensional datasets, a basis for assignment of NMR resonances, results in long data acquisition times during which substantial degradation of a protein sample might occur. Here we propose a method applicable for such a protein for automatic assignment of backbone resonances by direct inspection of multidimensional NMR spectra. In order to establish an optimal balance between completeness of resonance assignment and losses of cross-peaks due to dynamic processes/degradation of protein, assignment of backbone resonances is set as a stirring criterion for dynamically controlled targeted nonlinear NMR data acquisition. The result is demonstrated with the 12 kDa (13)C,(15) N-labeled apo-form of heme chaperone protein CcmE, where hydrolytic cleavage of 29 C-terminal amino acids is detected. For this protein, 90 and 98% of manually assignable resonances are automatically assigned within 10 and 40 h of nonlinear sampling of five 3D NMR spectra, respectively, instead of 600 h needed to complete the full time domain grid. In addition, resonances stemming from degradation products are identified. This study indicates that automatic resonance assignment might serve as a guiding criterion for optimal run-time allocation of NMR resources in applications to proteins prone to degradation.

  16. Automatic assignment of protein backbone resonances by direct spectrum inspection in targeted acquisition of NMR data

    Energy Technology Data Exchange (ETDEWEB)

    Wong, Leo E. [Nanyang Technological University, School of Biological Sciences (Singapore); Masse, James E. [National Institutes of Health (United States); Jaravine, Victor [J. W. Goethe-University Frankfurt, Institute of Biophysical Chemistry (Germany); Orekhov, Vladislav [Gothenburg University, Swedish NMR Centre (Sweden); Pervushin, Konstantin [Nanyang Technological University, School of Biological Sciences (Singapore)], E-mail: kpervushin@ntu.edu.sg

    2008-10-15

    The necessity to acquire large multidimensional datasets, a basis for assignment of NMR resonances, results in long data acquisition times during which substantial degradation of a protein sample might occur. Here we propose a method applicable for such a protein for automatic assignment of backbone resonances by direct inspection of multidimensional NMR spectra. In order to establish an optimal balance between completeness of resonance assignment and losses of cross-peaks due to dynamic processes/degradation of protein, assignment of backbone resonances is set as a stirring criterion for dynamically controlled targeted nonlinear NMR data acquisition. The result is demonstrated with the 12 kDa {sup 13}C,{sup 15} N-labeled apo-form of heme chaperone protein CcmE, where hydrolytic cleavage of 29 C-terminal amino acids is detected. For this protein, 90 and 98% of manually assignable resonances are automatically assigned within 10 and 40 h of nonlinear sampling of five 3D NMR spectra, respectively, instead of 600 h needed to complete the full time domain grid. In addition, resonances stemming from degradation products are identified. This study indicates that automatic resonance assignment might serve as a guiding criterion for optimal run-time allocation of NMR resources in applications to proteins prone to degradation.

  17. Cellulose nanofiber backboned Prussian blue nanoparticles as powerful adsorbents for the selective elimination of radioactive cesium

    Science.gov (United States)

    Vipin, Adavan Kiliyankil; Fugetsu, Bunshi; Sakata, Ichiro; Isogai, Akira; Endo, Morinobu; Li, Mingda; Dresselhaus, Mildred S.

    2016-11-01

    On 11 March 2011, the day of the unforgettable disaster of the 9 magnitude Tohoku earthquake and quickly followed by the devastating Tsunami, a damageable amount of radionuclides had dispersed from the Fukushima Daiichi’s damaged nuclear reactors. Decontamination of the dispersed radionuclides from seawater and soil, due to the huge amounts of coexisting ions with competitive functionalities, has been the topmost difficulty. Ferric hexacyanoferrate, also known as Prussian blue (PB), has been the most powerful material for selectively trapping the radioactive cesium ions; its high tendency to form stable colloids in water, however, has made PB to be impossible for the open-field radioactive cesium decontamination applications. A nano/nano combinatorial approach, as is described in this study, has provided an ultimate solution to this intrinsic colloid formation difficulty of PB. Cellulose nanofibers (CNF) were used to immobilize PB via the creation of CNF-backboned PB. The CNF-backboned PB (CNF/PB) was found to be highly tolerant to water and moreover, it gave a 139 mg/g capability and a million (106) order of magnitude distribution coefficient (Kd) for absorbing of the radioactive cesium ion. Field studies on soil and seawater decontaminations in Fukushima gave satisfactory results, demonstrating high capabilities of CNF/PB for practical applications.

  18. Protonation–deprotonation of the glycine backbone as followed by Raman scattering and multiconformational analysis

    Energy Technology Data Exchange (ETDEWEB)

    Hernández, Belén; Pflüger, Fernando [Groupe de Biophysique Moléculaire, UFR Santé-Médecine-Biologie Humaine, Université Paris 13, Sorbonne Paris Cité, 74 rue Marcel Cachin, 93017 Bobigny cedex (France); Kruglik, Sergei G. [Laboratoire Jean Perrin, FRE 3231, Université Pierre et Marie Curie (Paris 6), Case courrier 138, 75252 Paris Cedex 05 (France); Ghomi, Mahmoud, E-mail: mahmoud.ghomi@univ-paris13.fr [Groupe de Biophysique Moléculaire, UFR Santé-Médecine-Biologie Humaine, Université Paris 13, Sorbonne Paris Cité, 74 rue Marcel Cachin, 93017 Bobigny cedex (France)

    2013-11-08

    Highlights: • New pH-dependent Raman spectra in the middle wavenumber region (1800-300 cm{sup −1}). • New quantum mechanical calculations for exploring the Gly conformational landscape. • Construction of muticonformation based theoretical Raman spectra. - Abstract: Because of the absence of the side chain in its chemical structure and its well defined Raman spectra, glycine was selected here to follow its backbone protonation–deprotonation. The scan of the recorded spectra in the 1800–300 cm{sup −1} region led us to assign those obtained at pH 1, 6 and 12 to the cationic, zwitterionic and anionic species, respectively. These data complete well those previously published by Bykov et al. (2008) [16] devoted to the high wavenumber Raman spectra (>2500 cm{sup −1}). To reinforce our discussion, DFT calculations were carried out on the clusters of glycine + 5H{sub 2}O, mimicking reasonably the first hydration shell of the amino acid. Geometry optimization of 141 initial clusters, reflecting plausible combinations of the backbone torsion angles, allowed exploration of the conformational features, as well as construction of the theoretical Raman spectra by considering the most stable clusters containing each glycine species.

  19. Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting.

    Science.gov (United States)

    Margreitter, Christian; Oostenbrink, Chris

    2016-09-26

    Molecular dynamics simulations depend critically on the accuracy of the underlying force fields in properly representing biomolecules. Hence, it is crucial to validate the force-field parameter sets in this respect. In the context of the GROMOS force field, this is usually achieved by comparing simulation data to experimental observables for small molecules. In this study, we develop new amino acid backbone dihedral angle potential energy parameters based on the widely used 54A7 parameter set by matching to experimental J values and secondary structure propensity scales. In order to find the most appropriate backbone parameters, close to 100 000 different combinations of parameters have been screened. However, since the sheer number of combinations considered prohibits actual molecular dynamics simulations for each of them, we instead predicted the values for every combination using Hamiltonian reweighting. While the original 54A7 parameter set fails to reproduce the experimental data, we are able to provide parameters that match significantly better. However, to ensure applicability in the context of larger peptides and full proteins, further studies have to be undertaken.

  20. On the role of thermal backbone fluctuations in myoglobin ligand gate dynamics

    CERN Document Server

    Krokhotin, Andrey; Peng, Xubiao

    2012-01-01

    We construct an energy function that describes the crystallographic structure of spermwhale myoglobin backbone. As a model in our construction, we use the Protein Data Bank entry 1ABS that has been measured at liquid helium temperature. Consequently the thermal B-factor fluctuations are very small, which is an advantage in our construction. The energy function that we utilize resembles that of the discrete non-linear Schrodinger equation. Likewise, ours supports solitons as local minimum energy configurations. We describe the 1ABS backbone in terms of solitons with a precision that deviates from 1ABS by an average root-mean-square distance, which is less than the experimentally observed Debye-Waller B-factor fluctuation distance. We then subject the multisoliton solution to extensive numerical heating and cooling experiments, over a very wide range of temperatures. We concentrate in particular to temperatures above 300K and below the theta-point unfolding temperature, which is around 348K. We confirm that the...

  1. RNA-Redesign: a web server for fixed-backbone 3D design of RNA.

    Science.gov (United States)

    Yesselman, Joseph D; Das, Rhiju

    2015-07-01

    RNA is rising in importance as a design medium for interrogating fundamental biology and for developing therapeutic and bioengineering applications. While there are several online servers for design of RNA secondary structure, there are no tools available for the rational design of 3D RNA structure. Here we present RNA-Redesign (http://rnaredesign.stanford.edu), an online 3D design tool for RNA. This resource utilizes fixed-backbone design to optimize the sequence identity and nucleobase conformations of an RNA to match a desired backbone, analogous to fundamental tools that underlie rational protein engineering. The resulting sequences suggest thermostabilizing mutations that can be experimentally verified. Further, sequence preferences that differ between natural and computationally designed sequences can suggest whether natural sequences possess functional constraints besides folding stability, such as cofactor binding or conformational switching. Finally, for biochemical studies, the designed sequences can suggest experimental tests of 3D models, including concomitant mutation of base triples. In addition to the designs generated, detailed graphical analysis is presented through an integrated and user-friendly environment.

  2. Influence of Backbone Fluorination in Regioregular Poly(3-alkyl-4-fluoro)thiophenes

    KAUST Repository

    Fei, Zhuping

    2015-06-03

    © 2015 American Chemical Society. We report two strategies toward the synthesis of 3-alkyl-4-fluorothiophenes containing straight (hexyl and octyl) and branched (2-ethylhexyl) alkyl groups. We demonstrate that treatment of the dibrominated monomer with 1 equiv of alkyl Grignard reagent leads to the formation of a single regioisomer as a result of the pronounced directing effect of the fluorine group. Polymerization of the resulting species affords highly regioregular poly(3-alkyl-4-fluoro)thiophenes. Comparison of their properties to those of the analogous non-fluorinated polymers shows that backbone fluorination leads to an increase in the polymer ionization potential without a significant change in optical band gap. Fluorination also results in an enhanced tendency to aggregate in solution, which is ascribed to a more co-planar backbone on the basis of Raman and DFT calculations. Average charge carrier mobilities in field-effect transistors are found to increase by up to a factor of 5 for the fluorinated polymers.

  3. Improving VANETs Connectivity with a Totally Ad Hoc Living Mobile Backbone

    Directory of Open Access Journals (Sweden)

    Joilson Alves Junior

    2015-01-01

    Full Text Available The vehicular ad hoc network (VANET for intelligent transportation systems is an emerging concept to improve transportation security, reliability, and management. The network behavior can be totally different in topological aspects because of the mobility of vehicular nodes. The topology can be fully connected when the flow of vehicles is high and may have low connectivity or be invalid when the flow of vehicles is low or unbalanced. In big cities, the metropolitan buses that travel on exclusive lanes may be used to set up a metropolitan vehicular data network (backbone, raising the connectivity among the vehicles. Therefore, this paper proposes the implementation of a living mobile backbone, totally ad hoc (MOB-NET, which will provide infrastructure and raise the network connectivity. In order to show the viability of MOB-NET, statistical analyses were made with real data of express buses that travel through exclusive lanes, besides evaluations through simulations and analytic models. The statistic, analytic, and simulation results prove that the buses that travel through exclusive lanes can be used to build a communication network totally ad hoc and provide connectivity in more than 99% of the time, besides raising the delivery rate up to 95%.

  4. HIV-1 phenotypic reverse transcriptase inhibitor drug resistance test interpretation is not dependent on the subtype of the virus backbone.

    Directory of Open Access Journals (Sweden)

    Michelle Bronze

    Full Text Available To date, the majority of HIV-1 phenotypic resistance testing has been performed with subtype B virus backbones (e.g. HXB2. However, the relevance of using this backbone to determine resistance in non-subtype B HIV-1 viruses still needs to be assessed. From 114 HIV-1 subtype C clinical samples (36 ARV-naïve, 78 ARV-exposed, pol amplicons were produced and analyzed for phenotypic resistance using both a subtype B- and C-backbone in which the pol fragment was deleted. Phenotypic resistance was assessed in resulting recombinant virus stocks (RVS for a series of antiretroviral drugs (ARV's and expressed as fold change (FC, yielding 1660 FC comparisons. These Antivirogram® derived FC values were categorized as having resistant or sensitive susceptibility based on biological cut-off values (BCOs. The concordance between resistance calls obtained for the same clinical sample but derived from two different backbones (i.e. B and C accounted for 86.1% (1429/1660 of the FC comparisons. However, when taking the assay variability into account, 95.8% (1590/1660 of the phenotypic data could be considered as being concordant with respect to their resistance call. No difference in the capacity to detect resistance associated with M184V, K103N and V106M mutations was noted between the two backbones. The following was concluded: (i A high level of concordance was shown between the two backbone phenotypic resistance profiles; (ii Assay variability is largely responsible for discordant results (i.e. for FC values close to BCO; (iii Confidence intervals should be given around the BCO's, when assessing resistance in HIV-1 subtype C; (iv No systematic resistance under- or overcalling of subtype C amplicons in the B-backbone was observed; (v Virus backbone subtype sequence variability outside the pol region does not contribute to phenotypic FC values. In conclusion the HXB2 virus backbone remains an acceptable vector for phenotyping HIV-1 subtype C pol amplicons.

  5. Tuning backbones and side-chains of cationic conjugated polymers for optical signal amplification of fluorescent DNA detection.

    Science.gov (United States)

    Huang, Yan-Qin; Liu, Xing-Fen; Fan, Qu-Li; Wang, Lihua; Song, Shiping; Wang, Lian-Hui; Fan, Chunhai; Huang, Wei

    2009-06-15

    Three cationic conjugated polymers (CCPs) exhibiting different backbone geometries and charge densities were used to investigate how their conjugated backbone and side chain properties, together with the transitions of DNA amphiphilic properties, interplay in the CCP/DNA-C* (DNA-C*: fluorophore-labeled DNA) complexes to influence the optical signal amplification of fluorescent DNA detection based on Förster resonance energy transfer (FRET). By examining the FRET efficiencies to dsDNA-C* (dsDNA: double-stranded DNA) and ssDNA-C* (ssDNA: single-stranded DNA) for each CCP, twisted conjugated backbones and higher charge densities were proved to facilitate electrostatic attraction in CCP/dsDNA-C* complexes, and induced improved sensitivity to DNA hybridization. Especially, by using the CCP with twisted conjugated backbone and the highest charge density, a more than 7-fold higher efficiency of FRET to dsDNA-C* was found than to ssDNA-C*, indicating a high signal amplification for discriminating between dsDNA and ssDNA. By contrast, linear conjugated backbones and lower charge density were demonstrated to favor hydrophobic interactions in CCP/ssDNA-C* complexes. These findings provided guidelines for the design of novel sensitive CCP, which can be useful to recognize many other important DNA activities involving transitions of DNA amphiphilic properties like DNA hybridization, such as specific DNA binding with ions, some secondary or tertiary structural changes of DNA, and so forth.

  6. Polarizable Simulations with Second order Interaction Model (POSSIM) force field: Developing parameters for alanine peptides and protein backbone

    Science.gov (United States)

    Ponomarev, Sergei Y.; Kaminski, George A.

    2011-01-01

    A previously introduced POSSIM (POlarizable Simulations with Second order Interaction Model) force field has been extended to include parameters for alanine peptides and protein backbones. New features were introduced into the fitting protocol, as compared to the previous generation of the polarizable force field for proteins. A reduced amount of quantum mechanical data was employed in fitting the electrostatic parameters. Transferability of the electrostatics between our recently developed NMA model and the protein backbone was confirmed. Binding energy and geometry for complexes of alanine dipeptide with a water molecule were estimated and found in a good agreement with high-level quantum mechanical results (for example, the intermolecular distances agreeing within ca. 0.06Å). Following the previously devised procedure, we calculated average errors in alanine di- and tetra-peptide conformational energies and backbone angles and found the agreement to be adequate (for example, the alanine tetrapeptide extended-globular conformational energy gap was calculated to be 3.09 kcal/mol quantim mechanically and 3.14 kcal/mol with the POSSIM force field). However, we have now also included simulation of a simple alpha-helix in both gas-phase and water as the ultimate test of the backbone conformational behavior. The resulting alanine and protein backbone force field is currently being employed in further development of the POSSIM fast polarizable force field for proteins. PMID:21743799

  7. Effect of backbone chemistry on hybridization thermodynamics of oligonucleic acids: a coarse-grained molecular dynamics simulation study.

    Science.gov (United States)

    Ghobadi, Ahmadreza F; Jayaraman, Arthi

    2016-02-28

    In this paper we study how varying oligonucleic acid backbone chemistry affects the hybridization/melting thermodynamics of oligonucleic acids. We first describe the coarse-grained (CG) model with tunable parameters that we developed to enable the study of both naturally occurring oligonucleic acids, such as DNA, and their chemically-modified analogues, such as peptide nucleic acids (PNAs) and locked nucleic acids (LNAs). The DNA melting curves obtained using such a CG model and molecular dynamics simulations in an implicit solvent and with explicit ions match with the melting curves obtained using the empirical nearest-neighbor models. We use these CG simulations to then elucidate the effect of backbone flexibility, charge, and nucleobase spacing along the backbone on the melting curves, potential energy and conformational entropy change upon hybridization and base-pair hydrogen bond residence time. We find that increasing backbone flexibility decreases duplex thermal stability and melting temperature mainly due to increased conformational entropy loss upon hybridization. Removing charges from the backbone enhances duplex thermal stability due to the elimination of electrostatic repulsion and as a result a larger energetic gain upon hybridization. Lastly, increasing nucleobase spacing decreases duplex thermal stability due to decreasing stacking interactions that are important for duplex stability.

  8. Comb-type prepolymers consisting of a polyacrylamide backbone and poly(L-lysine) graft chains for multivalent ligands.

    Science.gov (United States)

    Asayama, S; Maruyama, A; Akaike, T

    1999-01-01

    The comb-type copolymers consisting of a polyacrylamide (PAAm) backbone and poly(L-lysine) (PLL) graft chains have been prepared as the "prepolymer" for designing multivalent ligands. To regulate the length and density of the clusters of primary amino groups, the Nalpha-carboxyanhydride of Nepsilon-carbobenzoxy (CBZ)-L-lysine was first polymerized using p-vinylbenzylamine as an initiator. The resulting poly(CBZ-L-lysine) macromonomer was then radically copolymerized with AAm, followed by the deprotection of amino groups. For the model study, the reactive clusters of primary amino groups were completely converted into anion clusters by the reaction with succinic anhydride. The model multivalent ligands having the biotin label on the PAAm backbone were prepared by the terpolymerization of the macromonomer, AAm, and the biotin derivative having a vinyl group. The enzyme-linked immunosorbent assay showed that the biotin with no spacer on the PAAm backbone was recognized by the avidin-peroxidase conjugate specifically. Therefore, the highly sensitive detection of the interaction between cells and various model multivalent ligands was possible. The selective labeling onto the PAAm backbone revealed that the converted anion clusters of graft chains interacted exclusively with the cell and that the backbone was inert to the interaction with the cell. These results indicate that the various PAAm-graft-PLL comb-type copolymers with the defined length and density of the PLL-grafts are the potential prepolymers to investigate and to optimize the affinity of the multivalent ligands for receptors.

  9. CORBA and MPI-based 'backbone' for coupling advanced simulation tools

    Energy Technology Data Exchange (ETDEWEB)

    Seydaliev, M.; Caswell, D., E-mail: marat.seydaliev@cnl.ca [Canadian Nuclear Laboratories, Chalk River, Ontario (Canada)

    2014-12-01

    There is a growing international interest in using coupled, multidisciplinary computer simulations for a variety of purposes, including nuclear reactor safety analysis. Reactor behaviour can be modeled using a suite of computer programs simulating phenomena or predicting parameters that can be categorized into disciplines such as Thermalhydraulics, Neutronics, Fuel, Fuel Channels, Fission Product Release and Transport, Containment and Atmospheric Dispersion, and Severe Accident Analysis. Traditionally, simulations used for safety analysis individually addressed only the behaviour within a single discipline, based upon static input data from other simulation programs. The limitation of using a suite of stand-alone simulations is that phenomenological interdependencies or temporal feedback between the parameters calculated within individual simulations cannot be adequately captured. To remove this shortcoming, multiple computer simulations for different disciplines must exchange data during runtime to address these interdependencies. This article describes the concept of a new framework, which we refer to as the 'Backbone', to provide the necessary runtime exchange of data. The Backbone, currently under development at AECL for a preliminary feasibility study, is a hybrid design using features taken from the Common Object Request Broker Architecture (CORBA), a standard defined by the Object Management Group, and the Message Passing Interface (MPI), a standard developed by a group of researchers from academia and industry. Both have well-tested and efficient implementations, including some that are freely available under the GNU public licenses. The CORBA component enables individual programs written in different languages and running on different platforms within a network to exchange data with each other, thus behaving like a single application. MPI provides the process-to-process intercommunication between these programs. This paper outlines the different

  10. Comparison of backbone dynamics of the type III antifreeze protein and antifreeze-like domain of human sialic acid synthase

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Yong-Geun [Gyeongsang National University, Department of Chemistry and Research Institute of Natural Science (Korea, Republic of); Park, Chin-Ju [Gwangju Institute of Science and Technology, Division of Liberal Arts and Sciences and Department of Chemistry (Korea, Republic of); Kim, Hee-Eun; Seo, Yeo-Jin; Lee, Ae-Ree; Choi, Seo-Ree; Lee, Shim Sung; Lee, Joon-Hwa, E-mail: joonhwa@gnu.ac.kr [Gyeongsang National University, Department of Chemistry and Research Institute of Natural Science (Korea, Republic of)

    2015-02-15

    Antifreeze proteins (AFPs) are found in a variety of cold-adapted (psychrophilic) organisms to promote survival at subzero temperatures by binding to ice crystals and decreasing the freezing temperature of body fluids. The type III AFPs are small globular proteins that consist of one α-helix, three 3{sub 10}-helices, and two β-strands. Sialic acids play important roles in a variety of biological functions, such as development, recognition, and cell adhesion and are synthesized by conserved enzymatic pathways that include sialic acid synthase (SAS). SAS consists of an N-terminal catalytic domain and a C-terminal antifreeze-like (AFL) domain, which is similar to the type III AFPs. Despite having very similar structures, AFL and the type III AFPs exhibit very different temperature-dependent stability and activity. In this study, we have performed backbone dynamics analyses of a type III AFP (HPLC12 isoform) and the AFL domain of human SAS (hAFL) at various temperatures. We also characterized the structural/dynamic properties of the ice-binding surfaces by analyzing the temperature gradient of the amide proton chemical shift and its correlation with chemical shift deviation from random coil. The dynamic properties of the two proteins were very different from each other. While HPLC12 was mostly rigid with a few residues exhibiting slow motions, hAFL showed fast internal motions at low temperature. Our results provide insight into the molecular basis of thermostability and structural flexibility in homologous psychrophilic HPLC12 and mesophilic hAFL proteins.

  11. Characterization of the Burkholderia mallei tonB Mutant and Its Potential as a Backbone Strain for Vaccine Development.

    Directory of Open Access Journals (Sweden)

    Tiffany M Mott

    Full Text Available In this study, a Burkholderia mallei tonB mutant (TMM001 deficient in iron acquisition was constructed, characterized, and evaluated for its protective properties in acute inhalational infection models of murine glanders and melioidosis.Compared to the wild-type, TMM001 exhibits slower growth kinetics, siderophore hyper-secretion and the inability to utilize heme-containing proteins as iron sources. A series of animal challenge studies showed an inverse correlation between the percentage of survival in BALB/c mice and iron-dependent TMM001 growth. Upon evaluation of TMM001 as a potential protective strain against infection, we found 100% survival following B. mallei CSM001 challenge of mice previously receiving 1.5 x 10(4 CFU of TMM001. At 21 days post-immunization, TMM001-treated animals showed significantly higher levels of B. mallei-specific IgG1, IgG2a and IgM when compared to PBS-treated controls. At 48 h post-challenge, PBS-treated controls exhibited higher levels of serum inflammatory cytokines and more severe pathological damage to target organs compared to animals receiving TMM001. In a cross-protection study of acute inhalational melioidosis with B. pseudomallei, TMM001-treated mice were significantly protected. While wild type was cleared in all B. mallei challenge studies, mice failed to clear TMM001.Although further work is needed to prevent chronic infection by TMM001 while maintaining immunogenicity, our attenuated strain demonstrates great potential as a backbone strain for future vaccine development against both glanders and melioidosis.

  12. Probing the role of backbone hydrogen bonds in protein-peptide interactions by amide-to-ester mutations

    DEFF Research Database (Denmark)

    Eildal, Jonas N N; Hultqvist, Greta; Balle, Thomas;

    2013-01-01

    -protein interactions, those of the PDZ domain family involve formation of intermolecular hydrogen bonds: C-termini or internal linear motifs of proteins bind as β-strands to form an extended antiparallel β-sheet with the PDZ domain. Whereas extensive work has focused on the importance of the amino acid side chains...... of the protein ligand, the role of the backbone hydrogen bonds in the binding reaction is not known. Using amide-to-ester substitutions to perturb the backbone hydrogen-bonding pattern, we have systematically probed putative backbone hydrogen bonds between four different PDZ domains and peptides corresponding...... to natural protein ligands. Amide-to-ester mutations of the three C-terminal amides of the peptide ligand severely affected the affinity with the PDZ domain, demonstrating that hydrogen bonds contribute significantly to ligand binding (apparent changes in binding energy, ΔΔG = 1.3 to >3.8 kcal mol(-1...

  13. On correlation between protein secondary structure, backbone bond angles, and side-chain orientations

    CERN Document Server

    Lundgren, Martin

    2012-01-01

    We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C$_\\alpha$ carbon of a protein backbone, and for this we develop new visualization techniques to analyze high resolution X-ray structures in Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse grained energy function to describe the ensuing side-chain geometry in terms of the C$_\\beta$ carbon orientations. The energy function can model the side-chain geometry with a sub-atomic precision. As an example we construct the C$_\\alpha$-C$_\\beta$ structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 \\.A in root-mean-square distance from the experimental X-ray structure.

  14. A renormalization approach to describe charge transport in quasiperiodic dangling backbone ladder (DBL)-DNA molecules

    Energy Technology Data Exchange (ETDEWEB)

    Sarmento, R.G. [Departamento de Fisica, Universidade Federal do Rio Grande do Norte, 59072-970 Natal, RN (Brazil); Fulco, U.L. [Departamento de Biofisica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal, RN (Brazil); Albuquerque, E.L., E-mail: eudenilson@gmail.com [Departamento de Biofisica e Farmacologia, Universidade Federal do Rio Grande do Norte, 59072-970 Natal, RN (Brazil); Caetano, E.W.S. [Instituto Federal de Educacao, Ciencia e Tecnologia do Ceara, 60040-531 Fortaleza, CE (Brazil); Freire, V.N. [Departamento de Fisica, Universidade Federal do Ceara, 60455-760 Fortaleza, CE (Brazil)

    2011-10-31

    Highlights: → One-step renormalization approach to describe the DBL-DNA molecule. → Electronic tight-binding Hamiltonian model. → A quasiperiodic sequence to mimic the DNA nucleotides arrangement. → Electronic transmission spectra. → I-V characteristics. -- Abstract: We study the charge transport properties of a dangling backbone ladder (DBL)-DNA molecule focusing on a quasiperiodic arrangement of its constituent nucleotides forming a Rudin-Shapiro (RS) and Fibonacci (FB) Poly (CG) sequences, as well as a natural DNA sequence (Ch22) for the sake of comparison. Making use of a one-step renormalization process, the DBL-DNA molecule is modeled in terms of a one-dimensional tight-binding Hamiltonian to investigate its transmissivity and current-voltage (I-V) profiles. Beyond the semiconductor I-V characteristics, a striking similarity between the electronic transport properties of the RS quasiperiodic structure and the natural DNA sequence was found.

  15. Polystyrene Backbone Polymers Consisting of Alkyl-Substituted Triazine Side Groups for Phosphorescent OLEDs

    Directory of Open Access Journals (Sweden)

    Beatrice Ch. D. Salert

    2012-01-01

    Full Text Available This paper describes the synthesis of new electron-transporting styrene monomers and their corresponding polystyrenes all with a 2,4,6-triphenyl-1,3,5-triazine basic structure in the side group. The monomers differ in the alkyl substitution and in the meta-/paralinkage of the triazine to the polymer backbone. The thermal and spectroscopic properties of the new electron-transporting polymers are discussed in regard to their chemical structures. Phosphorescent OLEDs were prepared using the obtained electron-transporting polymers as the emissive layer material in blend systems together with a green iridium-based emitter 13 and a small molecule as an additional cohost with wideband gap characteristics (CoH-001. The performance of the OLEDs was characterized and discussed in regard to the chemical structure of the new electron-transporting polymers.

  16. The Effects of NHC-Backbone Substitution on Efficiency in Ruthenium-based Olefin Metathesis

    Science.gov (United States)

    Kuhn, Kevin M.; Bourg, Jean-Baptiste; Chung, Cheol K.; Virgil, Scott C.; Grubbs, Robert H.

    2009-01-01

    A series of ruthenium olefin metathesis catalysts bearing N-heterocyclic carbene (NHC) ligands with varying degrees of backbone and N-aryl substitution have been prepared. These complexes show greater resistance to decomposition through C–H activation of the N-aryl group, resulting in increased catalyst lifetimes. This work has utilized robotic technology to examine the activity and stability of each catalyst in metathesis, providing insights into the relationship between ligand architecture and enhanced efficiency. The development of this robotic methodology has also shown that, under optimized conditions, catalyst loadings as low as 25 ppm can lead to 100% conversion in the ring-closing metathesis of diethyl diallylmalonate. PMID:19351207

  17. Extensive Air Showers: from the muonic smoking guns to the hadronic backbone

    Directory of Open Access Journals (Sweden)

    Cazon L.

    2013-06-01

    Full Text Available Extensive Air Showers are complex macroscopic objects initiated by single ultra-high energy particles. They are the result of millions of high energy reactions in the atmosphere and can be described as the superposition of hadronic and electromagnetic cascades. The hadronic cascade is the air shower backbone, and it is mainly made of pions. Decays of neutral pions initiate electromagnetic cascades, while the decays of charged pions produce muons which leave the hadronic core and travel many kilometers almost unaffected. Muons are smoking guns of the hadronic cascade: the energy, transverse momentum, spatial distribution and depth of production are key to reconstruct the history of the air shower. In this work, we overview the phenomenology of muons on the air shower and its relation to the hadronic cascade. We briefly review the experimental efforts to analyze muons within air showers and discuss possible paths to use this information.

  18. A recombinant, chimeric tetravalent dengue vaccine candidate based on a dengue virus serotype 2 backbone.

    Science.gov (United States)

    Osorio, Jorge E; Wallace, Derek; Stinchcomb, Dan T

    2016-01-01

    Dengue fever is caused by infection with one of four dengue virus (DENV) serotypes (DENV-1-4), necessitating tetravalent dengue vaccines that can induce protection against all four DENV. Takeda's live attenuated tetravalent dengue vaccine candidate (TDV) comprises an attenuated DENV-2 strain plus chimeric viruses containing the prM and E genes of DENV-1, -3 and -4 cloned into the attenuated DENV-2 'backbone'. In Phase 1 and 2 studies, TDV was well tolerated by children and adults aged 1.5-45 years, irrespective of prior dengue exposure; mild injection-site symptoms were the most common adverse events. TDV induced neutralizing antibody responses and seroconversion to all four DENV as well as cross-reactive T cell-mediated responses that may be necessary for broad protection against dengue fever.

  19. A renormalization approach to describe charge transport in quasiperiodic dangling backbone ladder (DBL)-DNA molecules

    Science.gov (United States)

    Sarmento, R. G.; Fulco, U. L.; Albuquerque, E. L.; Caetano, E. W. S.; Freire, V. N.

    2011-10-01

    We study the charge transport properties of a dangling backbone ladder (DBL)-DNA molecule focusing on a quasiperiodic arrangement of its constituent nucleotides forming a Rudin-Shapiro (RS) and Fibonacci (FB) Poly (CG) sequences, as well as a natural DNA sequence (Ch22) for the sake of comparison. Making use of a one-step renormalization process, the DBL-DNA molecule is modeled in terms of a one-dimensional tight-binding Hamiltonian to investigate its transmissivity and current-voltage (I-V) profiles. Beyond the semiconductor I-V characteristics, a striking similarity between the electronic transport properties of the RS quasiperiodic structure and the natural DNA sequence was found.

  20. Solid-phase synthesis of lidocaine and procainamide analogues using backbone amide linker (BAL) anchoring.

    Science.gov (United States)

    Shannon, Simon K; Peacock, Mandy J; Kates, Steven A; Barany, George

    2003-01-01

    New solid-phase strategies have been developed for the synthesis of lidocaine (1) and procainamide (2) analogues, using backbone amide linker (BAL) anchoring. Both sets were prepared starting from a common resin-bound intermediate, followed by four general steps: (i) attachment of a primary aliphatic or aromatic amine to the solid support via reductive amination (as monitored by a novel test involving reaction of 2,4-dinitrophenylhydrazine with residual aldehyde groups); (ii) acylation of the resultant secondary amine; (iii) displacement of halide with an amine; and (iv) trifluoroacetic acid-mediated release from the support. A manual parallel strategy was followed to provide 60 novel compounds, of which two dozen have not been previously described. In most cases, initial crude purities were >80%, and overall isolated yields were in the 40-88% range.

  1. Design of a sialylglycopolymer with a chitosan backbone having efficient inhibitory activity against influenza virus infection.

    Science.gov (United States)

    Umemura, Myco; Itoh, Masae; Makimura, Yutaka; Yamazaki, Kohji; Umekawa, Midori; Masui, Ayano; Matahira, Yoshiharu; Shibata, Mari; Ashida, Hisashi; Yamamoto, Kenji

    2008-08-14

    We verified here the inhibitory activity of a sialylglycopolymer prepared from natural products, chitosan and hen egg yolk, against influenza virus infection and estimated the requirements of the molecule for efficient inhibition. The inhibitory activity clearly depended on two factors, the length (the degree of polymerization: DP) of the chitosan backbone and the amount (the degree of substitution: DS) of conjugated sialyloligosaccharide side chain. The inhibitory efficiency increased in accordance with the DP value, with the highest inhibitory activity obtained when the DP was 1430. The inhibition of virus infection reached more than 90% as the DS value increased up to 15.6% when the neighboring sialyloligosaccharide side chains came as close as 4 nm, which was nearly the distance between two receptor-binding pockets in a hemagglutinin trimer. These results demonstrate that the sialylglycopolymer could be an excellent candidate of the safe and efficient anti-influenza drug.

  2. Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles.

    Science.gov (United States)

    Ostermeir, Katja; Zacharias, Martin

    2014-01-15

    A Hamiltonian Replica-Exchange Molecular Dynamics (REMD) simulation method has been developed that employs a two-dimensional backbone and one-dimensional side chain biasing potential specifically to promote conformational transitions in peptides. To exploit the replica framework optimally, the level of the biasing potential in each replica was appropriately adapted during the simulations. This resulted in both high exchange rates between neighboring replicas and improved occupancy/flow of all conformers in each replica. The performance of the approach was tested on several peptide and protein systems and compared with regular MD simulations and previous REMD studies. Improved sampling of relevant conformational states was observed for unrestrained protein and peptide folding simulations as well as for refinement of a loop structure with restricted mobility of loop flanking protein regions.

  3. Sequential backbone assignment based on dipolar amide-to-amide correlation experiments.

    Science.gov (United States)

    Xiang, ShengQi; Grohe, Kristof; Rovó, Petra; Vasa, Suresh Kumar; Giller, Karin; Becker, Stefan; Linser, Rasmus

    2015-07-01

    Proton detection in solid-state NMR has seen a tremendous increase in popularity in the last years. New experimental techniques allow to exploit protons as an additional source of information on structure, dynamics, and protein interactions with their surroundings. In addition, sensitivity is mostly improved and ambiguity in assignment experiments reduced. We show here that, in the solid state, sequential amide-to-amide correlations turn out to be an excellent, complementary way to exploit amide shifts for unambiguous backbone assignment. For a general assessment, we compare amide-to-amide experiments with the more common (13)C-shift-based methods. Exploiting efficient CP magnetization transfers rather than less efficient INEPT periods, our results suggest that the approach is very feasible for solid-state NMR.

  4. Sequential backbone assignment based on dipolar amide-to-amide correlation experiments

    Energy Technology Data Exchange (ETDEWEB)

    Xiang, ShengQi; Grohe, Kristof; Rovó, Petra; Vasa, Suresh Kumar; Giller, Karin; Becker, Stefan; Linser, Rasmus, E-mail: rali@nmr.mpibpc.mpg.de [Max Planck Institute for Biophysical Chemistry, Department for NMR-Based Structural Biology (Germany)

    2015-07-15

    Proton detection in solid-state NMR has seen a tremendous increase in popularity in the last years. New experimental techniques allow to exploit protons as an additional source of information on structure, dynamics, and protein interactions with their surroundings. In addition, sensitivity is mostly improved and ambiguity in assignment experiments reduced. We show here that, in the solid state, sequential amide-to-amide correlations turn out to be an excellent, complementary way to exploit amide shifts for unambiguous backbone assignment. For a general assessment, we compare amide-to-amide experiments with the more common {sup 13}C-shift-based methods. Exploiting efficient CP magnetization transfers rather than less efficient INEPT periods, our results suggest that the approach is very feasible for solid-state NMR.

  5. Modification of rifamycin polyketide backbone leads to improved drug activity against rifampicin-resistant Mycobacterium tuberculosis.

    Science.gov (United States)

    Nigam, Aeshna; Almabruk, Khaled H; Saxena, Anjali; Yang, Jongtae; Mukherjee, Udita; Kaur, Hardeep; Kohli, Puneet; Kumari, Rashmi; Singh, Priya; Zakharov, Lev N; Singh, Yogendra; Mahmud, Taifo; Lal, Rup

    2014-07-25

    Rifamycin B, a product of Amycolatopsis mediterranei S699, is the precursor of clinically used antibiotics that are effective against tuberculosis, leprosy, and AIDS-related mycobacterial infections. However, prolonged usage of these antibiotics has resulted in the emergence of rifamycin-resistant strains of Mycobacterium tuberculosis. As part of our effort to generate better analogs of rifamycin, we substituted the acyltransferase domain of module 6 of rifamycin polyketide synthase with that of module 2 of rapamycin polyketide synthase. The resulting mutants (rifAT6::rapAT2) of A. mediterranei S699 produced new rifamycin analogs, 24-desmethylrifamycin B and 24-desmethylrifamycin SV, which contained modification in the polyketide backbone. 24-Desmethylrifamycin B was then converted to 24-desmethylrifamycin S, whose structure was confirmed by MS, NMR, and X-ray crystallography. Subsequently, 24-desmethylrifamycin S was converted to 24-desmethylrifampicin, which showed excellent antibacterial activity against several rifampicin-resistant M. tuberculosis strains.

  6. Quality of service estimation based on maximum bottleneck algorithm for domain aggregation in backbone networks

    Institute of Scientific and Technical Information of China (English)

    WANG Yang; ZHAN Yi-chun; YU Shao-hua

    2007-01-01

    This paper investigates the routing among autonomous systems (ASs) with quality of service (QoS) requirements. To avoid the intractability of the problem, abstract QoS capability must be informed among ASs, because the routhing which constrained QoS has been proved to be nondeterministic polynomial-time (NP) hard even inside an AS. This paper employs the modified Dijkstra algorithm to compute the maximum bottleneck bandwidth inside an AS. This approach lays a basis for the AS-level switching capability on which interdomain advertisement can be performed. Furthermore, the paper models the aggregated traffic in backbone network with fractional Brownian motion (FBM), and by integrating along the time axis in short intervals, a good estimation of the distribution of queue length in the next short intervals can be obtained. The proposed advertisement mechanism can be easily implemented with the current interdomain routing protocols. Numerical study indicates that the presented scheme is effective and feasible.

  7. Side chain and backbone contributions of Phe508 to CFTR folding

    Energy Technology Data Exchange (ETDEWEB)

    Thibodeau, Patrick H.; Brautigam, Chad A.; Machius, Mischa; Thomas, Philip J. (U. of Texas-SMED)

    2010-12-07

    Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an integral membrane protein, cause cystic fibrosis (CF). The most common CF-causing mutant, deletion of Phe508, fails to properly fold. To elucidate the role Phe508 plays in the folding of CFTR, missense mutations at this position were generated. Only one missense mutation had a pronounced effect on the stability and folding of the isolated domain in vitro. In contrast, many substitutions, including those of charged and bulky residues, disrupted folding of full-length CFTR in cells. Structures of two mutant nucleotide-binding domains (NBDs) reveal only local alterations of the surface near position 508. These results suggest that the peptide backbone plays a role in the proper folding of the domain, whereas the side chain plays a role in defining a surface of NBD1 that potentially interacts with other domains during the maturation of intact CFTR.

  8. RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone.

    Science.gov (United States)

    Wang, Xueyi; Kapral, Gary; Murray, Laura; Richardson, David; Richardson, Jane; Snoeyink, Jack

    2008-01-01

    Although accurate details in RNA structure are of great importance for understanding RNA function, the backbone conformation is difficult to determine, and most existing RNA structures show serious steric clashes (>or= 0.4 A overlap) when hydrogen atoms are taken into account. We have developed a program called RNABC (RNA Backbone Correction) that performs local perturbations to search for alternative conformations that avoid those steric clashes or other local geometry problems. Its input is an all-atom coordinate file for an RNA crystal structure (usually from the MolProbity web service), with problem areas specified. RNABC rebuilds a suite (the unit from sugar to sugar) by anchoring the phosphorus and base positions, which are clearest in crystallographic electron density, and reconstructing the other atoms using forward kinematics. Geometric parameters are constrained within user-specified tolerance of canonical or original values, and torsion angles are constrained to ranges defined through empirical database analyses. Several optimizations reduce the time required to search the many possible conformations. The output results are clustered and presented to the user, who can choose whether to accept one of the alternative conformations. Two test evaluations show the effectiveness of RNABC, first on the S-motifs from 42 RNA structures, and second on the worst problem suites (clusters of bad clashes, or serious sugar pucker outliers) in 25 unrelated RNA structures. Among the 101 S-motifs, 88 had diagnosed problems, and RNABC produced clash-free conformations with acceptable geometry for 71 of those (about 80%). For the 154 worst problem suites, RNABC proposed alternative conformations for 72. All but 8 of those were judged acceptable after examining electron density (where available) and local conformation. Thus, even for these worst cases, nearly half the time RNABC suggested corrections suitable to initiate further crystallographic refinement. The program is

  9. Contribution of Peptide Backbone to Anti-Citrullinated Peptide Antibody Reactivity.

    Directory of Open Access Journals (Sweden)

    Nicole Hartwig Trier

    Full Text Available Rheumatoid arthritis (RA is one of the most common autoimmune diseases, affecting approximately 1-2% of the world population. One of the characteristic features of RA is the presence of autoantibodies. Especially the highly specific anti-citrullinated peptide antibodies (ACPAs, which have been found in up to 70% of RA patients' sera, have received much attention. Several citrullinated proteins are associated with RA, suggesting that ACPAs may react with different sequence patterns, separating them from traditional antibodies, whose reactivity usually is specific towards a single target. As ACPAs have been suggested to be involved in the development of RA, knowledge about these antibodies may be crucial. In this study, we examined the influence of peptide backbone for ACPA reactivity in immunoassays. The antibodies were found to be reactive with a central Cit-Gly motif being essential for ACPA reactivity and to be cross-reactive between the selected citrullinated peptides. The remaining amino acids within the citrullinated peptides were found to be of less importance for antibody reactivity. Moreover, these findings indicated that the Cit-Gly motif in combination with peptide backbone is essential for antibody reactivity. Based on these findings it was speculated that any amino acid sequence, which brings the peptide into a properly folded structure for antibody recognition is sufficient for antibody reactivity. These findings are in accordance with the current hypothesis that structural homology rather than sequence homology are favored between citrullinated epitopes. These findings are important in relation to clarifying the etiology of RA and to determine the nature of ACPAs, e.g., why some Cit-Gly-containing sequences are not targeted by ACPAs.

  10. Effects of Tryptophan Content and Backbone Spacing on the Uptake Efficiency of Cell-Penetrating Peptides

    KAUST Repository

    Rydberg, Hanna A.

    2012-07-10

    Cell-penetrating peptides (CPPs) are able to traverse cellular membranes and deliver macromolecular cargo. Uptake occurs through both endocytotic and nonendocytotic pathways, but the molecular requirements for efficient internalization are not fully understood. Here we investigate how the presence of tryptophans and their position within an oligoarginine influence uptake mechanism and efficiency. Flow cytometry and confocal fluorescence imaging are used to estimate uptake efficiency, intracellular distribution and toxicity in Chinese hamster ovarian cells. Further, membrane leakage and lipid membrane affinity are investigated. The peptides contain eight arginine residues and one to four tryptophans, the tryptophans positioned either at the N-terminus, in the middle, or evenly distributed along the amino acid sequence. Our data show that the intracellular distribution varies among peptides with different tryptophan content and backbone spacing. Uptake efficiency is higher for the peptides with four tryptophans in the middle, or evenly distributed along the peptide sequence, than for the peptide with four tryptophans at the N-terminus. All peptides display low cytotoxicity except for the one with four tryptophans at the N-terminus, which was moderately toxic. This finding is consistent with their inability to induce efficient leakage of dye from lipid vesicles. All peptides have comparable affinities for lipid vesicles, showing that lipid binding is not a decisive parameter for uptake. Our results indicate that tryptophan content and backbone spacing can affect both the CPP uptake efficiency and the CPP uptake mechanism. The low cytotoxicity of these peptides and the possibilities of tuning their uptake mechanism are interesting from a therapeutic point of view. © 2012 American Chemical Society.

  11. Preparation of stable spherical micelles with rigid backbones based on polyaryletherketone copolymers containing lateral pyridyl groups

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Shuling; Liu, Lingzhi; Guo, Yunliang; Jiang, Zhenhua; Wang, Guibin, E-mail: wgb@jlu.edu.cn

    2013-07-15

    A new bisphenol monomer, 3-(3,4-dihydroxyphenylimine) pyridine (PYPH), was synthesized via a deoxidization reaction of an amine. A series of novel polyaryletherketone copolymers containing lateral pyridyl groups (PY-PAEKs) based on PYPH, 2,2-di(4-hydroxyphenyl)propane and 4,4′-difluorobenzophenone were prepared by nucleophilic aromatic substitution polycondensation reactions. Furthermore, spherical micelles with rigid PY-PAEKs as the inner cores and flexible polyacrylic acid (PAA) as the outer shells were obtained in a selective solvent (H{sub 2}O) successfully. The formation of the spherical micelles was confirmed by scanning electron and transmission electron microscopy as well as by surface tension measurements. The formation and size of the spherical micelles depended on the weight ratio of PAA/PY-PAEK, the concentration and pH value of the mixed solution containing the PY-PAEK and PAA, and the number of pyridyl groups in the PY-PAEK. The structure of the spherical micelles could be stabilized by a cross-linking reaction between the pyridyl groups of the PY-PAEKs and 1,4-dibromobutane. The diameter of the spherical micelles decreased because of the removal of the PAA shell from the PY-PAEK core after the cross-linking reaction. The resulting stable spherical micelles with rigid backbones did not dissolve in a number of polar solvents and remained unaffected by changes in the pH values. - Graphical abstract: Display Omitted - Highlights: • Polyaryletherketone copolymers containing lateral pyridyl groups were synthesized. • Spherical micelles were prepared using these copolymers and polyacrylic acid. • The copolymers and polyacrylic acid formed the core and the shell of the micelles, respectively. • The obtained micelles were stabilized by a cross-linking reaction. • The cross-linked micelles had rigid backbones, independent of solvents and pH values.

  12. Backbone-hydrazone-containing biodegradable copolymeric micelles for anticancer drug delivery

    Science.gov (United States)

    Xu, Jing; Luan, Shujuan; Qin, Benkai; Wang, Yingying; Wang, Kai; Qi, Peilan; Song, Shiyong

    2016-11-01

    Well-defined biodegradable, pH-sensitive amphiphilic block polymers, poly(ethylene glycol)-Hyd-poly(lactic acid) (mPEG-Hyd-PLA) which have acid-cleavable linkages in their backbones, were synthesized via ring-opening polymerization initiated from hydrazone-containing macroinitiators. Introducing a hydrazone bond onto the backbone of an amphiphilic copolymer will find a broad-spectrum encapsulation of hydrophobic drugs. Dynamic light scattering (DLS) and transmission electron microscopy showed that the diblock copolymers self-assembled into stable micelles with average diameters of 100 nm. The mean diameters and size distribution of the hydrazone-containing micelles changed obviously in mildly acidic pH (multiple peaks from 1 to 202 nm appeared under a pH 4.0 condition) than in neutral, while there were no changes in the case of non-sensitive ones. Doxorubicin (DOX) and paclitaxel (PTX) were loaded with drug loading content ranging from 2.4 to 3.5 %, respectively. Interestingly, the anticancer drugs released from mPEG-Hyd-PLA micelles could also be promoted by the increased acidity. An in vitro cytotoxicity study showed that the DOX-loaded mPEG-Hyd-PLA micelles have significantly enhanced cytotoxicity against HepG2 cells compared with the non-sensitive poly(ethylene glycol)-block-poly(lactic acid) (mPEG-PLA) micelles. Confocal microscopy observation indicated that more DOX were delivered into the nuclei of cells following 6 or 12 h incubation with DOX-loaded mPEG-Hyd-PLA micelles. In vivo studies on H22-bearing Swiss mice demonstrated the superior anticancer activity of DOX-loaded mPEG-Hyd-PLA micelles over free DOX and DOX-loaded mPEG-PLA micelles. These hydrazone-containing pH-responsive degradable micelles provide a useful strategy for antitumor drug delivery.

  13. Subpicosecond protein backbone changes detected during the green-absorbing proteorhodopsin primary photoreaction.

    Science.gov (United States)

    Amsden, Jason J; Kralj, Joel M; Chieffo, Logan R; Wang, Xihua; Erramilli, Shyamsunder; Spudich, Elena N; Spudich, John L; Ziegler, Lawrence D; Rothschild, Kenneth J

    2007-10-11

    Recent studies demonstrate that photoactive proteins can react within several picoseconds to photon absorption by their chromophores. Faster subpicosecond protein responses have been suggested to occur in rhodopsin-like proteins where retinal photoisomerization may impulsively drive structural changes in nearby protein groups. Here, we test this possibility by investigating the earliest protein structural changes occurring in proteorhodopsin (PR) using ultrafast transient infrared (TIR) spectroscopy with approximately 200 fs time resolution combined with nonperturbing isotope labeling. PR is a recently discovered microbial rhodopsin similar to bacteriorhodopsin (BR) found in marine proteobacteria and functions as a proton pump. Vibrational bands in the retinal fingerprint (1175-1215 cm(-1)) and ethylenic stretching (1500-1570 cm(-1)) regions characteristic of all-trans to 13-cis chromophore isomerization and formation of a red-shifted photointermediate appear with a 500-700 fs time constant after photoexcitation. Bands characteristic of partial return to the ground state evolve with a 2.0-3.5 ps time constant. In addition, a negative band appears at 1548 cm(-1) with a time constant of 500-700 fs, which on the basis of total-15N and retinal C15D (retinal with a deuterium on carbon 15) isotope labeling is assigned to an amide II peptide backbone mode that shifts to near 1538 cm(-1) concomitantly with chromophore isomerization. Our results demonstrate that one or more peptide backbone groups in PR respond with a time constant of 500-700 fs, almost coincident with the light-driven retinylidene chromophore isomerization. The protein changes we observe on a subpicosecond time scale may be involved in storage of the absorbed photon energy subsequently utilized for proton transport.

  14. Enhanced biosynthetically directed fractional carbon-13 enrichment of proteins for backbone NMR assignments.

    Science.gov (United States)

    Wenrich, Broc R; Sonstrom, Reilly E; Gupta, Riju A; Rovnyak, David

    2015-11-01

    Routes to carbon-13 enrichment of bacterially expressed proteins include achieving uniform or positionally selective (e.g. ILV-Me, or (13)C', etc.) enrichment. We consider the potential for biosynthetically directed fractional enrichment (e.g. carbon-13 incorporation in the protein less than 100%) for performing routine n-(D)dimensional NMR spectroscopy of proteins. First, we demonstrate an approach to fractional isotope addition where the initial growth media containing natural abundance glucose is replenished at induction with a small amount (e.g. 10%(w/w)u-(13)C-glucose) of enriched nutrient. The approach considered here is to add 10% (e.g. 200mg for a 2g/L culture) u-(13)C-glucose at the induction time (OD600=0.8), resulting in a protein with enhanced (13)C incorporation that gives almost the same NMR signal levels as an exact 20% (13)C sample. Second, whereas fractional enrichment is used for obtaining stereospecific methyl assignments, we find that (13)C incorporation levels no greater than 20%(w/w) yield (13)C and (13)C-(13)C spin pair incorporation sufficient to conduct typical 3D-bioNMR backbone experiments on moderate instrumentation (600 MHz, RT probe). Typical 3D-bioNMR experiments of a fractionally enriched protein yield expected backbone connectivities, and did not show amino acid biases in this work, with one exception. When adding 10% u-(13)C glucose to expression media at induction, there is poor preservation of (13)Cα-(13)Cβ spin pairs in the amino acids ILV, leading to the absence of Cβ signals in HNCACB spectra for ILV, a potentially useful editing effect. Enhanced fractional carbon-13 enrichment provides lower-cost routes to high throughput protein NMR studies, and makes modern protein NMR more cost-accessible.

  15. Structural dynamics of protein backbone {phi} angles: extended molecular dynamics simulations versus experimental {sup 3}J scalar couplings

    Energy Technology Data Exchange (ETDEWEB)

    Markwick, Phineus R. L. [CNRS/CEA/UJF, Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel UMR 5075 (France); Showalter, Scott A. [Florida State University, Department of Chemistry and Biochemistry, NHMFL (United States); Bouvignies, Guillaume [CNRS/CEA/UJF, Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel UMR 5075 (France); Brueschweiler, Rafael [Florida State University, Department of Chemistry and Biochemistry, NHMFL (United States)], E-mail: bruschweiler@magnet.fsu.edu; Blackledge, Martin [CNRS/CEA/UJF, Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel UMR 5075 (France)], E-mail: martin.blackledge@ibs.fr

    2009-09-15

    {sup 3}J scalar couplings report on the conformational averaging of backbone {phi} angles in peptides and proteins, and therefore represent a potentially powerful tool for studying the details of both structure and dynamics in solution. We have compared an extensive experimental dataset with J-couplings predicted from unrestrained molecular dynamics simulation using enhanced sampling available from accelerated molecular dynamics or using long timescale trajectories (200 ns). The dynamic fluctuations predicted to be present along the backbone, in agreement with residual dipolar coupling analysis, are compatible with the experimental {sup 3}J scalar couplings providing a slightly better reproduction of these experimental parameters than a high-resolution static structure.

  16. Backbone dynamics of reduced plastocyanin from the cyanobacterium Anabaena variabilis: Regions involved in electron transfer have enhanced mobility

    DEFF Research Database (Denmark)

    Ma, L.X.; Hass, M.A.S.; Vierick, N.;

    2003-01-01

    The dynamics of the backbone of the electron-transfer protein plastocyanin from the cyanobacterium Anabaena variabilis were determined from the N-15 and C-13(alpha) R-1 and R-2) relaxation rates and steady-state [H-1]-N-15 and [H-1]-C-13 nuclear Overhauser effects (NOEs) using the model-free appr......The dynamics of the backbone of the electron-transfer protein plastocyanin from the cyanobacterium Anabaena variabilis were determined from the N-15 and C-13(alpha) R-1 and R-2) relaxation rates and steady-state [H-1]-N-15 and [H-1]-C-13 nuclear Overhauser effects (NOEs) using the model...

  17. The extension of a DNA double helix by an additional Watson-Crick base pair on the same backbone

    DEFF Research Database (Denmark)

    Kumar, P.; Sharma, P. K.; Madsen, Charlotte S.

    2013-01-01

    Additional base pair: The DNA duplex can be extended with an additional Watson-Crick base pair on the same backbone by the use of double-headed nucleotides. These also work as compressed dinucleotides and form two base pairs with cognate nucleobases on the opposite strand.......Additional base pair: The DNA duplex can be extended with an additional Watson-Crick base pair on the same backbone by the use of double-headed nucleotides. These also work as compressed dinucleotides and form two base pairs with cognate nucleobases on the opposite strand....

  18. A Multi-Objective Approach for Protein Structure Prediction Based on an Energy Model and Backbone Angle Preferences.

    Science.gov (United States)

    Tsay, Jyh-Jong; Su, Shih-Chieh; Yu, Chin-Sheng

    2015-07-03

    Protein structure prediction (PSP) is concerned with the prediction of protein tertiary structure from primary structure and is a challenging calculation problem. After decades of research effort, numerous solutions have been proposed for optimisation methods based on energy models. However, further investigation and improvement is still needed to increase the accuracy and similarity of structures. This study presents a novel backbone angle preference factor, which is one of the factors inducing protein folding. The proposed multiobjective optimisation approach simultaneously considers energy models and backbone angle preferences to solve the ab initio PSP. To prove the effectiveness of the multiobjective optimisation approach based on the energy models and backbone angle preferences, 75 amino acid sequences with lengths ranging from 22 to 88 amino acids were selected from the CB513 data set to be the benchmarks. The data sets were highly dissimilar, therefore indicating that they are meaningful. The experimental results showed that the root-mean-square deviation (RMSD) of the multiobjective optimization approach based on energy model and backbone angle preferences was superior to those of typical energy models, indicating that the proposed approach can facilitate the ab initio PSP.

  19. A Multi-Objective Approach for Protein Structure Prediction Based on an Energy Model and Backbone Angle Preferences

    Directory of Open Access Journals (Sweden)

    Jyh-Jong Tsay

    2015-07-01

    Full Text Available Protein structure prediction (PSP is concerned with the prediction of protein tertiary structure from primary structure and is a challenging calculation problem. After decades of research effort, numerous solutions have been proposed for optimisation methods based on energy models. However, further investigation and improvement is still needed to increase the accuracy and similarity of structures. This study presents a novel backbone angle preference factor, which is one of the factors inducing protein folding. The proposed multiobjective optimisation approach simultaneously considers energy models and backbone angle preferences to solve the ab initio PSP. To prove the effectiveness of the multiobjective optimisation approach based on the energy models and backbone angle preferences, 75 amino acid sequences with lengths ranging from 22 to 88 amino acids were selected from the CB513 data set to be the benchmarks. The data sets were highly dissimilar, therefore indicating that they are meaningful. The experimental results showed that the root-mean-square deviation (RMSD of the multiobjective optimization approach based on energy model and backbone angle preferences was superior to those of typical energy models, indicating that the proposed approach can facilitate the ab initio PSP.

  20. Backbone amide linker strategy for the synthesis of 1,4-triazole-containing cyclic tetra- and pentapeptides

    NARCIS (Netherlands)

    Springer, J.; de Cuba, K.R.; Calvet-Vitale, S.; Geenevasen, J.A.J.; Hermkens, P.H.H.; Hiemstra, H.; van Maarseveen, J.H.

    2008-01-01

    A backbone amide linker strategy was chosen for the solid-phase synthesis of triazole-containing Cyclic tetra- and pentapeptides. An alkyne-substituted linker derived from 4-hydroxy-2-methoxybenzaldehyde was elongated by using standard "Fmoc-based" solid phase chemistry and terminated by coupling of

  1. Alkali metal salts of formazanate ligands : diverse coordination modes as a result of the nitrogen-rich [NNCNN] ligand backbone

    NARCIS (Netherlands)

    Travieso-Puente, Raquel; Chang, Mu-Chieh; Otten, Edwin

    2014-01-01

    Alkali metal salts of redox-active formazanate ligands were prepared, and their structures in the solid-state and in solution are determined. The nitrogen-rich [NNCNN] backbone of formazanates results in a varied coordination chemistry, with both the internal and terminal nitrogen atoms available fo

  2. VPLS: alternativa de interconexión a través del backbone IP/MPLS de ETECSA

    Directory of Open Access Journals (Sweden)

    Osmel Barreto Prieto

    2013-03-01

    Full Text Available La Empresa de Telecomunicaciones de Cuba (ETECSA maneja en condiciones de exclusividad la infraestructura de telecomunicaciones del país, por lo que el resto de los proveedores necesitan utilizar dicha infraestructura como soporte para la interconexión de los nodos que componen sus redes. Teniendo en cuenta el desarrollo de las tecnologías de las telecomunicaciones, ETECSA ha apostado por la implementación de un backbone IP/MPLS (Internet Protocol over  MultiProtocol Label Switching: Protocolo de Internet sobre Conmutación Multiprotocolo basada en Etiquetas en su red, el cual se espera absorba todos los servicios actualmente soportados por el backbone ATM (Asynchronous Transfer Mode/Frame Relay. Sin embargo, en estos momentos, la red IP/MPLS solamente oferta servicios VPN (Virtual Private Network: Red Privada Virtual a nivel de red (nivel tres del modelo OSI, cuestión que, para los otros proveedores, resulta inadmisible. El presente artículo describe una propuesta de implementación de una entidad VPLS (Virtual Private LAN Service: Servicio de LAN Privada Virtual como alternativa para la migración de los servicios de VPN de nivel dos que actualmente se soportan sobre el backbone ATM/Frame Relay, hacia el backbone IP/MPLS, variante que garantiza la independencia por parte de los proveedores que son clientes de ETECSA en la operación y enrutamiento de su red.

  3. Tailor-made synthesis of various backbone-substituted imidazolinium salts by triflic anhydride mediated intramolecular cyclisation.

    Science.gov (United States)

    Zhang, Jun; Su, Xiaolong; Fu, Jun; Qin, Xinke; Zhao, Meixin; Shi, Min

    2012-09-21

    We have found a Tf(2)O-mediated intramolecular cyclization reaction and have revealed an intriguing stereoselectivity and a regioselectivity during the preparation of intermediate alcohols, which allow for the tailor-made synthesis of various backbone-substituted imidazolinium salts, and structurally specific syn-4,5-disubstituted imidazolinium salts.

  4. Interaction of Al-induced peptide backbone ring structure with the sidechains of His, Phe, Trp and Tyr

    Institute of Scientific and Technical Information of China (English)

    吴清雷; 宋波

    2015-01-01

    Aluminium is widely used as an antimicrobial coagulant, food additive, and cookware. However, many reports indicate that aluminium may be a critical factor in many amyloid diseases, such as Alzheimer’s disease and Parkinson’s disease. Unfortunately, the underlying mechanism is still poorly understood, which limits efforts to prevent and treat these diseases. In this paper, using an ab initio method, we studied the interaction of Al-backbone ring structure with theπ-electron-rich sidechains of His, Phe, Trp, and Tyr. We found that in the absence of water, the Al-backbone ring can stably bind with those sidechains. In the presence of water, the Al-backbone ring can bind to the His sidechain and cannot bind to the other sidechains. As revealed by further investigations, this could be attributed to the fact that there was a coordinate bond of the Al-backbone ring with the His sidechain, while there were theπ-πstacking and cation-π-like interactions with the other sidechains. These findings potentially provide a molecular understanding of Al-related toxicity, and may be helpful in designing drugs for those aforementioned aluminum-linked diseases and encourage treatment of Al-polluted water.

  5. In the Near Future Backbone Aluminum Enterprises will Close Down About 2.4 million Tonnes of Capacity

    Institute of Scientific and Technical Information of China (English)

    2015-01-01

    On August 21,China Nonferrous Metals Industry Association Aluminum Industry Branch assembled some backbone aluminum enterprises and Henan Nonferrous Metal Industry Association to hold a discussion meeting in Beijing over the current operation trend of aluminum industry,dilemma and opportunity ahead and measures to diffuse surplus capacity,the meeting also discussed the

  6. Backbone, side chain and heme resonance assignments of cytochrome OmcF from Geobacter sulfurreducens.

    Science.gov (United States)

    Dantas, Joana M; Silva E Sousa, Marta; Salgueiro, Carlos A; Bruix, Marta

    2015-10-01

    Gene knockout studies on Geobacter sulfurreducens (Gs) cells showed that the outer membrane cytochrome OmcF is involved in respiratory pathways leading to the extracellular reduction of Fe(III) citrate and U(VI) oxide. In addition, microarray analysis of OmcF-deficient mutant versus the wild-type strain revealed that many of the genes with decreased transcript level were those whose expression is upregulated in cells grown with a graphite electrode as electron acceptor. This suggests that OmcF also regulates the electron transfer to electrode surfaces and the concomitant electrical current production by Gs in microbial fuel cells. Extracellular electron transfer processes (EET) constitute nowadays the foundations to develop biotechnological applications in biofuel production, bioremediation and bioenergy. Therefore, the structural characterization of OmcF is a fundamental step to understand the mechanisms underlying EET. Here, we report the complete assignment of the heme proton signals together with (1)H, (13)C and (15)N backbone and side chain assignments of the OmcF, excluding the hydrophobic residues of the N-terminal predicted lipid anchor.

  7. Phylogenomics resolves a spider backbone phylogeny and rejects a prevailing paradigm for orb web evolution.

    Science.gov (United States)

    Bond, Jason E; Garrison, Nicole L; Hamilton, Chris A; Godwin, Rebecca L; Hedin, Marshal; Agnarsson, Ingi

    2014-08-04

    Spiders represent an ancient predatory lineage known for their extraordinary biomaterials, including venoms and silks. These adaptations make spiders key arthropod predators in most terrestrial ecosystems. Despite ecological, biomedical, and biomaterial importance, relationships among major spider lineages remain unresolved or poorly supported. Current working hypotheses for a spider "backbone" phylogeny are largely based on morphological evidence, as most molecular markers currently employed are generally inadequate for resolving deeper-level relationships. We present here a phylogenomic analysis of spiders including taxa representing all major spider lineages. Our robust phylogenetic hypothesis recovers some fundamental and uncontroversial spider clades, but rejects the prevailing paradigm of a monophyletic Orbiculariae, the most diverse lineage, containing orb-weaving spiders. Based on our results, the orb web either evolved much earlier than previously hypothesized and is ancestral for a majority of spiders or else it has multiple independent origins, as hypothesized by precladistic authors. Cribellate deinopoid orb weavers that use mechanically adhesive silk are more closely related to a diverse clade of mostly webless spiders than to the araneoid orb-weaving spiders that use adhesive droplet silks. The fundamental shift in our understanding of spider phylogeny proposed here has broad implications for interpreting the evolution of spiders, their remarkable biomaterials, and a key extended phenotype--the spider web.

  8. Is there a Climate Network - A Backbone of the Climate System? (Invited)

    Science.gov (United States)

    Kurths, J.

    2010-12-01

    We consider an inverse problem: Is there a backbone-like structure underlying the climate system? For this we propose a method to reconstruct and analyze a complex network from data generated by a spatio-temporal dynamical system. This technique is then applied to reanalysis and model surface air temperature data. Parameters of this network, as betweenness centrality, uncover relations to global circulation patterns in oceans and atmosphere. We especially study the role of hubs and of long range connections, called teleconnections, in the flows of energy and matter in the climate system. The global scale view on climate networks offers promising new perspectives for detecting dynamical structures based on nonlinear physical processes in the climate system. References Arenas, A., A. Diaz-Guilera, J. Kurths, Y. Moreno, and C. Zhou, Phys. Reports 2008, 469, 93. Donges, J., Y. Zou, N. Marwan, and J. Kurths, Europ. Phys. J. ST 2009, 174, 157-179. Donges, J., Y. Zou, N. Marwan, and J. Kurths, Europhys. Lett. 2009, 87, 48007. Nawrath, J. et al., Phys. Rev. Lett. 2010, 104, 038701. Donner, R., Y. Zou, J. Donges, N. Marwan, and J. Kurths, Phys. Rev. E 2010, 81, 015101(R ).

  9. APSY-NMR for protein backbone assignment in high-throughput structural biology

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, Samit Kumar; Serrano, Pedro; Proudfoot, Andrew; Geralt, Michael [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States); Pedrini, Bill [Paul Scherrer Institute (PSI), SwissFEL Project (Switzerland); Herrmann, Torsten [Université de Lyon, Institut des Sciences Analytiques, Centre de RMN à Très Hauts Champs, UMR 5280 CNRS, ENS Lyon, UCB Lyon 1 (France); Wüthrich, Kurt, E-mail: wuthrich@scripps.edu [The Scripps Research Institute, Department of Integrative Structural and Computational Biology (United States)

    2015-01-15

    A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90 % of the residues. For most proteins the APSY data acquisition was completed in less than 30 h. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [{sup 1}H,{sup 1}H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination.

  10. An Enhanced Backbone-Assisted Reliable Framework for Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Amna Ali

    2010-03-01

    Full Text Available An extremely reliable source to sink communication is required for most of the contemporary WSN applications especially pertaining to military, healthcare and disaster-recovery. However, due to their intrinsic energy, bandwidth and computational constraints, Wireless Sensor Networks (WSNs encounter several challenges in reliable source to sink communication. In this paper, we present a novel reliable topology that uses reliable hotlines between sensor gateways to boost the reliability of end-to-end transmissions. This reliable and efficient routing alternative reduces the number of average hops from source to the sink. We prove, with the help of analytical evaluation, that communication using hotlines is considerably more reliable than traditional WSN routing. We use reliability theory to analyze the cost and benefit of adding gateway nodes to a backbone-assisted WSN. However, in hotline assisted routing some scenarios where source and the sink are just a couple of hops away might bring more latency, therefore, we present a Signature Based Routing (SBR scheme. SBR enables the gateways to make intelligent routing decisions, based upon the derived signature, hence providing lesser end-to-end delay between source to the sink communication. Finally, we evaluate our proposed hotline based topology with the help of a simulation tool and show that the proposed topology provides manifold increase in end-to-end reliability.

  11. Structure and backbone dynamics of a microcrystalline metalloprotein by solid-state NMR.

    Science.gov (United States)

    Knight, Michael J; Pell, Andrew J; Bertini, Ivano; Felli, Isabella C; Gonnelli, Leonardo; Pierattelli, Roberta; Herrmann, Torsten; Emsley, Lyndon; Pintacuda, Guido

    2012-07-10

    We introduce a new approach to improve structural and dynamical determination of large metalloproteins using solid-state nuclear magnetic resonance (NMR) with (1)H detection under ultrafast magic angle spinning (MAS). The approach is based on the rapid and sensitive acquisition of an extensive set of (15)N and (13)C nuclear relaxation rates. The system on which we demonstrate these methods is the enzyme Cu, Zn superoxide dismutase (SOD), which coordinates a Cu ion available either in Cu(+) (diamagnetic) or Cu(2+) (paramagnetic) form. Paramagnetic relaxation enhancements are obtained from the difference in rates measured in the two forms and are employed as structural constraints for the determination of the protein structure. When added to (1)H-(1)H distance restraints, they are shown to yield a twofold improvement of the precision of the structure. Site-specific order parameters and timescales of motion are obtained by a gaussian axial fluctuation (GAF) analysis of the relaxation rates of the diamagnetic molecule, and interpreted in relation to backbone structure and metal binding. Timescales for motion are found to be in the range of the overall correlation time in solution, where internal motions characterized here would not be observable.

  12. Noise assisted excitation energy transfer in a linear model of a selectivity filter backbone strand.

    Science.gov (United States)

    Bassereh, Hassan; Salari, Vahid; Shahbazi, Farhad

    2015-07-15

    In this paper, we investigate the effect of noise and disorder on the efficiency of excitation energy transfer (EET) in a N = 5 sites linear chain with 'static' dipole-dipole couplings. In fact, here, the disordered chain is a toy model for one strand of the selectivity filter backbone in ion channels. It has recently been discussed that the presence of quantum coherence in the selectivity filter is possible and can play a role in mediating ion-conduction and ion-selectivity in the selectivity filter. The question is 'how a quantum coherence can be effective in such structures while the environment of the channel is dephasing (i.e. noisy)?' Basically, we expect that the presence of the noise should have a destructive effect in the quantum transport. In fact, we show that such expectation is valid for ordered chains. However, our results indicate that introducing the dephasing in the disordered chains leads to the weakening of the localization effects, arising from the multiple back-scatterings due to the randomness, and then increases the efficiency of quantum energy transfer. Thus, the presence of noise is crucial for the enhancement of EET efficiency in disordered chains. We also show that the contribution of both classical and quantum mechanical effects are required to improve the speed of energy transfer along the chain. Our analysis may help for better understanding of fast and efficient functioning of the selectivity filters in ion channels.

  13. Quantitative residue-specific protein backbone torsion angle dynamics from concerted measurement of 3J couplings.

    Science.gov (United States)

    Lee, Jung Ho; Li, Fang; Grishaev, Alexander; Bax, Ad

    2015-02-04

    Three-bond (3)J(C'C') and (3)J(HNHα) couplings in peptides and proteins are functions of the intervening backbone torsion angle ϕ. In well-ordered regions, (3)J(HNHα) is tightly correlated with (3)J(C'C'), but the presence of large ϕ angle fluctuations differentially affects the two types of couplings. Assuming the ϕ angles follow a Gaussian distribution, the width of this distribution can be extracted from (3)J(C'C') and (3)J(HNHα), as demonstrated for the folded proteins ubiquitin and GB3. In intrinsically disordered proteins, slow transverse relaxation permits measurement of (3)J(C'C') and (3)J(HNH) couplings at very high precision, and impact of factors other than the intervening torsion angle on (3)J will be minimal, making these couplings exceptionally valuable structural reporters. Analysis of α-synuclein yields rather homogeneous widths of 69 ± 6° for the ϕ angle distributions and (3)J(C'C') values that agree well with those of a recent maximum entropy analysis of chemical shifts, J couplings, and (1)H-(1)H NOEs. Data are consistent with a modest (≤30%) population of the polyproline II region.

  14. STARD6 on steroids: solution structure, multiple timescale backbone dynamics and ligand binding mechanism

    Science.gov (United States)

    Létourneau, Danny; Bédard, Mikaël; Cabana, Jérôme; Lefebvre, Andrée; Lehoux, Jean-Guy; Lavigne, Pierre

    2016-06-01

    START domain proteins are conserved α/β helix-grip fold that play a role in the non-vesicular and intracellular transport of lipids and sterols. The mechanism and conformational changes permitting the entry of the ligand into their buried binding sites is not well understood. Moreover, their functions and the identification of cognate ligands is still an active area of research. Here, we report the solution structure of STARD6 and the characterization of its backbone dynamics on multiple time-scales through 15N spin-relaxation and amide exchange studies. We reveal for the first time the presence of concerted fluctuations in the Ω1 loop and the C-terminal helix on the microsecond-millisecond time-scale that allows for the opening of the binding site and ligand entry. We also report that STARD6 binds specifically testosterone. Our work represents a milestone for the study of ligand binding mechanism by other START domains and the elucidation of the biological function of STARD6.

  15. Amino acid preference against beta sheet through allowing backbone hydration enabled by the presence of cation

    CERN Document Server

    Sharley, John N

    2016-01-01

    It is known that steric blocking by peptide sidechains of hydrogen bonding, HB, between water and peptide groups, PGs, in beta sheets accords with an amino acid intrinsic beta sheet preference. The present observations with Quantum Molecular Dynamics, QMD, simulation with quantum mechanical treatment of every water molecule solvating a beta sheet that would be transient in nature suggest that this steric blocking is not applicable in a hydrophobic region unless a cation is present, so that the amino acid beta sheet preference due to this steric blocking is only effective in the presence of a cation. We observed backbone hydration in a polyalanine and to a lesser extent polyvaline alpha helix without a cation being present, but a cation could increase the strength of these HBs. Parallel beta sheets have a greater tendency than antiparallel beta sheets of equivalent small size to retain regular structure in solvated QMD, and a 4 strand 4 inter-PG HB chain parallel beta sheet was used. Stability was reinforced b...

  16. Comparison of the backbone dynamics of a natural and a consensus designed 3-TPR domain.

    Science.gov (United States)

    Jarymowycz, Virginia A; Cortajarena, Aitziber L; Regan, Lynne; Stone, Martin J

    2008-07-01

    The tetratricopeptide repeat (TPR) is a 34-amino acid helix-turn-helix motif that occurs in tandem arrays in numerous proteins. Here we compare the backbone dynamics of a natural 3-repeat TPR domain, from the protein UBP, with the behavior of a designed protein CTPR3, which consists of three identical consensus TPR units. Although the three tandem TPR repeats in both CTPR3 and UBP behave as a single unit, with no evidence of independent repeat motions, the data indicate that certain positions in UBP are significantly more flexible than are the corresponding positions in CTPR3. Most of the dynamical changes occur at or adjacent to positions that are involved in intra-repeat packing interactions. These observations lead us to suggest that the three-TPR domain of UBP does not incorporate optimized packing, compared to that seen in the idealized CTPR. The natural TPR domain is not only less stable overall than CTPR3, but also presents increased local flexibility at the positions where the sequences differs from the conserved consensus.

  17. Noise assisted excitation energy transfer in a linear model of a selectivity filter backbone strand

    Science.gov (United States)

    Bassereh, Hassan; Salari, Vahid; Shahbazi, Farhad

    2015-07-01

    In this paper, we investigate the effect of noise and disorder on the efficiency of excitation energy transfer (EET) in a N=5 sites linear chain with ‘static’ dipole-dipole couplings. In fact, here, the disordered chain is a toy model for one strand of the selectivity filter backbone in ion channels. It has recently been discussed that the presence of quantum coherence in the selectivity filter is possible and can play a role in mediating ion-conduction and ion-selectivity in the selectivity filter. The question is ‘how a quantum coherence can be effective in such structures while the environment of the channel is dephasing (i.e. noisy)?’ Basically, we expect that the presence of the noise should have a destructive effect in the quantum transport. In fact, we show that such expectation is valid for ordered chains. However, our results indicate that introducing the dephasing in the disordered chains leads to the weakening of the localization effects, arising from the multiple back-scatterings due to the randomness, and then increases the efficiency of quantum energy transfer. Thus, the presence of noise is crucial for the enhancement of EET efficiency in disordered chains. We also show that the contribution of both classical and quantum mechanical effects are required to improve the speed of energy transfer along the chain. Our analysis may help for better understanding of fast and efficient functioning of the selectivity filters in ion channels.

  18. The Deuterator: software for the determination of backbone amide deuterium levels from H/D exchange MS data

    Directory of Open Access Journals (Sweden)

    Tsinoremas NF

    2007-05-01

    Full Text Available Abstract Background The combination of mass spectrometry and solution phase amide hydrogen/deuterium exchange (H/D exchange experiments is an effective method for characterizing protein dynamics, and protein-protein or protein-ligand interactions. Despite methodological advancements and improvements in instrumentation and automation, data analysis and display remains a tedious process. The factors that contribute to this bottleneck are the large number of data points produced in a typical experiment, each requiring manual curation and validation, and then calculation of the level of backbone amide exchange. Tools have become available that address some of these issues, but lack sufficient integration, functionality, and accessibility required to address the needs of the H/D exchange community. To date there is no software for the analysis of H/D exchange data that comprehensively addresses these issues. Results We have developed an integrated software system for the automated analysis and representation of H/D exchange data that has been titled "The Deuterator". Novel approaches have been implemented that enable high throughput analysis, automated determination of deuterium incorporation, and deconvolution of overlapping peptides. This has been achieved by using methods involving iterative theoretical envelope fitting, and consideration of peak data within expected m/z ranges. Existing common file formats have been leveraged to allow compatibility with the output from the myriad of MS instrument platforms and peptide sequence database search engines. A web-based interface is used to integrate the components of The Deuterator that are able to analyze and present mass spectral data from instruments with varying resolving powers. The results, if necessary, can then be confirmed, adjusted, re-calculated and saved. Additional tools synchronize the curated calculation parameters with replicate time points, increasing throughput. Saved results can then

  19. Dolutegravir treatment response by baseline viral load and NRTI backbone in treatment-naïve HIV-infected individuals

    Directory of Open Access Journals (Sweden)

    C Small

    2012-11-01

    Full Text Available Background: In two 48-week studies in naïve subjects, dolutegravir with NRTI of choice has shown non-inferiority to raltegravir and, with ABC/3TC, superiority to Atripla. Factors that influenced choice of NRTIs included viral load, resistance and safety. Methods: We analysed response rates and time to virologic failure by NRTI backbone and baseline viral load in the pivotal DTG-naïve studies. SPRING-2 randomized participants to DTG 50 mg QD or RAL 400 mg BID, each in combination with investigator-selected NRTIs (TDF/FTC or ABC/3TC. SINGLE randomised participants to DTG 50 mg+ABC/3TC QD or TDF/FTC/EFV (Atripla QD. In SPRING-2, changes in serum creatinine were examined by INI and NRTI backbone. Results: The two studies randomized and treated 1655 subjects, of whom 249 (15% were female, 388 (23% non-white, 495 (30% had HIV-1 RNA >100,000 c/ml, and 224 (14% had CD4+ count <200 cells/mm3. Primary analyses demonstrated non-inferiority of DTG to RAL in SPRING-2 (Δ=2.5%; 95% CI:−2.2% to +7.1%, excluding −10%, and superiority of the DTG regimen in SINGLE (7.4%; +2.5% to +12.3%. In SPRING-2, response rates by NRTI backbone were comparable in each viral load stratum. In SINGLE, a 7% difference in response (favoring DTG+ABC/3TC was observed in each viral load stratum. Exploratory analyses examining time-to-virologic failure showed no difference in response rates between the NRTIs irrespective of baseline viral load or study. Resistance to INIs or NRTIs was not demonstrated in any subject on DTG-based therapy through 48 weeks. Withdrawals due to AEs on DTG-based regimen were few (2% in both studies. In SPRING-2, no significant differences were observed in serum creatinine change from baseline to Week 48 by NRTI backbones. Conclusions: In SPRING-2 and SINGLE, DTG was effective with both ABC/3TC and TDF/FTC, and in subjects with high and low viral load. DTG was well tolerated in both studies. Renal safety also was similar by NRTI backbone. DTG is a once

  20. A new mixed-backbone oligonucleotide against glucosylceramide synthase sensitizes multidrug-resistant tumors to apoptosis.

    Directory of Open Access Journals (Sweden)

    Gauri A Patwardhan

    Full Text Available Enhanced ceramide glycosylation catalyzed by glucosylceramide synthase (GCS limits therapeutic efficiencies of antineoplastic agents including doxorubicin in drug-resistant cancer cells. Aimed to determine the role of GCS in tumor response to chemotherapy, a new mixed-backbone oligonucleotide (MBO-asGCS with higher stability and efficiency has been generated to silence human GCS gene. MBO-asGCS was taken up efficiently in both drug-sensitive and drug-resistant cells, but it selectively suppressed GCS overexpression, and sensitized drug-resistant cells. MBO-asGCS increased doxorubicin sensitivity by 83-fold in human NCI/ADR-RES, and 43-fold in murine EMT6/AR1 breast cancer cells, respectively. In tumor-bearing mice, MBO-asGCS treatment dramatically inhibited the growth of multidrug-resistant NCI/ADR-RE tumors, decreasing tumor volume to 37%, as compared with scrambled control. Furthermore, MBO-asGCS sensitized multidrug-resistant tumors to chemotherapy, increasing doxorubicin efficiency greater than 2-fold. The sensitization effects of MBO-asGCS relied on the decreases of gene expression and enzyme activity of GCS, and on the increases of C(18-ceramide and of caspase-executed apoptosis. MBO-asGCS was accumulation in tumor xenografts was greater in other tissues, excepting liver and kidneys; but MBO-asGCS did not exert significant toxic effects on liver and kidneys. This study, for the first time in vivo, has demonstrated that GCS is a promising therapeutic target for cancer drug resistance, and MBO-asGCS has the potential to be developed as an antineoplastic agent.

  1. Soluble and Membrane-Bound β-Glucosidases Are Involved in Trimming the Xyloglucan Backbone.

    Science.gov (United States)

    Sampedro, Javier; Valdivia, Elene R; Fraga, Patricia; Iglesias, Natalia; Revilla, Gloria; Zarra, Ignacio

    2017-02-01

    In many flowering plants, xyloglucan is a major component of primary cell walls, where it plays an important role in growth regulation. Xyloglucan can be degraded by a suite of exoglycosidases that remove specific sugars. In this work, we show that the xyloglucan backbone, formed by (1→4)-linked β-d-glucopyranosyl residues, can be attacked by two different Arabidopsis (Arabidopsis thaliana) β-glucosidases from glycoside hydrolase family 3. While BGLC1 (At5g20950; for β-glucosidase active against xyloglucan 1) is responsible for all or most of the soluble activity, BGLC3 (At5g04885) is usually a membrane-anchored protein. Mutations in these two genes, whether on their own or combined with mutations in other exoglycosidase genes, resulted in the accumulation of partially digested xyloglucan subunits, such as GXXG, GXLG, or GXFG. While a mutation in BGLC1 had significant effects on its own, lack of BGLC3 had only minor effects. On the other hand, double bglc1 bglc3 mutants revealed a synergistic interaction that supports a role for membrane-bound BGLC3 in xyloglucan metabolism. In addition, bglc1 bglc3 was complemented by overexpression of either BGLC1 or BGLC3 In overexpression lines, BGLC3 activity was concentrated in a microsome-enriched fraction but also was present in soluble form. Finally, both genes were generally expressed in the same cell types, although, in some cases, BGLC3 was expressed at earlier stages than BGLC1 We propose that functional specialization could explain the separate localization of both enzymes, as a membrane-bound β-glucosidase could specifically digest soluble xyloglucan without affecting the wall-bound polymer.

  2. Backbone structures in human milk oligosaccharides: trans-glycosylation by metagenomic β-N-acetylhexosaminidases.

    Science.gov (United States)

    Nyffenegger, Christian; Nordvang, Rune Thorbjørn; Zeuner, Birgitte; Łężyk, Mateusz; Difilippo, Elisabetta; Logtenberg, Madelon J; Schols, Henk A; Meyer, Anne S; Mikkelsen, Jørn Dalgaard

    2015-10-01

    This paper describes the discovery and characterization of two novel β-N-acetylhexosaminidases HEX1 and HEX2, capable of catalyzing the synthesis of human milk oligosaccharides (HMO) backbone structures with fair yields using chitin oligomers as β-N-acetylglucosamine (GlcNAc) donor. The enzyme-encoding genes were identified by functional screening of a soil-derived metagenomic library. The β-N-acetylhexosaminidases were expressed in Escherichia coli with an N-terminal His6-tag and were purified by nickel affinity chromatography. The sequence similarities of the enzymes with their respective closest homologues are 59 % for HEX1 and 51 % for HEX2 on the protein level. Both β-N-acetylhexosaminidases are classified into glycosyl hydrolase family 20 (GH 20) are able to hydrolyze para-nitrophenyl-β-N-acetylglucosamine (pNP-GlcNAc) as well as para-nitrophenyl-β-N-acetylgalactosamine (pNP-GalNAc) and exhibit pH optima of 8 and 6 for HEX1 and HEX2, respectively. The enzymes are able to hydrolyze N-acetylchitooligosaccharides with a degree of polymerization of two, three, and four. The major findings were, that HEX1 and HEX2 catalyze trans-glycosylation reactions with lactose as acceptor, giving rise to the human milk oligosaccharide precursor lacto-N-triose II (LNT2) with yields of 2 and 8 % based on the donor substrate. In total, trans-glycosylation reactions were tested with the disaccharide acceptors β-lactose, sucrose, and maltose, as well as with the monosaccharides galactose and glucose resulting in the successful attachment of GlcNAc to the acceptor in all cases.

  3. Role of monomer sequence and backbone structure in polypeptoid and polypeptide polymers for anti-fouling applications

    Science.gov (United States)

    Patterson, Anastasia; Rizis, Georgios; Wenning, Brandon; Finlay, John; Ober, Christopher; Segalman, Rachel

    Polymeric coatings rely on a fine balance of surface properties to achieve biofouling resistance. Bioinsipired polymers and oligomers provide a modular strategy for the inclusion of multiple functionalities with controlled architecture, sequence and surface properties. In this work, polypeptoid and polypeptide functionalized coatings based on PEO and PDMS block copolymers were compared with respect to surface presentation and fouling by Ulva linza. While polypeptoids and polypeptides are simple isomers of each other, the lack of backbone chirality and hydrogen bonding in polypeptoids leads to surprisingly different surface behavior. Specifically, the polypeptoids surface segregate much more strongly than analogous polypeptide functionalized polymers, which in turn affects the performance of the coating. Indeed, polypeptoid functionalized surfaces were significantly better both in terms of anti-fouling and fouling release than the corresponding polypeptide-bearing polymers. The role of specific monomer sequence and backbone chemistry will be further discussed in this poster.

  4. Progress in palladium-based catalytic systems for the sustainable synthesis of annulated heterocycles: a focus on indole backbones.

    Science.gov (United States)

    Platon, Mélanie; Amardeil, Régine; Djakovitch, Laurent; Hierso, Jean-Cyrille

    2012-05-21

    A survey highlighting the most recent palladium catalytic systems produced and their performances for progress in direct synthesis of indole backbones by heterocarbocyclization of reactive substrates is provided. The discussion is developed in relation with the principles of sustainable chemistry concerning atom and mass economy. In this respect, the general convergent character of the syntheses is of particular interest (one-pot, domino, cascade or tandem reactions), and the substrates accessibility and reactivity, together with the final waste production, are also important. This critical review clearly indicates that the development of ligand chemistry, mainly phosphines and carbenes, in the last few decades gave a significant impetus to powerful functionalization of indoles at virtually all positions of this ubiquitous backbone (118 references).

  5. Direct measurement of the correlated dynamics of the protein-backbone and proximal waters of hydration in mechanically strained elastin

    CERN Document Server

    Sun, Cheng; Huang, Jiaxin; Boutis, Gregory S

    2011-01-01

    We report on the direct measurement of the correlation times of the protein backbone carbons and proximal waters of hydration in mechanically strained elastin by nuclear magnetic resonance methods. The experimental data indicate a decrease in the correlation times of the carbonyl carbons as the strain on the biopolymer is increased. These observations are in good agreement with short 4ns molecular dynamics simulations of (VPGVG)3, a well studied mimetic peptide of elastin. The experimental results also indicate a reduction in the correlation time of proximal waters of hydration with increasing strain applied to the elastomer. A simple model is suggested that correlates the increase in the motion of proximal waters of hydration to the increase in frequency of libration of the protein backbone that develops with increasing strain. Together, the reduction in the protein entropy accompanied with the increase in entropy of the proximal waters of hydration with increasing strain, support the notion that the source ...

  6. Reduced Dimensionality (4,3)D-hnCOCANH Experiment: An Efficient Backbone Assignment tool for NMR studies of Proteins

    CERN Document Server

    Kumar, Dinesh

    2013-01-01

    Sequence specific resonance assignment and secondary structure determination of proteins form the basis for variety of structural and functional proteomics studies by NMR. In this context, an efficient standalone method for rapid assignment of backbone (1H, 15N, 13Ca and 13C') resonances and secondary structure determination of proteins has been presented here. Compared to currently available strategies used for the purpose, the method employs only a single reduced dimensionality (RD) experiment -(4,3)D-hnCOCANH and exploits the linear combinations of backbone (13Ca and 13C') chemical shifts to achieve a dispersion relatively better compared to those of individual chemical shifts (see the text) for efficient and rapid data analysis. Further, the experiment leads to the spectrum with direct distinction of self (intra-residue) and sequential (inter-residue) carbon correlation peaks; these appear opposite in signs and therefore can easily be discriminated without using an additional complementary experiment. On ...

  7. Generation of marker- and/or backbone-free transgenic wheat plants via Agrobacterium-mediated transformation

    Directory of Open Access Journals (Sweden)

    Wang Genping

    2016-09-01

    Full Text Available Horizontal transfer of antibiotic resistance genes to animals and vertical transfer of herbicide resistance genes to the weedy relatives are perceived as major biosafety concerns in genetically modified (GM crops. In this study, five novel vectors which used gusA and bar as a reporter gene and a selection marker gene, respectively, were constructed based on the pCLEAN dual binary vector system. Among these vectors, 1G7B and 5G7B carried two T-DNAs located on two respective plasmids with 5G7B possessing an additional virGwt gene. 5LBTG154 and 5TGTB154 carried two T-DNAs in the target plasmid with either one or double right borders, and 5BTG154 carried the selectable marker gene on the backbone outside of the T-DNA left border in the target plasmid. In addition, 5BTG154, 5LBTG154 and 5TGTB154 used pAL154 as a helper plasmid which contains Komari fragment to facilitate transformation. These five dual binary vector combinations were transformed into Agrobacterium strain AGL1 and used to transform durum wheat cv Stewart 63. Evaluation of the co-transformation efficiencies, the frequencies of marker-free transgenic plants and integration of backbone sequences in the obtained transgenic lines indicated that two vectors (5G7B and 5TGTB154 were more efficient in generating marker-free transgenic wheat plants with no or minimal integration of backbone sequences in the wheat genome. The vector series developed in this study for generation of marker- and/or backbone-free transgenic wheat plants via Agrobacterium-mediated transformation will be useful to facilitate the creation of ‘clean’ GM wheat containing only the foreign genes of agronomic importance.

  8. Generation of Marker- and/or Backbone-Free Transgenic Wheat Plants via Agrobacterium-Mediated Transformation

    Science.gov (United States)

    Wang, Gen-Ping; Yu, Xiu-Dao; Sun, Yong-Wei; Jones, Huw D.; Xia, Lan-Qin

    2016-01-01

    Horizontal transfer of antibiotic resistance genes to animals and vertical transfer of herbicide resistance genes to the weedy relatives are perceived as major biosafety concerns in genetically modified (GM) crops. In this study, five novel vectors which used gusA and bar as a reporter gene and a selection marker gene, respectively, were constructed based on the pCLEAN dual binary vector system. Among these vectors, 1G7B and 5G7B carried two T-DNAs located on two respective plasmids with 5G7B possessing an additional virGwt gene. 5LBTG154 and 5TGTB154 carried two T-DNAs in the target plasmid with either one or double right borders, and 5BTG154 carried the selectable marker gene on the backbone outside of the T-DNA left border in the target plasmid. In addition, 5BTG154, 5LBTG154, and 5TGTB154 used pAL154 as a helper plasmid which contains Komari fragment to facilitate transformation. These five dual binary vector combinations were transformed into Agrobacterium strain AGL1 and used to transform durum wheat cv Stewart 63. Evaluation of the co-transformation efficiencies, the frequencies of marker-free transgenic plants, and integration of backbone sequences in the obtained transgenic lines indicated that two vectors (5G7B and 5TGTB154) were more efficient in generating marker-free transgenic wheat plants with no or minimal integration of backbone sequences in the wheat genome. The vector series developed in this study for generation of marker- and/or backbone-free transgenic wheat plants via Agrobacterium-mediated transformation will be useful to facilitate the creation of “clean” GM wheat containing only the foreign genes of agronomic importance. PMID:27708648

  9. The Role of Backbone Hydrogen Bonds in the Transition State for Protein Folding of a PDZ Domain.

    Directory of Open Access Journals (Sweden)

    Søren W. Pedersen

    Full Text Available Backbone hydrogen bonds are important for the structure and stability of proteins. However, since conventional site-directed mutagenesis cannot be applied to perturb the backbone, the contribution of these hydrogen bonds in protein folding and stability has been assessed only for a very limited set of small proteins. We have here investigated effects of five amide-to-ester mutations in the backbone of a PDZ domain, a 90-residue globular protein domain, to probe the influence of hydrogen bonds in a β-sheet for folding and stability. The amide-to-ester mutation removes NH-mediated hydrogen bonds and destabilizes hydrogen bonds formed by the carbonyl oxygen. The overall stability of the PDZ domain generally decreased for all amide-to-ester mutants due to an increase in the unfolding rate constant. For this particular region of the PDZ domain, it is therefore clear that native hydrogen bonds are formed after crossing of the rate-limiting barrier for folding. Moreover, three of the five amide-to-ester mutants displayed an increase in the folding rate constant suggesting that the hydrogen bonds are involved in non-native interactions in the transition state for folding.

  10. The determinants of bond angle variability in protein/peptide backbones: A comprehensive statistical/quantum mechanics analysis.

    Science.gov (United States)

    Improta, Roberto; Vitagliano, Luigi; Esposito, Luciana

    2015-11-01

    The elucidation of the mutual influence between peptide bond geometry and local conformation has important implications for protein structure refinement, validation, and prediction. To gain insights into the structural determinants and the energetic contributions associated with protein/peptide backbone plasticity, we here report an extensive analysis of the variability of the peptide bond angles by combining statistical analyses of protein structures and quantum mechanics calculations on small model peptide systems. Our analyses demonstrate that all the backbone bond angles strongly depend on the peptide conformation and unveil the existence of regular trends as function of ψ and/or φ. The excellent agreement of the quantum mechanics calculations with the statistical surveys of protein structures validates the computational scheme here employed and demonstrates that the valence geometry of protein/peptide backbone is primarily dictated by local interactions. Notably, for the first time we show that the position of the H(α) hydrogen atom, which is an important parameter in NMR structural studies, is also dependent on the local conformation. Most of the trends observed may be satisfactorily explained by invoking steric repulsive interactions; in some specific cases the valence bond variability is also influenced by hydrogen-bond like interactions. Moreover, we can provide a reliable estimate of the energies involved in the interplay between geometry and conformations.

  11. Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity.

    Directory of Open Access Journals (Sweden)

    Noah Ollikainen

    Full Text Available Interactions between small molecules and proteins play critical roles in regulating and facilitating diverse biological functions, yet our ability to accurately re-engineer the specificity of these interactions using computational approaches has been limited. One main difficulty, in addition to inaccuracies in energy functions, is the exquisite sensitivity of protein-ligand interactions to subtle conformational changes, coupled with the computational problem of sampling the large conformational search space of degrees of freedom of ligands, amino acid side chains, and the protein backbone. Here, we describe two benchmarks for evaluating the accuracy of computational approaches for re-engineering protein-ligand interactions: (i prediction of enzyme specificity altering mutations and (ii prediction of sequence tolerance in ligand binding sites. After finding that current state-of-the-art "fixed backbone" design methods perform poorly on these tests, we develop a new "coupled moves" design method in the program Rosetta that couples changes to protein sequence with alterations in both protein side-chain and protein backbone conformations, and allows for changes in ligand rigid-body and torsion degrees of freedom. We show significantly increased accuracy in both predicting ligand specificity altering mutations and binding site sequences. These methodological improvements should be useful for many applications of protein-ligand design. The approach also provides insights into the role of subtle conformational adjustments that enable functional changes not only in engineering applications but also in natural protein evolution.

  12. Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning.

    Science.gov (United States)

    Heffernan, Rhys; Paliwal, Kuldip; Lyons, James; Dehzangi, Abdollah; Sharma, Alok; Wang, Jihua; Sattar, Abdul; Yang, Yuedong; Zhou, Yaoqi

    2015-01-01

    Direct prediction of protein structure from sequence is a challenging problem. An effective approach is to break it up into independent sub-problems. These sub-problems such as prediction of protein secondary structure can then be solved independently. In a previous study, we found that an iterative use of predicted secondary structure and backbone torsion angles can further improve secondary structure and torsion angle prediction. In this study, we expand the iterative features to include solvent accessible surface area and backbone angles and dihedrals based on Cα atoms. By using a deep learning neural network in three iterations, we achieved 82% accuracy for secondary structure prediction, 0.76 for the correlation coefficient between predicted and actual solvent accessible surface area, 19° and 30° for mean absolute errors of backbone φ and ψ angles, respectively, and 8° and 32° for mean absolute errors of Cα-based θ and τ angles, respectively, for an independent test dataset of 1199 proteins. The accuracy of the method is slightly lower for 72 CASP 11 targets but much higher than those of model structures from current state-of-the-art techniques. This suggests the potentially beneficial use of these predicted properties for model assessment and ranking.

  13. Unconventional N-H…N Hydrogen Bonds Involving Proline Backbone Nitrogen in Protein Structures.

    Science.gov (United States)

    Deepak, R N V Krishna; Sankararamakrishnan, Ramasubbu

    2016-05-10

    Contrary to DNA double-helical structures, hydrogen bonds (H-bonds) involving nitrogen as the acceptor are not common in protein structures. We systematically searched N-H…N H-bonds in two different sets of protein structures. Data set I consists of neutron diffraction and ultrahigh-resolution x-ray structures (0.9 Å resolution or better) and the hydrogen atom positions in these structures were determined experimentally. Data set II contains structures determined using x-ray diffraction (resolution ≤ 1.8 Å) and the positions of hydrogen atoms were generated using a computational method. We identified 114 and 14,347 potential N-H…N H-bonds from these two data sets, respectively, and 56-66% of these were of the Ni+1-Hi+1…Ni type, with Ni being the proline backbone nitrogen. To further understand the nature of such unusual contacts, we performed quantum chemical calculations on the model compound N-acetyl-L-proline-N-methylamide (Ace-Pro-NMe) with coordinates taken from the experimentally determined structures. A potential energy profile generated by varying the ψ dihedral angle in Ace-Pro-NMe indicates that the conformation with the N-H…N H-bond is the most stable. An analysis of H-bond-forming proline residues reveals that more than 30% of the proline carbonyl groups are also involved in n → π(∗) interactions with the carbonyl carbon of the preceding residue. Natural bond orbital analyses demonstrate that the strength of N-H…N H-bonds is less than half of that observed for a conventional H-bond. This study clearly establishes the H-bonding capability of proline nitrogen and its prevalence in protein structures. We found many proteins with multiple instances of H-bond-forming prolines. With more than 15% of all proline residues participating in N-H…N H-bonds, we suggest a new, to our knowledge, structural role for proline in providing stability to loops and capping regions of secondary structures in proteins.

  14. Occultation observations of atmosphere and climate change from space: a backbone for the GCOS

    Science.gov (United States)

    Kirchengast, G.

    2003-04-01

    , involving the heavily calibration-dependent Microwave Sounding Unit (MSU) data, could have been presumably saved had suitable occultation data been available. This talk will highlight, along the lines outlined above, the general principles, properties, capabilities, and exploitation possibilities of occultation methods with a focus on how they provide key contributions to a better understanding of the Earth's climate system and to better prediction of its future evolution. A properly designed occultation observing system has the capacity to become the leading backbone of the Global Climate Observing System (GCOS) for monitoring climate change and variability in fundamental atmospheric variables such as temperature, humidity, ozone, and geopotential height from global scales to meso-scales (order 100 km) and from the planetary boundary layer to the mesopause.

  15. 军队文职护理骨干护理科研现状的调查与分析%A Survey and Analysis on Status of Nursing Research for Backbone of Army Civilian Nurses

    Institute of Scientific and Technical Information of China (English)

    唐洪钦; 魏巍; 谢文娟; 乐惠飞

    2012-01-01

    Objective To explore the status of nursing research for the backbone of the army civilian nurses. Methods An investigation of status of nursing research for the backbone of the army civilian nurses was conducted among 83 civilian nurses in the third batch of army civilian nursing backbone of the professional education courses in April 2011. Results The backbone of the army civilian nurses raised a positive attitude towards nursing research activities but participated in less nursing research activities. The major difficulties in nursing research activities included inadequate regard from leadership, lack of mentors and difficulties in research design. Conclusion To improve the ability and positivity of nursing research, relevant departments should carry out a series of countermeasures such as organizing research training class and scientific steering group,creating academic atmosphere and establish encouragement systems.%目的 了解军队文职护理骨干护理科研的现状.方法 2011年4月采用自制“军队文职护理骨干护理科研现状调查表”对参加全军第3批文职护理骨干任职教育培训班的83名学员进行调查.结果 所有文职护理骨干对开展护理科研活动持积极态度,但参加护理科研活动较少,文职护理骨干护理科研活动中存在的困难主要有:领导不够重视、缺乏指导者、科研方案设计困难等.结论 相关部门可以从组织科研培训班、成立科研指导小组、营造学术氛围、建立奖励激励制度人手,提高文职护理骨干的护理科研能力和科研积极性.

  16. Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA.

    Science.gov (United States)

    Zgarbová, Marie; Šponer, Jiří; Otyepka, Michal; Cheatham, Thomas E; Galindo-Murillo, Rodrigo; Jurečka, Petr

    2015-12-01

    Z-DNA duplexes are a particularly complicated test case for current force fields. We performed a set of explicit solvent molecular dynamics (MD) simulations with various AMBER force field parametrizations including our recent refinements of the ε/ζ and glycosidic torsions. None of these force fields described the ZI/ZII and other backbone substates correctly, and all of them underpredicted the population of the important ZI substate. We show that this underprediction can be attributed to an inaccurate potential for the sugar-phosphate backbone torsion angle β. We suggest a refinement of this potential, β(OL1), which was derived using our recently introduced methodology that includes conformation-dependent solvation effects. The new potential significantly increases the stability of the dominant ZI backbone substate and improves the overall description of the Z-DNA backbone. It also has a positive (albeit small) impact on another important DNA form, the antiparallel guanine quadruplex (G-DNA), and improves the description of the canonical B-DNA backbone by increasing the population of BII backbone substates, providing a better agreement with experiment. We recommend using β(OL1) in combination with our previously introduced corrections, εζ(OL1) and χ(OL4), (the combination being named OL15) as a possible alternative to the current β torsion potential for more accurate modeling of nucleic acids.

  17. Impact of Backbone Rigidity on the Photomechanical Response of Glassy, Azobenzene-Functionalized Polyimides (Postprint)

    Science.gov (United States)

    2014-01-13

    filter cake was washed with ethyl acetate, and then the filtrate was evaporated to dryness on a rotary evaporator to afford 4.214 g (95%) of off...5−8 Polyimides represent an important class of heat- resistant polymers useful in a variety of applications deriving from their excellent combination...h and filtered. The filtrate was diluted with ethyl acetate (1200 mL), and the organic layer was separated. The organic layer was washed three times

  18. Aptamer-Functionalized and Backbone Redox-Responsive Hyperbranched Polymer for Targeted Drug Delivery in Cancer Therapy.

    Science.gov (United States)

    Zhuang, Yuanyuan; Deng, Hongping; Su, Yue; He, Lin; Wang, Ruibin; Tong, Gangsheng; He, Dannong; Zhu, Xinyuan

    2016-06-13

    A novel type of backbone redox-responsive hyperbranched poly(2-((2-(acryloyloxy)ethyl)disulfanyl)ethyl 4-cyano-4-(((propylthio)carbonothioyl)-thio)-pentanoate-co-poly(ethylene glycol) methacrylate) (HPAEG) has been designed and prepared successfully via the combination of reversible addition-fragmentation chain-transfer (RAFT) polymerization and self-condensing vinyl polymerization (SCVP). Owing to the existence of surface vinyl groups, HPAEG could be efficiently functionalized by DNA aptamer AS1411 via Michael addition reaction to obtain an active tumor targeting drug delivery carrier (HPAEG-AS1411). The amphiphilic HPAEG-AS1411 could form nanoparticles by macromolecular self-assembly strategy. Cell Counting Kit-8 (CCK-8) assay illustrated that HPAEG-AS1411 nanoparticles had low cytotoxicity to normal cell line. Flow cytometry and confocal laser scanning microscopy (CLSM) results demonstrated that HPAEG-AS1411 nanoparticles could be internalized into tumor cells via aptamer-mediated endocytosis. Compared with pure HPAEG nanoparticles, HPAEG-AS1411 nanoparticles displayed enhanced tumor cell uptake. When the HPAEG-AS1411 nanoparticles loaded with anticancer drug doxorubicin (DOX) were internalized into tumor cells, the disulfide bonds in the backbone of HPAEG-AS1411 were cleaved by glutathione (GSH) in the cytoplasm, so that DOX was released rapidly. Therefore, DOX-loaded HPAEG-AS1411 nanoparticles exhibited a high tumor cellular proliferation inhibition rate and low cytotoxicity to normal cells. This aptamer-functionalized and backbone redox-responsive hyperbranched polymer provides a promising platform for targeted drug delivery in cancer therapy.

  19. Design and synthesis of peptide YY analogues with c-terminal backbone amide-to-ester modifications

    DEFF Research Database (Denmark)

    Albertsen, Louise; Andersen, J.J.; Paulsson, J.F.;

    2013-01-01

    Peptide YY (PYY) is a gut hormone that activates the G protein-coupled neuropeptide Y (NPY) receptors, and because of its appetite reducing actions, it is evaluated as an antiobesity drug candidate. The C-terminal tail of PYY is crucial for activation of the NPY receptors. Here, we describe...... the design and preparation of a series of PYY(3-36) depsipeptide analogues, in which backbone amide-to-ester modifications were systematically introduced in the C-terminal. Functional NPY receptor assays and circular dichroism revealed that the ψ(CONH) bonds at positions 30-31 and 33-34 are particularly...

  20. 1H, 15N and 13C backbone resonance assignments of the archetypal serpin α1-antitrypsin.

    Science.gov (United States)

    Nyon, Mun Peak; Kirkpatrick, John; Cabrita, Lisa D; Christodoulou, John; Gooptu, Bibek

    2012-10-01

    Alpha(1)-antitrypsin is a 45-kDa (394-residue) serine protease inhibitor synthesized by hepatocytes, which is released into the circulatory system and protects the lung from the actions of neutrophil elastase via a conformational transition within a dynamic inhibitory mechanism. Relatively common point mutations subvert this transition, causing polymerisation of α(1)-antitrypsin and deficiency of the circulating protein, predisposing carriers to severe lung and liver disease. We have assigned the backbone resonances of α(1)-antitrypsin using multidimensional heteronuclear NMR spectroscopy. These assignments provide the starting point for a detailed solution state characterization of the structural properties of this highly dynamic protein via NMR methods.

  1. Backbone structures in human milk oligosaccharides: trans-glycosylation by metagenomic β-N-acetylhexosaminidases

    DEFF Research Database (Denmark)

    Nyffenegger, Christian; Nordvang, Rune Thorbjørn; Zeuner, Birgitte

    2015-01-01

    This paper describes the discovery and characterization of two novel β-N-acetylhexosaminidases HEX1 and HEX2, capable of catalyzing the synthesis of human milk oligosaccharides (HMO) backbone structures with fair yields using chitin oligomers as β-N-acetylglucosamine (GlcNAc) donor. The enzyme......-encoding genes were identified by functional screening of a soil-derived metagenomic library. The β-N-acetylhexosaminidases were expressed in Escherichia coli with an N-terminal His6-tag and were purified by nickel affinity chromatography. The sequence similarities of the enzymes with their respective closest...

  2. Conformation-specific spectroscopy of capped glutamine-containing peptides: role of a single glutamine residue on peptide backbone preferences.

    Science.gov (United States)

    Walsh, Patrick S; Dean, Jacob C; McBurney, Carl; Kang, Hyuk; Gellman, Samuel H; Zwier, Timothy S

    2016-04-28

    The conformational preferences of a series of short, aromatic-capped, glutamine-containing peptides have been studied under jet-cooled conditions in the gas phase. This work seeks a bottom-up understanding of the role played by glutamine residues in directing peptide structures that lead to neurodegenerative diseases. Resonant ion-dip infrared (RIDIR) spectroscopy is used to record single-conformation infrared spectra in the NH stretch, amide I and amide II regions. Comparison of the experimental spectra with the predictions of calculations carried out at the DFT M05-2X/6-31+G(d) level of theory lead to firm assignments for the H-bonding architectures of a total of eight conformers of four molecules, including three in Z-Gln-OH, one in Z-Gln-NHMe, three in Ac-Gln-NHBn, and one in Ac-Ala-Gln-NHBn. The Gln side chain engages actively in forming H-bonds with nearest-neighbor amide groups, forming C8 H-bonds to the C-terminal side, C9 H-bonds to the N-terminal side, and an amide-stacked geometry, all with an extended (C5) peptide backbone about the Gln residue. The Gln side chain also stabilizes an inverse γ-turn in the peptide backbone by forming a pair of H-bonds that bridge the γ-turn and stabilize it. Finally, the entire conformer population of Ac-Ala-Gln-NHBn is funneled into a single structure that incorporates the peptide backbone in a type I β-turn, stabilized by the Gln side chain forming a C7 H-bond to the central amide group in the β-turn not otherwise involved in a hydrogen bond. This β-turn backbone structure is nearly identical to that observed in a series of X-(AQ)-Y β-turns in the protein data bank, demonstrating that the gas-phase structure is robust to perturbations imposed by the crystalline protein environment.

  3. Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins

    DEFF Research Database (Denmark)

    Maragakis, Paul; Lindorff-Larsen, Kresten; Eastwood, Michael P

    2008-01-01

    methods. However, apparent systematic discrepancies between order parameters extracted from simulations and experiments are common, particularly for elements of noncanonical secondary structure. In this paper, results from a 1.2 micros explicit solvent MD simulation of the protein ubiquitin are compared...... with previously determined backbone order parameters derived from NMR relaxation experiments [Tjandra, N.; Feller, S. E.; Pastor, R. W.; Bax, A. J. Am. Chem. Soc. 1995, 117, 12562-12566]. The simulation reveals fluctuations in three loop regions that occur on time scales comparable to or longer than...

  4. IMMUNOMODULATION OF SYNTHESIZED POLYMERS CONTAINING PHOSPHORUS IN THE BACKBONE —EFFECT ON THE PROLIFERATION OF LYMPHOCYTES

    Institute of Scientific and Technical Information of China (English)

    ZhuoRenxi; WangJun; 等

    1997-01-01

    The immunomodulation of several Charged synthetic polymers containing phosphorus in the backbone was studied in vitro through examining their inhibition or promotion effect on the proliferatioin of both T and B lymphocytes,It is found that polymers based on long chain alkyl ester of tyrosine exhibit immunomodulative activity.Negatively charged polymers show stimulative activity on LPS-induced B lymphocytes proliferation.Positively charged polymers exhibit inhibitory activity on both Con A-induced T lymphocytes and LPS-induced B lymplhyocytes proliferation.

  5. Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity

    Science.gov (United States)

    Ollikainen, Noah; de Jong, René M.; Kortemme, Tanja

    2015-01-01

    Interactions between small molecules and proteins play critical roles in regulating and facilitating diverse biological functions, yet our ability to accurately re-engineer the specificity of these interactions using computational approaches has been limited. One main difficulty, in addition to inaccuracies in energy functions, is the exquisite sensitivity of protein–ligand interactions to subtle conformational changes, coupled with the computational problem of sampling the large conformational search space of degrees of freedom of ligands, amino acid side chains, and the protein backbone. Here, we describe two benchmarks for evaluating the accuracy of computational approaches for re-engineering protein-ligand interactions: (i) prediction of enzyme specificity altering mutations and (ii) prediction of sequence tolerance in ligand binding sites. After finding that current state-of-the-art “fixed backbone” design methods perform poorly on these tests, we develop a new “coupled moves” design method in the program Rosetta that couples changes to protein sequence with alterations in both protein side-chain and protein backbone conformations, and allows for changes in ligand rigid-body and torsion degrees of freedom. We show significantly increased accuracy in both predicting ligand specificity altering mutations and binding site sequences. These methodological improvements should be useful for many applications of protein – ligand design. The approach also provides insights into the role of subtle conformational adjustments that enable functional changes not only in engineering applications but also in natural protein evolution. PMID:26397464

  6. Thermodynamic contribution of backbone conformational entropy in the binding between SH3 domain and proline-rich motif.

    Science.gov (United States)

    Zeng, Danyun; Shen, Qingliang; Cho, Jae-Hyun

    2017-02-26

    Biological functions of intrinsically disordered proteins (IDPs), and proteins containing intrinsically disordered regions (IDRs) are often mediated by short linear motifs, like proline-rich motifs (PRMs). Upon binding to their target proteins, IDPs undergo a disorder-to-order transition which is accompanied by a large conformational entropy penalty. Hence, the molecular mechanisms underlying control of conformational entropy are critical for understanding the binding affinity and selectivity of IDPs-mediated protein-protein interactions (PPIs). Here, we investigated the backbone conformational entropy change accompanied by binding of the N-terminal SH3 domain (nSH3) of CrkII and PRM derived from guanine nucleotide exchange factor 1 (C3G). In particular, we focused on the estimation of conformational entropy change of disordered PRM upon binding to the nSH3 domain. Quantitative characterization of conformational dynamics of disordered peptides like PRMs is limited. Hence, we combined various methods, including NMR model-free analysis, δ2D, DynaMine, and structure-based calculation of entropy loss. This study demonstrates that the contribution of backbone conformational entropy change is significant in the PPIs mediated by IDPs/IDRs.

  7. Improved site-specific recombinase-based method to produce selectable marker- and vector-backbone-free transgenic cells

    Science.gov (United States)

    Yu, Yuan; Tong, Qi; Li, Zhongxia; Tian, Jinhai; Wang, Yizhi; Su, Feng; Wang, Yongsheng; Liu, Jun; Zhang, Yong

    2014-02-01

    PhiC31 integrase-mediated gene delivery has been extensively used in gene therapy and animal transgenesis. However, random integration events are observed in phiC31-mediated integration in different types of mammalian cells; as a result, the efficiencies of pseudo attP site integration and evaluation of site-specific integration are compromised. To improve this system, we used an attB-TK fusion gene as a negative selection marker, thereby eliminating random integration during phiC31-mediated transfection. We also excised the selection system and plasmid bacterial backbone by using two other site-specific recombinases, Cre and Dre. Thus, we generated clean transgenic bovine fetal fibroblast cells free of selectable marker and plasmid bacterial backbone. These clean cells were used as donor nuclei for somatic cell nuclear transfer (SCNT), indicating a similar developmental competence of SCNT embryos to that of non-transgenic cells. Therefore, the present gene delivery system facilitated the development of gene therapy and agricultural biotechnology.

  8. Multi-source micro-friction identification for a class of cable-driven robots with passive backbone

    Science.gov (United States)

    Tjahjowidodo, Tegoeh; Zhu, Ke; Dailey, Wayne; Burdet, Etienne; Campolo, Domenico

    2016-12-01

    This paper analyses the dynamics of cable-driven robots with a passive backbone and develops techniques for their dynamic identification, which are tested on the H-Man, a planar cabled differential transmission robot for haptic interaction. The mechanism is optimized for human-robot interaction by accounting for the cost-benefit-ratio of the system, specifically by eliminating the necessity of an external force sensor to reduce the overall cost. As a consequence, this requires an effective dynamic model for accurate force feedback applications which include friction behavior in the system. We first consider the significance of friction in both the actuator and backbone spaces. Subsequently, we study the required complexity of the stiction model for the application. Different models representing different levels of complexity are investigated, ranging from the conventional approach of Coulomb to an advanced model which includes hysteresis. The results demonstrate each model's ability to capture the dynamic behavior of the system. In general, it is concluded that there is a trade-off between model accuracy and the model cost.

  9. Circular permutation prediction reveals a viable backbone disconnection for split proteins: an approach in identifying a new functional split intein.

    Directory of Open Access Journals (Sweden)

    Yun-Tzai Lee

    Full Text Available Split-protein systems have emerged as a powerful tool for detecting biomolecular interactions and reporting biological reactions. However, reliable methods for identifying viable split sites are still unavailable. In this study, we demonstrated the feasibility that valid circular permutation (CP sites in proteins have the potential to act as split sites and that CP prediction can be used to search for internal permissive sites for creating new split proteins. Using a protein ligase, intein, as a model, CP predictor facilitated the creation of circular permutants in which backbone opening imposes the least detrimental effects on intein folding. We screened a series of predicted intein CPs and identified stable and native-fold CPs. When the valid CP sites were introduced as split sites, there was a reduction in folding enthalpy caused by the new backbone opening; however, the coincident loss in entropy was sufficient to be compensated, yielding a favorable free energy for self-association. Since split intein is exploited in protein semi-synthesis, we tested the related protein trans-splicing (PTS activities of the corresponding split inteins. Notably, a novel functional split intein composed of the N-terminal 36 residues combined with the remaining C-terminal fragment was identified. Its PTS activity was shown to be better than current reported two-piece intein with a short N-terminal segment. Thus, the incorporation of in silico CP prediction facilitated the design of split intein as well as circular permutants.

  10. Hydrogen-deuterium exchange mass spectrometry for investigation of backbone dynamics of oxidized and reduced cytochrome P450cam.

    Science.gov (United States)

    Hamuro, Yoshitomo; Molnar, Kathleen S; Coales, Stephen J; OuYang, Bo; Simorellis, Alana K; Pochapsky, Thomas C

    2008-02-01

    Backbone dynamics of the camphor monoxygenase cytochrome P450(cam) (CYP101) as a function of oxidation/ligation state of the heme iron were investigated via hydrogen/deuterium exchange (H/D exchange) as monitored by mass spectrometry. Main chain amide NH hydrogens can exchange readily with solvent and the rate of this exchange depends upon, among other things, dynamic fluctuations in local structural elements. A fluxional region of the polypeptide will exchange more quickly with solvent than one that is more constrained. In most regions of the enzyme, exchange rates were similar between oxidized high-spin camphor-bound and reduced camphor- and CO-bound CYP101 (CYP-S and CYP-S-CO, respectively). However, in regions of the protein that have previously been implicated in substrate access by structural and molecular dynamics investigations, the reduced enzyme shows significantly slower exchange rates than the oxidized CYP-S. This observation corresponds to increased flexibility of the oxidized enzyme relative to the reduced form. Structural features previously found to be perturbed in CYP-S-CO upon binding of the biologically relevant effector and reductant putidaredoxin (Pdx) as determined by nuclear magnetic resonance are also more protected from exchange in the reduced state. To our knowledge, this study represents the first experimental investigation of backbone dynamics within the P450 family using this methodology.

  11. The Critical Role of Organic Chemistry in Drug Discovery.

    Science.gov (United States)

    Rotella, David P

    2016-10-19

    Small molecules remain the backbone for modern drug discovery. They are conceived and synthesized by medicinal chemists, many of whom were originally trained as organic chemists. Support from government and industry to provide training and personnel for continued development of this critical skill set has been declining for many years. This Viewpoint highlights the value of organic chemistry and organic medicinal chemists in the complex journey of drug discovery as a reminder that basic science support must be restored.

  12. Protein folding and the organization of the protein topology universe

    DEFF Research Database (Denmark)

    Lindorff-Larsen,, Kresten; Røgen, Peter; Paci, Emanuele

    2005-01-01

    of protein folds that is based on the topological features of the polypeptide backbone, rather than the conventional view that depends on the arrangement of different types of secondary-structure elements. By linking the folding process to the organization of the protein structure universe, we propose...

  13. An employment karate - one of backbone factors of psychohygiene of youth.

    Directory of Open Access Journals (Sweden)

    Uskov S.V.

    2011-08-01

    Full Text Available The analysis of the scientifically-methodical and special literature on a research problem is carried out. Questions of preservation and perfection of psychological health of schoolboys and the students, solved by means of employment by single combats are opened. Methodical workings out on formation of the psychophysiological qualities necessary for healthy development of youth are offered. At the correct organization they can essentially increase stability to stressful situations, stability of the central nervous system and other important psychological qualities.

  14. Solid State Nuclear Magnetic Resonance Investigation of Polymer Backbone Dynamics in Poly(Ethylene Oxide) Based Lithium and Sodium Polyether-ester-sulfonate Ionomers

    Energy Technology Data Exchange (ETDEWEB)

    Roach, David J.; Dou, Shichen; Colby, Ralph H.; Mueller, Karl T.

    2013-01-01

    Polymer backbone dynamics of single ion conducting poly(ethylene oxide) (PEO)-based ionomer samples with low glass transition temperatures (Tg) have been investigated using solid-state nuclear magnetic resonance (NMR). Experiments detecting 13C with 1H decoupling under magic angle spinning (MAS) conditions identified the different components of the polymer backbone (PEO spacer and isophthalate groups) and their relative mobilities for a suite of lithium- and sodium-containing ionomer samples with varying cation contents. Variable temperature (203-373 K) 1H-13C cross-polarization MAS (CP-MAS) experiments also provided qualitative assessment of the differences in the motions of the polymer backbone components as a function of cation content and identity. Each of the main backbone components exhibit distinct motions, following the trends expected for motional characteristics based on earlier Quasi Elastic Neutron Scattering and 1H spin-lattice relaxation rate measurements. Previous 1H and 7Li spin-lattice relaxation measurements focused on both the polymer backbone and cation motion on the nanosecond timescale. The studies presented here assess the slower timescale motion of the polymer backbone allowing for a more comprehensive understanding of the polymer dynamics. The temperature dependences of 13C linewidths were used to both qualitatively and quantitatively examine the effects of cation content and identity on PEO spacer mobility. Variable contact time 1H-13C CP-MAS experiments were used to further assess the motions of the polymer backbone on the microsecond timescale. The motion of the PEO spacer, reported via the rate of magnetization transfer from 1H to 13C nuclei, becomes similar for T ≳ 1.1 Tg in all ionic samples, indicating that at similar elevated reduced temperatures the motions of the polymer backbones on the microsecond timescale become insensitive to ion interactions. These results present an improved picture, beyond those of previous findings, for

  15. High performance and highly durable infiltrated cathodes using Pr-modified Ce0.9Gd0.1O1.95 backbone

    DEFF Research Database (Denmark)

    Samson, Alfred Junio; Søgaard, Martin; Bonanos, Nikolaos;

    2014-01-01

    the CGO backbone with Pr through infiltration into the structure followed by firing. The Pr – modified CGO backbone is then infiltrated with LSC. The electrochemical performance of the infiltrated cathodes with and without Pr modification in the backbone was studied by impedance spectroscopy on symmetric...... °C (without Pr: Rp from 0.094 to 0.45 Ω cm2, Rs from 0.74 to 0.79 Ω cm2; with Pr: Rp from 0.051 to 0.32 Ω cm2, Rs from 0.74 to 0.71 Ω cm2). The improved performance and heat treatment tolerance is thought to originate from the imparted electronic conductivity into the CGO backbone by introducing Pr.......Infiltration of electrocatalysts into ionic conducting backbones (e.g. Sr – doped LaCoO3 (LSC) into Ce0.9Gd0.1O1.95 (CGO)) is becoming a widely popular means of preparing composite cathodes for SOFCs. The high surface area nanoparticle grains of the electrocatalyst obtained using the method...

  16. Laccase-assisted grafting of poly(3-hydroxybutyrate) onto the bacterial cellulose as backbone polymer: development and characterisation.

    Science.gov (United States)

    Iqbal, Hafiz M N; Kyazze, Godfrey; Tron, Thierry; Keshavarz, Tajalli

    2014-11-26

    Bacterial cellulose (BC) exhibits high purity, mechanical strength and an ultra-fine fibrous 3-D network structure with bio-compatible and bio-degradable characteristics, while P(3 HB) are a bio-degradable matrix material derived from natural resources. Herein, we report a mild and eco-friendly fabrication of indigenously isolated P(3 HB) based novel composites consisting of BC (a straight-chain polysaccharide) as a backbone polymer and laccase was used as a grafting tool. The resulting composites were characterised by Fourier-transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), X-ray diffraction (XRD), differential scanning calorimetry (DSC), dynamic mechanical analyser (DMA) and water contact angle analyser (WCA). The FTIR spectra of the pure P(3 HB) and P(3 HB) containing graft composites [P(3 HB)-g-BC] showed their strong characteristic bands at 3358 cm(-1), 1721 cm(-1) and 1651 cm(-1), respectively. A homogenous dispersion of P(3 HB) in the backbone polymer of BC was achieved as evident by the SEM micrographs. XRD pattern for P(3 HB) showed distinct peaks at 2θ values that represent the crystalline nature of P(3 HB). While, in comparison with those of neat P(3 HB), the degree of crystallinity for P(3 HB)-g-BC decreased and this reduction is mainly because of the new cross-linking of P(3 HB) within the backbone polymer that changes the morphology and destroys the crystallites. Laccase-assisted graft composite prepared from P(3 HB) and BC was fairly flexible and strong, judged by the tensile strength (64.5 MPa), elongations at break (15.7%), and Young's modulus (0.98 GPa) because inherently high strength of BC allowed the mechanical properties of P(3 HB) to improve in the P(3 HB)-g-BC composite. The hydrophilic property of the P(3 HB)-g-BC was much better than that of the individual counterparts which is also a desired characteristic to enhance the biocompatibility of the materials for proper cell adhesion and proliferation.

  17. Study on Developing Students' Backbone Leadership in Learning Class Building%学习型班级建设中的学生骨干领导力培养研究

    Institute of Scientific and Technical Information of China (English)

    刘萍; 周曦

    2012-01-01

    Learning classes by the development of learning organization theory, its research aims to combine the current situation of social development, in-depth exploration of traditional classroom education management philosophy. Learning class construction, students backbone of leadership training is essential is the key to success in shaping the learning class organization. This article explores the learning classroom building theory and practical application of learning class building and students backbone of lead- ership combined with cultivation of viable ideas to create a more cohesive and continuous leaxning class group.%学习型班级由学习型组织理论发展而来,其研究目的在于结合当前社会发展形势,对传统班级教育管理理念进行深入探索。在学习型班级建设中,对学生骨干领导力的培养至关重要,是成功塑造学习型班级组织的关键。为此,本文探讨了学习型班级建设理论和实践应用,提出了将学习型班级建设和学生骨干领导力培养相结合的可行思路,以打造更具凝聚力和持续学习能力的班集体。

  18. Synthesis and characterization of a novel carboxyl group containing (copolyimide with sulfur in the polymer backbone

    Directory of Open Access Journals (Sweden)

    Miroslav Mrsevic

    2012-05-01

    Full Text Available Soluble functional (copolyimides are of great interest in the area of separation processes or optical applications, due to their excellent mechanical-, thermal- and optical properties, their superior processability and the ability to adapt their properties to a wide range of special applications. Therefore, two series of novel (copolyimides containing fluorinated sulfur- and carboxylic acid groups consisting of 4,4′-(hexafluoroisopropylidenedi(phthalic anhydride (6FDA, 3,5-diaminobenzoic acid (DABA, 4,4′-diaminodiphenylsulfide (4,4′-SDA and 3,3′-diaminodiphenylsulfone (3,3′-DDS were synthesized in a two-step polycondensation reaction. The synthesized copolymers were characterized by using NMR, FTIR, GPC, and DSC. Furthermore, with regard to processing and potential applications, the thermal stability, solubility in common organic solvents, moisture uptake, and transparency were investigated. Compared to commercially available transparent polymers, i.e., polymethylmethacrylate and cycloolefin polymers, the sulfur (copolyimides containing carboxyl groups showed much higher glass-transition temperatures, comparably low moisture uptake and high transmission at the sodium D-line. Furthermore, good solubility in commonly used organic solvents makes them very attractive as high-performance coating materials.

  19. Thermoresponsive Poly(2-oxazoline) Molecular Brushes by Living Ionic Polymerization: Kinetic Investigations of Pendant Chain Grafting and Cloud Point Modulation by Backbone and Side Chain Length Variation

    KAUST Repository

    Zhang, Ning

    2012-04-17

    Molecular brushes of poly(2-oxazoline)s were prepared by living anionic polymerization of 2-iso-propenyl-2-oxazoline to form the backbone and subsequent living cationic ring-opening polymerization of 2-n- or 2-iso-propyl-2-oxazoline for pendant chain grafting. In situ kinetic studies indicate that the initiation efficiency and polymerization rates are independent from the number of initiator functions per initiator molecule. This was attributed to the high efficiency of oxazolinium salt and the stretched conformation of the backbone, which is caused by the electrostatic repulsion of the oxazolinium moieties along the macroinitiator. The resulting molecular brushes showed thermoresponsive properties, that is, having a defined cloud point (CP). The dependence of the CP as a function of backbone and side chain length as well as concentration was studied. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Modernización del IP Backbone del Core de Voz para Telefónica Ecuador

    OpenAIRE

    Echeverria Medina, Jorge Leonardo

    2015-01-01

    En el mercado de las telecomunicaciones, la alta disponibilidad de las redes celulares hace muchos años atrás dejó de ser una meta y hoy en día es un requisito básico para cualquier operador. Siguiendo el continuo evolucionar de las empresas celulares consideradas grandes a nivel mundial, la compañía Telefónica Ecuador a mediados del año 2014 entró en un proceso de modernización de toda su red, modernización que incluyó el Backbone IP para su red de Voz a nivel nacional. Telefónica Ecuador cu...

  1. Purification, crystallization and preliminary crystallographic analysis of the SpaA backbone-pilin subunit from probiotic Lactobacillus rhamnosus GG.

    Science.gov (United States)

    Singh, Deepak; von Ossowski, Ingemar; Palva, Airi; Krishnan, Vengadesan

    2013-10-01

    Lactobacillus rhamnosus GG, a widely used Gram-positive probiotic strain, is clinically well known for its perceived health-promoting effects. It has recently been shown to display proteinaceous pilus fibres (called SpaCBA) on its cell surface. Structurally, SpaCBA pili possess a characteristic three-pilin polymerized architecture, with repeating SpaA major pilins that form the backbone and two types of minor subunits (SpaB and SpaC). In this study, recombinant SpaA protein was purified, characterized and crystallized. The crystals diffracted to a resolution of 2.0 Å and belonged to space group C2, with unit-cell parameters a=227.9, b=63.2, c=104.3 Å, β=95.1°.

  2. Proton-detected MAS NMR experiments based on dipolar transfers for backbone assignment of highly deuterated proteins

    Science.gov (United States)

    Chevelkov, Veniamin; Habenstein, Birgit; Loquet, Antoine; Giller, Karin; Becker, Stefan; Lange, Adam

    2014-05-01

    Proton-detected solid-state NMR was applied to a highly deuterated insoluble, non-crystalline biological assembly, the Salmonella typhimurium type iii secretion system (T3SS) needle. Spectra of very high resolution and sensitivity were obtained at a low protonation level of 10-20% at exchangeable amide positions. We developed efficient experimental protocols for resonance assignment tailored for this system and the employed experimental conditions. Using exclusively dipolar-based interspin magnetization transfers, we recorded two sets of 3D spectra allowing for an almost complete backbone resonance assignment of the needle subunit PrgI. The additional information provided by the well-resolved proton dimension revealed the presence of two sets of resonances in the N-terminal helix of PrgI, while in previous studies employing 13C detection only a single set of resonances was observed.

  3. TACN-based cationic lipids with amino acid backbone and double tails: materials for non-viral gene delivery.

    Science.gov (United States)

    Wang, Bing; Yi, Wen-Jing; Zhang, Ji; Zhang, Qin-Fang; Xun, Miao-Miao; Yu, Xiao-Qi

    2014-04-01

    Cationic lipids have become an efficient type of non-viral vectors for gene delivery. In this Letter, four cationic lipids containing 1,4,7-triazacyclononane (TACN) headgroup, glutamic/aspartic acid backbone and dioleyl tails were designed and synthesized. The TACN headgroup gives these lipids excellent pH buffering capacities, which were higher than branched 25 kDa PEI. Cationic liposomes prepared from these lipids and DOPE showed good DNA affinity, and full DNA condensation was found at N/P ratio of 3 via agarose gel electrophoresis. The lipoplexes were characterized by dynamic light scattering (DLS) assay, which gave proper particle sizes and zeta-potentials for transfection. In vitro gene transfection results in two cell lines reveal that TAN (with aspartic acid and amide bond in the structure) shows the best transfection efficiency, which is close to commercially available transfection agent Lipofectamine 2000.

  4. BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks

    DEFF Research Database (Denmark)

    Alkan, Ferhat; Erten, Cesim

    2014-01-01

    MOTIVATION: Global many-to-many alignment of biological networks has been a central problem in comparative biological network studies. Given a set of biological interaction networks, the informal goal is to group together related nodes. For the case of protein-protein interaction networks...... are conserved across the input networks. We provide a formal definition of the global many-to-many alignment of multiple protein-protein interaction networks that captures this informal objective. We show the computational intractability of the suggested definition. We provide a heuristic method based...... on backbone extraction and merge strategy (BEAMS) for the problem. We finally show, through experiments based on biological significance tests, that the proposed BEAMS algorithm performs better than the state-of-the-art approaches. Furthermore, the computational burden of the BEAMS algorithm in terms...

  5. Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation

    Energy Technology Data Exchange (ETDEWEB)

    Marassi, Francesca M., E-mail: fmarassi@sbmri.org; Ding, Yi [Sanford-Burnham Medical Research Institute (United States); Schwieters, Charles D. [National Institutes of Health, Division of Computational Bioscience, Center for Information Technology (United States); Tian, Ye; Yao, Yong [Sanford-Burnham Medical Research Institute (United States)

    2015-09-15

    The outer membrane protein Ail (attachment invasion locus) is a virulence factor of Yersinia pestis that mediates cell invasion, cell attachment and complement resistance. Here we describe its three-dimensional backbone structure determined in decyl-phosphocholine (DePC) micelles by NMR spectroscopy. The NMR structure was calculated using the membrane function of the implicit solvation potential, eefxPot, which we have developed to facilitate NMR structure calculations in a physically realistic environment. We show that the eefxPot force field guides the protein towards its native fold. The resulting structures provide information about the membrane-embedded global position of Ail, and have higher accuracy, higher precision and improved conformational properties, compared to the structures calculated with the standard repulsive potential.

  6. Comparison of solid-state dipolar couplings and solution relaxation data provides insight into protein backbone dynamics.

    Science.gov (United States)

    Chevelkov, Veniamin; Xue, Yi; Linser, Rasmus; Skrynnikov, Nikolai R; Reif, Bernd

    2010-04-14

    Analyses of solution (15)N relaxation data and solid-state (1)H(N)-(15)N dipolar couplings from a small globular protein, alpha-spectrin SH3 domain, produce a surprisingly similar pattern of order parameters. This result suggests that there is little or no ns-mus dynamics throughout most of the sequence and, in particular, in the structured portion of the backbone. At the same time, evidence of ns-mus motions is found in the flexible loops and termini. These findings, corroborated by the MD simulations of alpha-spectrin SH3 in a hydrated crystalline environment and in solution, are consistent with the picture of protein dynamics that has recently emerged from the solution studies employing residual dipolar couplings.

  7. Formation of Hierarchical Structure Composed of (Co/Ni)Mn-LDH Nanosheets on MWCNT Backbones for Efficient Electrocatalytic Water Oxidation.

    Science.gov (United States)

    Jia, Gan; Hu, Yingfei; Qian, Qinfeng; Yao, Yingfang; Zhang, Shiying; Li, Zhaosheng; Zou, Zhigang

    2016-06-15

    Active, stable, and cost-effective electrocatalysts are attractive alternatives to the noble metal oxides that have been used in water splitting. The direct nucleation and growth of electrochemically active LDH materials on chemically modified MWCNTs exhibit considerable electrocatalytic activity toward oxygen evolution from water oxidation. CoMn-based and NiMn-based hybrids were synthesized using a facile chemical bath deposition method and the as-synthesized materials exhibited three-dimensional hierarchical configurations with tunable Co/Mn and Ni/Mn ratio. Benefiting from enhanced electrical conductivity with MWCNT backbones and LDH lamellar structure, the Co5Mn-LDH/MWCNT and Ni5Mn-LDH/MWCNT could generated a current density of 10 mA cm(-2) at overpotentials of ∼300 and ∼350 mV, respectively, in 1 M KOH. In addition, the materials also exhibited outstanding long-term electrocatalytic stability.

  8. Marburg virus VP35 can both fully coat the backbone and cap the ends of dsRNA for interferon antagonism.

    Directory of Open Access Journals (Sweden)

    Shridhar Bale

    2012-09-01

    Full Text Available Filoviruses, including Marburg virus (MARV and Ebola virus (EBOV, cause fatal hemorrhagic fever in humans and non-human primates. All filoviruses encode a unique multi-functional protein termed VP35. The C-terminal double-stranded (dsRNA-binding domain (RBD of VP35 has been implicated in interferon antagonism and immune evasion. Crystal structures of the VP35 RBD from two ebolaviruses have previously demonstrated that the viral protein caps the ends of dsRNA. However, it is not yet understood how the expanses of dsRNA backbone, between the ends, are masked from immune surveillance during filovirus infection. Here, we report the crystal structure of MARV VP35 RBD bound to dsRNA. In the crystal structure, molecules of dsRNA stack end-to-end to form a pseudo-continuous oligonucleotide. This oligonucleotide is continuously and completely coated along its sugar-phosphate backbone by the MARV VP35 RBD. Analysis of dsRNA binding by dot-blot and isothermal titration calorimetry reveals that multiple copies of MARV VP35 RBD can indeed bind the dsRNA sugar-phosphate backbone in a cooperative manner in solution. Further, MARV VP35 RBD can also cap the ends of the dsRNA in solution, although this arrangement was not captured in crystals. Together, these studies suggest that MARV VP35 can both coat the backbone and cap the ends, and that for MARV, coating of the dsRNA backbone may be an essential mechanism by which dsRNA is masked from backbone-sensing immune surveillance molecules.

  9. Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution.

    Science.gov (United States)

    Desai, Bijoy J; Goto, Yuki; Cembran, Alessandro; Fedorov, Alexander A; Almo, Steven C; Gao, Jiali; Suga, Hiroaki; Gerlt, John A

    2014-10-21

    Hydrogen bonds between backbone amide groups of enzymes and their substrates are often observed, but their importance in substrate binding and/or catalysis is not easy to investigate experimentally. We describe the generation and kinetic characterization of a backbone amide to ester substitution in the orotidine 5'-monophosphate (OMP) decarboxylase from Methanobacter thermoautotrophicum (MtOMPDC) to determine the importance of a backbone amide-substrate hydrogen bond. The MtOMPDC-catalyzed reaction is characterized by a rate enhancement (∼10(17)) that is among the largest for enzyme-catalyzed reactions. The reaction proceeds through a vinyl anion intermediate that may be stabilized by hydrogen bonding interaction between the backbone amide of a conserved active site serine residue (Ser-127) and oxygen (O4) of the pyrimidine moiety and/or electrostatic interactions with the conserved general acidic lysine (Lys-72). In vitro translation in conjunction with amber suppression using an orthogonal amber tRNA charged with L-glycerate ((HO)S) was used to generate the ester backbone substitution (S127(HO)S). With 5-fluoro OMP (FOMP) as substrate, the amide to ester substitution increased the value of Km by ∼1.5-fold and decreased the value of kcat by ∼50-fold. We conclude that (i) the hydrogen bond between the backbone amide of Ser-127 and O4 of the pyrimidine moiety contributes a modest factor (∼10(2)) to the 10(17) rate enhancement and (ii) the stabilization of the anionic intermediate is accomplished by electrostatic interactions, including its proximity of Lys-72. These conclusions are in good agreement with predictions obtained from hybrid quantum mechanical/molecular mechanical calculations.

  10. General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Qing; Shi, Chaowei [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Yu, Lu [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui, 230031 (China); Zhang, Longhua [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Xiong, Ying, E-mail: yxiong73@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Tian, Changlin, E-mail: cltian@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui, 230031 (China)

    2015-02-13

    Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of {sup 15}N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S{sup 2}) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in a defined hydrated box at neutral pH were conducted and the general order parameters (S{sup 2}) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S{sup 2} values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S{sup 2} parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S{sup 2} calculated from the experimental NMR relaxation measurements, in a site-specific manner. - Highlights: • Correlation analysis between NMR relaxation measurements and MD simulations. • General order parameter (S{sup 2}) as common reference between the two methods. • Different protein dynamics with different Histidine charge states in neutral pH. • Different protein dynamics with different water models.

  11. Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny.

    Science.gov (United States)

    Chen, Meng-Yun; Liang, Dan; Zhang, Peng

    2015-11-01

    Incongruence between different phylogenomic analyses is the main challenge faced by phylogeneticists in the genomic era. To reduce incongruence, phylogenomic studies normally adopt some data filtering approaches, such as reducing missing data or using slowly evolving genes, to improve the signal quality of data. Here, we assembled a phylogenomic data set of 58 jawed vertebrate taxa and 4682 genes to investigate the backbone phylogeny of jawed vertebrates under both concatenation and coalescent-based frameworks. To evaluate the efficiency of extracting phylogenetic signals among different data filtering methods, we chose six highly intractable internodes within the backbone phylogeny of jawed vertebrates as our test questions. We found that our phylogenomic data set exhibits substantial conflicting signal among genes for these questions. Our analyses showed that non-specific data sets that are generated without bias toward specific questions are not sufficient to produce consistent results when there are several difficult nodes within a phylogeny. Moreover, phylogenetic accuracy based on non-specific data is considerably influenced by the size of data and the choice of tree inference methods. To address such incongruences, we selected genes that resolve a given internode but not the entire phylogeny. Notably, not only can this strategy yield correct relationships for the question, but it also reduces inconsistency associated with data sizes and inference methods. Our study highlights the importance of gene selection in phylogenomic analyses, suggesting that simply using a large amount of data cannot guarantee correct results. Constructing question-specific data sets may be more powerful for resolving problematic nodes.

  12. The backbone of the post-synaptic density originated in a unicellular ancestor of choanoflagellates and metazoans

    Directory of Open Access Journals (Sweden)

    Manuel Michaël

    2010-02-01

    Full Text Available Abstract Background Comparative genomics of the early diverging metazoan lineages and of their unicellular sister-groups opens new window to reconstructing the genetic changes which preceded or accompanied the evolution of multicellular body plans. A recent analysis found that the genome of the nerve-less sponges encodes the homologues of most vertebrate post-synaptic proteins. In vertebrate excitatory synapses, these proteins assemble to form the post-synaptic density, a complex molecular platform linking membrane receptors, components of their signalling pathways, and the cytoskeleton. Newly available genomes from Monosiga brevicollis (a member of Choanoflagellata, the closest unicellular relatives of animals and Trichoplax adhaerens (a member of Placozoa: besides sponges, the only nerve-less metazoans offer an opportunity to refine our understanding of post-synaptic protein evolution. Results Searches for orthologous proteins and reconstruction of gene gains/losses based on the taxon phylogeny indicate that post-synaptic proteins originated in two main steps. The backbone scaffold proteins (Shank, Homer, DLG and some of their partners were acquired in a unicellular ancestor of choanoflagellates and metazoans. A substantial additional set appeared in an exclusive ancestor of the Metazoa. The placozoan genome contains most post-synaptic genes but lacks some of them. Notably, the master-scaffold protein Shank might have been lost secondarily in the placozoan lineage. Conclusions The time of origination of most post-synaptic proteins was not concomitant with the acquisition of synapses or neural-like cells. The backbone of the scaffold emerged in a unicellular context and was probably not involved in cell-cell communication. Based on the reconstructed protein composition and potential interactions, its ancestral function could have been to link calcium signalling and cytoskeleton regulation. The complex later became integrated into the evolving

  13. Unraveling the complexity of protein backbone dynamics with combined (13)C and (15)N solid-state NMR relaxation measurements.

    Science.gov (United States)

    Lamley, Jonathan M; Lougher, Matthew J; Sass, Hans Juergen; Rogowski, Marco; Grzesiek, Stephan; Lewandowski, Józef R

    2015-09-14

    Typically, protein dynamics involve a complex hierarchy of motions occurring on different time scales between conformations separated by a range of different energy barriers. NMR relaxation can in principle provide a site-specific picture of both the time scales and amplitudes of these motions, but independent relaxation rates sensitive to fluctuations in different time scale ranges are required to obtain a faithful representation of the underlying dynamic complexity. This is especially pertinent for relaxation measurements in the solid state, which report on dynamics in a broader window of time scales by more than 3 orders of magnitudes compared to solution NMR relaxation. To aid in unraveling the intricacies of biomolecular dynamics we introduce (13)C spin-lattice relaxation in the rotating frame (R1ρ) as a probe of backbone nanosecond-microsecond motions in proteins in the solid state. We present measurements of (13)C'R1ρ rates in fully protonated crystalline protein GB1 at 600 and 850 MHz (1)H Larmor frequencies and compare them to (13)C'R1, (15)N R1 and R1ρ measured under the same conditions. The addition of carbon relaxation data to the model free analysis of nitrogen relaxation data leads to greatly improved characterization of time scales of protein backbone motions, minimizing the occurrence of fitting artifacts that may be present when (15)N data is used alone. We also discuss how internal motions characterized by different time scales contribute to (15)N and (13)C relaxation rates in the solid state and solution state, leading to fundamental differences between them, as well as phenomena such as underestimation of picosecond-range motions in the solid state and nanosecond-range motions in solution.

  14. Assignment of congested NMR spectra: Carbonyl backbone enrichment via the Entner Doudoroff pathway

    Science.gov (United States)

    Goldbourt, Amir; Day, Loren A.; McDermott, Ann E.

    2007-12-01

    In NMR spectra of complex proteins, sparse isotope enrichment can be important, in that the removal of many 13C- 13C homonuclear J-couplings can narrow the lines and thereby facilitate the process of spectral assignment and structure elucidation. We present a simple scheme for selective yet extensive isotopic enrichment applicable for production of proteins in organisms utilizing the Entner-Doudoroff (ED) metabolic pathway. An enrichment scheme so derived is demonstrated in the context of a magic-angle spinning solid-state NMR (MAS SSNMR) study of Pf1 bacteriophage, the host of which is Pseudomonas aeruginosa, strain K (PAK), an organism that uses the ED pathway for glucose catabolism. The intact and infectious Pf1 phage in this study was produced by infected PAK cells grown on a minimal medium containing 1- 13C D-glucose ( 13C in position 1) as the sole carbon source, as well as 15NH 4Cl as the only nitrogen source. The 37 MDa Pf1 phage consists of about 93% major coat protein, 1% minor coat proteins, and 6% single-stranded, circular DNA. As a consequence of this composition and the enrichment scheme, the resonances in the MAS SSNMR spectra of the Pf1 sample were almost exclusively due to carbonyl carbons in the major coat protein. Moreover, 3D heteronuclear NCOCX correlation experiments also show that the amino acids leucine, serine, glycine, and tyrosine were not isotopically enriched in their carbonyl positions (although most other amino acids were), which is as expected based upon considerations of the ED metabolic pathway. 3D NCOCX NMR data and 2D 15N- 15N data provided strong verification of many previous assignments of 15N amide and 13C carbonyl shifts in this highly congested spectrum; both the semi-selective enrichment patterns and the narrowed linewidths allowed for greater certainty in the assignments as compared with use of uniformly enriched samples alone.

  15. Backbone dynamics of a biologically active human FGF-1 monomer, complexed to a hexasaccharide heparin-analogue, by {sup 15}N NMR relaxation methods

    Energy Technology Data Exchange (ETDEWEB)

    Canales-Mayordomo, Angeles; Fayos, Rosa [Centro de Investigaciones Biologicas, CSIC, Departamento de Estructura y Funcion de Proteinas (Spain); Angulo, Jesus; Ojeda, Rafael [Instituto de Investigaciones Quimicas, CSIC, Grupo de Carbohidratos (Spain); Martin-Pastor, Manuel [Unidad de RM y Unidad de RMN de Biomoleculas Asociada al CSIC, Laboratorio de Estructura e Estructura de Biomoleculas Jose Carracido (Spain); Nieto, Pedro M.; Martin-Lomas, Manuel [Instituto de Investigaciones Quimicas, CSIC, Grupo de Carbohidratos (Spain); Lozano, Rosa; Gimenez-Gallego, Guillermo; Jimenez-Barbero, Jesus [Centro de Investigaciones Biologicas, CSIC, Departamento de Estructura y Funcion de Proteinas (Spain)], E-mail: jjbarbero@cib.csic.es

    2006-08-15

    The binding site and backbone dynamics of a bioactive complex formed by the acidic fibroblast growth factor (FGF-1) and a specifically designed heparin hexasaccharide has been investigated by HSQC and relaxation NMR methods. The comparison of the relaxation data for the free and bound states has allowed showing that the complex is monomeric, and still induces mutagenesis, and that the protein backbone presents reduced motion in different timescale in its bound state, except in certain points that are involved in the interaction with the fibroblast growth factor receptor (FGFR)

  16. Subnetworks of percolation backbones to model karst systems around Tulum, Mexico

    Science.gov (United States)

    Hendrick, Martin; Renard, Philippe

    2016-11-01

    Karstic caves, which play a key role in groundwater transport, are often organized as complex connected networks resulting from the dissolution of carbonate rocks. In this work, we propose a new model to describe and study the structures of the two largest submersed karst networks in the world. Both of these networks are located in the area of Tulum (Quintana Roo, Mexico). In a previous work te{hendrick2016fractal} we showed that these networks behave as self-similar structures exhibiting well-defined scaling behaviours. In this paper, we suggest that these networks can be modeled using substructures of percolation clusters (θ-subnetworks) having similar structural behaviour (in terms of fractal dimension and conductivity exponent) to those observed in Tulum's karst networks. We show in addition that these θ-subnetworks correspond to structures that minimise a global function, where this global function includes energy dissipation by the viscous forces when water flows through the network, and the cost of network formation itself.

  17. Anatomy as the backbone of an integrated first year medical curriculum: design and implementation.

    Science.gov (United States)

    Klement, Brenda J; Paulsen, Douglas F; Wineski, Lawrence E

    2011-01-01

    Morehouse School of Medicine chose to restructure its first year medical curriculum in 2005. The anatomy faculty had prior experience in integrating courses, stemming from the successful integration of individual anatomical sciences courses into a single course called Human Morphology. The integration process was expanded to include the other first year basic science courses (Biochemistry, Physiology, and Neurobiology) as we progressed toward an integrated curriculum. A team, consisting of the course directors, a curriculum coordinator, and the Associate Dean for Educational and Faculty Affairs, was assembled to build the new curriculum. For the initial phase, the original course titles were retained but the lecture order was reorganized around the Human Morphology topic sequence. The material from all four courses was organized into four sequential units. Other curricular changes included placing laboratories and lectures more consistently in the daily routine, reducing lecture time from 120 to 90 minute blocks, eliminating unnecessary duplication of content, and increasing the amount of independent study time. Examinations were constructed to include questions from all courses on a single test, reducing the number of examination days in each block from three to one. The entire restructuring process took two years to complete, and the revised curriculum was implemented for the students entering in 2007. The outcomes of the restructured curriculum include a reduction in the number of contact hours by 28%, higher or equivalent subject examination average scores, enhanced student satisfaction, and a first year curriculum team better prepared to move forward with future integration.

  18. Sphingolipid-dependent fusion of Semliki Forest virus with cholesterol-containing liposomes requires both the 3-hydroxyl group and the double bond of the sphingolipid backbone

    DEFF Research Database (Denmark)

    Corver, J; Moesby, Lise; Erukulla, R K;

    1995-01-01

    , we demonstrate that sphingolipid-dependent fusion of SFV with cholesterol-containing liposomes exhibits remarkable molecular specificity, the 3-hydroxyl group and the 4,5-trans carbon-carbon double bond of the sphingosine backbone being critical for the sphingolipid to mediate the process...

  19. Investigation of novel solid oxide fuel cell cathodes based on impregnation of SrTixFe1-xO3-δ into ceria-based backbones

    DEFF Research Database (Denmark)

    Brinch-Larsen, Mathias; Søgaard, Martin; Hjelm, Johan;

    2013-01-01

    and electrochemical stability as a thin film electrode have been reported for these materials. XRD measurements showed a high degree of secondary phase formation in the infiltrate as well as reaction with the CGO backbone. Microstructural analysis showed that the STF infiltrate had formed a coating on the CGO...

  20. Typing of core and backbone domains of mucin-type oligosaccharides from human ovarian-cyst glycoproteins by 500-MHz 1H-NMR spectroscopy

    NARCIS (Netherlands)

    Vliegenthart, J.F.G.; Mutsaers, J.H.G.M.; Halbeek, H. van; Wu, A.M.; Kabat, E.A.

    1986-01-01

    Human blood-group A active glycoproteins from ovarian-cyst fluid were subjected to Smith degradation and subsequent beta-elimination. The resulting oligosaccharide-alditols represent the core and backbone domains of the O-linked carbohydrate chains. Nine of these, ranging in size from disaccharides

  1. The ortho backbone amide linker (o-BAL) is an easily prepared and highly acid-labile handle for solid-phase synthesis

    DEFF Research Database (Denmark)

    Boas, Ulrik; Brask, Jesper; Christensen, J.B.;

    2002-01-01

    The tris(alkoxy)benzyl backbone amide linker (BAL) has found widespread application in solid-phase synthesis. The key intermediate for preparation of para BAL (p-BAL) is 2,6-dimethoxy-4-hydroxybenzaldehyde; several reports on its synthesis have appeared. However, the ortho analogue of the handle (o...

  2. Peptide backbone orientation and dynamics in spider dragline silk and two-photon excitation in nuclear magnetic and quadrupole resonance

    Energy Technology Data Exchange (ETDEWEB)

    Eles, P.T

    2005-07-01

    In the first part of the dissertation, spider dragline silk is studied by solid state NMR techniques. The dependence of NMR frequency on molecular orientation is exploited using the DECODER experiment to determine the orientation of the protein backbone within the silk fibre. Practical experimental considerations require that the silk fibres be wound about a cylindrical axis perpendicular to the external magnetic field, complicating the reconstruction of the underlying orientation distribution and necessitating the development of numerical techniques for this purpose. A two-component model of silk incorporating static b-sheets and polyglycine II helices adequately fits the NMR data and suggests that the b-sheets are well aligned along the silk axis (20 FWHM) while the helices are poorly aligned (68 FWHM). The effects of fibre strain, draw rate and hydration on orientation are measured. Measurements of the time-scale for peptide backbone motion indicate that when wet, a strain-dependent fraction of the poorly aligned component becomes mobile. This suggests a mechanism for the supercontraction of silk involving latent entropic springs that undergo a local strain-dependent phase transition, driving supercontraction. In the second part of this dissertation a novel method is developed for exciting NMR and nuclear quadrupole resonance (NQR) by rf irradiation at multiple frequencies that sum to (or differ by) the resonance frequency. This is fundamentally different than traditional NMR experiments where irradiation is applied on-resonance. With excitation outside the detection bandwidth, two-photon excitation allows for detection of free induction signals during excitation, completely eliminating receiver dead-time. A theoretical approach to describing two-photon excitation is developed based on average Hamiltonian theory. An intuition for two-photon excitation is gained by analogy to the coherent absorption of multiple photons requiring conservation of total energy and

  3. Broadly Neutralizing Anti-Influenza Virus Antibodies: Enhancement of Neutralizing Potency in Polyclonal Mixtures and IgA Backbones

    Science.gov (United States)

    He, Wenqian; Mullarkey, Caitlin E.; Duty, J. Andrew; Moran, Thomas M.; Palese, Peter

    2015-01-01

    ABSTRACT Current influenza virus vaccines rely upon the accurate prediction of circulating virus strains months in advance of the actual influenza season in order to allow time for vaccine manufacture. Unfortunately, mismatches occur frequently, and even when perfect matches are achieved, suboptimal vaccine efficacy leaves several high-risk populations vulnerable to infection. However, the recent discovery of broadly neutralizing antibodies that target the hemagglutinin (HA) stalk domain has renewed hope that the development of “universal” influenza virus vaccines may be within reach. Here, we examine the functions of influenza A virus hemagglutinin stalk-binding antibodies in an endogenous setting, i.e., as polyclonal preparations isolated from human sera. Relative to monoclonal antibodies that bind to the HA head domain, the neutralization potency of monoclonal stalk-binding antibodies was vastly inferior in vitro but was enhanced by several orders of magnitude in the polyclonal context. Furthermore, we demonstrated a surprising enhancement in IgA-mediated HA stalk neutralization relative to that achieved by antibodies of IgG isotypes. Mechanistically, this could be explained in two ways. Identical variable regions consistently neutralized virus more potently when in an IgA backbone compared to an IgG backbone. In addition, HA-specific memory B cells isolated from human peripheral blood were more likely to be stalk specific when secreting antibodies of IgA isotypes compared to those secreting IgG. Taken together, our data provide strong evidence that HA stalk-binding antibodies perform optimally when in a polyclonal context and that the targeted elicitation of HA stalk-specific IgA should be an important consideration during “universal” influenza virus vaccine design. IMPORTANCE Influenza viruses remain one of the most worrisome global public health threats due to their capacity to cause pandemics. While seasonal vaccines fail to protect against the

  4. Constructing d-Hop 2-Connected Dominating Sets for Fault-Tolerant Backbone in Wireless Sensor Networks%无线传感器网络中d-Hop2-连通容错支配集的分布式构造算法

    Institute of Scientific and Technical Information of China (English)

    郑婵; 尹令; 孙世新

    2012-01-01

    Wireless sensor networks are self-maintaining and self-organizing structures with sensors nodes moving around. The virtual backbone base on connected dominating sets (CDS) helps to optimize multi-level hierarchical networks from flat models. However the size of CDS nodes is still large in large-scale wireless sensor networks. Thus d-hop CDS which is generalized from the concept of CDS can further reduce the virtual backbones. Otherwise virtual backbones are often very vulnerable due to frequent node failure and link broken,which are inherent in wireless networks. It is desirable that the virtual backbone is fault tolerant since the nodes in the virtual backbone need to carry other node's traffic. A distributed algorithm of d-hop 2-connected dominating set construction was proposed in unit disk graph network model in this paper. The major strategy we used was clustering partition. A d-hop dominating set was selected from each cluster firstly,and then some connector nodes were added to make final sub-solutions 2-connected.The complexity,approximation ratio and performance of the algorithm were given through theoretical analysis and simulations.%无线传感器网络随节点移动组成自我维持的自组织系统,采用连通支配集的虚拟骨干技术可使平面网络系统层次化而简化节点路由、管理和维护.但大规模无线传感器网络的连通支配集节点数目依然庞大,d-hop连通支配集可以大大减小支配集节点数目.另外,由于存在节点失效、链路断裂等无线特性,虚拟骨干网需要具备一定的容错性.在单位圆盘图网络模型中为构建精简且具有容错能力的虚拟骨干网,提出d-hop 2-连通支配集的分布式构造算法,先构造d-hop独立支配集后再连通形成d-hop 2-连通支配集.并从理论和仿真上对算法的复杂度、近似比和算法性能作了进一步探讨和验证.

  5. Positional distribution of fatty acids on the glycerol backbone during the biosynthesis of glycerolipids in Ectocarpus fasciculatus

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The biosynthesis of glycolipids in E. fasciculatus was studied by 14C label and chase. The fatty acids in sulphoquinovosyl diacylglycerol (SQDG) were almost 16-car- bon and 18-carbon ones. In addition to the two fatty acids, monogalactosyl diacylglycerol (MGDG) and digalactosyl diacylglycerol (DGDG) contained 8.5 mol% and 31.0 mol% of eicosapentaenoic acid (20∶5), respectively, and this fatty acid was usually distributed in the sn-1 position of the glycerol backbone. When plants were incubated with [2-14C] acetate, differences existed in the positional distribution of the labeled fatty acids in sn-1 and sn-2 among the three glycerolipids. In SQDG, 14C-labeled fatty acids were distributed uniformly in the sn-1 and sn-2 positions. In DGDG, 14C-labeled fatty acids were mainly distributed in the sn-2 position. In MGDG, the radioactivity of fatty acids in sn-1 position was far greater than that in sn-2 position after a 30 min pulse label, and the difference in radioactivity between the two positions decreased rapidly. The above results indicated that differences in the positional distribution of 14C-labeled fatty acids between sn-1 and sn-2 positions might be related to 20∶5 and the biosynthesis of DGDG. Our results also suggested that E. fasciculatus had the same DGDG biosynthetic pathway as that in higher plants and galactosyl transferase was selective for MGDG.

  6. Impairment assessment of orthogonal frequency division multiplexing over dispersion-managed links in backbone and backhaul networks

    Science.gov (United States)

    Tamilarasan, Ilavarasan; Saminathan, Brindha; Murugappan, Meenakshi

    2016-04-01

    The past decade has seen the phenomenal usage of orthogonal frequency division multiplexing (OFDM) in the wired as well as wireless communication domains, and it is also proposed in the literature as a future proof technique for the implementation of flexible resource allocation in cognitive optical networks. Fiber impairment assessment and adaptive compensation becomes critical in such implementations. A comprehensive analytical model for impairments in OFDM-based fiber links is developed. The proposed model includes the combined impact of laser phase fluctuations, fiber dispersion, self phase modulation, cross phase modulation, four-wave mixing, the nonlinear phase noise due to the interaction of amplified spontaneous emission with fiber nonlinearities, and the photodetector noises. The bit error rate expression for the proposed model is derived based on error vector magnitude estimation. The performance analysis of the proposed model is presented and compared for dispersion compensated and uncompensated backbone/backhaul links. The results suggest that OFDM would perform better for uncompensated links than the compensated links due to the negligible FWM effects and there is a need for flexible compensation. The proposed model can be employed in cognitive optical networks for accurate assessment of fiber-related impairments.

  7. Structure of the exceptionally large nonrepetitive carbohydrate backbone of the lipopolysaccharide of Pectinatus frisingensis strain VTT E-82164.

    Science.gov (United States)

    Vinogradov, Evgeny; Petersen, Bent O; Sadovskaya, Irina; Jabbouri, Said; Duus, Jens Ø; Helander, Ilkka M

    2003-07-01

    The structures of the oligosaccharides obtained after acetic acid hydrolysis and alkaline deacylation of the rough-type lipopolysaccharide (LPS) from Pectinatus frisingensis strain VTT E-82164 were analysed using NMR spectroscopy, MS and chemical methods. The LPS contains two major structural variants, differing by a decasaccharide fragment, and some minor variants lacking the terminal glucose residue. The largest structure of the carbohydrate backbone of the LPS that could be deduced from experimental results consists of 25 monosaccharides (including the previously found Ara4NP residue in lipid A) arranged in a well-defined nonrepetitive structure: We presume that the shorter variant with R1 = H represents the core-lipid A part of the LPS, and the additional fragment is present instead of the O-specific polysaccharide. Structures of this type have not been previously described. Analysis of the deacylation products obtained from the LPS of the smooth strain, VTT E-79100T, showed that it contains a very similar core but with one different glycosidic linkage.

  8. Conformational energetics of cationic backbone rearrangements in triterpenoid biosynthesis provide an insight into enzymatic control of product.

    Science.gov (United States)

    Kürti, László; Chein, Rong-Jie; Corey, E J

    2008-07-16

    2,3-( S)-Oxidosqualene (C 30H 50O) serves as a versatile starting point for the remarkable biosynthesis of many isomeric naturally occurring triterpenoids of formula C 30H 50O. These biosyntheses all involve polycyclization via cationic intermediates. The fully cyclized primary products then are converted to various structures by cationic rearrangements involving the polycyclic backbone. The energetics of these rearrangements has been examined by B3LYP 6-31 G* DFT calculations and by ab initio Hartree-Fock calculations at the 6-31G* or 3-21G(*) level. The results have led to the conclusion that the biosynthesis of friedelin, the most drastically rearranged of the pentacyclic triterpenes, involves a complex nonstop process, with no stable intermediates between 2,3-( S)-oxidosqualene and friedelin. It is proposed that this single-reaction biosynthesis consists of pentacyclization to the lupanyl cation followed directly by a sequence of 10 suprafacial 1,2-shifts of carbon and hydrogen, driven by the large exergonicity of the pentacyclization and electrostatic acceleration of the rearrangement steps.

  9. Alkali metal salts of formazanate ligands: diverse coordination modes as a result of the nitrogen-rich [NNCNN] ligand backbone.

    Science.gov (United States)

    Travieso-Puente, Raquel; Chang, Mu-Chieh; Otten, Edwin

    2014-12-28

    Alkali metal salts of redox-active formazanate ligands were prepared, and their structures in the solid-state and in solution are determined. The nitrogen-rich [NNCNN] backbone of formazanates results in a varied coordination chemistry, with both the internal and terminal nitrogen atoms available for bonding with the alkali metal. The potassium salt K[PhNNC(p-tol)NNPh]·2THF (1-K) is dimeric in the solid state and even in THF solution, as a result of the K atom bridging via interaction with a terminal N atom and the aromatic ring of a second unit. Conversely, for the compounds Na[MesNNC(CN)NNMes]·2THF (2-Na) and Na[PhNNC((t)Bu)NNPh] (3-Na) polymeric and hexameric structures are found in the solid state respectively. The preference for binding the alkali metal through internal N atoms (1-K and 2-Na) to give a 4-membered chelate, or via internal/external N atoms (5-membered chelate in 3-Na), contrasts with the 6-membered chelate mode observed in our recently reported formazanate zinc complexes.

  10. MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data

    Energy Technology Data Exchange (ETDEWEB)

    Mantsyzov, Alexey B. [M.V. Lomonosov Moscow State University, Faculty of Fundamental Medicine (Russian Federation); Shen, Yang; Lee, Jung Ho [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Hummer, Gerhard [Max Planck Institute of Biophysics (Germany); Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2015-09-15

    MERA (Maximum Entropy Ramachandran map Analysis from NMR data) is a new webserver that generates residue-by-residue Ramachandran map distributions for disordered proteins or disordered regions in proteins on the basis of experimental NMR parameters. As input data, the program currently utilizes up to 12 different parameters. These include three different types of short-range NOEs, three types of backbone chemical shifts ({sup 15}N, {sup 13}C{sup α}, and {sup 13}C′), six types of J couplings ({sup 3}J{sub HNHα}, {sup 3}J{sub C′C′}, {sup 3}J{sub C′Hα}, {sup 1}J{sub HαCα}, {sup 2}J{sub CαN} and {sup 1}J{sub CαN}), as well as the {sup 15}N-relaxation derived J(0) spectral density. The Ramachandran map distributions are reported in terms of populations of their 15° × 15° voxels, and an adjustable maximum entropy weight factor is available to ensure that the obtained distributions will not deviate more from a newly derived coil library distribution than required to account for the experimental data. MERA output includes the agreement between each input parameter and its distribution-derived value. As an application, we demonstrate performance of the program for several residues in the intrinsically disordered protein α-synuclein, as well as for several static and dynamic residues in the folded protein GB3.

  11. Aggregation and Gelation of Aromatic Polyamides with Parallel and Anti-parallel Alignment of Molecular Dipole Along the Backbone

    Science.gov (United States)

    Zhu, Dan; Shang, Jing; Ye, Xiaodong; Shen, Jian

    2016-12-01

    The understanding of macromolecular structures and interactions is important but difficult, due to the facts that a macromolecules are of versatile conformations and aggregate states, which vary with environmental conditions and histories. In this work two polyamides with parallel or anti-parallel dipoles along the linear backbone, named as ABAB (parallel) and AABB (anti-parallel) have been studied. By using a combination of methods, the phase behaviors of the polymers during the aggregate and gelation, i.e., the forming or dissociation processes of nuclei and fibril, cluster of fibrils, and cluster-cluster aggregation have been revealed. Such abundant phase behaviors are dominated by the inter-chain interactions, including dispersion, polarity and hydrogen bonding, and correlatd with the solubility parameters of solvents, the temperature, and the polymer concentration. The results of X-ray diffraction and fast-mode dielectric relaxation indicate that AABB possesses more rigid conformation than ABAB, and because of that AABB aggregates are of long fibers while ABAB is of hairy fibril clusters, the gelation concentration in toluene is 1 w/v% for AABB, lower than the 3 w/v% for ABAB.

  12. N-H stretching modes around 3300 wavenumber from peptide backbones observed by chiral sum frequency generation vibrational spectroscopy.

    Science.gov (United States)

    Fu, Li; Wang, Zhuguang; Yan, Elsa C Y

    2014-09-01

    We present a detailed analysis of the molecular origin of the chiral sum frequency generation (SFG) signals of proteins and peptides at interfaces in the N-H stretching vibrational region. The N-H stretching can be a probe for investigating structural and functional properties of proteins, but remains technically difficult to analyze due to the overlapping with the O-H stretching of water molecules. Chiral SFG spectroscopy offers unique tools to study the N-H stretching from proteins at interfaces without interference from the water background. However, the molecular origin of the N-H stretching signals of proteins is still unclear. This work provides a justification of the origin of chiral N-H signals by analyzing the vibrational frequencies, examining chiral SFG theory, studying proton (hydrogen/deuterium) exchange kinetics, and performing optical control experiments. The results demonstrate that the chiral N-H stretching signals at ~3300 cm(-1) originate from the amide group of the protein backbones. This chiral N-H stretching signal offers an in situ, real-time, and background-free probe for interrogating the protein structures and dynamics at interfaces at the molecular level.

  13. a Proposal for a General Method for Determining Semi-Experimental Equilibrium Structures of Carbon Atom Backbones

    Science.gov (United States)

    Craig, Norman C.

    2010-06-01

    Semi-experimental equilibrium structures are determined from ground state rotational constants derived from the analysis of rotational transitions in high-resolution spectra and from the quantum chemical calculation of spectroscopic alphas. In the full application of this method, spectra of numerous isotopic species must be investigated. Most of these isotopic species require specialized synthesis. We now propose focusing on the carbon atoms, for which microwave spectroscopy routinely yields spectra for polar molecules with 13C substitution in natural abundance. Needed spectroscopic alphas can be computed with Gaussian software. Application of the Kraitchman substitution relationships gives Cartesian coordinates for the carbon atoms and thence bond parameters for the carbon backbone. This method will be evaluated with ethylene, 1,1-difluoroethylene, 1,1-difluorocyclopropane, propene, and butadiene. The method will then be applied to cis-hexatriene and the two conformers of glycidol. R. D. Suenram, B. H. Pate, A. Lessari, J. L. Neill, S. Shipman, R. A. Holmes, M. C. Leyden, and N. C. Craig, J. Phys. Chem. A 113, 1864-1868 (2009). A. R. Conrad, N. H. Teumelsan, P. E. Wang, and M. J. Tubergen, J. Phys. Chem. A 114, 336-342 (2010).

  14. Design of an all-fiber erbium-doped laser system for simulating power load in backbone networks

    Science.gov (United States)

    Pobořil, Radek; Bednárek, Lukáš; Vanderka, Aleš; Hájek, Lukáš; Zbořil, Ondřej; Vašinek, Vladimír

    2016-12-01

    This article is focused on the design of an all-fiber laser that was supposed to be used for simulating power load similar to the power load in backbone networks. The first part of the article is a brief introduction to the topic of lasers and erbium doped fiber amplifiers. The following parts present design of a fiber laser with ring cavity, and measuring the ideal length of a doped fiber and the split ratio of the output coupler. After proposing the first stage -a laser- we focused on the construction of the two following stages -EDFA preamplifier and EDFA amplifier. There were used fibers with various levels of erbium ion density, namely ISO-GAIN I6, and Liekki ER110-4/125. The resulting output power of the whole system was 320 mW. This value is sufficient when we take into account that we used only single-mode fibers with energy pumped directly to the fiber core. The output wavelength of the whole laser system was 1559 nm.

  15. An improved algorithm for finding community structure in networks with an application to IPv6 backbone network

    Institute of Scientific and Technical Information of China (English)

    GUO Yingxin; XU Ke

    2007-01-01

    The discovery of community structure in a large number of complex networks has attracted lots of interest in recent years.One category of algorithms for detecting community structure,the divisive algorithms,has been proposed and improved impressively.In this paper,we propose an improved divisive algorithm,the basic idea of which is to take more than one parameters into consideration to describe the networks from different points of view.Although its basic idea appears to be a little simple,it is shown experimentally that it outperforms some other algorithms when it is applied to the networks with a relatively obscure community structure.We also demonstrate its effectiveness by applying it to IPv6 backbone network.The communities detected by our algorithm indicate that although underdeveloped compared with IPv4 network,IPv6 network has already exhibited a preliminary community structure.Moreover,our algorithm can be further extended and adapted in the future.In fact,it suggests a simple yet possibly efficient way to improve algorithms.

  16. A Network Flow Approach to Predict Protein Targets and Flavonoid Backbones to Treat Respiratory Syncytial Virus Infection

    Directory of Open Access Journals (Sweden)

    José Eduardo Vargas

    2015-01-01

    Full Text Available Background. Respiratory syncytial virus (RSV infection is the major cause of respiratory disease in lower respiratory tract in infants and young children. Attempts to develop effective vaccines or pharmacological treatments to inhibit RSV infection without undesired effects on human health have been unsuccessful. However, RSV infection has been reported to be affected by flavonoids. The mechanisms underlying viral inhibition induced by these compounds are largely unknown, making the development of new drugs difficult. Methods. To understand the mechanisms induced by flavonoids to inhibit RSV infection, a systems pharmacology-based study was performed using microarray data from primary culture of human bronchial cells infected by RSV, together with compound-proteomic interaction data available for Homo sapiens. Results. After an initial evaluation of 26 flavonoids, 5 compounds (resveratrol, quercetin, myricetin, apigenin, and tricetin were identified through topological analysis of a major chemical-protein (CP and protein-protein interacting (PPI network. In a nonclustered form, these flavonoids regulate directly the activity of two protein bottlenecks involved in inflammation and apoptosis. Conclusions. Our findings may potentially help uncovering mechanisms of action of early RSV infection and provide chemical backbones and their protein targets in the difficult quest to develop new effective drugs.

  17. High resolution 4D HPCH experiment for sequential assignment of {sup 13}C-labeled RNAs via phosphodiester backbone

    Energy Technology Data Exchange (ETDEWEB)

    Saxena, Saurabh; Stanek, Jan [University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre (Poland); Cevec, Mirko; Plavec, Janez [National Institute of Chemistry, Slovenian NMR Centre (Slovenia); Koźmiński, Wiktor, E-mail: kozmin@chem.uw.edu.pl [University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre (Poland)

    2015-11-15

    The three-dimensional structure determination of RNAs by NMR spectroscopy requires sequential resonance assignment, often hampered by assignment ambiguities and limited dispersion of {sup 1}H and {sup 13}C chemical shifts, especially of C4′/H4′. Here we present a novel through-bond 4D HPCH NMR experiment involving phosphate backbone where C4′–H4′ correlations are resolved along the {sup 1}H3′–{sup 31}P spectral planes. The experiment provides high peak resolution and effectively removes ambiguities encountered during assignments. Enhanced peak dispersion is provided by the inclusion of additional {sup 31}P and {sup 1}H3′ dimensions and constant-time evolution of chemical shifts. High spectral resolution is obtained by using non-uniform sampling in three indirect dimensions. The experiment fully utilizes the isotopic {sup 13}C-labeling with evolution of C4′ carbons. Band selective {sup 13}C inversion pulses are used to achieve selectivity and prevent signal dephasing due to the C4′–C3′ and C4′–C5′ homonuclear couplings. Multiple quantum line narrowing is employed to minimize sensitivity loses. The 4D HPCH experiment is verified and successfully applied to a non-coding 34-nt RNA consisting typical structure elements and a 14-nt RNA hairpin capped by cUUCGg tetraloop.

  18. Three-Dimensional Protein Fold Determination from Backbone Amide Pseudocontact Shifts Generated by Lanthanide Tags at Multiple Sites

    KAUST Repository

    Yagi, Hiromasa

    2013-06-01

    Site-specific attachment of paramagnetic lanthanide ions to a protein generates pseudocontact shifts (PCS) in the nuclear magnetic resonance (NMR) spectra of the protein that are easily measured as changes in chemical shifts. By labeling the protein with lanthanide tags at four different sites, PCSs are observed for most amide protons and accurate information is obtained about their coordinates in three-dimensional space. The approach is demonstrated with the chaperone ERp29, for which large differences have been reported between X-ray and NMR structures of the C-terminal domain, ERp29-C. The results unambiguously show that the structure of rat ERp29-C in solution is similar to the crystal structure of human ERp29-C. PCSs of backbone amides were the only structural restraints required. Because these can be measured for more dilute protein solutions than other NMR restraints, the approach greatly widens the range of proteins amenable to structural studies in solution. © 2013 Elsevier Ltd. All rights reserved.

  19. Pressure dependence of backbone chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH2.

    Science.gov (United States)

    Erlach, Markus Beck; Koehler, Joerg; Crusca, Edson; Kremer, Werner; Munte, Claudia E; Kalbitzer, Hans Robert

    2016-06-01

    For a better understanding of nuclear magnetic resonance (NMR) detected pressure responses of folded as well as unstructured proteins the availability of data from well-defined model systems are indispensable. In this work we report the pressure dependence of chemical shifts of the backbone atoms (1)H(α), (13)C(α) and (13)C' in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of these nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The polynomial pressure coefficients B 1 and B 2 are dependent on the type of amino acid studied. The coefficients of a given nucleus show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure are also weakly correlated.

  20. Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar-phosphate backbone and their comparison with modern density functional theory.

    Science.gov (United States)

    Mládek, Arnošt; Krepl, Miroslav; Svozil, Daniel; Cech, Petr; Otyepka, Michal; Banáš, Pavel; Zgarbová, Marie; Jurečka, Petr; Sponer, Jiří

    2013-05-21

    The DNA sugar-phosphate backbone has a substantial influence on the DNA structural dynamics. Structural biology and bioinformatics studies revealed that the DNA backbone in experimental structures samples a wide range of distinct conformational substates, known as rotameric DNA backbone conformational families. Their correct description is essential for methods used to model nucleic acids and is known to be the Achilles heel of force field computations. In this study we report the benchmark database of MP2 calculations extrapolated to the complete basis set of atomic orbitals with aug-cc-pVTZ and aug-cc-pVQZ basis sets, MP2(T,Q), augmented by ΔCCSD(T)/aug-cc-pVDZ corrections. The calculations are performed in the gas phase as well as using a COSMO solvent model. This study includes a complete set of 18 established and biochemically most important families of DNA backbone conformations and several other salient conformations that we identified in experimental structures. We utilize an electronically sufficiently complete DNA sugar-phosphate-sugar (SPS) backbone model system truncated to prevent undesired intramolecular interactions. The calculations are then compared with other QM methods. The BLYP and TPSS functionals supplemented with Grimme's D3(BJ) dispersion term provide the best tradeoff between computational demands and accuracy and can be recommended for preliminary conformational searches as well as calculations on large model systems. Among the tested methods, the best agreement with the benchmark database has been obtained for the double-hybrid DSD-BLYP functional in combination with a quadruple-ζ basis set, which is, however, computationally very demanding. The new hybrid density functionals PW6B95-D3 and MPW1B95-D3 yield outstanding results and even slightly outperform the computationally more demanding PWPB95 double-hybrid functional. B3LYP-D3 is somewhat less accurate compared to the other hybrids. Extrapolated MP2(D,T) calculations are not as

  1. Energies and 2'-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations.

    Science.gov (United States)

    Mládek, Arnošt; Banáš, Pavel; Jurečka, Petr; Otyepka, Michal; Zgarbová, Marie; Šponer, Jiří

    2014-01-14

    Sugar-phosphate backbone is an electronically complex molecular segment imparting RNA molecules high flexibility and architectonic heterogeneity necessary for their biological functions. The structural variability of RNA molecules is amplified by the presence of the 2'-hydroxyl group, capable of forming multitude of intra- and intermolecular interactions. Bioinformatics studies based on X-ray structure database revealed that RNA backbone samples at least 46 substates known as rotameric families. The present study provides a comprehensive analysis of RNA backbone conformational preferences and 2'-hydroxyl group orientations. First, we create a benchmark database of estimated CCSD(T)/CBS relative energies of all rotameric families and test performance of dispersion-corrected DFT-D3 methods and molecular mechanics in vacuum and in continuum solvent. The performance of the DFT-D3 methods is in general quite satisfactory. The B-LYP-D3 method provides the best trade-off between accuracy and computational demands. B3-LYP-D3 slightly outperforms the new PW6B95-D3 and MPW1B95-D3 and is the second most accurate density functional of the study. The best agreement with CCSD(T)/CBS is provided by DSD-B-LYP-D3 double-hybrid functional, although its large-scale applications may be limited by high computational costs. Molecular mechanics does not reproduce the fine energy differences between the RNA backbone substates. We also demonstrate that the differences in the magnitude of the hyperconjugation effect do not correlate with the energy ranking of the backbone conformations. Further, we investigated the 2'-hydroxyl group orientation preferences. For all families, we conducted a QM and MM hydroxyl group rigid scan in gas phase and solvent. We then carried out set of explicit solvent MD simulations of folded RNAs and analyze 2'-hydroxyl group orientations of different backbone families in MD. The solvent energy profiles determined primarily by the sugar pucker match well with the

  2. Backbone.js cookbook

    CERN Document Server

    Mirgorod, Vadim

    2013-01-01

    Written in a friendly, example driven Beginner's Guide format, there are plenty of step-by-step instructions to get you started fast!Pentaho 4.0 By Example: Beginner's Guide is the ideal companion for a wide-variety of developers. Whether you are new to the world of Business Intelligence reporting, or an experienced BI analyst, this book will guide you through the creation of your first reports in Pentaho. We assume some knowledge of the SQL language and database systems.

  3. Dicyclopropylmethyl peptide backbone protectant.

    Science.gov (United States)

    Carpino, Louis A; Nasr, Khaled; Abdel-Maksoud, Adel Ali; El-Faham, Ayman; Ionescu, Dumitru; Henklein, Peter; Wenschuh, Holger; Beyermann, Michael; Krause, Eberhard; Bienert, Michael

    2009-08-20

    The N-dicyclopropylmethyl (Dcpm) residue, introduced into amino acids via reaction of dicyclopropylmethanimine hydrochloride with an amino acid ester followed by sodium cyanoborohydride or triacetoxyborohydride reduction, can be used as an amide bond protectant for peptide synthesis. Examples which demonstrate the amelioration of aggregation effects include syntheses of the alanine decapeptide and the prion peptide (106-126). Avoidance of cyclization to the aminosuccinimide followed substitution of Fmoc-(Dcpm)Gly-OH for Fmoc-Gly-OH in the assembly of sequences containing the sensitive Asp-Gly unit.

  4. Backbone.js essentials

    CERN Document Server

    Walker, Jeremy

    2015-01-01

    If you are a developer with baseline JavaScript proficiency and are familiar with the jQuery library, then this book is ideal for you. Whether you've tried building complex web applications before and been frustrated by the challenge of doing so without the proper tools, or whether you've only built simple websites and are now looking to create full-featured web applications, this book has everything you need to get ahead of the curve.

  5. Backbone amide linker strategy

    DEFF Research Database (Denmark)

    Shelton, Anne Pernille Tofteng; Jensen, Knud Jørgen

    2013-01-01

    amino acid residue by reductive amination. This can be used as a general approach for the introduction of other C-terminal modifications as well as functionalities, such as fluorophors. The second step is an acylation of a secondary amine, followed by standard Fmoc-based solid-phase synthesis...

  6. Nitrogen Backbone Oligomers.

    Science.gov (United States)

    Wang, Hongbo; Eremets, Mikhail I; Troyan, Ivan; Liu, Hanyu; Ma, Yanming; Vereecken, Luc

    2015-08-19

    We found that nitrogen and hydrogen directly react at room temperature and pressures of ~35 GPa forming chains of single-bonded nitrogen atom with the rest of the bonds terminated with hydrogen atoms - as identified by IR absorption, Raman, X-ray diffraction experiments and theoretical calculations. At releasing pressures below ~10 GPa, the product transforms into hydrazine. Our findings might open a way for the practical synthesis of these extremely high energetic materials as the formation of nitrogen-hydrogen compounds is favorable already at pressures above 2 GPa according to the calculations.

  7. Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY

    KAUST Repository

    Jang, Richard

    2012-03-21

    Background: Chemical shift mapping is an important technique in NMR-based drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule\\'s introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically, which is not efficient for high-throughput drug screening.Results: We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C-labeling, to resolve the ambiguities for a one-to-one mapping. On the three proteins, it achieves an average accuracy of 94% or better.Conclusions: Our mathematical programming approach for modeling chemical shift mapping as a graph problem, while modeling the errors directly, is potentially a time- and cost-effective first step for high-throughput drug screening based on limited NMR data and homologous 3D structures. 2012 Jang et al.; licensee BioMed Central Ltd.

  8. Backbone resonance assignments for G protein α(i3) subunit in the GDP-bound state.

    Science.gov (United States)

    Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

    2014-10-01

    Guanine-nucleotide binding proteins (G proteins) serve as molecular switches in signaling pathways, by coupling the activation of G protein-coupled receptors (GPCRs) at the cell surface to intracellular responses. In the resting state, G protein forms a heterotrimer, consisting of the G protein α subunit with GDP (Gα·GDP) and the G protein βγ subunit (Gβγ). Ligand binding to GPCRs promotes the GDP-GTP exchange on Gα, leading to the dissociation of the GTP-bound form of Gα (Gα·GTP) and Gβγ. Then, Gα·GTP and Gβγ bind to their downstream effector enzymes or ion channels and regulate their activities, leading to a variety of cellular responses. Finally, Gα hydrolyzes the bound GTP to GDP and returns to the resting state by re-associating with Gβγ. The G proteins are classified with four major families based on the amino acid sequences of Gα: i/o, s, q/11, and 12/13. Here, we established the backbone resonance assignments of human Gαi3, a member of the i/o family with a molecular weight of 41 K, in complex with GDP. The chemical shifts were compared with those of Gα(i3) in complex with a GTP-analogue, GTPγS, which we recently reported, indicating that the residues with significant chemical shift differences are mostly consistent with the regions with the structural differences between the GDP- and GTPγS-bound states, as indicated in the crystal structures. The assignments of Gα(i3)·GDP would be useful for the analyses of the dynamics of Gα(i3) and its interactions with various target molecules.

  9. Structural basis for the enhanced stability of protein model compounds and peptide backbone unit in ammonium ionic liquids.

    Science.gov (United States)

    Vasantha, T; Attri, Pankaj; Venkatesu, Pannuru; Devi, R S Rama

    2012-10-04

    Protein folding/unfolding is a fascinating study in the presence of cosolvents, which protect/disrupt the native structure of protein, respectively. The structure and stability of proteins and their functional groups may be modulated by the addition of cosolvents. Ionic liquids (ILs) are finding a vast array of applications as novel cosolvents for a wide variety of biochemical processes that include protein folding. Here, the systematic and quantitative apparent transfer free energies (ΔG'(tr)) of protein model compounds from water to ILs through solubility measurements as a function of IL concentration at 25 °C have been exploited to quantify and interpret biomolecular interactions between model compounds of glycine peptides (GPs) with ammonium based ILs. The investigated aqueous systems consist of zwitterionic glycine peptides: glycine (Gly), diglycine (Gly(2)), triglycine (Gly(3)), tetraglycine (Gly(4)), and cyclic glycylglycine (c(GG)) in the presence of six ILs such as diethylammonium acetate (DEAA), diethylammonium hydrogen sulfate (DEAS), triethylammonium acetate (TEAA), triethylammonium hydrogen sulfate (TEAS), triethylammonium dihydrogen phosphate (TEAP), and trimethylammonium acetate (TMAA). We have observed positive values of ΔG'(tr) for GPs from water to ILs, indicating that interactions between ILs and GPs are unfavorable, which leads to stabilization of the structure of model protein compounds. Moreover, our experimental data ΔG'(tr) is used to obtain transfer free energies (Δg'(tr)) of the peptide backbone unit (or glycyl unit) (-CH(2)C═ONH-), which is the most numerous group in globular proteins, from water to IL solutions. To obtain the mechanism events of the ILs' role in enhancing the stability of the model compounds, we have further obtained m-values for GPs from solubility limits. These results explicitly elucidate that all alkyl ammonium ILs act as stabilizers for model compounds through the exclusion of ILs from model compounds of

  10. Soluble and Membrane-Bound β-Glucosidases Are Involved in Trimming the Xyloglucan Backbone1[OPEN

    Science.gov (United States)

    Fraga, Patricia

    2017-01-01

    In many flowering plants, xyloglucan is a major component of primary cell walls, where it plays an important role in growth regulation. Xyloglucan can be degraded by a suite of exoglycosidases that remove specific sugars. In this work, we show that the xyloglucan backbone, formed by (1→4)-linked β-d-glucopyranosyl residues, can be attacked by two different Arabidopsis (Arabidopsis thaliana) β-glucosidases from glycoside hydrolase family 3. While BGLC1 (At5g20950; for β-glucosidase active against xyloglucan 1) is responsible for all or most of the soluble activity, BGLC3 (At5g04885) is usually a membrane-anchored protein. Mutations in these two genes, whether on their own or combined with mutations in other exoglycosidase genes, resulted in the accumulation of partially digested xyloglucan subunits, such as GXXG, GXLG, or GXFG. While a mutation in BGLC1 had significant effects on its own, lack of BGLC3 had only minor effects. On the other hand, double bglc1 bglc3 mutants revealed a synergistic interaction that supports a role for membrane-bound BGLC3 in xyloglucan metabolism. In addition, bglc1 bglc3 was complemented by overexpression of either BGLC1 or BGLC3. In overexpression lines, BGLC3 activity was concentrated in a microsome-enriched fraction but also was present in soluble form. Finally, both genes were generally expressed in the same cell types, although, in some cases, BGLC3 was expressed at earlier stages than BGLC1. We propose that functional specialization could explain the separate localization of both enzymes, as a membrane-bound β-glucosidase could specifically digest soluble xyloglucan without affecting the wall-bound polymer. PMID:27956490

  11. Solution NMR analysis of the interaction between the actinoporin sticholysin I and DHPC micelles--correlation with backbone dynamics.

    Science.gov (United States)

    López-Castilla, Aracelys; Pazos, Fabiola; Schreier, Shirley; Pires, José Ricardo

    2014-06-01

    Sticholysin I (StI), an actinoporin expressed as a water-soluble protein by the sea anemone Stichodactyla helianthus, binds to natural and model membranes, forming oligomeric pores. It is proposed that the first event of a multistep pore formation mechanism consists of the monomeric protein attachment to the lipid bilayer. To date there is no high-resolution structure of the actinoporin pore or other membrane-bound form available. Here we evaluated StI:micelle complexes of variable lipid composition to look for a suitable model for NMR studies. Micelles of pure or mixed lysophospholipids and of dihexanoyl phosphatidylcholine (DHPC) were examined. The StI:DHPC micelle was found to be the best system, yielding a stable sample and good quality spectra. A comprehensive chemical shift perturbation analysis was performed to map the StI membrane recognition site in the presence of DHPC micelles. The region mapped (residues F(51), R(52), S(53) in loop 3; F(107), D(108), Y(109), W(111), Y(112), W(115) in loop 7; Q(129), Y(132), D(134), M(135), Y(136), Y(137), G(138) in helix-α2) is in agreement with previously reported data, but additional residues were found to interact, especially residues V(81), A(82), T(83), G(84) in loop 5, and A(85), A(87) in strand-β5. Backbone dynamics measurements of StI free in solution and bound to micelles highlighted the relevance of protein flexibility for membrane binding and suggested that a conformer selection process may take place during protein-membrane interaction. We conclude that the StI:DHPC micelles system is a suitable model for further characterization of an actinoporin membrane-bound form by solution NMR.

  12. Combining ambiguous chemical shift mapping with structure-based backbone and NOE assignment from 15N-NOESY

    KAUST Repository

    Jang, Richard

    2011-01-01

    Chemical shift mapping is an important technique in NMRbased drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule\\'s introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically. However, automated methods are necessary for high-throughput drug screening. We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C- labeling, to resolve the ambiguities for a one-toone mapping. On the three proteins, it achieves an average accuracy of 94% or better. Copyright © 2011 ACM.

  13. Sulfur-infiltrated graphene-backboned mesoporous carbon nanosheets with a conductive polymer coating for long-life lithium-sulfur batteries

    Science.gov (United States)

    Dong, Yanfeng; Liu, Shaohong; Wang, Zhiyu; Liu, Yang; Zhao, Zongbin; Qiu, Jieshan

    2015-04-01

    Sandwich-type, two-dimensional hybrid nanosheets were fabricated by the infiltration of nanosized sulfur into graphene-backboned mesoporous carbon with a PPy nanocoating. They exhibit a high reversible capacity for as long as 400 cycles with an ultra slow decay rate of 0.05% per cycle at the high rate of 1-3 C due to the efficient immobilization of polysulfides.Sandwich-type, two-dimensional hybrid nanosheets were fabricated by the infiltration of nanosized sulfur into graphene-backboned mesoporous carbon with a PPy nanocoating. They exhibit a high reversible capacity for as long as 400 cycles with an ultra slow decay rate of 0.05% per cycle at the high rate of 1-3 C due to the efficient immobilization of polysulfides. Electronic supplementary information (ESI) available: Experimental details, BET, SEM, XPS and more electrochemical data. See DOI: 10.1039/c5nr01015b

  14. 1H, 15N and 13C backbone assignments of GDP-bound human H-Ras mutant G12V.

    Science.gov (United States)

    Amin, Nader; Chiarparin, Elisabetta; Coyle, Joe; Nietlispach, Daniel; Williams, Glyn

    2016-04-01

    Harvey Ras (H-Ras) is a membrane-associated GTPase with critical functions in cell proliferation and differentiation. The G12V mutant of H-Ras is one of the most commonly encountered oncoproteins in human cancer. This mutation disrupts the GTPase activity of H-Ras, leading to constitutive activation and aberrant downstream signalling. Here we report the backbone resonance assignments of human H-Ras mutant G12V lacking the C-terminal membrane attachment domain.

  15. Study on softening Tilapia backbone by high pressure steam cooking%高压蒸煮软化罗非鱼鱼骨的研究

    Institute of Scientific and Technical Information of China (English)

    吴克刚; 张文祥; 柴向华; 何文龙

    2013-01-01

    To study softening Tilapia backbone by high pressure steam cooking,with pH,cooking pressure,steaming time and material/water ratio for study factors,the hardness of Tilapia backbone was evaluated with its maximum bearable pressure on universal testing machine.Results of single-factor experiments and orthogonal experiments showed that the softening effect of backbone was the best with the treatment condition of pH6.5,pressure of 0.13MPa,steaming time of 75min and material/water ratio of 1∶1.Under this condition,the hardness of Tilapia backbone was 33.0N.%以罗非鱼鱼骨为实验对象,以pH、蒸煮压力、蒸煮时间以及料液比为研究因素,采用万能试验机测量鱼骨最大承受压力来评价其硬度,研究高压蒸煮软化工艺.通过单因素实验及正交实验表明:当pH为6.5、蒸煮压力为0.13MPa、时间为75min、料液比为1∶1时,对鱼骨的软化效果最好,此工艺下所得鱼骨硬度为33.0N.

  16. Selective Acid Hydrolysis Condition for the Composition and Linkage with a Fructofuranosyl Backbone of a Polysaccharide from Angelica sinensis (Oliv) Diels

    Institute of Scientific and Technical Information of China (English)

    Gui Yun XU; Yang CHEN; Ru Xian CHEN

    2006-01-01

    A new polysaccharide was extracted and purified from the roots of Angelica sinensis (Oliv) Diels (ASD). Its composition and linkage was elucidated by selective hydrolysis and GC/MS analysis of its derivatives. The polysaccharide was made of→1) Fruf(2→and→6) GlCp (1→as its backbone with highly branched structure. To our best knowledge, this is the first report of the fructose residue in polysaccharides from the roots of the ASD.

  17. Rapid analysis of protein backbone resonance assignments using cryogenic probes, a distributed Linux-based computing architecture, and an integrated set of spectral analysis tools.

    Science.gov (United States)

    Monleón, Daniel; Colson, Kimberly; Moseley, Hunter N B; Anklin, Clemens; Oswald, Robert; Szyperski, Thomas; Montelione, Gaetano T

    2002-01-01

    Rapid data collection, spectral referencing, processing by time domain deconvolution, peak picking and editing, and assignment of NMR spectra are necessary components of any efficient integrated system for protein NMR structure analysis. We have developed a set of software tools designated AutoProc, AutoPeak, and AutoAssign, which function together with the data processing and peak-picking programs NMRPipe and Sparky, to provide an integrated software system for rapid analysis of protein backbone resonance assignments. In this paper we demonstrate that these tools, together with high-sensitivity triple resonance NMR cryoprobes for data collection and a Linux-based computer cluster architecture, can be combined to provide nearly complete backbone resonance assignments and secondary structures (based on chemical shift data) for a 59-residue protein in less than 30 hours of data collection and processing time. In this optimum case of a small protein providing excellent spectra, extensive backbone resonance assignments could also be obtained using less than 6 hours of data collection and processing time. These results demonstrate the feasibility of high throughput triple resonance NMR for determining resonance assignments and secondary structures of small proteins, and the potential for applying NMR in large scale structural proteomics projects.

  18. Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by guided-learning through a two-layer neural network.

    Science.gov (United States)

    Faraggi, Eshel; Xue, Bin; Zhou, Yaoqi

    2009-03-01

    This article attempts to increase the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins through improved learning. Most methods developed for improving the backpropagation algorithm of artificial neural networks are limited to small neural networks. Here, we introduce a guided-learning method suitable for networks of any size. The method employs a part of the weights for guiding and the other part for training and optimization. We demonstrate this technique by predicting residue solvent accessibility and real-value backbone torsion angles of proteins. In this application, the guiding factor is designed to satisfy the intuitive condition that for most residues, the contribution of a residue to the structural properties of another residue is smaller for greater separation in the protein-sequence distance between the two residues. We show that the guided-learning method makes a 2-4% reduction in 10-fold cross-validated mean absolute errors (MAE) for predicting residue solvent accessibility and backbone torsion angles, regardless of the size of database, the number of hidden layers and the size of input windows. This together with introduction of two-layer neural network with a bipolar activation function leads to a new method that has a MAE of 0.11 for residue solvent accessibility, 36 degrees for psi, and 22 degrees for phi. The method is available as a Real-SPINE 3.0 server in http://sparks.informatics.iupui.edu.

  19. In Sup35p filaments (the [PSI+] prion), the globular C-terminal domains are widely offset from the amyloid fibril backbone

    Energy Technology Data Exchange (ETDEWEB)

    Baxa, U.; Wall, J.; Keller, P. W.; Cheng, N.; Steven, A. C.

    2011-01-01

    In yeast cells infected with the [PSI+] prion, Sup35p forms aggregates and its activity in translation termination is downregulated. Transfection experiments have shown that Sup35p filaments assembled in vitro are infectious, suggesting that they reproduce or closely resemble the prion. We have used several EM techniques to study the molecular architecture of filaments, seeking clues as to the mechanism of downregulation. Sup35p has an N-terminal 'prion' domain; a highly charged middle (M-)domain; and a C-terminal domain with the translation termination activity. By negative staining, cryo-EM and scanning transmission EM (STEM), filaments of full-length Sup35p show a thin backbone fibril surrounded by a diffuse 65-nm-wide cloud of globular C-domains. In diameter ({approx}8 nm) and appearance, the backbones resemble amyloid fibrils of N-domains alone. STEM mass-per-unit-length data yield -1 subunit per 0.47 nm for N-fibrils, NM-filaments and Sup35p filaments, further supporting the fibril backbone model. The 30 nm radial span of decorating C-domains indicates that the M-domains assume highly extended conformations, offering an explanation for the residual Sup35p activity in infected cells, whereby the C-domains remain free enough to interact with ribosomes.

  20. A maximum entropy approach to the study of residue-specific backbone angle distributions in α-synuclein, an intrinsically disordered protein

    Science.gov (United States)

    Mantsyzov, Alexey B; Maltsev, Alexander S; Ying, Jinfa; Shen, Yang; Hummer, Gerhard; Bax, Ad

    2014-01-01

    α-Synuclein is an intrinsically disordered protein of 140 residues that switches to an α-helical conformation upon binding phospholipid membranes. We characterize its residue-specific backbone structure in free solution with a novel maximum entropy procedure that integrates an extensive set of NMR data. These data include intraresidue and sequential HN–Hα and HN–HN NOEs, values for 3JHNHα, 1JHαCα, 2JCαN, and 1JCαN, as well as chemical shifts of 15N, 13Cα, and 13C′ nuclei, which are sensitive to backbone torsion angles. Distributions of these torsion angles were identified that yield best agreement to the experimental data, while using an entropy term to minimize the deviation from statistical distributions seen in a large protein coil library. Results indicate that although at the individual residue level considerable deviations from the coil library distribution are seen, on average the fitted distributions agree fairly well with this library, yielding a moderate population (20–30%) of the PPII region and a somewhat higher population of the potentially aggregation-prone β region (20–40%) than seen in the database. A generally lower population of the αR region (10–20%) is found. Analysis of 1H–1H NOE data required consideration of the considerable backbone diffusion anisotropy of a disordered protein. PMID:24976112

  1. Sulfolobus acidocaldarius UDG Can Remove dU from the RNA Backbone: Insight into the Specific Recognition of Uracil Linked with Deoxyribose

    Directory of Open Access Journals (Sweden)

    Gang-Shun Yi

    2017-01-01

    Full Text Available Sulfolobus acidocaldarius encodes family 4 and 5 uracil-DNA glycosylase (UDG. Two recombinant S. acidocaldarius UDGs (SacUDG were prepared and biochemically characterized using oligonucleotides carrying a deaminated base. Both SacUDGs can remove deoxyuracil (dU base from both double-stranded DNA and single-stranded DNA. Interestingly, they can remove U linked with deoxyribose from single-stranded RNA backbone, suggesting that the riboses on the backbone have less effect on the recognition of dU and hydrolysis of the C-N glycosidic bond. However, the removal of rU from DNA backbone is inefficient, suggesting strong steric hindrance comes from the 2′ hydroxyl of ribose linked to uracil. Both SacUDGs cannot remove 2,2′-anhydro uridine, hypoxanthine, and 7-deazaxanthine from single-stranded DNA and single-stranded DNA. Compared with the family 2 MUG, other family UDGs have an extra N-terminal structure consisting of about 50 residues. Removal of the 46 N-terminal residues of family 5 SacUDG resulted in only a 40% decrease in activity, indicating that the [4Fe-4S] cluster and truncated secondary structure are not the key elements in hydrolyzing the glycosidic bond. Combining our biochemical and structural results with those of other groups, we discussed the UDGs’ catalytic mechanism and the possible repair reactions of deaminated bases in prokaryotes.

  2. Sulfolobus acidocaldarius UDG Can Remove dU from the RNA Backbone: Insight into the Specific Recognition of Uracil Linked with Deoxyribose.

    Science.gov (United States)

    Yi, Gang-Shun; Wang, Wei-Wei; Cao, Wei-Guo; Wang, Feng-Ping; Liu, Xi-Peng

    2017-01-18

    Sulfolobus acidocaldarius encodes family 4 and 5 uracil-DNA glycosylase (UDG). Two recombinant S. acidocaldarius UDGs (SacUDG) were prepared and biochemically characterized using oligonucleotides carrying a deaminated base. Both SacUDGs can remove deoxyuracil (dU) base from both double-stranded DNA and single-stranded DNA. Interestingly, they can remove U linked with deoxyribose from single-stranded RNA backbone, suggesting that the riboses on the backbone have less effect on the recognition of dU and hydrolysis of the C-N glycosidic bond. However, the removal of rU from DNA backbone is inefficient, suggesting strong steric hindrance comes from the 2' hydroxyl of ribose linked to uracil. Both SacUDGs cannot remove 2,2'-anhydro uridine, hypoxanthine, and 7-deazaxanthine from single-stranded DNA and single-stranded DNA. Compared with the family 2 MUG, other family UDGs have an extra N-terminal structure consisting of about 50 residues. Removal of the 46 N-terminal residues of family 5 SacUDG resulted in only a 40% decrease in activity, indicating that the [4Fe-4S] cluster and truncated secondary structure are not the key elements in hydrolyzing the glycosidic bond. Combining our biochemical and structural results with those of other groups, we discussed the UDGs' catalytic mechanism and the possible repair reactions of deaminated bases in prokaryotes.

  3. A maximum entropy approach to the study of residue-specific backbone angle distributions in α-synuclein, an intrinsically disordered protein.

    Science.gov (United States)

    Mantsyzov, Alexey B; Maltsev, Alexander S; Ying, Jinfa; Shen, Yang; Hummer, Gerhard; Bax, Ad

    2014-09-01

    α-Synuclein is an intrinsically disordered protein of 140 residues that switches to an α-helical conformation upon binding phospholipid membranes. We characterize its residue-specific backbone structure in free solution with a novel maximum entropy procedure that integrates an extensive set of NMR data. These data include intraresidue and sequential H(N) − H(α) and H(N) − H(N) NOEs, values for (3) JHNHα, (1) JHαCα, (2) JCαN, and (1) JCαN, as well as chemical shifts of (15)N, (13)C(α), and (13)C' nuclei, which are sensitive to backbone torsion angles. Distributions of these torsion angles were identified that yield best agreement to the experimental data, while using an entropy term to minimize the deviation from statistical distributions seen in a large protein coil library. Results indicate that although at the individual residue level considerable deviations from the coil library distribution are seen, on average the fitted distributions agree fairly well with this library, yielding a moderate population (20-30%) of the PPII region and a somewhat higher population of the potentially aggregation-prone β region (20-40%) than seen in the database. A generally lower population of the αR region (10-20%) is found. Analysis of (1)H − (1)H NOE data required consideration of the considerable backbone diffusion anisotropy of a disordered protein.

  4. Using MUSIC and CC(CONH for Backbone Assignment of Two Medium-Sized Proteins Not Fully Accessible to Standard 3D NMR

    Directory of Open Access Journals (Sweden)

    Annette K. Brenner

    2014-06-01

    Full Text Available The backbone assignment of medium-sized proteins is rarely as straightforward as that of small proteins, and thus often requires creative solutions. Here, we describe the application of a combination of standard 3D heteronuclear methods with CC(CONH and a variety of MUltiplicity Selective In-phase Coherence transfer (MUSIC experiments. Both CC(CONH and MUSIC are, in theory, very powerful methods for the backbone assignment of proteins. Due to low sensitivity, their use has usually been linked to small proteins only. However, we found that combining CC(CONH and MUSIC experiments simplified the assignment of two challenging medium-sized proteins of 13 and 19.5 kDa, respectively. These methods are to some extent complementary to each other: CC(CONH acquired with a long isotropic mixing time can identify amino acids with large aliphatic side chains. Whereas the most sensitive MUSIC experiments identify amino acid types that cannot be detected by CC(CONH, comprising the residues with acid and amide groups, and aromatic rings in their side chains. Together these methods provide a means of identifying the majority of peaks in the 2D 15N HSQC spectrum which simplifies the backbone assignment work even for proteins, e.g., small kinases, whose standard spectra resulted in little spectral resolution and low signal intensities.

  5. n Silico Analysis of Envelope Dengue Virus-2 and Envelope Dengue Virus-3 Protein as the Backbone of Dengue Virus Tetravalent Vaccine by Using Homology Modeling Method

    Directory of Open Access Journals (Sweden)

    Rizky I. Taufik

    2009-01-01

    Full Text Available Problem statement: Dengue fever, which was caused by Dengue virus infection, had became a major public health problem in the tropic and subtropical countries. Dengue virus (DENV had four serotypes (DENV-1, DENV-2, DENV-3 and DENV-4, based on their immunogenic in the human body. Preventive measure will be necessary to decrease the prevalence of dengue fever, by developing modern vaccine. Approach: This research was focused on in silico study of dengue virus vaccines, by using envelope (E protein of DENV-2 and DENV-3 as their backbones. T cell epitope prediction was determined by using MULTIPRED server and B cell epitope prediction was determined by using Conformational Epitope Prediction server (CEP. Homology modeling study of E DENV-3 protein as the vaccine backbone had produced six dengue vaccine peptides (HMM Vaccine 1-6. Moreover, homology modeling study of E DENV-2 protein as vaccine backbone had produced six dengue vaccine peptides (ANN vaccine 1-6. Results: The BLAST analysis of HMM and ANN vaccines had produced 93% and 91% identity, respectively. The Ramachandran Plot of both vaccines had shown less than 15% non glycine residue in the disallowed region, therefore it showed the solid stability of the proteins. The VAST analysis of E DENV-3 backbone vaccines had determined, that HMM4 and HMM6 had the highest structure similarity with native E DENV-3. HMM4 and HMM6 had the highest VAST score of 64.5. Moreover, the VAST analysis of E DENV-2 backbone vaccines had determined, that ANN1, ANN3, ANN4, ANN5 and ANN6 had the highest structure similarity with native E DENV-2. ANN1, ANN3, ANN4, ANN5 and ANN6 have the highest VAST score of 64.7. Conclusion/Recommendation: It could be inferred from this research that HMM4; HMM6; ANN1; ANN3; ANN4; ANN5; and ANN6 were the best in silico vaccine design, based on their similarity with native E DENV Proteins. This research could be applied for the wet

  6. Tridentate Lewis Acids Based on 1,3,5-Trisilacyclohexane Backbones and an Example of Their Host-Guest Chemistry.

    Science.gov (United States)

    Weisheim, Eugen; Reuter, Christian G; Heinrichs, Peter; Vishnevskiy, Yury V; Mix, Andreas; Neumann, Beate; Stammler, Hans-Georg; Mitzel, Norbert W

    2015-08-24

    Directed tridentate Lewis acids based on the 1,3,5-trisilacyclohexane skeleton with three ethynyl groups [CH2Si(Me)(C2H)]3 were synthesised and functionalised by hydroboration with HB(C6F5)2, yielding the ethenylborane {CH2Si(Me)[C2H2B(C6F5)2]}3, and by metalation with gallium and indium organyls affording {CH2Si(Me)[C2M(R)2]}3 (M = Ga, In, R = Me, Et). In the synthesis of the backbone the influence of substituents (MeO, EtO and iPrO groups at Si) on the orientation of the methyl group was studied with the aim to increase the abundance of the all-cis isomer. New compounds were identified by elemental analyses, multi-nuclear NMR spectroscopy and in some cases by IR spectroscopy. Crystal structures were obtained for cis-trans-[CH2Si(Me)(Cl)]3, all-cis-[CH2Si(Me)(H)]3, all-cis-[CH2Si(Me)(C2H)]3, cis-trans-[CH2Si(Me)(C2H)]3 and all-cis-[CH2Si(Me)(C2SiMe3)]3. A gas-phase electron diffraction experiment for all-cis-[CH2Si(Me)(C2H)]3 provides information on the relative stabilities of the all-equatorial and all-axial form; the first is preferred in both solid and gas phase. The gallium-based Lewis acid {CH2Si(Me)[C2Ga(Et)2]}3 was reacted with a tridentate Lewis base (1,3,5-trimethyl-1,3,5-triazacyclohexane) in an NMR titration experiment. The generated host-guest complexes involved in the equilibria during this reaction were identified by DOSY NMR spectroscopy by comparing measured diffusion coefficients with those of the suitable reference compounds of same size and shape.

  7. Photochemical stability of random poly(3-hexylthiophene-co-3-cyanothiophene) and its use in roll coated ITO-free organic photovoltaics

    DEFF Research Database (Denmark)

    Roth, Bérenger; Rudenko, Andrey E.; Thompson, Barry C.;

    2015-01-01

    The photochemical stability of the active layer blend for organic solar cells was explored by introducing electron withdrawing cyano groups into the backbone of poly-3-hexylthiophene (P3HT). Random copolymerization of 2-bromo-3-hexyl-5-trimethylstannylthiophene and 2-bromo-3-cyano-5-trimethylstan......The photochemical stability of the active layer blend for organic solar cells was explored by introducing electron withdrawing cyano groups into the backbone of poly-3-hexylthiophene (P3HT). Random copolymerization of 2-bromo-3-hexyl-5-trimethylstannylthiophene and 2-bromo-3-cyano-5...

  8. [Current organization of disaster medicine].

    Science.gov (United States)

    Julien, Henri

    2013-12-01

    The concept of disaster medicine, derivedfrom medical management of casualties caused by terrorist attacks or earthquakes, began to be taught in medical school in 1982. It adapts military intervention tactics to civilian practices, and differentiates major disasters (in which preformed teams are sent to the scene) from disasters with limited effects (predefined plans form the backbone of the rescue organization). Management of blast and crush syndromes, triage, care of numerous burn victims, on-site amputation, necrotomy, medicopsychological support, mass decontamination, and rescue management are some of the aspects with which physicians should be familiar. Predefined intervention teams and ad hoc materials have been created to provide autonomous logistic support. Regulations, ethical aspects and managerial methods still need to be refined, and research and teaching must be given a new impetus.

  9. 1H, 13C and 15N backbone and side-chain chemical shift assignment of the Fyn SH2 domain and its complex with a phosphotyrosine peptide.

    Science.gov (United States)

    Huculeci, Radu; Buts, Lieven; Lenaerts, Tom; van Nuland, Nico A J

    2011-10-01

    SH2 domains are interaction modules uniquely dedicated to recognize phosphotyrosine sites, playing a central role in for instance the activation of tyrosine kinases or phosphatases. Here we report the (1)H, (15)N and (13)C backbone and side-chain chemical shift assignments of the SH2 domain of the human protein tyrosine kinase Fyn, both in its free state and bound to a high-affinity phosphotyrosine peptide corresponding to a specific sequence in the hamster middle-T antigen. The BMRB accession numbers are 17,368 and 17,369, respectively.

  10. Direct Formation of the C5′-Radical in the Sugar-Phosphate Backbone of DNA by High Energy Radiation

    Science.gov (United States)

    Adhikary, Amitava; Becker, David; Palmer, Brian J.; Heizer, Alicia N.; Sevilla, Michael D.

    2012-01-01

    Neutral sugar radicals formed in DNA sugar-phosphate backbone are well-established as precursors of biologically important damage such as DNA-strand scission and crosslinking. In this work, we present electron spin resonance (ESR) evidence showing that the sugar radical at C5′ (C5′•) is one of the most abundant (ca. 30%) sugar radicals formed by γ- and Ar ion-beam irradiated hydrated DNA samples. Taking dimethyl phosphate as a model of sugar-phosphate backbone, ESR and theoretical (DFT) studies of γ-irradiated dimethyl phosphate were carried out. CH3OP(O2−)OCH2• is formed via deprotonation from the methyl group of directly ionized dimethyl phosphate at 77 K. Formation of CH3OP(O2−)OCH2• is independent of dimethyl phosphate concentration (neat or in aqueous solution) or pH. ESR spectra of C5′• found in DNA and of CH3OP(O2−)OCH2• do not show an observable β-phosphorous hyperfine coupling (HFC). Further, C5′• found in DNA does not show a significant C4′-H β–proton HFC. Applying the DFT/B3LYP/6-31G(d) method, a study of conformational dependence of the phosphorous HFC in CH3OP(O2−)OCH2• shows that in its minimum energy conformation, CH3OP(O2−)OCH2• has a negligible β-phosphorous HFC. Based on these results, formation of radiation-induced C5′• is proposed to occur via a very rapid deprotonation from the directly ionized sugar-phosphate backbone and rate of this deprotonation must be faster than that of energetically downhill transfer of the unpaired spin (hole) from ionized sugar-phosphate backbone to the DNA bases. Moreover, C5′• in irradiated DNA is found to be in a conformation that does not exhibit β proton or β phosphorous HFCs. PMID:22553971

  11. Effects of a vanadium post-metallocene catalyst-induced polymer backbone inhomogeneity on UV oxidative degradation of the resulting polyethylene film

    KAUST Repository

    Atiqullah, M.

    2012-07-01

    A Group 5 post-metallocene precatalyst, (ONO)VCl(THF) 2 (ONO = a bis(phenolate)pyridine LX 2 pincer ligand), activated with modified methylaluminoxane (MMAO-3A) produced a linear ethylene homopolymer (nm-HomoPE)and an unusual inhomogeneous copolymer (nm-CopolyPE) with 1-hexene having very low backbone unsaturation. The nm-CopolyPE inhomogeneity was reflected in the distributions of short chain branches, 1-hexene composition, and methylene sequence length. The 1-hexene incorporation into the polyethylene backbone strongly depended on the molecular weight of the growing polymer chain. (ONO)VCl(THF) 2, because of site diversity and easier removal of a tertiary (vs. a secondary) hydrogen, produced a skewed short chain branching (SCB) profile, incorporating 1-hexene more efficiently in the low molecular weight region than in the high molecular weight region. The significant decrease in molecular weight by 1-hexene showed that the (ONO)VCl(THF) 2 catalytic sites were also highly responsive to chain-transfer directly to 1-hexene itself, producing vinyl and trans-vinylene termini. Subsequently, the effect of backbone inhomogeneity on the UV oxidative degradation of films made from both polyethylenes was investigated. The major functional group accumulated in the branched nm-CopolyPE film was carbonyl followed by carboxyl, then vinyl/ester, whereas that in the linear nm-HomoPE film was carboxyl. However, (carbonyl, carboxyl, vinyl, and ester) nm-CopolyPE film >> (carboxyl) nm-HomoPE film). The distributions of the tertiary C-H sites and methylene sequence length in the branched nm-CopolyPE film enhanced abstraction of H, decomposition of hydroperoxide group ROOH, and generation of carbonyl compounds as compared with those in the linear nm-HomoPE film. This clearly establishes the role played by the backbone inhomogeneity. The effect of short chain branches and sequence length distributions on peak melting temperature T pm, and most probably lamellar thickness L o, was

  12. Residual dipolar couplings in short peptidic foldamers: combined analyses of backbone and side-chain conformations and evaluation of structure coordinates of rigid unnatural amino acids.

    Science.gov (United States)

    Schmid, Markus B; Fleischmann, Matthias; D'Elia, Valerio; Reiser, Oliver; Gronwald, Wolfram; Gschwind, Ruth M

    2009-02-13

    A flexible tool for rigid systems. Residual dipolar couplings (RDCs) have proven to be valuable NMR structural parameters that provide insights into the backbone conformations of short linear peptidic foldamers, as illustrated here. This study demonstrates that RDCs at natural abundance can provide essential structural information even in the case of short linear peptides with unnatural amino acids. In addition, they allow for the detection of proline side-chain conformations and are used as a quality check for the parameterizations of rigid unnatural amino acids.

  13. An Organ System Approach to Explore the Antioxidative, Anti-Inflammatory, and Cytoprotective Actions of Resveratrol

    OpenAIRE

    Ashim Malhotra; Sundeep Bath; Fawzy Elbarbry

    2015-01-01

    Resveratrol is a phenolic phytochemical, with a stilbene backbone, derived from edible plants such as grape and peanut. It is a bioactive molecule with physiological effects on multiple organ systems. Its effects range from the neuroprotective to the nephroprotective, including cardiovascular, neuronal, and antineoplastic responses as a part of its broad spectrum of action. In this review, we examine the effects of resveratrol on the following organ systems: the central nervous system, includ...

  14. Organization within Organization Studies

    DEFF Research Database (Denmark)

    Lopdrup-Hjorth, Thomas

    This paper explores how prevalent contemporary problematizations of organizations coincide with a widespread assessment that Organization Studies (OS) has run out of steam. This impasse, the paper argues, is largely due to the emergence of an organization-phobia that has come to seize several...... strands of theorizing. By attending to the wide-ranging and far-reaching history of this organization-phobia, the paper argues that OS has become increasingly incapable of speaking about its core object. I show how organizations went from being conceptualized as entities of major importance to becoming...... associated with all kinds of ills. Through this history, organizations as distinct entities have been rendered so problematic that they have gradually come to be removed from the center of OS. The costs of this have been rather significant. Besides undermining the grounds that gave OS intellectual...

  15. A luminescent metal-organic framework with an open cubic cage and eight-coordinate cadmium nodes

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Self-assembly of cadmium ions and the rigid bridging ligand 4,4′-methylenebis(3-hydroxy-2-naphthoic acid) (pamoic acid, H4PA) leads to a one-dimensional metal-organic framework with open cube-like M2(H2PA)2 cages within its backbone, and exhibiting interesting yellow fluorescence.

  16. Knowledge Organization = Information Organization?

    DEFF Research Database (Denmark)

    Hjørland, Birger

    Are the terms ―information organization‖ (IO), ―organization of information‖ (OI) and ―information architecture‖ (IA) synonyms for knowledge organization (KO)? This study uses bibliometric methods, among others, to determine some relations between these terms and their meanings. Apparently the data...

  17. 繁忙铁路干线区段TDCS升级方案%TDCS Upgrading Scheme of Heavy Traffic Backbone Railway Line

    Institute of Scientific and Technical Information of China (English)

    苗义烽; 王涛; 赵随海; 严频

    2011-01-01

    已开通TDCS的繁忙铁路干线区段,由于车流密度大、沿线各站客货作业繁忙、调度区段管辖里程长等特点,行车指挥工作对TDCS系统的依赖度很高,由TDCS系统升级到CTC系统,必须要保障运输生产秩序不受影响,做到平稳、无缝的过渡。以北京局管内京九线为例探讨了TDCS升级为CTC系统的解决方案。%As for open backbone railway lines,the train dispatching and command operation relies deeply on TDCS because of the characteristics of railway backbone lines,namely great train density,busy passenger transportation and freight operations,and long-distance of dispatching section.Upgrading from the TDCS to a CTC system,it was guaranteed that the order of transportation production should not be affected and steady and seamless transition should be steady and no-breaking.In the case of Beijing-Kowloon line,this article explored the upgrading solution from TDCS to CTC system.

  18. Significant Role of DNA Backbone in Mediating the Transition Origin of Electronic Excitations of B-DNA - Implication from Long Range Corrected TDDFT and Quantified NTO Analysis

    CERN Document Server

    Li, Jian-Hao; Guo, Guang-Yu; Hayashi, Michitoshi

    2011-01-01

    We systematically investigate the possible complex transition origin of electronic excitations of giant molecular systems by using the recently proposed QNTO analysis [J.-H. Li, J.-D. Chai, G. Y. Guo and M. Hayashi, Chem. Phys. Lett., 2011, 514, 362.] combined with long-range corrected TDDFT calculations. Thymine (Thy) related excitations of biomolecule B-DNA are then studied as examples, where the model systems have been constructed extracting from the perfect or a X-ray crystal (PDB code 3BSE) B-DNA structure with at least one Thy included. In the first part, we consider the systems composed of a core molecular segment (e.g. Thy, di-Thy) and a surrounding physical/chemical environment of interest (e.g. backbone, adjacent stacking nucleobases) and examine how the excitation properties of the core vary in response to the environment. We find that the orbitals contributed from DNA backbone and surrounding nucleobases often participate in a transition of Thy-related excitations affecting their composition, abso...

  19. Molecular Data for a Biochemical Model of DNA Radiation Damage: Electron Impact Ionization and Dissociative Ionization of DNA Bases and Sugar-Phosphate Backbone

    Science.gov (United States)

    Dateo, Christopher E.; Fletcher, Graham D.

    2004-01-01

    As part of the database for building up a biochemical model of DNA radiation damage, electron impact ionization cross sections of sugar-phosphate backbone and DNA bases have been calculated using the improved binary-encounter dipole (iBED) model. It is found that the total ionization cross sections of C3'- and C5'-deoxyribose-phospate, two conformers of the sugar-phosphate backbone, are close to each other. Furthermore, the sum of the ionization cross sections of the separate deoxyribose and phosphate fragments is in close agreement with the C3'- and C5'-deoxyribose-phospate cross sections, differing by less than 10%. Of the four DNA bases, the ionization cross section of guanine is the largest, then in decreasing order, adenine, thymine, and cytosine. The order is in accordance with the known propensity of oxidation of the bases by ionizing radiation. Dissociative ionization (DI), a process that both ionizes and dissociates a molecule, is investigated for cytosine. The DI cross section for the formation of H and (cytosine-Hl)(+), with the cytosine ion losing H at the 1 position, is also reported. The threshold of this process is calculated to be 17.1 eV. Detailed analysis of ionization products such as in DI is important to trace the sequential steps in the biochemical process of DNA damage.

  20. Differential Gelation and Self-Sorting Properties of Two Isomeric Polyamides Due to the Parallel vs Anti-Parallel Alignment of Backbone Dipoles.

    Science.gov (United States)

    Leung, Chui-Fan; Chow, Hak-Fun

    2017-02-14

    Two isomeric bottlebrush polyamides P-1 and A-1 having the same repeating monomer dipole units aligned along the polymer backbone in pseudo-parallel and pseudo-anti-parallel, respectively, were synthesized and characterized. Both polymers can form thermoreversible gels with aromatic solvents but P-1 was found to show inferior gelation strength as compared to that of A-1. Furthermore, despite their close structural resemblance, a 1:1 mixture of the P-1 and A-1 polymers was shown to exhibit self-sorting in the gel state. Gel formation was found to be a kinetically trapped process via H-bonding, π-π stacking interactions and side chain interdigitation. The differential gelation and self-sorting properties can be explained by the local dipole-dipole interactions originated from the different modes of backbone dipole alignment. In single gel systems, the antiparallel-aligned dipoles in A-1 facilitated a more compact molecular packing due to the enthalpically more favorable polymer chain association. On the other hand, the parallel-aligned dipoles in P-1 gave rise to a less stable head-to-head packing, which had difficulties to convert to the more stable head-to-tail packing in a kinetically trapped environment. In the mixed gel system, it is the unfavorable hetero-polymer mismatch dipole-dipole interaction that inhibited the mixing of the A-1 and P-1 polymers and led to self-sorting.

  1. A facile route to backbone-tethered N-heterocyclic carbene (NHC) ligands via NHC to aNHC rearrangement in NHC silicon halide adducts.

    Science.gov (United States)

    Schneider, Heidi; Schmidt, David; Radius, Udo

    2015-02-09

    The reaction of 1,3-diisopropylimidazolin-2-ylidene (iPr2 Im) with diphenyldichlorosilane (Ph2 SiCl2 ) leads to the adduct (iPr2 Im)SiCl2 Ph2 1. Prolonged heating of isolated 1 at 66 °C in THF affords the backbone-tethered bis(imidazolium) salt [((a) HiPr2 Im)2 SiPh2 ](2+)  2 Cl(-) 2 ("(a) " denotes "abnormal" coordination of the NHC), which can be synthesized in high yields in one step starting from two equivalents of iPr2 Im and Ph2 SiCl2 . Imidazolium salt 2 can be deprotonated in THF at room temperature using sodium hydride as a base and catalytic amounts of sodium tert-butoxide to give the stable N-heterocyclic dicarbene ((a) iPr2 Im)2 SiPh2 3, in which two NHCs are backbone-tethered with a SiPh2 group. This easy-to-synthesize dicarbene 3 can be used as a novel ligand type in transition metal chemistry for the preparation of dinuclear NHC complexes, as exemplified by the synthesis of the homodinuclear copper(I) complex [{(a) (ClCuiPr2 Im)}2 SiPh2 ] 4.

  2. Rational design of a cytotoxic dinuclear Cu2 complex that binds by molecular recognition at two neighboring phosphates of the DNA backbone.

    Science.gov (United States)

    Jany, Thomas; Moreth, Alexander; Gruschka, Claudia; Sischka, Andy; Spiering, Andre; Dieding, Mareike; Wang, Ying; Samo, Susan Haji; Stammler, Anja; Bögge, Hartmut; Fischer von Mollard, Gabriele; Anselmetti, Dario; Glaser, Thorsten

    2015-03-16

    The mechanism of the cytotoxic function of cisplatin and related anticancer drugs is based on their binding to the nucleobases of DNA. The development of new classes of anticancer drugs requires establishing other binding modes. Therefore, we performed a rational design for complexes that target two neighboring phosphates of the DNA backbone by molecular recognition resulting in a family of dinuclear complexes based on 2,7-disubstituted 1,8-naphthalenediol. This rigid backbone preorganizes the two metal ions for molecular recognition at the distance of two neighboring phosphates in DNA of 6-7 Å. Additionally, bulky chelating pendant arms in the 2,7-position impede nucleobase complexation by steric hindrance. We successfully synthesized the Cu(II)2 complex of the designed family of dinuclear complexes and studied its binding to dsDNA by independent ensemble and single-molecule methods like gel electrophoresis, precipitation, and titration experiments followed by UV-vis spectroscopy, atomic force microscopy (AFM), as well as optical tweezers (OT) and magnetic tweezers (MT) DNA stretching. The observed irreversible binding of our dinuclear Cu(II)2 complex to dsDNA leads to a blocking of DNA synthesis as studied by polymerase chain reactions and cytotoxicity for human cancer cells.

  3. Organ Donation

    Science.gov (United States)

    Organ donation takes healthy organs and tissues from one person for transplantation into another. Experts say that the organs ... and bone marrow Cornea Most organ and tissue donations occur after the donor has died. But some ...

  4. Synthesis and characterization of a novel carboxyl group containing (co)polyimide with sulfur in the polymer backbone.

    Science.gov (United States)

    Mrsevic, Miroslav; Düsselberg, David; Staudt, Claudia

    2012-01-01

    Soluble functional (co)polyimides are of great interest in the area of separation processes or optical applications, due to their excellent mechanical-, thermal- and optical properties, their superior processability and the ability to adapt their properties to a wide range of special applications. Therefore, two series of novel (co)polyimides containing fluorinated sulfur- and carboxylic acid groups consisting of 4,4'-(hexafluoroisopropylidene)di(phthalic anhydride) (6FDA), 3,5-diaminobenzoic acid (DABA), 4,4'-diaminodiphenylsulfide (4,4'-SDA) and 3,3'-diaminodiphenylsulfone (3,3'-DDS) were synthesized in a two-step polycondensation reaction. The synthesized copolymers were characterized by using NMR, FTIR, GPC, and DSC. Furthermore, with regard to processing and potential applications, the thermal stability, solubility in common organic solvents, moisture uptake, and transparency were investigated. Compared to commercially available transparent polymers, i.e., polymethylmethacrylate and cycloolefin polymers, the sulfur (co)polyimides containing carboxyl groups showed much higher glass-transition temperatures, comparably low moisture uptake and high transmission at the sodium D-line. Furthermore, good solubility in commonly used organic solvents makes them very attractive as high-performance coating materials.

  5. 项目化管理在国家骨干校建设中的运用%Application of Projectized Management in Building the National Backbone School

    Institute of Scientific and Technical Information of China (English)

    孙怀忠

    2011-01-01

    项目化管理是从项目管理的逐步深入中发展起来的.在当前国家骨干校的建设中运用项目化管理能够确保建设目标的如期实现,有利于提高工作效率、降低管理成本,能够充分调动项目团队成员的工作积极性、充分释放人的能量.%Projectized management is developed from project management gradually. To use projectized management in the construction of national backbone school can ensure the achievement of construction objectives on schedule, is helpful to improve efficiency and reduce management costs, and can fully mobilize the enthusiasm of the project team members for work and release the person's energy.

  6. Adding liraglutide to the backbone therapy of biguanide in patients with coronary artery disease and newly diagnosed type-2 diabetes (the AddHope2 study)

    DEFF Research Database (Denmark)

    Anholm, Christian; Kumarathurai, Preman; Klit, Malene S;

    2014-01-01

    INTRODUCTION: Newly diagnosed type 2 diabetes mellitus (T2DM) in patients with coronary artery disease (CAD) more than doubles the risk of death compared with otherwise matched glucose tolerant patients. The biguanide metformin is the drug of choice in treatment of T2DM and has shown to ameliorate......), liraglutide, is currently used for treatment of T2DM but its potential effect on cardiac function has not been investigated in detail. We hypothesised that liraglutide added to metformin backbone therapy in patients with CAD and newly diagnosed T2DM will improve β-cell function and left ventricular systolic...... function during dobutamine stress. METHODS AND ANALYSES: 40 patients with CAD and newly diagnosed T2DM will receive the intervention liraglutide+metformin and placebo+metformin in this investigator-initiated, double blind, randomised, placebo-controlled, cross-over 12 plus 12 weeks intervention study...

  7. NMR solution structure and backbone dynamics of domain III of the E protein of tick-borne Langat flavivirus suggests a potential site for molecular recognition.

    Science.gov (United States)

    Mukherjee, Munia; Dutta, Kaushik; White, Mark A; Cowburn, David; Fox, Robert O

    2006-06-01

    Flaviviruses cause many human diseases, including dengue fever, yellow fever, West Nile viral encephalitis, and hemorrhagic fevers, and are transmitted to their vertebrate hosts by infected mosquitoes and ticks. Domain III of the envelope protein (E-D3) is considered to be the primary viral determinant involved in the virus-host-cell receptor interaction, and thus represents an excellent target for antiviral drug development. Langat (LGT) virus is a naturally attenuated BSL-2 TBE virus and is a model for the pathogenic BSL-3 and BSL-4 viruses in the serogroup. We have determined the solution structure of LGT-E-D3 using heteronuclear NMR spectroscopy. The backbone dynamics of LGT-E-D3 have been investigated using 15N relaxation measurements. A detailed analysis of the solution structure and dynamics of LGT-E-D3 suggests potential residues that could form a surface for molecular recognition, and thereby represent a target site for antiviral therapeutics design.

  8. Impact of neoadjuvant single or dual HER2 inhibition and chemotherapy backbone upon pathological complete response in operable and locally advanced breast cancer: Sensitivity analysis of randomized trials.

    Science.gov (United States)

    Bria, Emilio; Carbognin, Luisa; Furlanetto, Jenny; Pilotto, Sara; Bonomi, Maria; Guarneri, Valentina; Vicentini, Cecilia; Brunelli, Matteo; Nortilli, Rolando; Pellini, Francesca; Sperduti, Isabella; Giannarelli, Diana; Pollini, Giovanni Paolo; Conte, Pierfranco; Tortora, Giampaolo

    2014-08-01

    The role of the dual HER2 inhibition, and the best chemotherapy backbone for neoadjuvant chemotherapy still represent an issue for clinical practice. A literature-based meta-analysis exploring single versus dual HER2 inhibition in terms of pathological complete response (pCR, breast plus axilla) rate and testing the interaction according to the chemotherapy (anthracyclines-taxanes or taxanes) was conducted. In addition, an event-based pooled analysis by extracting activity and safety events and deriving 95% confidence intervals (CI) was accomplished. Fourteen trials (4149 patients) were identified, with 6 trials (1820 patients) included in the meta-analysis and 31 arms (14 trials, 3580 patients) in the event-based pooled analysis. The dual HER2 inhibition significantly improves pCR rate, in the range of 16-19%, regardless of the chemotherapy backbone (relative risk 1.37, 95% CI 1.23-1.53, p<0.0001); pCR was significantly higher in the hormonal receptor negative population, regardless of the HER2 inhibition and type of chemotherapy. pCR and the rate of breast conserving surgery was higher when anthracyclines were added to taxanes, regardless of the HER2 inhibition. Severe neutropenia was higher with the addition of anthracyclines to taxanes, with an absolute difference of 19.7%, despite no differences in febrile neutropenia. While no significant differences according to the HER2 inhibition were found in terms of cardiotoxicity, a slightly difference for grade 3-4 (1.2%) against the addition of anthracyclines was calculated. The dual HER2 inhibition for the neoadjuvant treatment of HER2-positive breast cancer significantly increases pCR; the combination of anthracyclines, taxanes and anti-Her2 agents should be currently considered the standard of care.

  9. Trappist: european project dedicated to an open backbone structure for NDT expertise; Trappist: un projet europeen pour realiser une structure de gestion des donnees de CND

    Energy Technology Data Exchange (ETDEWEB)

    Nouailhas, B.; Vailhen, O.

    1993-12-31

    Non Destructive Testing (NDT) on critical components such as the reactor vessel, primary coolant pipes and steam generators have already been, and are still the subject of many development concerning the improvement of measuring techniques, data processing and on site operation. The tools developed for these tests are generally closed, difficult to extend and of proprietary type. Productivity could be increased if an open backbone structure common to several types of test were available. Moreover, these components are generally submitted to a test involving a single method. In certain cases, the produced information is an insufficient basis for drawing up a satisfactory diagnosis: the test operator or expert often faces problems in extracting more information from signals that are generally noisy. It may prove necessary to complete the inspection with another NDT method based on different principles in order to obtain better performances. It is then by combining the information obtained by two complementary methods that it will be possible to draw up a more reliable diagnosis. These components have also a complex shape. In the case of ultrasonic testing, the accurate following of probe paths requires 3D representation of the geometry, as it is built, to position and display the data obtained from the inspection. To take these geometric constraints into account, it is imperative to use computer tools allowing the three-dimensional representation of the reconstructed information on the components` actual geometry. This specific difficulty, which has long been appreciated, is the subject of developments resulting to industrial products that are more or less satisfactory. The aim of the European Project TRAPPIST (Race Program) is to study an open backbone structure. A mock-up of an analysis station dedicated to NDT expertise will be built and evaluated with specific examples. (authors). 6 figs., 1 ref.

  10. Backbone dynamics of a bacterially expressed peptide from the receptor binding domain of Pseudomonas aeruginosa pilin strain PAK from heteronuclear 1H-15N NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Campbell, A. Patricia [University of Washington, Department of Medicinal Chemistry, School of Pharmacy (United States); Spyracopoulos, Leo [Department of Biochemistry (Canada); Irvin, Randall T. [University of Alberta, Department of Medical Microbiology and Immunology (Canada); Sykes, Brian D. [Department of Biochemistry (Canada)

    2000-07-15

    The backbone dynamics of a {sup 15}N-labeled recombinant PAK pilin peptide spanning residues 128-144 in the C-terminal receptor binding domain of Pseudomonas aeruginosa pilin protein strain PAK (Lys{sup 128}-Cys-Thr-Ser-Asp-Gln-Asp-Glu-Gln-Phe-Ile-Pro-Lys-Gly-Cys-Ser-Lys{sup 144}) were probed by measurements of {sup 15}N NMR relaxation. This PAK(128-144) sequence is a target for the design of a synthetic peptide vaccine effective against multiple strains of P. aeruginosa infection. The {sup 15}N longitudinal (T{sub 1}) and transverse (T{sub 2}) relaxation rates and the steady-state heteronuclear {l_brace}{sup 1}H{r_brace}-{sup 15}N NOE were measured at three fields (7.04, 11.74 and 14.1 Tesla), five temperatures (5, 10, 15, 20, and 25 deg. C ) and at pH 4.5 and 7.2. Relaxation data was analyzed using both the 'model-free' formalism [Lipari, G. and Szabo, A. (1982) J. Am. Chem. Soc., 104, 4546-4559 and 4559-4570] and the reduced spectral density mapping approach [Farrow, N.A., Szabo, A., Torchia, D.A. and Kay, L.E. (1995) J. Biomol. NMR, 6, 153-162]. The relaxation data, spectral densities and order parameters suggest that the type I and type II {beta}-turns spanning residues Asp{sup 134}-Glu-Gln-Phe{sup 137} and Pro{sup 139}-Lys-Gly-Cys{sup 142}, respectively, are the most ordered and structured regions of the peptide. The biological implications of these results will be discussed in relation to the role that backbone motions play in PAK pilin peptide immunogenicity, and within the framework of developing a pilin peptide vaccine capable of conferring broad immunity across P. aeruginosa strains.

  11. Determination of Equine Cytochrome c Backbone Amide Hydrogen/Deuterium Exchange Rates by Mass Spectrometry Using a Wider Time Window and Isotope Envelope

    Science.gov (United States)

    Hamuro, Yoshitomo

    2017-03-01

    A new strategy to analyze amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) data is proposed, utilizing a wider time window and isotope envelope analysis of each peptide. While most current scientific reports present HDX-MS data as a set of time-dependent deuteration levels of peptides, the ideal HDX-MS data presentation is a complete set of backbone amide hydrogen exchange rates. The ideal data set can provide single amide resolution, coverage of all exchange events, and the open/close ratio of each amide hydrogen in EX2 mechanism. Toward this goal, a typical HDX-MS protocol was modified in two aspects: measurement of a wider time window in HDX-MS experiments and deconvolution of isotope envelope of each peptide. Measurement of a wider time window enabled the observation of deuterium incorporation of most backbone amide hydrogens. Analysis of the isotope envelope instead of centroid value provides the deuterium distribution instead of the sum of deuteration levels in each peptide. A one-step, global-fitting algorithm optimized exchange rate and deuterium retention during the analysis of each amide hydrogen by fitting the deuterated isotope envelopes at all time points of all peptides in a region. Application of this strategy to cytochrome c yielded 97 out of 100 amide hydrogen exchange rates. A set of exchange rates determined by this approach is more appropriate for a patent or regulatory filing of a biopharmaceutical than a set of peptide deuteration levels obtained by a typical protocol. A wider time window of this method also eliminates false negatives in protein-ligand binding site identification.

  12. Molecular data for a biochemical model of DNA damage: Electron impact ionization and dissociative ionization cross sections of DNA bases and sugar-phosphate backbone

    Energy Technology Data Exchange (ETDEWEB)

    Huo, Winifred M. [NASA Ames Research Center, Mail Stop T27B-1, Moffett Field, CA 94035-1000 (United States)]. E-mail: whuo@mail.arc.nasa.gov; Dateo, Christopher E. [ELORET Corporation, Sunnyvale, CA (United States); Fletcher, Graham D. [ELORET Corporation, Sunnyvale, CA (United States)

    2006-10-15

    As part of the database for building up a biochemical model of DNA radiation damage, electron impact ionization cross sections of sugar-phosphate backbone and DNA bases have been calculated using the improved binary-encounter dipole (iBED) model. It is found that the total ionization cross sections of C{sub 3}{sup '}- and C{sub 5}{sup '}-deoxyribose-phosphate, two conformers of the sugar-phosphate backbone, are close to each other. Furthermore, the sum of the ionization cross sections of the separate deoxyribose and phosphate fragments is in close agreement with the C{sub 3}{sup '}- and C{sub 5}{sup '}-deoxyribose-phosphate cross sections, differing by less than 10%, an indication that a building-up principle may be applicable. Of the four DNA bases, the ionization cross section of guanine is the largest, then in decreasing order, adenine, thymine, and cytosine. The order is in accordance with the known propensity of oxidation of the bases by ionizing radiation. Dissociative ionization (DI), a process that both ionizes and dissociates a molecule, is investigated for cytosine. The DI cross section for the formation of H and (cytosine-H1){sup +}, with the cytosine ion losing H at the 1 position, is also reported. The threshold of this process is calculated to be 16.9eV. Detailed analysis of ionization products such as in DI is important to trace the sequential steps in the biochemical process of DNA damage.

  13. Properties of polyimide liquid crystal alignment layer with different backbone structure%聚酰亚胺主链结构对液晶取向膜性能的影响

    Institute of Scientific and Technical Information of China (English)

    刘露露; 刘明; 龚世铭; 汪映寒

    2015-01-01

    A series polyimides (PIs)were prepared by one-step method.These PIs were comprised of a functional diamine N,N-bis (4-aminophenyl )-4-(dodecylo-xy-biphenyl )-4′-amino-phenylether (C1 2 -BAAPE),one of two commercially available diamines 2,2′-Bis(trifluoromethy-l)-4,4′-diaminobiphe-nyl (TFDB),4,4′-Oxydianiline (ODA)and one of two dianhydride 4,4′-(hexafluoroisopropylidene) diphthalic anhydride (6FDA)and 4,4′-Oxydiphthalic anhydride (ODPA)in order to get different backbone structures.The structures and thermo properties of these PIs were characterized by NMR, FT-IR,DSC and TGA.Pretilt angles and alignment abilities were carried out by pretilt angle tester and polarization microscope.Solubility of PIs was tested by dissolving PIs in various organic solvents. DSC and TGA curves showed that PI-2 had higher glass transition temperature (T g )and decomposi-tion temperature (T d )than PI-1 and PI-3.Three PI films presented vertical alignment before mechan-ical rubbing and only PI-2 maintained it after rubbing process.Conformations of these PIs were simu-lated by Material Studio (MS).The vertical conformation existed in PI-2 ’s backbones improved rubbing resistance and showed vertical alignment ability after rubbing.%采用一步法,以 N,N-二(4-氨基苯基)-4-(十二烷氧基联苯基)-4’-氨基苯醚(C12-BAAPE)为控制预倾角的功能性二胺,2,2’-双三氟甲基-4,4’-联苯二胺(TFDB)或4,4’-二氨基二苯醚(ODA)为辅助二胺,分别与2,2’-双(3,4-二羧苯基)六氟丙烷四羧酸二酐(6FDA)和4,4’-联苯醚二酐(ODPA)聚合,得到三种主链结构不同的聚酰亚胺(PI-1、PI-2和PI-3)。利用 NMR、FT-IR、DSC、TGA、偏光显微镜和预倾角测试仪对聚合物的结构、热性能以及制备的液晶盒的取向性进行了表征,同时测试了3种 PI 的溶解性能。结果表明,PI-2液晶取向膜的耐摩擦性能明显优于 PI-1和 PI-3,且具有更高的玻璃化转变温度(T g )和分解温度(T d ),更好

  14. 1H, 13C, and 15N backbone and side chain resonance assignments of thermophilic Geobacillus kaustophilus cyclophilin-A

    Energy Technology Data Exchange (ETDEWEB)

    Holliday, Michael; Zhang, Fengli; Isern, Nancy G.; Armstrong, Geoffrey S.; Eisenmesser, Elan Z.

    2014-04-01

    Cyclophilins catalyze the reversible peptidyl-prolyl isomerization of their substrates and are present across all kingdoms of life from humans to bacteria. Although numerous biological roles have now been discovered for cyclophilins, their function was initially ascribed to their chaperone-like activity in protein folding where they catalyze the often rate-limiting step of proline isomerization. This chaperone-like activity may be especially important under extreme conditions where cyclophilins are often over expressed, such as in tumors for human cyclophilins {Lee, 2010 #1167}, but also in organisms that thrive under extreme conditions, such as theromophilic bacteria. Moreover, the reversible nature of the peptidyl-prolyl isomerization reaction catalyzed by cyclophilins has allowed these enzymes to serve as model systems for probing the role of conformational changes during catalytic turnover {Eisenmesser, 2002 #20;Eisenmesser, 2005 #203}. Thus, we present here the resonance assignments of a thermophilic cyclophilin from Geobacillus kaustophilus derived from deep-sea sediment {Takami, 2004 #1384}. This thermophilic cyclophilin may now be studied at a variety of temperatures to provide insight into the comparative structure, dynamics, and catalytic mechanism of cyclophilins.

  15. 1H, 13C, and 15N backbone and side chain resonance assignments of thermophilic Geobacillus kaustophilus cyclophilin-A.

    Science.gov (United States)

    Holliday, Michael J; Zhang, Fengli; Isern, Nancy G; Armstrong, Geoffrey S; Eisenmesser, Elan Z

    2014-04-01

    Cyclophilins catalyze the reversible peptidyl-prolyl isomerization of their substrates and are present across all kingdoms of life from humans to bacteria. Although numerous biological roles have now been discovered for cyclophilins, their function was initially ascribed to their chaperone-like activity in protein folding where they catalyze the often rate-limiting step of proline isomerization. This chaperone-like activity may be especially important under extreme conditions where cyclophilins are often over expressed, such as in tumors for human cyclophilins (Lee Archiv Pharm Res 33(2): 181-187, 2010), but also in organisms that thrive under extreme conditions, such as theromophilic bacteria. Moreover, the reversible nature of the peptidyl-prolyl isomerization reaction catalyzed by cyclophilins has allowed these enzymes to serve as model systems for probing the role of conformational changes during catalytic turnover (Eisenmesser et al. Science 295(5559): 1520-1523, 2002; Eisenmesser et al. Nature 438(7064): 117-121, 2005). Thus, we present here the resonance assignments of a thermophilic cyclophilin from Geobacillus kaustophilus derived from deep-sea sediment (Takami et al. Extremophiles 8(5): 351-356, 2004). This thermophilic cyclophilin may now be studied at a variety of temperatures to provide insight into the comparative structure, dynamics, and catalytic mechanism of cyclophilins.

  16. Mechanical reliability of porous low-k dielectrics for advanced interconnect: Study of the instability mechanisms in porous low-k dielectrics and their mediation through inert plasma induced re-polymerization of the backbone structure

    Science.gov (United States)

    Sa, Yoonki

    catalysts for reactions that break the cross-linked backbone. Clearly, both changes in PLK chemistry and bond structure must be addressed in order for any repair method to be favorable. For this reason, Ar plasma treatment with low energy ions is employed to repair the plasma induced damage by creating the desired changes in the film matrix without a significant loss of other properties. Our approach of using inert plasma as a way for damage recovery is motivated by the realization that there is no possibility of chemical reaction with any organic species, driving the energy transfer only from the plasma species towards the respective film matrix. As results, after applying Ar plasma beam treatment followed by annealing on damaged PLK films, the resistance against thermal instability and viscoplastic deformation is found to be improved. Ball indentation depth of the films with Ar plasma process is drastically reduced at the identical condition. More noticeable is the fact that such alternation is converted towards a dehydration reaction under hydrostatic thermal pressure, which causes dielectric constant to decrease and films shrinkage to restore during reconstruction of polymer chains. It is suggested that the immediate event of an Ar plasma beam radiation is to deposit energy from the plasma species (ions, electrons) and this energy input produces the excited state species because Ar cannot chemically react with the film matrix. As a consequence, the radical sites are generated at the less stable area such as colony boundary or pore surface with the decay of the excited species, leading to the production of free radicals by an energy transfer to the bonds which are to be broken. Then, the activated sites experience chemical bond rearrangement by chain-scission, branching, or cross-linking. In our case, crosslink with C is involved with silylmethylene (Si-(CH 2)x-Si) groups and it is turned out that some of these groups are converted to methyl groups terminally bonded to

  17. BPTs: thiophene-flanked benzodipyrrolidone conjugated polymers for ambipolar organic transistors.

    Science.gov (United States)

    Rumer, Joseph W; Levick, Matthew; Dai, Sheng-Yao; Rossbauer, Stephan; Huang, Zhenggang; Biniek, Laure; Anthopoulos, Thomas D; Durrant, James R; Procter, David J; McCulloch, Iain

    2013-05-18

    A series of novel thiophene-flanked benzodipyrrolidone (BPT)-based alternating copolymers are synthesised, their optical and electrical properties evaluated. The BPT unit promotes a conjugated, planar polymer backbone, with a low bandgap, primarily due to low lying LUMO energy levels. Copolymerisation with thiophene exhibits well balanced ambipolar organic field-effect transistor performance, with electron and hole mobilities 0.1 and 0.2 cm(2) V(-1) s(-1), respectively.

  18. Energetic polymers and plasticizers based on organic azides, nitro groups and tetrazoles

    OpenAIRE

    Hartdegen, Vera

    2016-01-01

    The aim of this thesis was the development and investigation of new energetic polymers and plasticizers, on the basis of different polymer backbones or organic compounds with varying energetic or nitrogen-rich functional groups, along with the syntheses of suitable precursors for further (polymeric) processing. One of the main requirements of the newly developed compounds was their suitability as energetic binder or plasticizer, respectively, which includes high thermal and physical stabil...

  19. Ribosomal proteins L11 and L10.(L12)4 and the antibiotic thiostrepton interact with overlapping regions of the 23 S rRNA backbone in the ribosomal GTPase centre

    DEFF Research Database (Denmark)

    Rosendahl, G; Douthwaite, S

    1993-01-01

    The Escherichia coli ribosomal protein (r-protein) L11 and its binding site on 23 S ribosomal RNA (rRNA) are associated with ribosomal hydrolysis of guanosine 5'-triphosphate (GTP). We have used hydroxyl radical footprinting to map the contacts between L11 and the backbone riboses in 23 S rRNA, a...

  20. Comparative analysis of backbone curve models for loess soils%黄土骨干曲线模型比较分析

    Institute of Scientific and Technical Information of China (English)

    廖红建; 李涛; 马宗源; 刘健

    2009-01-01

    A series of dynamic triaxial tests were conducted on saturated remolded loess specimens under various loading conditions. A method of using hysteretic loops for each loading step to construct the backbone curve is developed. This method can utilize most of the testing information and reduce the randomicity of the tests compared with the traditional method of using only one hysteretic loop for each loading step. Hardin-Drnevich model, modified Hardin-Drnevich model and Martin-Darvidenkov model were then used to simulate the test results. Using this method, the accuracy and parameter sensibility of the above three backbone curve models were discussed respectively. Results show that Hardin-Drnevich Model can't always simulate test data accurately in different test conditions. Modified Hardin-Drnevich Model and Martin-Darvidenkov model are more effective to simulate test data and they can reflect the softening characteristics of the backbone curve. Considering that Martin-Darvidenkov model is more sensitive than modified Hardin-Drnevich model, modified Hardin-Drnevich model is suggested to be used in the dynamic simulation of loess under complex loads.%对饱和重塑黄土进行了一系列不同加载条件下的动三轴试验,研究了对每级荷载应用多个滞回圈构造骨干曲线的方法,该方法可以考虑更多的试验信息,减小试验随机性对模拟曲线的影响.并运用该方法对试验数据采用Hardin-Drnevich模型、修正Hardin-Drnevich模型和Martin-Darvidenkov模型3种不同的骨干曲线模型进行数值模拟,分析了不同的骨干曲线模型对试验数据模拟的准确性和参数敏感性.结果表明,在试验条件变化时Hardin-Drnevich模型并不能总是很好地模拟试验骨干曲线,而且在有些情况下偏离较多.修正Hardin-Drnevich模型和Martin-Darvidenkov模型相比于Hardin-Drnevich模型能更好地模拟试验数据.在对不规则动载下黄土动力反应的数值模拟中,可以考虑用

  1. 多约束条件下互联网骨干网路由器级拓扑生成方法%Router-level topology generation research for Internet backbone networks under multiple constraints

    Institute of Scientific and Technical Information of China (English)

    吴元立; 司光亚; 罗批

    2016-01-01

    互联网骨干网是网络流量的中枢传输系统,其路由器级拓扑结构对于网络抗毁性分析具有重要意义。由于难以获取互联网骨干网路由器级的真实拓扑,通过分析骨干网的形成因素,将地理位置、节点间联系强度、基础设施费用、鲁棒性等因素结合起来,提出一种多约束条件下的互联网骨干网路由器级拓扑生成方法。该方法既可以构造难以公开获取网络测量数据的骨干网,也可以用来生成某一骨干网的多种替身拓扑集。通过现实中的互联网骨干网作为实例,验证了方法的有效性。%The backbone network is the main part of the Internet traffic transfer system,and the router-level topology of backbone network is of great significance for the research on network survivability.Due to various reasons,it is difficult to get real Internet backbone router level topology.By analyzing the forming driving factors of backbone network,the geographical constraints,the exchanging strength of nodes, infrastructure cost and robustness,etc.were combined;the router-level topology generation method for Internet backbone networks under multiple constraints was proposed.The method can generate router level topology for network which cannot be inferred from publicly accessible measurement data,and can generate topology set that consists of realistic alternatives for a backbone network.Finally,the effectiveness of the method is verified by two real Internet backbone networks.

  2. Contribution of the mannan backbone of cryptococcal glucuronoxylomannan and a glycolytic enzyme of Staphylococcus aureus to contact-mediated killing of Cryptococcus neoformans.

    Science.gov (United States)

    Ikeda, Reiko; Saito, Fumito; Matsuo, Miki; Kurokawa, Kenji; Sekimizu, Kazuhisa; Yamaguchi, Masashi; Kawamoto, Susumu

    2007-07-01

    The fungal pathogen Cryptococcus neoformans is killed by the bacterium Staphylococcus aureus, and the killing is inhibited by soluble capsular polysaccharides. To investigate the mechanism of killing, cells in coculture were examined by scanning and transmission electron microscopy. S. aureus attached to the capsule of C. neoformans, and the ultrastructure of the attached C. neoformans cells was characteristic of dead cells. To identify the molecules that contributed to the fungal-bacterial interaction, we treated each with NaIO(4) or protease. Treatment of C. neoformans with NaIO(4) promoted adherence. It was inferred that cleavage of xylose and glucuronic acid side chains of glucuronoxylomannan (GXM) allowed S. aureus to recognize mannose residues in the backbone, which resisted periodate oxidation. On the other hand, treatment of S. aureus with protease decreased adherence, suggesting that protein contributed to attachment in S. aureus. In confirmation, side chain-cleaved polysaccharide or defined alpha-(1-->3)-mannan inhibited the killing at lower concentrations than native GXM did. Also, these polysaccharides reduced the adherence of the two species and induced clumping of pure S. aureus cells. alpha-(1-->3)-Mannooligosaccharides with a degree of polymerization (DP) of >/=3 induced cluster formation of S. aureus in a dose-dependent manner. Surface plasmon resonance analyses showed interaction of GXM and surface protein from S. aureus; the interaction was inhibited by oligosaccharides with a DP of > or =3. Conformations of alpha-(1-->3) oligosaccharides were predicted. The three-dimensional structures of mannooligosaccharides larger than triose appeared curved and could be imagined to be recognized by a hypothetical staphylococcal lectin. Native polyacrylamide gel electrophoresis of staphylococcal protein followed by electroblotting, enzyme-linked immunolectin assay, protein staining, and N-terminal amino acid sequencing suggested that the candidate protein was

  3. Comparison of the backbone dynamics of wild-type Hydrogenobacter thermophilus cytochrome c{sub 552} and its b-type variant

    Energy Technology Data Exchange (ETDEWEB)

    Tozawa, Kaeko; Ferguson, Stuart J.; Redfield, Christina, E-mail: christina.redfield@bioch.ox.ac.uk [University of Oxford, Department of Biochemistry (United Kingdom); Smith, Lorna J., E-mail: lorna.smith@chem.ox.ac.uk [University of Oxford, Department of Chemistry (United Kingdom)

    2015-06-15

    Cytochrome c{sub 552} from the thermophilic bacterium Hydrogenobacter thermophilus is a typical c-type cytochrome which binds heme covalently via two thioether bonds between the two heme vinyl groups and two cysteine thiol groups in a CXXCH sequence motif. This protein was converted to a b-type cytochrome by substitution of the two cysteine residues by alanines (Tomlinson and Ferguson in Proc Natl Acad Sci USA 97:5156–5160, 2000a). To probe the significance of the covalent attachment of the heme in the c-type protein, {sup 15}N relaxation and hydrogen exchange studies have been performed for the wild-type and b-type proteins. The two variants share very similar backbone dynamic properties, both proteins showing high {sup 15}N order parameters in the four main helices, with reduced values in an exposed loop region (residues 18–21), and at the C-terminal residue Lys80. Some subtle changes in chemical shift and hydrogen exchange protection are seen between the wild-type and b-type variant proteins, not only for residues at and neighbouring the mutation sites, but also for some residues in the heme binding pocket. Overall, the results suggest that the main role of the covalent linkages between the heme group and the protein chain must be to increase the stability of the protein.

  4. Robustness and backbone motif of a cancer network regulated by miR-17-92 cluster during the G1/S transition.

    Directory of Open Access Journals (Sweden)

    Lijian Yang

    Full Text Available Based on interactions among transcription factors, oncogenes, tumor suppressors and microRNAs, a Boolean model of cancer network regulated by miR-17-92 cluster is constructed, and the network is associated with the control of G1/S transition in the mammalian cell cycle. The robustness properties of this regulatory network are investigated by virtue of the Boolean network theory. It is found that, during G1/S transition in the cell cycle process, the regulatory networks are robustly constructed, and the robustness property is largely preserved with respect to small perturbations to the network. By using the unique process-based approach, the structure of this network is analyzed. It is shown that the network can be decomposed into a backbone motif which provides the main biological functions, and a remaining motif which makes the regulatory system more stable. The critical role of miR-17-92 in suppressing the G1/S cell cycle checkpoint and increasing the uncontrolled proliferation of the cancer cells by targeting a genetic network of interacting proteins is displayed with our model.

  5. Negative-ion Electrospray Tandem Mass Spectrometry and Microarray Analyses of Developmentally-regulated Antigens Based on Type 1 and Type 2 Backbone Sequences

    Science.gov (United States)

    Gao, Chao; Zhang, Yibing; Liu, Yan; Feizi, Ten; Chai, Wengang

    2016-01-01

    Type 1 (Galβ1-3GlcNAc) and type 2 (Galβ1-4GlcNAc) sequences are constituents of the backbones of a large family of glycans of glycoproteins and glycolipids whose branching and peripheral substitutions are developmentally-regulated. It is highly desirable to have micro-sequencing methods that can be used to precisely identify and monitor these oligosaccharide sequences with high sensitivity. Negative-ion electrospray tandem mass spectrometry with collision-induced dissociation has been used for characterization of branching points, peripheral substitutions and partial assignment of linkages in reducing oligosaccharides. We now extend this method to characterizing entire sequences of linear type 1 and type 2 chain-based glycans, focusing on the type 1 and -2 units in the internal regions including the linkages connecting type 1 and type 2 disaccharide units. We apply the principles to sequence analysis of closely related isomeric oligosaccharides and demonstrate by microarray analyses distinct binding activities of antibodies and a lectin toward various combinations of type 1 and 2 units joined by 1,3- and 1,6-linkages. These sequence-specific carbohydrate-binding proteins are in turn valuable tools for detecting and distinguishing the type 1 and type 2-based developmentally-regulated glycan sequences. PMID:26530895

  6. Negative-Ion Electrospray Tandem Mass Spectrometry and Microarray Analyses of Developmentally Regulated Antigens Based on Type 1 and Type 2 Backbone Sequences.

    Science.gov (United States)

    Gao, Chao; Zhang, Yibing; Liu, Yan; Feizi, Ten; Chai, Wengang

    2015-12-01

    Type 1 (Galβ1-3GlcNAc) and type 2 (Galβ1-4GlcNAc) sequences are constituents of the backbones of a large family of glycans of glycoproteins and glycolipids whose branching and peripheral substitutions are developmentally regulated. It is highly desirable to have microsequencing methods that can be used to precisely identify and monitor these oligosaccharide sequences with high sensitivity. Negative-ion electrospray tandem mass spectrometry with collision-induced dissociation has been used for characterization of branching points, peripheral substitutions, and partial assignment of linkages in reducing oligosaccharides. We now extend this method to characterizing entire sequences of linear type 1 and type 2 chain-based glycans, focusing on the type 1 and type 2 units in the internal regions including the linkages connecting type 1 and type 2 disaccharide units. We apply the principles to sequence analysis of closely related isomeric oligosaccharides and demonstrate by microarray analyses distinct binding activities of antibodies and a lectin toward various combinations of type 1 and 2 units joined by 1,3- and 1,6-linkages. These sequence-specific carbohydrate-binding proteins are in turn valuable tools for detecting and distinguishing the type 1 and type 2-based developmentally regulated glycan sequences.

  7. (nBuCp)2ZrCl2-catalyzed Ethylene-4M1P Copolymerization: Copolymer Backbone Structure, Melt Behavior, and Crystallization

    KAUST Repository

    Atiqullah, Muhammad

    2016-01-08

    The judicious design of methylaluminoxane (MAO) anions expands the scope for developing industrial metallocene catalysts. Therefore, the effects of MAO anion design on the backbone structure, melt behavior, and crystallization of ethylene−4-methyl-1-pentene (E−4M1P) copolymer were investigated. Ethylene was homopolymerized, as well as copolymerized with 4M1P, using (i) MAO anion A (unsupported [MAOCl2]−) premixed with dehydroxylated silica, (nBuCp)2ZrCl2, and Me2SiCl2; and (ii) MAO anion B (Si−O−Me2Si−[MAOCl2]−) supported with (nBuCp)2ZrCl2 on Me2SiCl2-functionalized silica. Unsupported Me2SiCl2, opposite to the supported analogue, acted as a co-chain transfer agent with 4M1P. The modeling of polyethylene melting and crystallization kinetics, including critical crystallite stability, produced insightful results. This study especially illustrates how branched polyethylene can be prepared from ethylene alone using particularly one metallocene-MAO ion pair, and how a compound, that functionalizes silica as well as terminates the chain, can synthesize ethylene−α-olefin copolymers with novel structures. Hence, it unfolds prospective future research niches in polyethyne systhesis. This article is protected by copyright. All rights reserved.

  8. A novel dengue virus serotype 1 vaccine candidate based on Japanese encephalitis virus vaccine strain SA14-14-2 as the backbone.

    Science.gov (United States)

    Yang, Huiqiang; Li, Zhushi; Lin, Hua; Wang, Wei; Yang, Jian; Liu, Lina; Zeng, Xianwu; Wu, Yonglin; Yu, Yongxin; Li, Yuhua

    2016-06-01

    To develop a potential dengue vaccine candidate, a full-length cDNA clone of a novel chimeric virus was constructed using recombinant DNA technology, with Japanese encephalitis virus (JEV) vaccine strain SA14-14-2 as the backbone, with its premembrane (prM) and envelope (E) genes substituted by their counterparts from dengue virus type 1 (DENV1). The chimeric virus (JEV/DENV1) was successfully recovered from primary hamster kidney (PHK) cells by transfection with the in vitro transcription products of JEV/DENV1 cDNA and was identified by complete genome sequencing and immunofluorescent staining. No neuroinvasiveness of this chimeric virus was observed in mice inoculated by the subcutaneous route (s.c.) or by the intraperitoneal route (i.p.), while some neurovirulence was displayed in mice that were inoculated directly by the intracerebral route (i.c.). The chimeric virus was able to stimulate high-titer production of antibodies against DENV1 and provided protection against lethal challenge with neuroadapted dengue virus in mice. These results suggest that the chimeric virus is a promising dengue vaccine candidate.

  9. Backbone and side chain NMR assignments of Geobacillus stearothermophilus ZapA allow identification of residues that mediate the interaction of ZapA with FtsZ.

    Science.gov (United States)

    Nogueira, Maria Luiza C; Sforça, Mauricio Luis; Chin, Yanni K-Y; Mobli, Mehdi; Handler, Aaron; Gorbatyuk, Vitaliy Y; Robson, Scott A; King, Glenn F; Gueiros-Filho, Frederico J; Zeri, Ana Carolina de Mattos

    2015-10-01

    Bacterial division begins with the formation of a contractile protein ring at midcell, which constricts the bacterial envelope to generate two daughter cells. The central component of the division ring is FtsZ, a tubulin-like protein capable of self-assembling into filaments which further associate into a higher order structure known as the Z ring. Proteins that bind to FtsZ play a crucial role in the formation and regulation of the Z ring. One such protein is ZapA, a widely conserved 21 kDa homodimeric protein that associates with FtsZ filaments and promotes their bundling. Although ZapA was discovered more than a decade ago, the structural details of its interaction with FtsZ remain unknown. In this work, backbone and side chain NMR assignments for the Geobacillus stearothermophilus ZapA homodimer are described. We titrated FtsZ into (15)N(2)H-ZapA and mapped ZapA residues whose resonances are perturbed upon FtsZ binding. This information provides a structural understanding of the interaction between FtsZ and ZapA.

  10. Iron-chelating backbone coupled with monoamine oxidase inhibitory moiety as novel pluripotential therapeutic agents for Alzheimer's disease: a tribute to Moussa Youdim.

    Science.gov (United States)

    Weinreb, Orly; Mandel, Silvia; Bar-Am, Orit; Amit, Tamar

    2011-03-01

    It is for these authors a great privilege to dedicate this review article to Moussa Youdim, who is one of the most imperative pharmacologists and pioneer investigators in the search and development of novel therapeutics for neurodegenerative diseases. 40 years ago, Moussa Youdim has started studying brain iron, catecholamine receptor and monoamine oxidase (MAO)-A and -B functions. Although Moussa Youdim succeeded in exploring the novel anti-Parkinsonian, selective MAO-B inhibitor drug, rasagiline (Azilect, Teva Pharmaceutical Co.), he did not stop searching for superior therapeutic approaches for neurodegenerative disorders. To date, Moussa Youdim and his research group are designing and synthesizing pluripotential drug candidates possessing diverse pharmacological properties that can act on multiple targets and pathological features ascribed to Parkinson's disease, Alzheimer's disease (AD) and amyotrophic lateral sclerosis. One such example is the multimodal non-toxic, brain-permeable iron-chelating compound, M30 (5-[N-methyl-N-propargylaminomethyl]-8-hydroxyquinoline), which amalgamates the propargyl moiety of rasagiline with the backbone of the potent iron chelator, VK28. This review discusses the multiple effects of several leading compounds of this series, concerning their neuroprotective/neurorestorative molecular mechanisms in vivo and in vitro, with a special focus on the pathological features ascribed to AD, including antioxidant and iron chelating activities, regulation of amyloid precursor protein and amyloid β peptide expression processing, activation of pro-survival signaling pathways and regulation of cell cycle and neurite outgrowth.

  11. Intra-residue interactions in proteins: interplay between serine or cysteine side chains and backbone conformations, revealed by laser spectroscopy of isolated model peptides.

    Science.gov (United States)

    Alauddin, Mohammad; Biswal, Himansu S; Gloaguen, Eric; Mons, Michel

    2015-01-21

    Intra-residue interactions play an important role in proteins by influencing local folding of the backbone. Taking advantage of the capability of gas phase experiments to provide relevant information on the intrinsic H-bonding pattern of isolated peptide chains, the intra-residue interactions of serine and cysteine residues, i.e., OH/SH···OC(i) C6 and NH(i···)O/S C5 interactions in Ser/Cys residues, are probed by laser spectroscopy of isolated peptides. The strength of these local side chain-main chain interactions, elegantly documented from their IR spectral features for well-defined conformations of the main chain, demonstrates that a subtle competition exists between the two types of intra-residue bond: the C6 H-bond is the major interaction with Ser, in contrast to Cys where C5 interaction takes over. The restricted number of conformers observed in the gas phase experiment with Ser compared to Cys (where both extended and folded forms are observed) also suggests a significant mediation role of these intra-residue interactions on the competition between the several main chain folding patterns.

  12. 浅析高职院校学生骨干力量的培养%The cultivation of students' the backbone force in Higher Vocational Colleges

    Institute of Scientific and Technical Information of China (English)

    江涛

    2015-01-01

    在学生团体里,学生干部扮演着重要角色,他们是骨干,是教师与学生之间的沟通桥梁.作为高校的学生干部,他们的工作本质上就是关爱以及恰当的方式进行管理学生,如此才能游刃有余的展开工作.那么对其在管理工作上,以沉着,诚心以及认真的态度给予其帮助,使他们解决难题,如此便可以让学生干部的工作和高校的管理工作达到双赢.%In the student group, the student cadres play an important role, they are the backbone, is the bridge of communication between teachers and students. As a collegestudent cadres, the nature of their work is the care and proper way of management of students, so to do a job with skill and ease of work. So the work in the management, tocalm, sincere and serious attitude and giving help, so that they solve the problem, so it can make the work of student cadres and university management to achieve a win-win situation.

  13. INCLUSION COMPLEX FORMATION BETWEEN α-CYCLODEXTRIN AND BIODEGRADABLE COMBLIKE COPOLYMERS WITH POLY(α,β-MALIC ACID) BACKBONES AND mPEG SIDE CHAINS

    Institute of Scientific and Technical Information of China (English)

    Jing Zeng; Yuan Li; Jia-jing Li; Rui Wang; Bin He; Yu Nie; Xiang-lin Luo; Zhi-rong Zhang; Zhong-wei Gua

    2009-01-01

    Inclusion complexes(ICs)composed of ocyclodextrins(α-CD)and biodegradable comblike copolymers with poly(α,β-malic acid)(PMA)backbones and methylated poly(ethylene glycol)(mPEG)side chains were prepared by the host-guest reaction.Two series of ICs with mPEG750 and mPEG2000 were prepared.The stoichiometry(EG/CD)of all the ICs in mPEG2000 series was 3.1,no matter what the graft degree was.While in mPEG750 series,the stoichiometry(EG/CD)was very different;it increased with the amount of mPEG decreasing.The decomposition temperatures of the fragments in ICs were closely related to graft degrees.The stack of α-CDs in ICs was a channel-type structure.The crystal of ICs was lamellar,and it could be reorganized to well-defined supermolecular structure.

  14. Reduced Dimensionality tailored HN(C)N Pulse Sequences for Efficient Backbone Resonance Assignment of Proteins through Rapid Identification of Sequential HSQC peaks

    CERN Document Server

    Kumar, Dinesh

    2013-01-01

    Two novel reduced dimensionality (RD) experiments -(4,3)D-hNCOcaNH and (4,3)D-hNcoCANH- have been presented here to facilitate the backbone resonance assignment of proteins both in terms of its accuracy and speed. The experiments basically represent an improvisation of previously reported HN(C)N experiment [Panchal et. al., J. Biomol. NMR. (2002), 20 (2), 135-147] and exploit the simple reduced dimensionality NMR concept [Szyperski et. al. (2002), Proc. Natl. Acad. Sci. U.S.A. 99(12), 8009-8014] to achieve (a) higher dispersion and resolution along the co-evolved F1 dimension and (b) rapid identification of sequential HSQC peaks on its F2(15N)- F3(1H) planes. The current implementation is based on the fact that the linear combination of 15N and 13CO/13Ca chemical shifts offers relatively better dispersion and randomness compared to the individual chemical shifts; thus enables the assignment of crowded HSQC spectra by resolving the ambiguities generally encountered in HNCN based assignment protocol because of ...

  15. In-depth sphingomyelin characterization using electron impact excitation of ions from organics and mass spectrometry.

    Science.gov (United States)

    Baba, Takashi; Campbell, J Larry; Le Blanc, J C Yves; Baker, Paul R S

    2016-05-01

    Electron impact excitation of ions from organics (EIEIO), also referred to as electron-induced dissociation, was applied to singly charged SM molecular species in the gas phase. Using ESI and a quadrupole TOF mass spectrometer equipped with an electron-ion reaction device, we found that SMs fragmented sufficiently to identify their lipid class, acyl group structure, and the location of double bond(s). Using this technique, nearly 200 SM molecular species were found in four natural lipid extracts: bovine milk, porcine brain, chicken egg yolk, and bovine heart. In addition to the most common backbone, d18:1, sphingosines with a range of carbon chain lengths, sphingadienes, and some sphinganine backbones were also detected. Modifications in natural SMs were also identified, including addition of iodine/methanol across a carbon-carbon double bond. This unparalleled new approach to SM analysis using EIEIO-MS shows promise as a unique and powerful tool for structural characterization.

  16. A Strong Backbone For Export

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    China Export & Credit Insurance Corp., founded in 2001, is the country’s only policy-oriented credit insurance company. In line with the state’s diplomatic, foreign trade and industrial policies, it supports the country’s commodity, technology and servic

  17. Fixing Beijing’s Backbone

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    Capital’s central axis will be renovated as part of World Cultural Heritage status application Whenever the layout of Beijing is mentioned,its iconic central axis will immediately come to mind.It is so important that the Beijing Government

  18. Transnational Organizing

    DEFF Research Database (Denmark)

    Henriksen, Lasse Folke; Seabrooke, Leonard

    2016-01-01

    should be treated and governed by organizations. Using network and career sequences methods, we provide a case of transnational organizing through professionals who attempt issue control and network management on transnational environmental sustainability certification. The article questions how...

  19. Organic chemistry

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2003-08-15

    This book with sixteen chapter explains organic chemistry on linkage isomerism such as alkane, cycloalkane, alkene, aromatic compounds, stereo selective isomerization, aromatic compounds, stereo selective isomerization, organic compounds, stereo selective isomerization, organic halogen compound, alcohol, ether, aldehyde and ketone, carboxylic acid, dicarboxylic acid, fat and detergent, amino, carbohydrate, amino acid and protein, nucleotide and nucleic acid and spectroscopy, a polymer and medical chemistry. Each chapter has introduction structure and characteristic and using of organic chemistry.

  20. Study on Lyophilized Protective for Recombinant Anti - artherosclerosis Protein on the Basis of SAK Backbone%重组SRH蛋白冻干保护剂的研究

    Institute of Scientific and Technical Information of China (English)

    邹民吉; 徐涛; 刘深; 付文亮; 徐东刚

    2011-01-01

    Objective To select a lyophilized protective for recombinant anti - artherosclerosis protein on the basis of SAK backbone. Methods Mannitol, dextran 40, sucrose,and glycine in their different concentrations were selected to make up a single recipe or different complex recipes of their concentrations. After lyophilization, the thrombolytic activity and plasticity change should be examined, in the meantime, the lyophilized sample was rapidly thowed at 371 and the changes of thrombolytic activity and plasticity also should be examined. Results The protective effects on the protein of interest were not significantly different between glyceral and dextran 40 in their different concentrations. Both of them possessed better protective effect, however, that of the sucrose and glycine in different concentrations were less effective. The complex recipe of dextran 40, sucrose and glycine displayed the best protective effect on the protein of interest among the complex recipes, but the complex of gyceral, sucrose and glycine in the different concentrations had no obvious protective effect. Conclusion The dextran 40, sucrose and gycine in differet concentrations possess a significantly protective effect on the lyophilized process of the recombinant anti - artherosclerosis protein on the basis of SAK backbone.%目的 筛选并优化重组SRH蛋白的冻千保护剂,使其能够保持良好的生物学活性.方法 选择不同浓度的冻干保护剂,包括甘露醇、右旋糖酐40、蔗糖和甘氨酸等组成不同浓度的单一和复合配方,冷冻干燥后检测冻干样品的溶栓活性和成型的变化,同时,冻干样品经过37℃加速实验后,检测其溶栓活性和成型状况的改变,对比分析各组保护剂的效果.结果 不同浓度的甘露醇和右旋糖苷40对SRH蛋白的保护作用良好,没有明显差异,而不同浓度的蔗糖和甘氨酸保护效果较差.复方中以右旋糖苷40、蔗糖和甘胺酸的复合对目的蛋白的保

  1. Structure-activity study for (bis)ureidopropyl- and (bis)thioureidopropyldiamine LSD1 inhibitors with 3-5-3 and 3-6-3 carbon backbone architectures.

    Science.gov (United States)

    Nowotarski, Shannon L; Pachaiyappan, Boobalan; Holshouser, Steven L; Kutz, Craig J; Li, Youxuan; Huang, Yi; Sharma, Shiv K; Casero, Robert A; Woster, Patrick M

    2015-04-01

    Methylation at specific histone lysine residues is a critical post-translational modification that alters chromatin architecture, and dysregulated lysine methylation/demethylation is associated with the silencing of tumor suppressor genes. The enzyme lysine-specific demethylase 1 (LSD1) complexed to specific transcription factors catalyzes the oxidative demethylation of mono- and dimethyllysine 4 of histone H3 (H3K4me and H3K4me2, respectively). We have previously reported potent (bis)urea and (bis)thiourea LSD1 inhibitors that increase cellular levels of H3K4me and H3K4me2, promote the re-expression of silenced tumor suppressor genes and suppress tumor growth in vitro. Here we report the design additional (bis)urea and (bis)thiourea LSD1 inhibitors that feature 3-5-3 or 3-6-3 carbon backbone architectures. Three of these compounds displayed single-digit IC50 values in a recombinant LSD1 assay. In addition, compound 6d exhibited an IC50 of 4.2μM against the Calu-6 human lung adenocarcinoma line, and 4.8μM against the MCF7 breast tumor cell line, in an MTS cell viability assay. Following treatment with 6b-6d, Calu-6 cells exhibited a significant increase in the mRNA expression for the silenced tumor suppressor genes SFRP2, HCAD and p16, and modest increases in GATA4 message. The compounds described in this paper represent the most potent epigenetic modulators in this series, and have potential for use as antitumor agents.

  2. Backbone metal cyclization: Novel {sup 99m}Tc labeled GnRH analog as potential SPECT molecular imaging agent in cancer

    Energy Technology Data Exchange (ETDEWEB)

    Barda, Yaniv; Cohen, Nasi; Lev, Vered; Ben-Aroya, Nurit; Koch, Yitzhak; Mishani, Eyal; Fridkin, Mati; Gilon, Chaim E-mail: gilon@vms.huji.ac.il

    2004-10-01

    Gonadotropin-releasing hormone (GnRH) is a decapeptide secreted to the pituitary where it binds to specific receptors on the gonadotropes to regulate gonadotropic hormones (luteinizing hormone (LH) and follicle-stimulating hormone (FSH)) synthesis and secretion. Specific GnRH receptors are overexpressed in breast, prostatic, ovarian, and other tumors. The aim of this study was to synthesize a cyclic GnRH analog with high affinity to GnRH receptors that can be radiolabeled with {sup 99m}Tc. A precyclic GnRH analog, [Cys-Gly]{sup 1}[D-Ala]{sup 6}[N{sup {alpha}}({eta}-Cys-amino hexyl)]{sup 10}GnRH (Gn-2), containing two hemi-chelator groups was synthesized. It was cyclized applying the recently reported backbone metal cyclization (BMC) approach, to obtain cyclo(Re(O)1-10)[Cys-Gly]{sup 1}[D-Ala]{sup 6}[N{sup {alpha}}({eta}-Cys-amino hexyl)]{sup 10}GnRH (cyclo[Re(O)-Gn-2]). For comparative evaluations, Gn-2 was oxidized on-resin to yield cyclo(S-S,1-10)[Cys-Gly]{sup 1}[D-Ala]{sup 6}[N{sup {alpha}}({eta}-Cys-amino hexyl)]{sup 10}GnRH, (cyclo[S-S-Gn-2]). The binding affinity of cyclo[Re(O)-Gn-2] to rat pituitary membranes showed IC{sub 50} of 50nM, compared to IC{sub 50} = 10 nM in the native GnRH. Cyclo({sup 99m}Tc(O)1-10)[Cys-Gly]{sup 1}[D-Ala]{sup 6}[N{sup {alpha}}({eta}-Cys-amino hexyl)]{sup 10}GnRH (cyclo[{sup 99m}Tc(O)-Gn-2]) was synthesized from Gn-2 and showed similar chromatographic behavior to its rhenium surrogate.

  3. Refined solution structure and backbone dynamics of 15N-labeled C12A-p8MTCP studied by NMR relaxation

    Energy Technology Data Exchange (ETDEWEB)

    Barthe, Philippe; Chiche, Laurent; Declerck, Nathalie; Delsuc, Marc-Andre [Universite de Montpellier I, Faculte de Pharmacie, Centre de Biochimie Structurale, CNRS-UMR 9955, INSERM-U414 (France); Lefevre, Jean-Francois [Universite Louis Pasteur, CNRS UPR-9003, ESBS (France); Malliavin, Therese [Universite de Montpellier I, Faculte de Pharmacie, Centre de Biochimie Structurale, CNRS-UMR 9955, INSERM-U414 (France); Mispelter, Joel [Centre Universitaire Bat 112, INSERM-U350, Institut Curie, Biologie (France); Stern, Marc-Henri [Hopital Saint-Louis, Unite INSERM-U462 (France); Lhoste, Jean-Marc; Roumestand, Christian [Universite de Montpellier I, Faculte de Pharmacie, Centre de Biochimie Structurale, CNRS-UMR 9955, INSERM-U414 (France)

    1999-12-15

    MTCP1 (for Mature-T-Cell Proliferation) was the first gene unequivocally identified in the group of uncommon leukemias with a mature phenotype. The three-dimensional solution structure of the human p8{sup MTCP} protein encoded by the MTCP1 oncogene has been previously determined by homonuclear proton two-dimensional NMR methods at 600 MHz: it consists of an original scaffold comprising three {alpha}-helices, associated with a new cysteine motif. Two of the helices are covalently paired by two disulfide bridges, forming an {alpha}-hairpin which resembles an antiparallel coiled-coil. The third helix is orientated roughly parallel to the plane defined by the {alpha}-antiparallel motif and appears less well defined. In order to gain more insight into the details of this new scaffold, we uniformly labeled with nitrogen-15 a mutant of this protein (C12A-p8{sup MTCP1}) in which the unbound cysteine at position 12 has been replaced by an alanine residue, thus allowing reproducibly high yields of recombinant protein. The refined structure benefits from 211 additional NOEs, extracted from {sup 15}N-edited 3D experiments, and from a nearly complete set of {phi} angular restraints allowing the estimation of the helical content of the structured part of the protein. Moreover, measurements of {sup 15} N spin relaxation times and heteronuclear {sup 15} N{sup 1}HNOEs provided additional insights into the dynamics of the protein backbone. The analysis of the linear correlation between J(0) and J({omega}) was used to interpret relaxation parameters. It appears that the apparent relative disorder seen in helix III is not simply due to a lack of experimental constraints, but associated with substantial contributions of sub-nanosecond motions in this segment.

  4. Combinations of various CpG motifs cloned into plasmid backbone modulate and enhance protective immunity of viral replicon DNA anthrax vaccines.

    Science.gov (United States)

    Yu, Yun-Zhou; Ma, Yao; Xu, Wen-Hui; Wang, Shuang; Sun, Zhi-Wei

    2015-08-01

    DNA vaccines are generally weak stimulators of the immune system. Fortunately, their efficacy can be improved using a viral replicon vector or by the addition of immunostimulatory CpG motifs, although the design of these engineered DNA vectors requires optimization. Our results clearly suggest that multiple copies of three types of CpG motifs or combinations of various types of CpG motifs cloned into a viral replicon vector backbone with strong immunostimulatory activities on human PBMC are efficient adjuvants for these DNA vaccines to modulate and enhance protective immunity against anthrax, although modifications with these different CpG forms in vivo elicited inconsistent immune response profiles. Modification with more copies of CpG motifs elicited more potent adjuvant effects leading to the generation of enhanced immunity, which indicated a CpG motif dose-dependent enhancement of antigen-specific immune responses. Notably, the enhanced and/or synchronous adjuvant effects were observed in modification with combinations of two different types of CpG motifs, which provides not only a contribution to the knowledge base on the adjuvant activities of CpG motifs combinations but also implications for the rational design of optimal DNA vaccines with combinations of CpG motifs as "built-in" adjuvants. We describe an efficient strategy to design and optimize DNA vaccines by the addition of combined immunostimulatory CpG motifs in a viral replicon DNA plasmid to produce strong immune responses, which indicates that the CpG-modified viral replicon DNA plasmid may be desirable for use as vector of DNA vaccines.

  5. Structural insights into the evolution of a sexy protein: novel topology and restricted backbone flexibility in a hypervariable pheromone from the red-legged salamander, Plethodon shermani.

    Directory of Open Access Journals (Sweden)

    Damien B Wilburn

    Full Text Available In response to pervasive sexual selection, protein sex pheromones often display rapid mutation and accelerated evolution of corresponding gene sequences. For proteins, the general dogma is that structure is maintained even as sequence or function may rapidly change. This phenomenon is well exemplified by the three-finger protein (TFP superfamily: a diverse class of vertebrate proteins co-opted for many biological functions - such as components of snake venoms, regulators of the complement system, and coordinators of amphibian limb regeneration. All of the >200 structurally characterized TFPs adopt the namesake "three-finger" topology. In male red-legged salamanders, the TFP pheromone Plethodontid Modulating Factor (PMF is a hypervariable protein such that, through extensive gene duplication and pervasive sexual selection, individual male salamanders express more than 30 unique isoforms. However, it remained unclear how this accelerated evolution affected the protein structure of PMF. Using LC/MS-MS and multidimensional NMR, we report the 3D structure of the most abundant PMF isoform, PMF-G. The high resolution structural ensemble revealed a highly modified TFP structure, including a unique disulfide bonding pattern and loss of secondary structure, that define a novel protein topology with greater backbone flexibility in the third peptide finger. Sequence comparison, models of molecular evolution, and homology modeling together support that this flexible third finger is the most rapidly evolving segment of PMF. Combined with PMF sequence hypervariability, this structural flexibility may enhance the plasticity of PMF as a chemical signal by permitting potentially thousands of structural conformers. We propose that the flexible third finger plays a critical role in PMF:receptor interactions. As female receptors co-evolve, this flexibility may allow PMF to still bind its receptor(s without the immediate need for complementary mutations. Consequently

  6. Structural insights into the evolution of a sexy protein: novel topology and restricted backbone flexibility in a hypervariable pheromone from the red-legged salamander, Plethodon shermani.

    Science.gov (United States)

    Wilburn, Damien B; Bowen, Kathleen E; Doty, Kari A; Arumugam, Sengodagounder; Lane, Andrew N; Feldhoff, Pamela W; Feldhoff, Richard C

    2014-01-01

    In response to pervasive sexual selection, protein sex pheromones often display rapid mutation and accelerated evolution of corresponding gene sequences. For proteins, the general dogma is that structure is maintained even as sequence or function may rapidly change. This phenomenon is well exemplified by the three-finger protein (TFP) superfamily: a diverse class of vertebrate proteins co-opted for many biological functions - such as components of snake venoms, regulators of the complement system, and coordinators of amphibian limb regeneration. All of the >200 structurally characterized TFPs adopt the namesake "three-finger" topology. In male red-legged salamanders, the TFP pheromone Plethodontid Modulating Factor (PMF) is a hypervariable protein such that, through extensive gene duplication and pervasive sexual selection, individual male salamanders express more than 30 unique isoforms. However, it remained unclear how this accelerated evolution affected the protein structure of PMF. Using LC/MS-MS and multidimensional NMR, we report the 3D structure of the most abundant PMF isoform, PMF-G. The high resolution structural ensemble revealed a highly modified TFP structure, including a unique disulfide bonding pattern and loss of secondary structure, that define a novel protein topology with greater backbone flexibility in the third peptide finger. Sequence comparison, models of molecular evolution, and homology modeling together support that this flexible third finger is the most rapidly evolving segment of PMF. Combined with PMF sequence hypervariability, this structural flexibility may enhance the plasticity of PMF as a chemical signal by permitting potentially thousands of structural conformers. We propose that the flexible third finger plays a critical role in PMF:receptor interactions. As female receptors co-evolve, this flexibility may allow PMF to still bind its receptor(s) without the immediate need for complementary mutations. Consequently, this unique

  7. {{text{C}}_{α }} - {text{C}} Bond Cleavage of the Peptide Backbone in MALDI In-Source Decay Using Salicylic Acid Derivative Matrices

    Science.gov (United States)

    Asakawa, Daiki; Takayama, Mitsuo

    2011-07-01

    The use of 5-formylsalicylic acid (5-FSA) and 5-nitrosalicylic acid (5-NSA) as novel matrices for in-source decay (ISD) of peptides in matrix-assisted laser desorption/ionization (MALDI) is described. The use of 5-FSA and 5-NSA generated a- and x-series ions accompanied by oxidized peptides [M - 2 H + H]+. The preferential formation of a- and x-series ions was found to be dependent on the hydrogen-accepting ability of matrix. The hydrogen-accepting ability estimated from the ratio of signal intensity of oxidized product [M - 2 H + H]+ to that of non-oxidized protonated molecule [M + H]+ of peptide was of the order 5-NSA > 5-FSA > 5-aminosalicylic acid (5-ASA) ≒ 2,5-dihydroxyl benzoic acid (2,5-DHB) ≒ 0. The results suggest that the hydrogen transfer reaction from peptide to 5-FSA and 5-NSA occurs during the MALDI-ISD processes. The hydrogen abstraction from peptides results in the formation of oxidized peptides containing a radical site on the amide nitrogen with subsequent radical-induced cleavage at the {{{C}}_{α }} - {{C}} bond, leading to the formation of a- and x-series ions. The most significant feature of MALDI-ISD with 5-FSA and 5-NSA is the specific cleavage of the {{{C}}_{α }} - {{C}} bond of the peptide backbone without degradation of side-chain and post-translational modifications (PTM). The matrix provides a useful complementary method to conventional MALDI-ISD for amino acid sequencing and site localization of PTMs in peptides.

  8. Peptaibol antiamoebin I: spatial structure, backbone dynamics, interaction with bicelles and lipid-protein nanodiscs, and pore formation in context of barrel-stave model.

    Science.gov (United States)

    Shenkarev, Zakhar O; Paramonov, Alexander S; Lyukmanova, Ekaterina N; Gizatullina, Albina K; Zhuravleva, Anastasia V; Tagaev, Andrey A; Yakimenko, Zoya A; Telezhinskaya, Irina N; Kirpichnikov, Mikhail P; Ovchinnikova, Tatiana V; Arseniev, Alexander S

    2013-05-01

    Antiamoebin I (Aam-I) is a membrane-active peptaibol antibiotic isolated from fungal species belonging to the genera Cephalosporium, Emericellopsis, Gliocladium, and Stilbella. In comparison with other 16-amino acid-residue peptaibols, e.g., zervamicin IIB (Zrv-IIB), Aam-I possesses relatively weak biological and channel-forming activities. In MeOH solution, Aam-I demonstrates fast cooperative transitions between right-handed and left-handed helical conformation of the N-terminal (1-8) region. We studied Aam-I spatial structure and backbone dynamics in the membrane-mimicking environment (DMPC/DHPC bicelles)(1) ) by heteronuclear (1) H,(13) C,(15) N-NMR spectroscopy. Interaction with the bicelles stabilizes the Aam-I right-handed helical conformation retaining significant intramolecular mobility on the ms-μs time scale. Extensive ms-μs dynamics were also detected in the DPC and DHPC micelles and DOPG nanodiscs. In contrast, Zrv-IIB in the DPC micelles demonstrates appreciably lesser mobility on the μs-ms time scale. Titration with Mn(2+) and 16-doxylstearate paramagnetic probes revealed Aam-I binding to the bicelle surface with the N-terminus slightly immersed into hydrocarbon region. Fluctuations of the Aam-I helix between surface-bound and transmembrane (TM) state were observed in the nanodisc membranes formed from the short-chain (diC12 : 0) DLPC/DLPG lipids. All the obtained experimental data are in agreement with the barrel-stave model of TM pore formation, similarly to the mechanism proposed for Zrv-IIB and other peptaibols. The observed extensive intramolecular dynamics explains the relatively low activity of Aam-I.

  9. Chemistry of Covalent Organic Frameworks.

    Science.gov (United States)

    Waller, Peter J; Gándara, Felipe; Yaghi, Omar M

    2015-12-15

    Linking organic molecules by covalent bonds into extended solids typically generates amorphous, disordered materials. The ability to develop strategies for obtaining crystals of such solids is of interest because it opens the way for precise control of the geometry and functionality of the extended structure, and the stereochemical orientation of its constituents. Covalent organic frameworks (COFs) are a new class of porous covalent organic structures whose backbone is composed entirely of light elements (B, C, N, O, Si) that represent a successful demonstration of how crystalline materials of covalent solids can be achieved. COFs are made by combination of organic building units covalently linked into extended structures to make crystalline materials. The attainment of crystals is done by several techniques in which a balance is struck between the thermodynamic reversibility of the linking reactions and their kinetics. This success has led to the expansion of COF materials to include organic units linked by these strong covalent bonds: B-O, C-N, B-N, and B-O-Si. Since the organic constituents of COFs, when linked, do not undergo significant change in their overall geometry, it has been possible to predict the structures of the resulting COFs, and this advantage has facilitated their characterization using powder X-ray diffraction (PXRD) techniques. It has also allowed for the synthesis of COF structures by design and for their formation with the desired composition, pore size, and aperture. In practice, the modeled PXRD pattern for a given expected COF is compared with the experimental one, and depending on the quality of the match, this is used as a starting point for solving and then refining the crystal structure of the target COF. These characteristics make COFs an attractive class of new porous materials. Accordingly, they have been used as gas storage materials for energy applications, solid supports for catalysis, and optoelectronic devices. A large and

  10. 高职骨干院校物流管理专业教学改革的构想%The Ideas of Teaching Reform of Logistics Management Major in Higher Vocational Backbone Colleges

    Institute of Scientific and Technical Information of China (English)

    刘佳

    2011-01-01

    本文提出了高职骨干院校物流管理专业培养目标,课程设置,并在参考国内高职院校实践教学体系经验的基础上,对高职骨干院校物流管理专业的校内外实训基地建设提出了初步构想.%This paper presents the training objectives and curriculum provision of logistics management major in higher vocational backbone colleges,and proposes preliminary ideas on practice bases for logistics management major inside and outside of higher vocational backbone colleges, on the basis of referring to the experience on practical teaching system in the domestic vocational colleges.

  11. Designing Organizations

    DEFF Research Database (Denmark)

    Book Description The design of organizations has been an ongoing concern of management theory and practice over the past several decades. Over this time, there has been little change in the fundamental theory, principles and concepts of Organization Design (OD). Recently organizational life has....... The individual chapters are organized into five sections: (1) Putting Contingency Theory in its Place, (2) Focus on Individuals who make up the Organization, (3) Innovation Processes and Organization Design, (4) Adaptation and Technology, and (5) Design for Performance. Each chapter examines aspects of the books...

  12. 艺术类大学生团学骨干培养的关键与模式%The Key of Art Students' League backbone Training and Mode

    Institute of Scientific and Technical Information of China (English)

    郑陈超

    2014-01-01

    Art Students' educational management is often a problem in universities, and art students' training mode of the backbone is particularly important. This article thinks that the cultivation of professional art groups to learn the backbone of the art students to combine the characteristics of attention and emotional education play a role in student management work, establish and improve a personalized training system based on personality and common on the coordinated development. This paper analyzes the Art Students League in critical backbone of culture, made echelon training mode suitable for arts groups to learn the backbone of the training model and encourage innovation.%艺术类大学生的教育管理通常是高校的一个难题,而艺术类学生中团学骨干的培养模式则尤为重要。文章认为对艺术类专业团学骨干的培养要结合艺术类专业学生的特点,重视和发挥情感教育在学生管理工作中的作用,在个性与共性协调发展的基础上建立健全个性化人才培养体系。本文分析了艺术类大学生团学骨干培养的关键,提出了适合艺术类团学骨干的梯队培养模式和鼓励创新培养模式。

  13. 省干SDH网络系统改造优化思路与方法探讨%Study of provincial backbone SDH network system’s optimization strategy and method

    Institute of Scientific and Technical Information of China (English)

    朱向刚

    2015-01-01

    It analyzes problems that exist in one operator’s provincial backbone SDH platform for network structure and system usage, considering of the background that group client business is the main increasing business in provincial backbone SDH platform, propose to the way of network system optimization and transformation in one operator’s provincial backbone SDH platform, as well as the implementation of specific strategies and methods.%深入分析了某运营商省干SDH平台现有网络结构和系统使用情况以及存在的问题,结合集客业务作为当下省干SDH平台主要新增业务的背景,提出了对某运营商省干SDH平台的网络改造和系统优化的思路,以及实施的具体策略和方法。

  14. Design of HIV-1 Protease Inhibitors with Amino-bis-tetrahydrofuran Derivatives as P2-Ligands to Enhance Backbone-Binding Interactions. Synthesis, Biological Evaluation, and Protein-Ligand X-ray Studies

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Arun K.; Martyr, Cuthbert D.; Osswald, Heather L.; Sheri, Venkat Reddy; Kassekert, Luke A.; Chen, Shujing; Agniswamy, Johnson; Wang, Yuan-Fang; Hayashi, Hironori; Aoki, Manabu; Weber, Irene T.; Mitsuya, Hiroaki (GSU); (Kumamoto); (Purdue)

    2015-10-30

    Structure-based design, synthesis, and biological evaluation of a series of very potent HIV-1 protease inhibitors are described. In an effort to improve backbone ligand–binding site interactions, we have incorporated basic-amines at the C4 position of the bis-tetrahydrofuran (bis-THF) ring. We speculated that these substituents would make hydrogen bonding interactions in the flap region of HIV-1 protease. Synthesis of these inhibitors was performed diastereoselectively. A number of inhibitors displayed very potent enzyme inhibitory and antiviral activity. Inhibitors 25f, 25i, and 25j were evaluated against a number of highly-PI-resistant HIV-1 strains, and they exhibited improved antiviral activity over darunavir. Two high resolution X-ray structures of 25f- and 25g-bound HIV-1 protease revealed unique hydrogen bonding interactions with the backbone carbonyl group of Gly48 as well as with the backbone NH of Gly48 in the flap region of the enzyme active site. These ligand–binding site interactions are possibly responsible for their potent activity.

  15. Site-specific protein backbone and side-chain NMR chemical shift and relaxation analysis of human vinexin SH3 domain using a genetically encoded {sup 15}N/{sup 19}F-labeled unnatural amino acid

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Pan [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China); School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Xi, Zhaoyong; Wang, Hu [School of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026 (China); Shi, Chaowei [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China); School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Xiong, Ying, E-mail: yxiong73@ustc.edu.cn [School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Tian, Changlin, E-mail: cltian@ustc.edu.cn [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China)

    2010-11-19

    Research highlights: {yields} Chemical synthesis of {sup 15}N/{sup 19}F-trifluomethyl phenylalanine. {yields} Site-specific incorporation of {sup 15}N/{sup 19}F-trifluomethyl phenylalanine to SH3. {yields} Site-specific backbone and side chain chemical shift and relaxation analysis. {yields} Different internal motions at different sites of SH3 domain upon ligand binding. -- Abstract: SH3 is a ubiquitous domain mediating protein-protein interactions. Recent solution NMR structural studies have shown that a proline-rich peptide is capable of binding to the human vinexin SH3 domain. Here, an orthogonal amber tRNA/tRNA synthetase pair for {sup 15}N/{sup 19}F-trifluoromethyl-phenylalanine ({sup 15}N/{sup 19}F-tfmF) has been applied to achieve site-specific labeling of SH3 at three different sites. One-dimensional solution NMR spectra of backbone amide ({sup 15}N){sup 1}H and side-chain {sup 19}F were obtained for SH3 with three different site-specific labels. Site-specific backbone amide ({sup 15}N){sup 1}H and side-chain {sup 19}F chemical shift and relaxation analysis of SH3 in the absence or presence of a peptide ligand demonstrated different internal motions upon ligand binding at the three different sites. This site-specific NMR analysis might be very useful for studying large-sized proteins or protein complexes.

  16. Organic electroluminescence

    CERN Document Server

    Kafafi, Zakya H

    2005-01-01

    Organic light-emitting diode(OLED) technology has achieved significant penetration in the commercial market for small, low-voltage and inexpensive displays. Present and future novel technologies based on OLEDs involve rigid and flexible flat panel displays, solid-state lighting, and lasers. Display applications may range from hand-held devices to large flat panel screens that can be rolled up or hung flat on a wall or a ceiling. Organic Electroluminescence gives an overview of the on-going research in the field of organic light-emitting materials and devices, covering the principles of electroluminescence in organic thin films, as well as recent trends, current applications, and future potential uses. The book begins by giving a background of organic electroluminescence in terms of history and basic principles. It offers details on the mechanism(s) of electroluminescence in thin organic films. It presentsin-depth discussions of the parameters that control the external electroluminescence quantum efficien...

  17. Organic optoelectronics

    CERN Document Server

    Hu, Wenping; Gong, Xiong; Zhan, Xiaowei; Fu, Hongbing; Bjornholm, Thomas

    2012-01-01

    Written by internationally recognized experts in the field with academic as well as industrial experience, this book concisely yet systematically covers all aspects of the topic.The monograph focuses on the optoelectronic behavior of organic solids and their application in new optoelectronic devices. It covers organic electroluminescent materials and devices, organic photonics, materials and devices, as well as organic solids in photo absorption and energy conversion. Much emphasis is laid on the preparation of functional materials and the fabrication of devices, from materials synthesis a

  18. Live virus vaccines based on a yellow fever vaccine backbone: standardized template with key considerations for a risk/benefit assessment.

    Science.gov (United States)

    Monath, Thomas P; Seligman, Stephen J; Robertson, James S; Guy, Bruno; Hayes, Edward B; Condit, Richard C; Excler, Jean Louis; Mac, Lisa Marie; Carbery, Baevin; Chen, Robert T

    2015-01-01

    The Brighton Collaboration Viral Vector Vaccines Safety Working Group (V3SWG) was formed to evaluate the safety of live, recombinant viral vaccines incorporating genes from heterologous viruses inserted into the backbone of another virus (so-called "chimeric virus vaccines"). Many viral vector vaccines are in advanced clinical trials. The first such vaccine to be approved for marketing (to date in Australia, Thailand, Malaysia, and the Philippines) is a vaccine against the flavivirus, Japanese encephalitis (JE), which employs a licensed vaccine (yellow fever 17D) as a vector. In this vaccine, two envelope proteins (prM-E) of YF 17D virus were exchanged for the corresponding genes of JE virus, with additional attenuating mutations incorporated into the JE gene inserts. Similar vaccines have been constructed by inserting prM-E genes of dengue and West Nile into YF 17D virus and are in late stage clinical studies. The dengue vaccine is, however, more complex in that it requires a mixture of four live vectors each expressing one of the four dengue serotypes. This vaccine has been evaluated in multiple clinical trials. No significant safety concerns have been found. The Phase 3 trials met their endpoints in terms of overall reduction of confirmed dengue fever, and, most importantly a significant reduction in severe dengue and hospitalization due to dengue. However, based on results that have been published so far, efficacy in preventing serotype 2 infection is less than that for the other three serotypes. In the development of these chimeric vaccines, an important series of comparative studies of safety and efficacy were made using the parental YF 17D vaccine virus as a benchmark. In this paper, we use a standardized template describing the key characteristics of the novel flavivirus vaccine vectors, in comparison to the parental YF 17D vaccine. The template facilitates scientific discourse among key stakeholders by increasing the transparency and comparability of

  19. Chemoenzymatic synthesis of artificial glycopolypeptides containing multivalent sialyloligosaccharides with a gamma-polyglutamic acid backbone and their effect on inhibition of infection by influenza viruses.

    Science.gov (United States)

    Ogata, Makoto; Murata, Takeomi; Murakami, Kouki; Suzuki, Takashi; Hidari, Kazuya I P J; Suzuki, Yasuo; Usui, Taichi

    2007-02-01

    Highly water-soluble, artificial glycopolypeptides with a gamma-polyglutamic acid (gamma-PGA) backbone derived from Bacillus subtilis sp. and multivalent sialyloligosaccharide units have been chemoenzymatically synthesized as potential polymeric inhibitors of infection by bird and human influenza viruses. 5-Trifluoroacetamidopentyl beta-N-acetyllactosaminide and 5-trifluoroacetamidopentyl beta-lactoside were enzymatically synthesized from LacNAc and lactose, respectively, by cellulase-mediated condensation with 5-trifluoroacetamido-1-pentanol. After deacetylation, the resulting 5-aminopentyl beta-LacNAc and beta-lactoside glycosides were coupled to the alpha-carboxyl groups of the gamma-PGA side chains. The artificial glycopolypeptides carrying LacNAc and lactose were further converted to Neu5Acalpha2-(3/6)Galbeta1-4Glcbeta and Neu5Acalpha2-(3/6)Galbeta1-4GlcNAcbeta sialyloligosaccharide units by alpha2,3- and alpha2,6-sialyltransferase, respectively. The interaction of these glycopolypeptides with various influenza virus strains has been investigated by three different methods. Glycopolypeptides carrying Neu5Acalpha2,6LacNAc inhibited hemagglutination mediated by influenza A and B viruses, and their relative binding affinities for hemagglutinin were 10(2)- to 10(4)-fold higher than that of the naturally occurring fetuin control. A glycopolypeptide carrying Neu5Acalpha2,6LacNAc inhibited infection by A/Memphis/1/71 (H3N2) 93 times more strongly than fetuin, as assessed by cytopathic effects on virus-infected MDCK cells. The avian virus [A/duck/Hong kong/4/78 (H5N3)] bound strongly to Neu5Acalpha2,3LacNAc/Lac-carrying glycopolypeptides, whereas the human virus [A/Memphis/1/71 (H3N2)] bound to Neu5Acalpha2,6LacNAc in preference to Neu5Acalpha2,6Lac. Taken together, these results indicate that the binding of viruses to terminal sialic acids is markedly affected by the structure of the asialo portion, in this case either LacNAc or lactose, in the sugar chain of

  20. 求解QAP问题的近似骨架导向快速蚁群算法%Approximate-Backbone Guided Fast Ant Algorithms to QAP

    Institute of Scientific and Technical Information of China (English)

    邹鹏; 周智; 陈国良; 江贺; 顾钧

    2005-01-01

    QAP(quadratic assignment problem)问题是经典的组合优化问题之一,广泛应用于许多领域中.针对QAP问题,提出了一种新的蚁群算法--近似骨架导向的快速蚁群算法(ABFANT).该算法的基本原理是通过对局部最优解的简单相交操作得到QAP问题实例的近似骨架(approximate-backbone),利用这些近似骨架可以极大地缩小QAP问题的搜索空间,而同时不降低搜索的性能,最后对这个缩小后的搜索空间,直接用当前求解QAP问题最好的启发式算法之一-快速蚁群算法(FANT)求解得到问题的解.在QAPLIB中的典型实例上的实验结果表明,近似骨架导向的快速蚁群算法明显优于快速蚁群算法.此外,指出基于近似骨架的算法思想可以很容易地被移植到其他求解QAP问题的启发式算法中.%Quadratic Assignment Problem (QAP) is one of the classical combinatorial optimization problems and is known for its diverse applications. This paper presents a new fast ant heuristic for the QAP, the approximatebackbone guided fast ant colony algorithm (ABFANT). The main idea is to fix the approximatebackbone which is the intersection of several local optimal permutations to the QAP. After fixing it, the authors can smooth the search space of the QAP instance without losing the search capability, and then solve the instance using the known fast ant colony algorithm (FANT) which is one of the best heuristics to the QAP in the much smoother search space. Comparisons of ABFANT and FANT within a given iteration number are performed on the publicly available QAP instances from QAPLIB. The result demonstrates that ABFANT significantly outperforms FANT.Furthermore, this idea is general and applicable to other heuristics of the QAP.

  1. Organic salmon

    DEFF Research Database (Denmark)

    Ankamah Yeboah, Isaac; Nielsen, Max; Nielsen, Rasmus

    The year 2016 is groundbreaking for organic aquaculture producers in EU, as it represents the deadline for implementing a full organic life cycle in the aquaculture production. Such a shift induces production costs for farmers and if it should be profitable, they must receive higher prices. This ...... is closer to organic labeled agriculture products than to ecolabelled capture fisheries products, it indicates that consumers value organic salmon as an agriculture product more than fisheries product.......The year 2016 is groundbreaking for organic aquaculture producers in EU, as it represents the deadline for implementing a full organic life cycle in the aquaculture production. Such a shift induces production costs for farmers and if it should be profitable, they must receive higher prices....... This study identifies the price premium on organic salmon in the Danish retail sale sector using consumer panel scanner data for households by applying the hedonic price model while permitting unobserved heterogeneity between households. A premium of 20% for organic salmon is found. Since this premium...

  2. Organic Synthesis

    OpenAIRE

    Romea, Pedro

    2014-01-01

    Organic Synthesis is a one-semester course of the fourth year of the Chemistry Degree at the Universitat de Barcelona. This course covers the most important transformations in Organic Chemistry, including a short introduction to the Retrosynthetic Analysis. The aim is to provide a solid knowledge of the main reactions and their mechanism, which could later be improved during Master studies.

  3. Spray printing of organic semiconducting single crystals

    Science.gov (United States)

    Rigas, Grigorios-Panagiotis; Payne, Marcia M.; Anthony, John E.; Horton, Peter N.; Castro, Fernando A.; Shkunov, Maxim

    2016-11-01

    Single-crystal semiconductors have been at the forefront of scientific interest for more than 70 years, serving as the backbone of electronic devices. Inorganic single crystals are typically grown from a melt using time-consuming and energy-intensive processes. Organic semiconductor single crystals, however, can be grown using solution-based methods at room temperature in air, opening up the possibility of large-scale production of inexpensive electronics targeting applications ranging from field-effect transistors and light-emitting diodes to medical X-ray detectors. Here we demonstrate a low-cost, scalable spray-printing process to fabricate high-quality organic single crystals, based on various semiconducting small molecules on virtually any substrate by combining the advantages of antisolvent crystallization and solution shearing. The crystals' size, shape and orientation are controlled by the sheer force generated by the spray droplets' impact onto the antisolvent's surface. This method demonstrates the feasibility of a spray-on single-crystal organic electronics.

  4. Model for Triplet State Engineering in Organic Light Emitting Diodes

    CERN Document Server

    Prodhan, Suryoday; Ramasesha, S

    2014-01-01

    Engineering the position of the lowest triplet state (T1) relative to the first excited singlet state (S1) is of great importance in improving the efficiencies of organic light emitting diodes and organic photovoltaic cells. We have carried out model exact calculations of substituted polyene chains to understand the factors that affect the energy gap between S1 and T1. The factors studied are backbone dimerisation, different donor-acceptor substitutions and twisted geometry. The largest system studied is an eighteen carbon polyene which spans a Hilbert space of about 991 million. We show that for reverse intersystem crossing (RISC) process, the best system involves substituting all carbon sites on one half of the polyene with donors and the other half with acceptors.

  5. Organic spintronics.

    Science.gov (United States)

    Bergenti, I; Dediu, V; Prezioso, M; Riminucci, A

    2011-08-13

    Organic semiconductors are emerging materials in the field of spintronics. Successful achievements include their use as a tunnel barrier in magnetoresistive tunnelling devices and as a medium for spin-polarized current in transport devices. In this paper, we give an overview of the basic concepts of spin transport in organic semiconductors and present the results obtained in the field, highlighting the open questions that have to be addressed in order to improve devices performance and reproducibility. The most challenging perspectives will be discussed and a possible evolution of organic spin devices featuring multi-functional operation is presented.

  6. Structural proteomics of minimal organisms: conservation ofprotein fold usage and evolutionary implications

    Energy Technology Data Exchange (ETDEWEB)

    Chandonia, John-Marc; Kim, Sung-Hou

    2006-03-15

    Background: Determining the complete repertoire of proteinstructures for all soluble, globular proteins in a single organism hasbeen one of the major goals of several structural genomics projects inrecent years. Results: We report that this goal has nearly been reachedfor several "minimal organisms"--parasites or symbionts with reducedgenomes--for which over 95 percent of the soluble, globular proteins maynow be assigned folds, overall 3-D backbone structures. We analyze thestructures of these proteins as they relate to cellular functions, andcompare conservation off old usage between functional categories. We alsocompare patterns in the conservation off olds among minimal organisms andthose observed between minimal organisms and other bacteria. Conclusion:We find that proteins performing essential cellular functions closelyrelated to transcription and translation exhibit a higher degree ofconservation in fold usage than proteins in other functional categories.Folds related to transcription and translation functional categories werealso over represented in minimal organisms compared to otherbacteria.

  7. Hydrogen-Bonded Organic Frameworks (HOFs): A New Class of Porous Crystalline Proton-Conducting Materials.

    Science.gov (United States)

    Karmakar, Avishek; Illathvalappil, Rajith; Anothumakkool, Bihag; Sen, Arunabha; Samanta, Partha; Desai, Aamod V; Kurungot, Sreekumar; Ghosh, Sujit K

    2016-08-26

    Two porous hydrogen-bonded organic frameworks (HOFs) based on arene sulfonates and guanidinium ions are reported. As a result of the presence of ionic backbones appended with protonic source, the compounds exhibit ultra-high proton conduction values (σ) 0.75× 10(-2)  S cm(-1) and 1.8×10(-2)  S cm(-1) under humidified conditions. Also, they have very low activation energy values and the highest proton conductivity at ambient conditions (low humidity and at moderate temperature) among porous crystalline materials, such as metal-organic frameworks (MOFs) and covalent organic frameworks (COFs). These values are not only comparable to the conventionally used proton exchange membranes, such as Nafion used in fuel cell technologies, but is also the highest value reported in organic-based porous architectures. Notably, this report inaugurates the usage of crystalline hydrogen-bonded porous organic frameworks as solid-state proton conducting materials.

  8. Organ Transplantation

    Science.gov (United States)

    ... of neurological criteria—the absence of brain activity. Brain death typically occurs after cardiopulmonary death, the cessation of ... it is medically more complex than donation after brain death because of the risk of organs being harmed ...

  9. Matching Organs

    Science.gov (United States)

    ... transplanted immediately. Also, a laboratory test to measure compatibility between the donor and potential recipient may be necessary. If the organ is refused for any reason, the transplant hospital of the next patient on the list ...

  10. Colloidal organization

    CERN Document Server

    Okubo, Tsuneo

    2015-01-01

    Colloidal Organization presents a chemical and physical study on colloidal organization phenomena including equilibrium systems such as colloidal crystallization, drying patterns as an example of a dissipative system and similar sized aggregation. This book outlines the fundamental science behind colloid and surface chemistry and the findings from the author's own laboratory. The text goes on to discuss in-depth colloidal crystallization, gel crystallization, drying dissipative structures of solutions, suspensions and gels, and similar-sized aggregates from nanosized particles. Special emphas

  11. Organic Conductors

    DEFF Research Database (Denmark)

    Andersen, Jan Rud; Jacobsen, Claus S.; Rindorf, Grethe;

    1975-01-01

    2,3,6,7-Tetramethyl-1,4,5,8-tetraselenafulvalene reacts with 2,5-dimethyl-7,7′,8,8′-tetracyano-p-quinodi-methane to give a highly conducting organic solid.......2,3,6,7-Tetramethyl-1,4,5,8-tetraselenafulvalene reacts with 2,5-dimethyl-7,7′,8,8′-tetracyano-p-quinodi-methane to give a highly conducting organic solid....

  12. Organic Computing

    CERN Document Server

    Würtz, Rolf P

    2008-01-01

    Organic Computing is a research field emerging around the conviction that problems of organization in complex systems in computer science, telecommunications, neurobiology, molecular biology, ethology, and possibly even sociology can be tackled scientifically in a unified way. From the computer science point of view, the apparent ease in which living systems solve computationally difficult problems makes it inevitable to adopt strategies observed in nature for creating information processing machinery. In this book, the major ideas behind Organic Computing are delineated, together with a sparse sample of computational projects undertaken in this new field. Biological metaphors include evolution, neural networks, gene-regulatory networks, networks of brain modules, hormone system, insect swarms, and ant colonies. Applications are as diverse as system design, optimization, artificial growth, task allocation, clustering, routing, face recognition, and sign language understanding.

  13. (1)H, (15)N, (13)C backbone resonance assignments of human soluble catechol O-methyltransferase in complex with S-adenosyl-L-methionine and 3,5-dinitrocatechol.

    Science.gov (United States)

    Czarnota, Sylwia; Baxter, Nicola J; Cliff, Matthew J; Waltho, Jonathan P; Scrutton, Nigel S; Hay, Sam

    2016-12-15

    Catechol O-methyltransferase (COMT) is an enzyme that plays a major role in catechol neurotransmitter deactivation. Inhibition of COMT can increase neurotransmitter levels, which provides a means of treatment for Parkinson's disease, schizophrenia and depression. COMT exists as two isozymes: a soluble cytoplasmic form (S-COMT), expressed in the liver and kidneys and a membrane-bound form (MB-COMT), found mostly in the brain. Here we report the backbone (1)H, (15)N and (13)C chemical shift assignments of S-COMT in complex with S-adenosyl-L-methionine, 3,5-dinitrocatechol and Mg(2+). Assignments were obtained by heteronuclear multidimensional NMR spectroscopy. In total, 97 % of all backbone resonances were assigned in the complex, with 205 out of a possible 215 residues assigned in the (1)H-(15)N TROSY spectrum. Prediction of solution secondary structure from a chemical shift analysis using the TALOS+ webserver is in good agreement with published X-ray crystal structures.

  14. (1)H, (13)C, and (15)N backbone resonance assignments of the full-length 40 kDa S. acidocaldarius Y-family DNA polymerase, dinB homolog.

    Science.gov (United States)

    Moro, Sean L; Cocco, Melanie J

    2015-10-01

    The dinB homolog (Dbh) is a member of the Y-family of translesion DNA polymerases, which are specialized to accurately replicate DNA across from a wide variety of lesions in living cells. Lesioned bases block the progression of high-fidelity polymerases and cause detrimental replication fork stalling; Y-family polymerases can bypass these lesions. The active site of the translesion synthesis polymerase is more open than that of a replicative polymerase; consequently Dbh polymerizes with low fidelity. Bypass polymerases also have low processivity. Short extension past the lesion allows the high-fidelity polymerase to switch back onto the site of replication. Dbh and the other Y-family polymerases have been used as structural models to investigate the mechanisms of DNA polymerization and lesion bypass. Many high-resolution crystal structures of Y-family polymerases have been reported. NMR dynamics studies can complement these structures by providing a measure of protein motions. Here we report the (15)N, (1)H, and (13)C backbone resonance assignments at two temperatures (35 and 50 °C) for Sulfolobus acidocaldarius Dbh polymerase. Backbone resonance assignments have been obtained for 86 % of the residues. The polymerase active site is assigned as well as the majority of residues in each of the four domains.

  15. TEMPO-Assisted Free Radical-Initiated Peptide Sequencing Mass Spectrometry (FRIPS MS) in Q-TOF and Orbitrap Mass Spectrometers: Single-Step Peptide Backbone Dissociations in Positive Ion Mode

    Science.gov (United States)

    Jang, Inae; Lee, Sun Young; Hwangbo, Song; Kang, Dukjin; Lee, Hookeun; Kim, Hugh I.; Moon, Bongjin; Oh, Han Bin

    2017-01-01

    The present study demonstrates that one-step peptide backbone fragmentations can be achieved using the TEMPO [2-(2,2,6,6-tetramethyl piperidine-1-oxyl)]-assisted free radical-initiated peptide sequencing (FRIPS) mass spectrometry in a hybrid quadrupole time-of-flight (Q-TOF) mass spectrometer and a Q-Exactive Orbitrap instrument in positive ion mode, in contrast to two-step peptide fragmentation in an ion-trap mass spectrometer (reference Anal. Chem. 85, 7044-7051 (30)). In the hybrid Q-TOF and Q-Exactive instruments, higher collisional energies can be applied to the target peptides, compared with the low collisional energies applied by the ion-trap instrument. The higher energy deposition and the additional multiple collisions in the collision cell in both instruments appear to result in one-step peptide backbone dissociations in positive ion mode. This new finding clearly demonstrates that the TEMPO-assisted FRIPS approach is a very useful tool in peptide mass spectrometry research.

  16. Organic Nanowires

    DEFF Research Database (Denmark)

    Balzer, Frank; Schiek, Manuela; Al-Shamery, Katharina;

    Single crystalline nanowires from fluorescing organic molecules like para-phenylenes or thiophenes are supposed to become key elements in future integrated optoelectronic devices [1]. For a sophisticated design of devices based on nanowires the basic principles of the nanowire formation have...

  17. An interactive integrative approach to translating knowledge and building a "learning organization" in health services management.

    Science.gov (United States)

    Chunharas, Somsak

    2006-08-01

    This paper proposes a basic approach to ensuring that knowledge from research studies is translated for use in health services management with a view towards building a "learning organization". (A learning organization is one in which the environment is structured in such a way as to facilitate learning as well as the sharing of knowledge among members or employees.) This paper highlights various dimensions that determine the complexity of knowledge translation, using the problem-solving cycle as the backbone for gaining a better understanding of how different types of knowledge interact in health services management. It is essential to use an integrated and interactive approach to ensure that knowledge from research is translated in a way that allows a learning organization to be built and that knowledge is not used merely to influence a single decision in isolation from the overall services and management of an organization.

  18. Relationship between band gap and bond length alternation in organic conjugated polymers

    Science.gov (United States)

    Bredas, J. L.

    1985-04-01

    A description is given of calculations of the evolution of the band gap as a function of geometry in conjugated polymers based on aromatic rings; polyparaphenylene, polypyrrole, polythiophene. The results demonstrate that the gap decreases as a function of increasing quinoid character of the backbone and is thus not minimal in the case of zero bond length alternation, in contrast to the situation found in polyacetylene-like compounds. The consequences of these results are stressed for the understanding of the effects of doping and for the design of new organic polymers with small gaps.

  19. 动载下饱和重塑黄土的骨干曲线变化研究%Study of variation of backbone curve of saturated remolded loess under dynamic loading

    Institute of Scientific and Technical Information of China (English)

    廖红建; 肖正华; 刘健

    2011-01-01

    针对饱和重塑黄土进行了一系列等向固结和偏压同结下的排水与不排水动三轴试验,分析了饱和重塑黄土的动力性质、骨干曲线模型及其影响因素.基于动三轴试验结果,探讨了在考虑累积塑性应变影响下,修正 Hardin-Drnevich模型的适用性.结果表明,考虑累积塑性应变时,修正Hardin-Drnevich模型能够较好地模拟饱和重塑黄土的骨干曲线试验结果.进而分析了等向固结和偏压固结、固结围压、波形和排水条件等因素对饱和重塑黄土骨干曲线的影响,得到偏压固结和同结围压的增大使骨干曲线上移,土体强度增加,而波形对骨干曲线的影响较小;排水条件下的骨干曲线较不排水条件下的有所上移,土体强度增加.所得结论可供工程设计人员参考.%A series of triaxial tests of saturated remolded loess under dynamic loading in isotropic and anisotropic consolidation stress states on condition of drain and undrain are performed to analyse its dynamic characteristics and backbone curves.Based on the dynamic triaxial test results, the effect of accumulated plastic strain is considered; and then the applicability of modified model of Hardin-Drnevich to saturated remolded loess is discussed.The results show that the modified model of Hardin-Drnevich could simulate the backbone curve of saturated remolded loess well.After that, the influences of isotropic and anisotropic consolidation stress states, confining pressure of consolidation, wave form and drain or undrain on the backbone curve for saturated remolded loess are also discussed.The backbone curves are all upper shift under anisotropic consolidation with the increasing confining pressure of consolidation; and it is shown that the strength of samples is increased; the impact of wave form on backbone curve is little; the effect of drain condition on it is upper shift comparing with undrained condition and this indicates that the strength of samples

  20. Organic photovoltaics

    DEFF Research Database (Denmark)

    Demming, Anna; Krebs, Frederik C; Chen, Hongzheng

    2013-01-01

    spectrum as possible can be converted into an electrical current', explains Mukundan Thelakkat and colleagues in Germany, the US and UK. In this special issue they report on how charge carrier mobility and morphology of the active blend layer in thin film organic solar cells correlate with device...... parameters [2]. The work contributes to a better understanding of the solar-cell characteristics of polymer:fullerene blends, which form the material basis for some of the most successful solution processable organic photovoltaic devices at present. Andrey E Rudenko, Sangtaik Noh, and Barry C Thompson...... Z and Wang L 2013 Fine tuning of the PCDTBT-OR:PC71BM blend nanoscale phase separation via selective solvent annealing toward high-performance polymer photovoltaics Nanotechnology 24 484004 [6] Arar M et al 2013 Influence of morphology and polymer:nanoparticle ratio on device performance of hybrid...

  1. Controlling the mode of operation of organic transistors through side-chain engineering

    KAUST Repository

    Giovannitti, Alexander

    2016-10-11

    Electrolyte-gated organic transistors offer low bias operation facilitated by direct contact of the transistor channel with an electrolyte. Their operation mode is generally defined by the dimensionality of charge transport, where a field-effect transistor allows for electrostatic charge accumulation at the electrolyte/semiconductor interface, whereas an organic electrochemical transistor (OECT) facilitates penetration of ions into the bulk of the channel, considered a slow process, leading to volumetric doping and electronic transport. Conducting polymer OECTs allow for fast switching and high currents through incorporation of excess, hygroscopic ionic phases, but operate in depletion mode. Here, we show that the use of glycolated side chains on a thiophene backbone can result in accumulation mode OECTs with high currents, transconductance, and sharp subthreshold switching, while maintaining fast switching speeds. Compared with alkylated analogs of the same backbone, the triethylene glycol side chains shift the mode of operation of aqueous electrolyte-gated transistors from interfacial to bulk doping/transport and show complete and reversible electrochromism and high volumetric capacitance at low operating biases. We propose that the glycol side chains facilitate hydration and ion penetration, without compromising electronic mobility, and suggest that this synthetic approach can be used to guide the design of organic mixed conductors.

  2. Organic Compounds

    Science.gov (United States)

    Shankland, Kenneth

    For many years, powder X-ray diffraction was used primarily as a fingerprinting method for phase identification in the context of molecular organic materials. In the early 1990s, with only a few notable exceptions, structures of even moderate complexity were not solvable from PXRD data alone. Global optimisation methods and highly-modified direct methods have transformed this situation by specifically exploiting some well-known properties of molecular compounds. This chapter will consider some of these properties.

  3. LEARNING ORGANIZATIONS: PREREQUISITE FOR SUCCESSFUL TOURISM ORGANIZATIONS

    Directory of Open Access Journals (Sweden)

    Natasa Kraleva

    2011-06-01

    Full Text Available Nowadays, each and every organization, including the tourism organizations should be learning organizations. The globalization and the competition affect the process of working of tourism organizations, where only the organizations which have knowledge, and are learning organizations can succeed. In a time of constant change, tourism organizations can have a competitive advantage only if they can do something or offer something different than their competitors. Many organizations in order to enable the learning process, should firstly undertake changes in the organization design, the organizational culture and the leadership style. The paper discusses the relevance of implementing the process of learning organizations as a concept for successful tourism organizations.

  4. LEARNING ORGANIZATIONS: PREREQUISITE FOR SUCCESSFUL TOURISM ORGANIZATIONS

    OpenAIRE

    Natasa Kraleva

    2011-01-01

    Nowadays, each and every organization, including the tourism organizations should be learning organizations. The globalization and the competition affect the process of working of tourism organizations, where only the organizations which have knowledge, and are learning organizations can succeed. In a time of constant change, tourism organizations can have a competitive advantage only if they can do something or offer something different than their competitors. Many organizations in order to ...

  5. Learning organizations: Prerequisite for successful tourism organizations

    OpenAIRE

    Natasa Kraleva

    2011-01-01

    Nowadays, each and every organization, including the tourism organizations should be learning organizations. The globalization and the competition affect the process of working of tourism organizations, where only the organizations which have knowledge, and are learning organizations can succeed. In a time of constant change, tourism organizations can have a competitive advantage only if they can do something or offer something different than their competitors. Many organizations in order to ...

  6. N-type organic electrochemical transistors with stability in water

    KAUST Repository

    Giovannitti, Alexander

    2016-10-07

    Organic electrochemical transistors (OECTs) are receiving significant attention due to their ability to efficiently transduce biological signals. A major limitation of this technology is that only p-type materials have been reported, which precludes the development of complementary circuits, and limits sensor technologies. Here, we report the first ever n-type OECT, with relatively balanced ambipolar charge transport characteristics based on a polymer that supports both hole and electron transport along its backbone when doped through an aqueous electrolyte and in the presence of oxygen. This new semiconducting polymer is designed specifically to facilitate ion transport and promote electrochemical doping. Stability measurements in water show no degradation when tested for 2 h under continuous cycling. This demonstration opens the possibility to develop complementary circuits based on OECTs and to improve the sophistication of bioelectronic devices.

  7. N-type organic electrochemical transistors with stability in water

    Science.gov (United States)

    Giovannitti, Alexander; Nielsen, Christian B.; Sbircea, Dan-Tiberiu; Inal, Sahika; Donahue, Mary; Niazi, Muhammad R.; Hanifi, David A.; Amassian, Aram; Malliaras, George G.; Rivnay, Jonathan; McCulloch, Iain

    2016-01-01

    Organic electrochemical transistors (OECTs) are receiving significant attention due to their ability to efficiently transduce biological signals. A major limitation of this technology is that only p-type materials have been reported, which precludes the development of complementary circuits, and limits sensor technologies. Here, we report the first ever n-type OECT, with relatively balanced ambipolar charge transport characteristics based on a polymer that supports both hole and electron transport along its backbone when doped through an aqueous electrolyte and in the presence of oxygen. This new semiconducting polymer is designed specifically to facilitate ion transport and promote electrochemical doping. Stability measurements in water show no degradation when tested for 2 h under continuous cycling. This demonstration opens the possibility to develop complementary circuits based on OECTs and to improve the sophistication of bioelectronic devices. PMID:27713414

  8. N-type organic electrochemical transistors with stability in water

    Science.gov (United States)

    Giovannitti, Alexander; Nielsen, Christian B.; Sbircea, Dan-Tiberiu; Inal, Sahika; Donahue, Mary; Niazi, Muhammad R.; Hanifi, David A.; Amassian, Aram; Malliaras, George G.; Rivnay, Jonathan; McCulloch, Iain

    2016-10-01

    Organic electrochemical transistors (OECTs) are receiving significant attention due to their ability to efficiently transduce biological signals. A major limitation of this technology is that only p-type materials have been reported, which precludes the development of complementary circuits, and limits sensor technologies. Here, we report the first ever n-type OECT, with relatively balanced ambipolar charge transport characteristics based on a polymer that supports both hole and electron transport along its backbone when doped through an aqueous electrolyte and in the presence of oxygen. This new semiconducting polymer is designed specifically to facilitate ion transport and promote electrochemical doping. Stability measurements in water show no degradation when tested for 2 h under continuous cycling. This demonstration opens the possibility to develop complementary circuits based on OECTs and to improve the sophistication of bioelectronic devices.

  9. Thin film encapsulation for organic light-emitting diodes using inorganic/organic hybrid layers by atomic layer deposition.

    Science.gov (United States)

    Zhang, Hao; Ding, He; Wei, Mengjie; Li, Chunya; Wei, Bin; Zhang, Jianhua

    2015-01-01

    A hybrid nanolaminates consisting of Al2O3/ZrO2/alucone (aluminum alkoxides with carbon-containing backbones) grown by atomic layer deposition (ALD) were reported for an encapsulation of organic light-emitting diodes (OLEDs). The electrical Ca test in this study was designed to measure the water vapor transmission rate (WVTR) of nanolaminates. We found that moisture barrier performance was improved with the increasing of the number of dyads (Al2O3/ZrO2/alucone) and the WVTR reached 8.5 × 10(-5) g/m(2)/day at 25°C, relative humidity (RH) 85%. The half lifetime of a green OLED with the initial luminance of 1,500 cd/m(2) reached 350 h using three pairs of the Al2O3 (15 nm)/ZrO2 (15 nm)/alucone (80 nm) as encapsulation layers.

  10. Organizing Process

    DEFF Research Database (Denmark)

    Hull Kristensen, Peer; Bojesen, Anders

    This paper invites to discuss the processes of individualization and organizing being carried out under what we might see as an emerging regime of change. The underlying argumentation is that in certain processes of change, competence becomes questionable at all times. The hazy characteristics...... of this regime of change are pursued through a discussion of competencies as opposed to qualifications illustrated by distinct cases from the Danish public sector in the search for repetitive mechanisms. The cases are put into a general perspective by drawing upon experiences from similar change processes...

  11. Entangling Organizations

    DEFF Research Database (Denmark)

    Strand, Anete Mikkala Camille

    2017-01-01

    The chapter accounts for the process of becoming of a changed practice within the area of disability care in the Municipality of Aalborg in Denmark. Across a period of a few months in the fall of 2015 a group of employees across the organization and an action researcher from Aalborg University (t....../ability and thereby the model opened the possibility for reworking the binary of ability/disability to the benefit of restorying the citizen’s ability in the practices of changing the disability care....

  12. (1)H, (13)C, (15)N backbone and side-chain resonance assignment of Nostoc sp. C139A variant of the heme-nitric oxide/oxygen binding (H-NOX) domain.

    Science.gov (United States)

    Alexandropoulos, Ioannis I; Argyriou, Aikaterini I; Marousis, Kostas D; Topouzis, Stavros; Papapetropoulos, Andreas; Spyroulias, Georgios A

    2016-10-01

    The H-NOX (Heme-nitric oxide/oxygen binding) domain is conserved across eukaryotes and bacteria. In human soluble guanylyl cyclase (sGC) the H-NOX domain functions as a sensor for the gaseous signaling agent nitric oxide (NO). sGC contains the heme-binding H-NOX domain at its N-terminus, which regulates the catalytic site contained within the C-terminal end of the enzyme catalyzing the conversion of GTP (guanosine 5'-triphosphate) to GMP (guanylyl monophosphate). Here, we present the backbone and side-chain assignments of the (1)H, (13)C and (15)N resonances of the 183-residue H-NOX domain from Nostoc sp. through solution NMR.

  13. 军队文职护理骨干护理科研培训需求调查%Investigation of the training requirements for military civilian nursing backbones in scientific nursing research

    Institute of Scientific and Technical Information of China (English)

    唐洪钦; 徐纪玲; 董琴; 何华; 欧崇阳

    2015-01-01

    目的:了解军队文职护理骨干护理科研培训需求情况。方法采用自制问卷表向全军第8批文职人员护理骨干任职教育培训班93名文职人员进行调查。结果90%文职护理骨干认为非常有必要开展护理科研培训,护理科研培训项目需求率前三的是:护理科研设计(89%)、医学统计学(83%)、论文写作技巧(80%);培训方式需求率排前三的是:科研培训班(85%)、专题讲座(82%)、专家指导(71%);科研培训适宜时间以2~4周为主。结论护理管理部门在文职护理骨干护理科研培训中应注重选择合适的科研培训项目和培训方式,合理安排培训时间,以提高文职护理骨干的护理科研能力。%Objective To investigate the training requirements of military civilian nursing backbones in scientific nursing re-search.Methods A questionnaire survey was conducted among the 93 military civilian personnel taking part in the 8t h working-post training class of military civilian nursing backbones by using the questionnaire specifically developed for the study.Results Ninety per cent of the military civilian nursing backbones held that it was absolutely necessary to conduct training on scientific nursing research. The top 3 training requirements for scientific nursing research were:scientific nursing research design (accounting for 89%),medical statistics (accounting for 83%)and thesis writing skill (accounting for 80%).The top 3 requirements of training forms were:scientific research training courses (accounting for 85%),seminars (accounting for 82%)and expert instruction (accounting for 71%).A 2 to 4-week training period was most appropriate for scientific research training.Conclusion Attention should be paid on the part of the nursing administration to the selection of appropriate scientific research training programs and training methods,as well as flexible ar-rangement of training time,so as to

  14. Organic photovoltaics

    Science.gov (United States)

    Demming, Anna; Krebs, Frederik C.; Chen, Hongzheng

    2013-12-01

    Energy inflation, the constant encouragement to economize on energy consumption and the huge investments in developing alternative energy resources might seem to suggest that there is a global shortage of energy. Far from it, the energy the Sun beams on the Earth each hour is equivalent to a year's supply, even at our increasingly ravenous rate of global energy consumption [1]. But it's not what you have got it's what you do with it. Hence the intense focus on photovoltaic research to find more efficient ways to harness energy from the Sun. Recently much of this research has centred on organic solar cells since they offer simple, low-cost, light-weight and large-area flexible photovoltaic structures. This issue with guest editors Frederik C Krebs and Hongzheng Chen focuses on some of the developments at the frontier of organic photovoltaic technology. Improving the power conversion efficiency of organic photovoltaic systems, while maintaining the inherent material, economic and fabrication benefits, has absorbed a great deal of research attention in recent years. Here significant progress has been made with reports now of organic photovoltaic devices with efficiencies of around 10%. Yet operating effectively across the electromagnetic spectrum remains a challenge. 'The trend is towards engineering low bandgap polymers with a wide optical absorption range and efficient hole/electron transport materials, so that light harvesting in the red and infrared region is enhanced and as much light of the solar spectrum as possible can be converted into an electrical current', explains Mukundan Thelakkat and colleagues in Germany, the US and UK. In this special issue they report on how charge carrier mobility and morphology of the active blend layer in thin film organic solar cells correlate with device parameters [2]. The work contributes to a better understanding of the solar-cell characteristics of polymer:fullerene blends, which form the material basis for some of the most

  15. Case Studies of Secondary School English Young Backbone Teachers' Professional Growth%中学英语青年骨干教师专业成长个案研究

    Institute of Scientific and Technical Information of China (English)

    王飞涛; 江苹

    2012-01-01

    It's a case study of the professional development of a young middle school English teacher. The study shows that profound professional knowledge and abilities form the base of being an excellent teacher; Second, only with strong desire to be an excellent teacher can a teacher keep pushing himself hard and being reflective and creative is also one of the core qualities of an excellent teacher. Third, specializing in self-regulated learning and reflection are the essential means of backbone teachers. Finally, creative problem solving and innovations enable teachers to improve the quality of teaching, is one of the core qualities of the backbone teachers.%本文是对一名中学英语青年骨干教师专业成长的个案研究。研究表明,首先青年教师应有深厚的专业知识和过硬的业务能力,这是成长为骨干教师的专业基础。其次,青年教师只有胸怀远大的专业理想,才会有源源不断的内驱力推动自己的专业水平不断朝前发展。第三,专业自主学习和反思是成就骨干教师的必经途径。最后,创新使教师能创造性解决问题和改进教学质量,是骨干教师的核心素养之一。

  16. hNCOcanH pulse sequence and a robust protocol for rapid and unambiguous assignment of backbone ((1)H(N), (15)N and (13)C') resonances in (15)N/(13)C-labeled proteins.

    Science.gov (United States)

    Kumar, Dinesh; Hosur, Ramakrishna V

    2011-09-01

    A three-dimensional nuclear magnetic resonance (NMR) pulse sequence named as hNCOcanH has been described to aid rapid sequential assignment of backbone resonances in (15)N/(13)C-labeled proteins. The experiment has been derived by a simple modification of the previously described HN(C)N pulse sequence [Panchal et al., J. Biomol. NMR 20 (2001) 135-147]; t2 evolution is used to frequency label (13)C' rather than (15)N (similar trick has also been used in the design of hNCAnH pulse sequence from hNcaNH [Frueh et al., JACS, 131 (2009) 12880-12881]). The modification results in a spectrum equivalent to HNCO, but in addition to inter-residue correlation peaks (i.e. Hi , Ci-1), the spectrum also contains additional intra-residue correlation peaks (i.e. Hi-1 , Ci-1) in the direct proton dimension which has maximum resolution. This is the main strength of the experiment and thus, even a small difference in amide (1) H chemical shifts (5-6 Hz) can be used for establishing a sequential connectivity. This experiment in combination with the HNN experiment described previously [Panchal et al., J. Biomol. NMR 20 (2001) 135-147] leads to a more robust assignment protocol for backbone resonances ((1) H(N) , (15)N) than could be derived from the combination of HNN and HN(C)N experiments [Bhavesh et al., Biochemistry, 40 (2001) 14727-14735]. Further, this new protocol enables assignment of (13)C' resonances as well. We believe that the experiment and the protocol presented here will be of immense value for structural-and functional-proteomics research by NMR. Performance of this experiment has been demonstrated using (13)C/(15)N labeled ubiquitin.

  17. 电力骨干通信网资源优化配置与仿真研究%Research and simulation on the resource optimization for the power communicaiton backbone network

    Institute of Scientific and Technical Information of China (English)

    周静; 刘贵荣; 赵子岩; 陈希

    2011-01-01

    For the power communication network, the main trend for its future backone optical transport network is the evolution from IP over SDH to IP over WDM. And so the Routing and Wavelength Assignment (RWA) will be one of key improtant problems. It has carried out the RWA simluation on a certain province electrical power communction backbone network, and both utilized wavelenth resource and network performance are compared for different network plan. Finally, a reasonable network plan schemes is recommanded.It is well shown that the appraoch should give a good reference to the choice of network optimization for power communication backbone optical network.%面向IP业务的新一代电力专网骨干传送网网络架构,总体趋势将从IP over SDH向IP overWDM演进,波长路由分配(Routing and Wavelength Assignment,RWA)问题成为电力骨干光传送网络中的核心问题之一.以某典型省电力公司2015年骨干传送网网目标网络架构为例,通过RWA仿真计算,综合分析比较了不同规划方案的网络资源占用率和网络性能指标,最后结合业务需求给出可选规划方案建议.研究方法可用于指导形成电力骨干光传送网的波长与路由配置的阶段性部署策略.

  18. Entangled Organizations

    DEFF Research Database (Denmark)

    Strand, Anete Mikkala Camille

    the model opened the possibility for reworking the binary. The offset of the becoming of the revised model for cooperation was taken from a quantum approach to organizational development and change coined as ‘Organizational scenography’ as part of the methodology of Material Storytelling (Strand 2012). Here...... to embrace other dis/ability care facilities and dis/ability care workers/professionals nearby as well as the neighborhood of the village of citizens surrounding these facilities. Thus reworking previously upheld cuts between areas of responsibility of the Municipality/relatives and of Municipality...... for the employees and thereby support the bringing about of a cultural transformation. A changed relationality indeed brought about though reworking the binary dis/able. From the standpoint of a diffractive methodology (Barad 2007) the paper accounts for this project by being organized in four parts that together...

  19. Macromolecular scaffolding: the relationship between nanoscale architecture and function in multichromophoric arrays for organic electronics.

    Science.gov (United States)

    Palermo, Vincenzo; Schwartz, Erik; Finlayson, Chris E; Liscio, Andrea; Otten, Matthijs B J; Trapani, Sara; Müllen, Klaus; Beljonne, David; Friend, Richard H; Nolte, Roeland J M; Rowan, Alan E; Samorì, Paolo

    2010-02-23

    The optimization of the electronic properties of molecular materials based on optically or electrically active organic building blocks requires a fine-tuning of their self-assembly properties at surfaces. Such a fine-tuning can be obtained on a scale up to 10 nm by mastering principles of supramolecular chemistry, i.e., by using suitably designed molecules interacting via pre-programmed noncovalent forces. The control and fine-tuning on a greater length scale is more difficult and challenging. This Research News highlights recent results we obtained on a new class of macromolecules that possess a very rigid backbone and side chains that point away from this backbone. Each side chain contains an organic semiconducting moiety, whose position and electronic interaction with neighboring moieties are dictated by the central macromolecular scaffold. A combined experimental and theoretical approach has made it possible to unravel the physical and chemical properties of this system across multiple length scales. The (opto)electronic properties of the new functional architectures have been explored by constructing prototypes of field-effect transistors and solar cells, thereby providing direct insight into the relationship between architecture and function.

  20. Hierarchical organization versus self-organization

    OpenAIRE

    Busseniers, Evo

    2014-01-01

    In this paper we try to define the difference between hierarchical organization and self-organization. Organization is defined as a structure with a function. So we can define the difference between hierarchical organization and self-organization both on the structure as on the function. In the next two chapters these two definitions are given. For the structure we will use some existing definitions in graph theory, for the function we will use existing theory on (self-)organization. In the t...

  1. CO2 Conversion: The Potential of Porous–Organic Polymers (POPs) for the cycloaddition of CO2 and epoxides

    KAUST Repository

    Alkordi, Mohamed Helmi

    2016-03-30

    Novel porous organic polymers (POPs) have been synthesized using functionalized Cr and Co-salen complexes as molecular building blocks. The integration of metalosalen catalysts into the porous polymers backbone permits the successful utilization of the materials as solid-state catalysts for CO2-epoxide cycloadditions reactions with excellent catalytic performance under mild conditions of temperature and pressure. The catalyst proved to be fully recyclable and robust thus showing the potential of POPs as smart functional materials for the heterogenization of key catalytic elements.

  2. Synthesis of the spacer-containing β-D-GalpNAc-(1→4)-β-D-GlcpNAc-(1→3)-α-D-Galp moiety, representing the non-fucosylated backbone trisaccharide of the glycocalyx glycan of the parasite Schistosoma mansoni

    NARCIS (Netherlands)

    Vliegenthart, J.F.G.; Halkes, K.M.; Lefeber, D.J.; Fransen, C.T.M.; Kamerling, J.P.

    1998-01-01

    The chemical synthesis of beta-d-GalpNAc-(1->4)-beta-d-GlcpNAc-(1->3)-beta-d-Galp-(1->O)- (CH2)5NH2 is described. This structure represents the nonfucosylated backbone trisaccharide of the glycocalyx glycan of the cercarial stage of the parasite Schistosoma mansoni. Synthesis of the trisaccharide wa

  3. 骨干网络中RoQ攻击的监测、定位和识别%MIL-RoQ:Monitoring,Identifying and Locating the RoQ Attack in Backbone Ne two rk

    Institute of Scientific and Technical Information of China (English)

    文坤; 杨家海; 程凤娟; 尹辉; 王健峰

    2015-01-01

    降质(reduction of quality ,RoQ)攻击是一种非典型拒绝服务攻击,它利用TCP自适应机制的安全漏洞能够显著降低或抑制TCP服务质量,且具有很强的隐蔽性。现有的研究集中在针对单条网络链路上的攻击和检测。但是,Ro Q攻击的对象并不局限于此,它既可以对单条链路发动攻击,也可以有选择的对多条链路(甚至整个网络)发起攻击,造成更大的危害,所以需要有一种能够从网络全局角度分析和识别的方法。为此,提出了一种基于骨干网络流量分析的异常监测、定位和识别的方法M IL‐Ro Q (monitoring ,identifying and locating the RoQ attack in backbone network )。主要使用主成分分析(principal component analysis ,PCA )和频谱分析(spectrum analysis)技术对骨干流量进行流量建模分析,从全局角度监测网络流量变化情况,能够同时分析和判断多条链路的异常情况,并能准确识别出Ro Q攻击。使用了CERNET骨干网络数据进行实验分析,结果表明该方法能够有效地定位和识别RoQ 攻击;同时,攻击识别时只需要使用局部的流量数据,因而能显著降低计算量和复杂度。%Reduction of quality (RoQ) attack is an atypical denial of service (DoS) attack ,which exploits the vulnerability of TCP's adaptive behavior that can seriously reduce or inhibit the throughput of TCP flows .While most of the defensive methods are studied on the single network access link (router) ,the RoQ attack can not only launch on the single network link ,but also attack towards several links or even entire network ,which causes more severe consequences .In order to obtain a global perspective from the network and identify the attack ,in this paper we propose a traffic anomaly analysis method to monitor ,identify and locate the RoQ attack in backbone network on the basis of principal component analysis (PCA ) and spectrum analysis

  4. Organic mixed conductors for bioelectronic applications (Conference Presentation)

    Science.gov (United States)

    Rivnay, Jonathan

    2016-09-01

    Direct measurement and stimulation of electrophysiological activity is a staple of neural and cardiac health monitoring, diagnosis and/or therapy. The ability to sensitively detect these signals can be enhanced by organic electronic materials that show mixed conduction properties (both electronic and ionic transport) in order to bridge the inherent mismatch that is prevalent between biological systems and traditional microelectronic materials/devices. Organic electrochemical transistors (OECTs) are one class of devices that utilize organic mixed conductors as the transistor channel, and have shown considerable promise as amplifying transducers due to their stability in aqueous conditions and high transconductance. These devices are fabricated in flexible, conformable form factors for in vivo recordings of epileptic activity, and for cutaneous EEG and ECG recordings in human subjects. The majority of high performance devices are based on conducting polymers such as poly(3,4-ethylenedioxythiophene) :poly(styrenesulfonate), PEDOT:PSS. By investigating PEDOT-based materials and devices, we are able to construct design rules for new formulations/materials. Introducing glycolated side chains to carefully selected semiconducting polymer backbones has enabled a new class high performance bioelectronic materials that feature high volumetric capacitance, transconductance >10mS (device dimensions ca. 10um), and steep subthreshold switching characteristics. A sub-set of these materials outperform PEDOT:PSS and shows significant promise for low power in vitro and in vivo biosensing applications.

  5. 军队文职人员护理骨干执行卫勤保障任务现状的调查%Investigation on Civilian Backbone Nurses in Military Medical Support Tasks

    Institute of Scientific and Technical Information of China (English)

    唐洪钦; 魏巍; 鱼敏; 化前珍; 谢文娟; 乐惠飞

    2011-01-01

    Objective To comprehend the problems for civilian backbone nurses in medical support tasks. Methods Questionnaires were used to investigate 83 civilian nurses of the professional education courses for 3rd batch of civilian backbone nures of PLA. The problems in implementing medical support tasks for cililian nures were listed as follows too few opportunities to perform large-scale medical support tasks, overweight workload,the obvious contradictions between work and training and unawareness of the purpose, objectives medical support tasks and scope of its responsibilities. Results Chances to implement large medical indemnity mission are too few, busy daily work and obvious contradiction between work and training, unclear about he purpose of the medical indemnity mission, objectives and scope of its responsibilities are three top major problems of implementing medical indemnity for nursing mainstay of civilian staffs. Conclusion To enhance the capacity of implementing medicla support tasks, the authorities should add more opportunities to perform large-scale medical support tasks,well coodinate the interdepartmental relationships, alleviate the contradictions between work and training and determine the purpose, objectives medical support tasks and scope of its responsibilities.%目的 了解军队文职人员护理骨干在执行卫勤保障任务中存在的问题.方法 采用自制的调查问卷对参加全军第3批文职人员护理骨干任职教育培训班的83名文职人员进行调查.结果 文职人员护理骨干在执行卫勤保障任务中存在的主要问题排在前三的依次是:执行大型卫勤保障任务的机会太少、平时科室工作繁忙、工作与训练矛盾突出,对卫勤保障任务的目的、目标及自身的职责范围不是很明确.结论 相关部门应适当增加文职人员执行大型卫勤保障任务的机会,部门之间搞好协调工作,缓解工作和训练的矛盾,在卫勤保障中明确任务的目的

  6. 河北广电光缆干线网动环监控系统的应用%The Application of Power & Environment Supervision System in Optical Fiber Transmission Backbone Network of Hebei Broadcasting & TV Information

    Institute of Scientific and Technical Information of China (English)

    宋立芳

    2014-01-01

    河北广电光缆传输干线网动环监控系统是根据河北广电网络的自身特点建设的,实现了对偏远山区无人值守站发电机的远程控制,利用省干线OTN公务语音通道解决了无人值守站动环监控信息的传送问题,切实做到了对全网站内动力环境的集中监控管理。应用该系统大大提高了网络维护的及时性和准确性,提高了维护水平和运维效率,节省了网络运营成本,达到了减员增效的目的,保障网络安全可靠运行。%The power&environment supervision system for optical fiber transmission backbone network is con -structed according to the characteristic of Hebei broadcasting& TV information network , which is different to the one of other carrier operator .The remote control of oil engine for no-duty station in remote mountain areas is implemented;and the no-duty station information transmission of power&environment supervision system is achieved by using OTN speech channel of province backbone lines network; and the centralized monitoring control management is feasibly realized in the whole network of Hebei broadcasting & TV information .By the application of the presented system , the timeliness and the accurateness of the network maintenance and the quality and efficiency of the network operation and maintenance are largely improved;the cost of the network operation is saved;the aim of increase efficiency by downsizing staff is achieved;and the reliability and safety of the network operation is guaranteed .

  7. Comb-like amphiphilic copolymers bearing acetal-functionalized backbones with the ability of acid-triggered hydrophobic-to-hydrophilic transition as effective nanocarriers for intracellular release of curcumin.

    Science.gov (United States)

    Zhao, Junqiang; Wang, Haiyang; Liu, Jinjian; Deng, Liandong; Liu, Jianfeng; Dong, Anjie; Zhang, Jianhua

    2013-11-11

    The pH-responsive micelles have enormous potential as nanosized drug carriers for cancer therapy due to their physicochemical changes in response to the tumor intracellular acidic microenvironment. Herein, a series of comb-like amphiphilic copolymers bearing acetal-functionalized backbone were developed based on poly[(2,4,6-trimethoxybenzylidene-1,1,1-tris(hydroxymethyl) ethane methacrylate-co-poly(ethylene glycol) methyl ether methacrylate] [P(TTMA-co-mPEGMA)] as effective nanocarriers for intracellular curcumin (CUR) release. P(TTMA-co-mPEGMA) copolymers with different hydrophobic-hydrophilic ratios were prepared by one-step reversible addition fragmentation chain transfer (RAFT) copolymerization of TTMA and mPEGMA. Their molecular structures and chemical compositions were confirmed by (1)H NMR, Fourier transform infrared spectroscopy (FT-IR) and gel permeation chromatography (GPC). P(TTMA-co-mPEGMA) copolymers could self-assemble into nanosized micelles in aqueous solution and displayed low critical micelle concentration (CMC). All P(TTMA-co-mPEGMA) micelles displayed excellent drug loading capacity, due to the strong π-π conjugate action and hydrophobic interaction between the PTTMA and CUR. Moreover, the hydrophobic PTTMA chain could be selectively hydrolyzed into a hydrophilic backbone in the mildly acidic environment, leading to significant swelling and final disassembly of the micelles. These morphological changes of P(TTMA-co-mPEGMA) micelles with time at pH 5.0 were determined by DLS and TEM. The in vitro CUR release from the micelles exhibited a pH-dependent behavior. The release rate of CUR was significantly accelerated at mildly acidic pH of 4.0 and 5.0 compared to that at pH 7.4. Toxicity test revealed that the P(TTMA-co-mPEGMA) copolymers exhibited low cytotoxicity, whereas the CUR-loaded micelles maintained high cytotoxicity for HepG-2 and EC-109 cells. The results indicated that the novel P(TTMA-co-mPEGMA) micelles with low CMC, small and tunable

  8. Expanded organic building units for the construction of highly porous metal-organic frameworks.

    Science.gov (United States)

    Kong, Guo-Qiang; Han, Zhi-Da; He, Yabing; Ou, Sha; Zhou, Wei; Yildirim, Taner; Krishna, Rajamani; Zou, Chao; Chen, Banglin; Wu, Chuan-De

    2013-10-25

    Two new organic building units that contain dicarboxylate sites for their self-assembly with paddlewheel [Cu2(CO2)4] units have been successfully developed to construct two isoreticular porous metal-organic frameworks (MOFs), ZJU-35 and ZJU-36, which have the same tbo topologies (Reticular Chemistry Structure Resource (RCSR) symbol) as HKUST-1. Because the organic linkers in ZJU-35 and ZJU-36 are systematically enlarged, the pores in these two new porous MOFs vary from 10.8 Å in HKUST-1 to 14.4 Å in ZJU-35 and 16.5 Å in ZJU-36, thus leading to their higher porosities with Brunauer-Emmett-Teller (BET) surface areas of 2899 and 4014 m(2) g(-1) for ZJU-35 and ZJU-36, respectively. High-pressure gas-sorption isotherms indicate that both ZJU-35 and ZJU-36 can take up large amounts of CH4 and CO2, and are among the few porous MOFs with the highest volumetric storage of CH4 under 60 bar and CO2 under 30 bar at room temperature. Their potential for high-pressure swing adsorption (PSA) hydrogen purification was also preliminarily examined and compared with several reported MOFs, thus indicating the potential of ZJU-35 and ZJU-36 for this important application. Studies show that most of the highly porous MOFs that can volumetrically take up the greatest amount of CH4 under 60 bar and CO2 under 30 bar at room temperature are those self-assembled from organic tetra- and hexacarboxylates that contain m-benzenedicarboxylate units with the [Cu2(CO2)4] units, because this series of MOFs can have balanced porosities, suitable pores, and framework densities to optimize their volumetric gas storage. The realization of the two new organic building units for their construction of highly porous MOFs through their self-assembly with [Cu2(CO2)4] units has provided great promise for the exploration of a large number of new tetra- and hexacarboxylate organic linkers based on these new organic building units in which different aromatic backbones can be readily incorporated

  9. Novel non-conjugated main-chain hole-transporting polymers for organic electronics application.

    Science.gov (United States)

    Schelter, Jürgen; Mielke, Georg Felix; Köhnen, Anne; Wies, Jenna; Köber, Sebastian; Nuyken, Oskar; Meerholz, Klaus

    2010-09-01

    A new class of hole-transporting polymers for use in organic electronic devices such as organic light-emitting diodes (OLEDs) or photorefractive holographic storage devices has been synthesized. The polymers contain tetraarylbenzidines or tetraarylphenylenediamines as charge-transporting units in the polymer backbone and are connected by non-conjugating fluorene bridges. For use in OLEDs the novel polymers were functionalized with oxetane groups that can be cross-linked via a cationic ring opening polymerization to yield insoluble networks. Such insoluble films are necessary for the fabrication of multilayer devices by wet deposition techniques. The novel materials feature improved film-formation properties as demonstrated in green-emitting double-layer OLEDs.

  10. Organic-inorganic hybrid protonic polymeric electrolytes grafted by sulfonic acid/sulfonamide moieties

    Energy Technology Data Exchange (ETDEWEB)

    Depre, L.; Poinsignon, C.; Popall, M.

    2000-07-01

    Thin proton conducting membranes of an organic-inorganic polymer electrolyte bearing sulphonamide and sulfonic groups are prepared by sol-gel process. Polycondensation of alkoxysilanes provides the inorganic silicate backbone whereas the organic network is formed from reactive functional groups R{prime}(({minus}DH{sub 2}){sub 3}-SO{sub 3}H) and [({minus}CH{sub 2}){sub 3}-SO{sub 2}NH{sub 2}] of alkoxysilanes of R{prime}Si[OR{sub 3}] type. Proton conductivity measured in the dry and wet state under controlled Temperature and Relative Humidity increases from 10{sup {minus}4} S/cm under vacuum to 6 10{sup {minus}2} S/cm at 70 C and 96% RH. Conductivity dependence on temperature and associated conduction mechanisms are discussed in both states.

  11. Efficient White Light Emission Using a Single Copolymer with Red and Green Chromophores on a Conjugated Polyfluorene Backbone Hybridized with InGaN-Based Light-Emitting Diodes

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yong; HOU Qiong; NIU Qiao-Li; ZHENG Shu-Wen; LI Shu-Ti; HE Miao; FAN Guang-Han

    2009-01-01

    We report an efficient white-light emission based on a single copolymer/InGaN hybrid light-emitting diode.The single copolymer consists of a conjugated polyfluorene backbone by incorporating 2,1,3-benzothiadiazole (BT) and 4, 7-bis(2-thienyl)-2,1,3-benzothiadiazole (DBT) as green and red light-emitting units, respectively. For the single eopolymer/lnGaN hybrid device, the Commission Internationale de l'Eclairage (CIE) coordinates,color temperature Tc and color rendering index Ra at 20mA are (0.323,0.329), 5960K and 86, respectively.In comparison with the performance of red copolymer PFO-DBT15 (DOF:DBT=85:15 with DOF being 9'9-dioctylfluorene) and green copolymer PFO-BT35 (DOF:BT=65:35) blend/InGaN hybrid white devices, it is concluded that the chemically doped copolymer hybridized device shows a higher emission intensity and spectral stability at a high driving current than the polymer blend.

  12. Emergence and spread of G3P[8] rotaviruses possessing an equine-like VP7 and a DS-1-like genetic backbone in the Basque Country (North of Spain), 2015.

    Science.gov (United States)

    Arana, Ainara; Montes, Milagrosa; Jere, Khuzwayo C; Alkorta, Miriam; Iturriza-Gómara, Miren; Cilla, Gustavo

    2016-10-01

    In March 2015, an atypical G3P[8] rotavirus with an equine-like VP7 gene was detected in Gipuzkoa (Basque Country, Spain) and spread contributing significantly to the seasonal epidemic. The strain was identified in fecal samples collected from 68 patients, mainly children from rural and urban settings with acute gastroenteritis, representing 14.9% of the 455 rotavirus strains genotyped between July 2014 and June 2015. Seven patients (10.3%) were hospitalized. Full genome analysis of six of these strains revealed a DS-1-like genotype constellation, G3-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2, and showed that most genome segments shared the highest nucleotide sequence identity with strains isolated in Japan, Thailand, Australia and the Philippines. The strains of Gipuzkoa were similar to novel G3P[8] reassortant rotaviruses with an equine-like VP7 gene and a DS-1-like genetic backbone that emerged in the Asia-Pacific Region in 2013. The study highlights the circulation of these atypical rotaviruses outside the Asia-Pacific Region of origin, and their emergence in a European Region. Due to their unusual genotype constellation, these strains pose a challenge for the rotavirus strain surveillance, since G-/P-typing, the most commonly used classification system, cannot identify this type of intergenogroup reassortants.

  13. Purification, crystallization and preliminary X-ray diffraction analysis of SpaD, a backbone-pilin subunit encoded by the fimbrial spaFED operon in Lactobacillus rhamnosus GG.

    Science.gov (United States)

    Chaurasia, Priyanka; von Ossowski, Ingemar; Palva, Airi; Krishnan, Vengadesan

    2015-01-01

    SpaD is the predicted backbone-pilin subunit of the SpaFED pilus, whose loci are encoded by the fimbrial spaFED operon in Lactobacillus rhamnosus GG, a Gram-positive gut-adapted commensal strain with perceived probiotic benefits. In this study, soluble recombinant SpaD protein was overproduced in Escherichia coli and then purified by Ni2+-chelating affinity and gel-filtration chromatography. After limited proteolysis with α-chymotrypsin, good-quality crystals of SpaD were obtained which diffracted beyond 2.0 Å resolution. These crystals belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a=50.11, b=83.27, c=149.65 Å. For phasing, sodium iodide-derivatized crystals were prepared using the halide quick-soaking method and diffraction data were collected in-house to a resolution of 2.2 Å. An interpretable electron-density map was successfully obtained using single-wavelength anomalous diffraction (SAD).

  14. Semiexperimental equilibrium structure for the C6 backbone of cis-1,3,5-hexatriene; structural evidence for greater pi-electron delocalization with increasing chain length in polyenes.

    Science.gov (United States)

    Suenram, Richard D; Pate, Brooks H; Lesarri, Alberto; Neill, Justin L; Shipman, Steven; Holmes, Robin A; Leyden, Matthew C; Craig, Norman C

    2009-03-05

    Twenty-five microwave lines were observed for cis-1,3,5-hexatriene (0.05 D dipole moment) and a smaller number for its three (13)C isotopomers in natural abundance. Ground-state rotational constants were fitted for all four species to a Watson-type rotational Hamiltonian for an asymmetric top (kappa = -0.9768). Vibration-rotation (alpha) constants were predicted with a B3LYP/cc-pVTZ model and used to adjust the ground-state rotational constants to equilibrium rotational constants. The small inertial defect for cis-hexatriene shows that the molecule is planar, despite significant H-H repulsion. The substitution method was applied to the equilibrium rotational constants to give a semiexperimental equilibrium structure for the C(6) backbone. This structure and one predicted with the B3LYP/cc-pVTZ model show structural evidence for increased pi-electron delocalization in comparison with butadiene, the first member of the polyene series.

  15. Gamma scintigraphy of {sup 111}In-labelled branched chain polypeptides (BCP) with a poly(L-lysine) backbone in mice with mammary carcinoma. Effect of charge on biodistribution and tumour imaging potential

    Energy Technology Data Exchange (ETDEWEB)

    Pimm, M.V.; Gribben, S.J. [University of Nottingham (United Kingdom); Perkins, A.C.; Mezo, G.; Gaal, D.; Hudecz, F.

    1995-11-01

    Radiolabelled synthetic branched chain polypeptides (BCP) represent a new and novel range of materials with potential as radiopharmaceuticals. Preliminary imaging studies have been undertaken with {sup 111}In-labelled BCP in mice with subcutaneously transplanted mammary carcinoma. Four polypeptides each with a poly(L-lysine) backbone and side chains of DL-alanine residues were studied. These were AK, which is polycationic, EAK which is amphoteric, having additional glutamic acid residues at the end of the side chains, and AcEAK (anionic) and SucEAK (highly polyanionic) where the terminal glutamic acid amino groups were acetylated or succinylated respectively. Radiolabelling was achieved by previous conjugation with DTPA. Serial images up to 48 hours showed marked retention of {sup 111}In-labelled polycationic AK and polyanionic SucEAK in the liver and spleen, with renal uptake also being visible in the case of AK. {sup 111}In-labelled EAK and AcEAK showed longer blood survival with some liver uptake, but tumour uptake was also visualized by 24 hours with both of these polypeptides. These studies demonstrate the feasibility of using {sup 111}In-labelled synthetic branched chain polypeptides as radiopharmaceuticals for gamma scintigraphy and the visualization of tumours by modification of the side chain structure. These materials warrant further study. (author).

  16. Efficient protocol for backbone and side-chain assignments of large, intrinsically disordered proteins: transient secondary structure analysis of 49.2 kDa microtubule associated protein 2c

    Energy Technology Data Exchange (ETDEWEB)

    Novacek, Jiri; Janda, Lubomir; Dopitova, Radka; Zidek, Lukas, E-mail: lzidek@chemi.muni.cz; Sklenar, Vladimir [Masaryk University, Faculty of Science, NCBR, and CEITEC (Czech Republic)

    2013-08-15

    Microtubule-associated proteins (MAPs) are abundantly present in axons and dendrites, and have been shown to play crucial role during the neuronal morphogenesis. The period of main dendritic outgrowth and synaptogenesis coincides with high expression levels of one of MAPs, the MAP2c, in rats. The MAP2c is a 49.2 kDa intrinsically disordered protein. To achieve an atomic resolution characterization of such a large protein, we have developed a protocol based on the acquisition of two five-dimensional {sup 13}C-directly detected NMR experiments. Our previously published 5D CACONCACO experiment (Novacek et al. in J Biomol NMR 50(1):1-11, 2011) provides the sequential assignment of the backbone resonances, which is not interrupted by the presence of the proline residues in the amino acid sequence. A novel 5D HC(CC-TOCSY)CACON experiment facilitates the assignment of the aliphatic side chain resonances. To streamline the data analysis, we have developed a semi-automated procedure for signal assignments. The obtained data provides the first atomic resolution insight into the conformational state of MAP2c and constitutes a model for further functional studies of MAPs.

  17. Organization of Nucleotides in Different Environments and the Formation of Pre-Polymers

    Science.gov (United States)

    Himbert, Sebastian; Chapman, Mindy; Deamer, David W.; Rheinstädter, Maikel C.

    2016-08-01

    RNA is a linear polymer of nucleotides linked by a ribose-phosphate backbone. Polymerization of nucleotides occurs in a condensation reaction in which phosphodiester bonds are formed. However, in the absence of enzymes and metabolism there has been no obvious way for RNA-like molecules to be produced and then encapsulated in cellular compartments. We investigated 5‧-adenosine monophosphate (AMP) and 5‧-uridine monophosphate (UMP) molecules confined in multi-lamellar phospholipid bilayers, nanoscopic films, ammonium chloride salt crystals and Montmorillonite clay, previously proposed to promote polymerization. X-ray diffraction was used to determine whether such conditions imposed a degree of order on the nucleotides. Two nucleotide signals were observed in all matrices, one corresponding to a nearest neighbour distance of 4.6 Å attributed to nucleotides that form a disordered, glassy structure. A second, smaller distance of 3.4 Å agrees well with the distance between stacked base pairs in the RNA backbone, and was assigned to the formation of pre-polymers, i.e., the organization of nucleotides into stacks of about 10 monomers. Such ordering can provide conditions that promote the nonenzymatic polymerization of RNA strands under prebiotic conditions. Experiments were modeled by Monte-Carlo simulations, which provide details of the molecular structure of these pre-polymers.

  18. Fluorinated polyimide gate dielectrics for the advancing the electrical stability of organic field-effect transistors.

    Science.gov (United States)

    Baek, Yonghwa; Lim, Sooman; Yoo, Eun Joo; Kim, Lae Ho; Kim, Haekyoung; Lee, Seung Woo; Kim, Se Hyun; Park, Chan Eon

    2014-09-10

    Organic field-effect transistors (OFETs) that operated with good electrical stability were prepared by synthesizing fluorinated polyimide (PI) gate dielectrics based on 6FDA-PDA-PDA PI and 6FDA-CF3Bz-PDA PI. 6FDA-PDA-PDA PI and 6FDA-CF3Bz-PDA PI contain 6 and 18 fluorine atoms per repeat unit, respectively. These fluorinated polymers provided smooth surface topographies and surface energies that decreased as the number of fluorine atoms in the polymer backbone increased. These properties led to a better crystalline morphology in the semiconductor film grown over their surfaces. The number of fluorine atoms in the PI backbone increased, the field-effect mobility improved, and the threshold voltage shifted toward positive values (from -0.38 to +2.21 V) in the OFETs with pentacene and triethylsilylethynyl anthradithiophene. In addition, the highly fluorinated polyimide dielectric showed negligible hysteresis and a notable gate bias stability under both a N2 environment and ambient air.

  19. Polyester based hybrid organic coatings

    Science.gov (United States)

    Wang, Xiaojiang

    Polyesters are a class of polymers widely used in organic coatings applications. In this work, four types of organic coatings based on polyester polyols were prepared: UV-curable polyester/poly(meth)acrylate coatings, thermal curable polyester polyurethane-urea coatings, thermal curable non-isocyanate polyurethane coatings, and UV-curable non-isocyanate polyurethane coatings. Polyester/poly(meth)acrylate block copolymers are synthesized using a combination of polycondensation and Atom-Transfer Radical Polymerization (ATRP). All block copolymers are characterized by means of Nuclear Magnetic Resonance (NMR) and Gel Permeation Chromatography (GPC). In the case of unsaturated-polyester-based block copolymers the main chain double bond in the polyester backbone remains almost unaffected during ATRP. The unsaturated block copolymers are crosslinkable and can form networks upon photo-irradiation in the presence of a suitable photoinitiator. These copolymers might be interesting candidates for coatings with better overall properties than those based on neat polyesters. Thermal curable polyester polyol based Polyurethane-Urea (PUU) coatings were formulated using Partially Blocked HDI isocyanurate (PBH), Isophorone Diamine (IPDA), and polyester polyol. As a comparison, the polyurethane coatings (PU) without adding IPDA were also prepared. The mechanical and viscoelastic properties of the PUU and PU coating were investigated by using tensile test and Dynamic Mechanical Thermal Analyzer (DMTA). It was found that PUU coating exhibited higher crosslink density, Tg, tensile modulus and strength than the corresponding PU coating. Thermal curable non-isocyanate polyurethane coatings were prepared by using polyamine and cyclic carbonate terminated polyester. Cyclic carbonate terminated polyester was synthesized from the reaction of the carbon dioxide and epoxidized polyester which was prepared from the polyester polyol. The properties of the epoxidized and cyclic carbonate

  20. Ordered organic-organic multilayer growth

    Science.gov (United States)

    Forrest, Stephen R; Lunt, Richard R

    2015-01-13

    An ordered multilayer crystalline organic thin film structure is formed by depositing at least two layers of thin film crystalline organic materials successively wherein the at least two thin film layers are selected to have their surface energies within .+-.50% of each other, and preferably within .+-.15% of each other, whereby every thin film layer within the multilayer crystalline organic thin film structure exhibit a quasi-epitaxial relationship with the adjacent crystalline organic thin film.

  1. The Legal Ethical Backbone of Conscientious Refusal

    DEFF Research Database (Denmark)

    Munthe, Christian; Nielsen, Morten Ebbe Juul

    2017-01-01

    This article analyzes the idea of a legal right to conscientious refusal for healthcare professionals from a basic legal ethical standpoint, using refusal to perform tasks related to legal abortion (in cases of voluntary employment) as a case in point. The idea of a legal right to conscientious...... refusal is distinguished from ideas regarding moral rights or reasons related to conscientious refusal, and none of the latter are found to support the notion of a legal right. Reasons for allowing some sort of room for conscientious refusal for healthcare professionals based on the importance of cultural...... identity and the fostering of a critical atmosphere might provide some support, if no countervailing factors apply. One such factor is that a legal right to healthcare professionals’ conscientious refusal must comply with basic legal ethical tenets regarding the rule of law and equal treatment...

  2. The backbone of the climate network

    Energy Technology Data Exchange (ETDEWEB)

    Donges, Jonathan Friedemann; Kurths, Juergen [Potsdam Institute for Climate Impact Research, P.O. Box 601203, 14412 Potsdam (Germany); Department of Physics, Humboldt University Berlin, Newtonstr. 15, 12489 Berlin (Germany); Zou, Yong; Marwan, Norbert [Potsdam Institute for Climate Impact Research, P.O. Box 601203, 14412 Potsdam (Germany)

    2010-07-01

    We propose a method to reconstruct and analyze a complex network from data generated by a spatio-temporal dynamical system, relying on the nonlinear mutual information of time series analysis and betweenness centrality of complex network theory. We show, that this approach reveals a rich internal structure in complex climate networks constructed from reanalysis and model surface air temperature data. Our novel method uncovers peculiar wave-like structures of high energy flow, that we relate to global surface ocean currents. This points to a major role of the oceanic surface circulation in coupling and stabilizing the global temperature field in the long term mean (140 years for the model run and 60 years for reanalysis data). We find that these results cannot be obtained using classical linear methods of multivariate data analysis, and have ensured their robustness by intensive significance testing.

  3. The backbone of the climate network

    CERN Document Server

    Donges, Jonathan F; Marwan, Norbert; Kurths, Juergen; 10.1209/0295-5075/87/48007

    2010-01-01

    We propose a method to reconstruct and analyze a complex network from data generated by a spatio-temporal dynamical system, relying on the nonlinear mutual information of time series analysis and betweenness centrality of complex network theory. We show, that this approach reveals a rich internal structure in complex climate networks constructed from reanalysis and model surface air temperature data. Our novel method uncovers peculiar wave-like structures of high energy flow, that we relate to global surface ocean currents. This points to a major role of the oceanic surface circulation in coupling and stabilizing the global temperature field in the long term mean (140 years for the model run and 60 years for reanalysis data). We find that these results cannot be obtained using classical linear methods of multivariate data analysis, and have ensured their robustness by intensive significance testing.

  4. Cervical Exercise: The Backbone of Spine Treatment

    Science.gov (United States)

    ... back of your neck and a sense of “crowding” your throat in front. Hold that “retracted” stretching position for 1-2 seconds and then release, allowing your head to return to neutral. Repeat that movement 8-10 times and perform 3-4 such ...

  5. Exercise: The Backbone of Spine Treatment

    Medline Plus

    Full Text Available ... provide quick and significant pain relief and speed recovery. Once your pain lessens or disappears, exercise can ... exercises recommended by physicians and therapists to help prevent and relieve low back pain. Privacy Policy | Terms ...

  6. The orientational preferences of backbones of proteins

    Institute of Scientific and Technical Information of China (English)

    CHEN Ying; WANG Jun; XUE Bin; WANG Wei

    2006-01-01

    The orientation between the backboneresidues of proteins is defined based on the local configurations and the corresponding preferences are analyzed by statistics. It is found that all the residue pairs have some specific preferences of orientations. The statistical analysis is mainly concentrated in the orientational distributions for two kinds of groupings of residues based on the hydrophobicity and secondary structural features. The statistics for such two types of groupings shows different orientational preferences. It is found that for the former grouping the orientational preference is rather weak,while for the later a kind of strong orientational preferences. This suggests that the formation of local structures and of secondary structures are highly related to the orientational preferences.

  7. The Dicyclopropylmethyl (Dcpm) Peptide Backbone Protectant†

    Science.gov (United States)

    Carpino, Louis A.; Nasr, Khaled; Abdel-Maksoud, Adel Ali; El-Faham, Ayman; Ionescu, Dumitru; Henklein, Peter; Wenschuh, Holger; Beyermann, Michael; Krause, Eberhard; Bienert, Michael

    2009-01-01

    The N-dicyclopropylmethyl (Dcpm) residue, introduced into amino acids via reaction of dicyclopropylmethanimine hydrochloride with an amino acid ester followed by sodium cyanoborohydride or triacetoxyborohydride reduction, can be used as an amide bond protectant for peptide synthesis. Examples which demonstrate the amelioration of aggregation effects include syntheses of the alanine decapeptide and the prion peptide (106–126). Avoidance of cyclization to the aminosuccinimide followed substitution of Fmoc-(Dcpm)Gly-OH for Fmoc-Gly-OH in the assembly of sequences containing the sensitive Asp-Gly unit. PMID:19719204

  8. Exercise: The Backbone of Spine Treatment

    Medline Plus

    Full Text Available ... Treatment | View Video Back About Video Struggling with Low Back Pain? Many people are surprised to learn that carefully ... physicians and therapists to help prevent and relieve low back pain. Privacy Policy | Terms of Use | Bookmark This Page | ...

  9. Core Backbone Convergence Mechanisms and Microloops Analysis

    Directory of Open Access Journals (Sweden)

    Abdelali Ala

    2012-07-01

    Full Text Available In this article we study approaches that can be used to minimise the convergence time, we also make a focus on microloops phenomenon, analysis and means to mitigate them. The convergence time reflects the time required by a network to react to a failure of a link or a router failure itself. When all nodes (routers have updated their respective routing and forwarding databases, we can say the network has converged. This study will help in building real-time and resilient network infrastructure, the goal is to make any evenement in the core network, as transparent as possible to any sensitive and real-time flows. This study is also, a deepening of earlier works presented in [10] and [11].

  10. The Legal Ethical Backbone of Conscientious Refusal.

    Science.gov (United States)

    Munthe, Christian; Nielsen, Morten Ebbe Juul

    2017-01-01

    This article analyzes the idea of a legal right to conscientious refusal for healthcare professionals from a basic legal ethical standpoint, using refusal to perform tasks related to legal abortion (in cases of voluntary employment) as a case in point. The idea of a legal right to conscientious refusal is distinguished from ideas regarding moral rights or reasons related to conscientious refusal, and none of the latter are found to support the notion of a legal right. Reasons for allowing some sort of room for conscientious refusal for healthcare professionals based on the importance of cultural identity and the fostering of a critical atmosphere might provide some support, if no countervailing factors apply. One such factor is that a legal right to healthcare professionals' conscientious refusal must comply with basic legal ethical tenets regarding the rule of law and equal treatment, and this requirement is found to create serious problems for those wishing to defend the idea under consideration. We conclude that the notion of a legal right to conscientious refusal for any profession is either fundamentally incompatible with elementary legal ethical requirements, or implausible because it undermines the functioning of a related professional sector (healthcare) or even of society as a whole.

  11. Topology Control within the Airborne Network Backbone

    Science.gov (United States)

    2009-10-01

    protocols resulting in infrequent topology control message exchange at the routing layer. The reactive protocols like ( AODV , TORA etc.) can also...each other. There are several ways MAToC interacts with different routing protocols : MAToC uses the Hello/Ack feedback mechanism of the proactive... routing protocols like OLSR and OSPF for monitoring links. The time dependent topology planned by deliberative MAToC is shared with proactive routing

  12. Foundry provides the network backbone for supercomputing

    CERN Multimedia

    2003-01-01

    Some of the results from the fourth annual High-Performance Bandwidth Challenge, held in conjunction with SC2003, the international conference on high-performance computing and networking which occurred last week in Phoenix, AZ (1/2 page).

  13. Organic and composite aerogels through ring opening metathesis polymerization (ROMP)

    Science.gov (United States)

    Mohite, Dhairyashil P.

    Aerogels are open-cell nanoporous materials, unique in terms of low density, low thermal conductivity, low dielectric constants and high acoustic attenuation. Those exceptional properties stem from their complex hierarchical solid framework (agglomerates of porous, fractal secondary nanoparticles), but they also come at a cost: low mechanical strength. This issue has been resolved by crosslinking silica aerogels with organic polymers. The crosslinking polymer has been assumed to form a conformal coating on the surface of the skeletal framework by covalent bridging elementary building blocks. However, "assuming" is not enough: for correlating nanostructure with bulk material properties, it is important to know the exact location of the polymer on the aerogel backbone. For that investigation, we synthesized a new norbornene derivative of triethoxysilane (Si-NAD) that can be attached to skeletal silica nanoparticles. Those norbornene-modified silica aerogels were crosslinked with polynorbornene by ring opening metathesis polymerization (ROMP). The detailed correlation between nanostructure and mechanical strength was probed with a wide array of characterization methods ranging from molecular to bulk through nano. Subsequently, it was reasoned that since the polymer dominates the exceptional mechanical properties of polymer crosslinked aerogels, purely organic aerogels with the same nanostructure and interparticle connectivity should behave similarly. That was explored and confirmed by: (a) synthesis of a difunctional nadimide monomer (bis-NAD), and preparation of robust polyimide aerogels by ROMP of its norbornene end-caps; and, (b) synthesis of dimensionally stable ROMP-derived polydicyclopentadiene aerogels by grafting the nanostructure with polymethylmethacrylate (PMMA) via free radical chemistry.

  14. Molecular Design of Benzodithiophene-Based Organic Photovoltaic Materials.

    Science.gov (United States)

    Yao, Huifeng; Ye, Long; Zhang, Hao; Li, Sunsun; Zhang, Shaoqing; Hou, Jianhui

    2016-06-22

    Advances in the design and application of highly efficient conjugated polymers and small molecules over the past years have enabled the rapid progress in the development of organic photovoltaic (OPV) technology as a promising alternative to conventional solar cells. Among the numerous OPV materials, benzodithiophene (BDT)-based polymers and small molecules have come to the fore in achieving outstanding power conversion efficiency (PCE) and breaking 10% efficiency barrier in the single junction OPV devices. Remarkably, the OPV device featured by BDT-based polymer has recently demonstrated an impressive PCE of 11.21%, indicating the great potential of this class of materials in commercial photovoltaic applications. In this review, we offered an overview of the organic photovoltaic materials based on BDT from the aspects of backbones, functional groups, alkyl chains, and device performance, trying to provide a guideline about the structure-performance relationship. We believe more exciting BDT-based photovoltaic materials and devices will be developed in the near future.

  15. Yersinia enterocolitica organism (image)

    Science.gov (United States)

    This picture shows the organism Yersinia enterocolitica . Yersinia organisms cause a wide range of disease but are most often associated with diarrhea or gastrointestinal symptoms. Yersinia infection is ...

  16. AN OPTIMISED LOW-RATE DISTRIBUTED DENIAL OF SERVICE ATTACK STRATEGY FOR INTERNET BACKBONE NETWORK%面向 Internet 骨干网的优化 LDDoS 策略

    Institute of Scientific and Technical Information of China (English)

    陈世云; 刘渊; 王晓锋

    2016-01-01

    低速率分布式拒绝服务攻击(LDDoS)正成为互联网的重要安全威胁之一。为更好地探索当前 Internet 存在的 LDDoS 隐患,以有效提升相应的防御策略,有必要研究面向 Internet 的 LDDoS 攻防策略。针对面向 Internet 骨干网的 LDDoS 攻击策略(CXPST)存在的攻击流量难以汇集于被攻击路径,从而导致攻击效果不明显的问题,提出一种优化的低速率分布式拒绝服务攻击部署策略。该策略基于路由信息,重点优化攻击流部署,从而能更有效地攻击关键路径。基于 GTNetS 进行仿真实验表明,与 CXPST策略相比,所提出的优化 LDDoS 策略能有效提升低速率拒绝服务攻击的精确性,实际的攻击效果更为明显。基于所提出的策略,进一步探讨面向 Internet 骨干网 LDDoS 的防御策略。%The low-rate distributed denial of service (LDDoS)attack is becoming one of the major threats to the Internet.In order to better explore the pitfalls of LDDoS existed in current Internet and to effectively enhance the corresponding defense strategy,it is necessary to study the Internet-oriented attack and defensive strategies of LDDoS.Aiming at the defect of CXPST,an attack strategy of LDDoS for Internet backbone network,that its attack traffic is hard to converge on the links to be attacked and this resulting in weak attacking effect,we present an optimised low-rate denial of service attacks deployment strategy.Based on routing information,the strategy focuses on the optimisation deployment of attack traffic,so that the critical paths can be attacked more effectively.It is demonstrated by the simulation experiment based on GTNetS that the optimised LDDoS attack deployment strategy proposed can effectively enhance the accuracy of the low-rate distributed denial of service attack compared with CXPST strategy,there is also a more obvious improvement in attacking effect.Based on the proposed strategy,we further

  17. 河北省小学科学骨干教师专业发展现状调查%Investigation and Analysis of the Professional Development Status of Elementary School Backbone Science Teachers in Hebei Province

    Institute of Scientific and Technical Information of China (English)

    张晓莹; 林长春; 梁国明; 吴育飞

    2013-01-01

      采用问卷调查对参加河北省“国培计划”的小学科学骨干教师的专业发展现状进行了调查。调查结果表明:河北省小学科学骨干教师年富力强,整体教龄较长,但科学教龄较短;大多数教师专业学科背景缺乏,专业知识结构与能力存在缺陷;专业发展途径不够完善,缺乏专业发展规划指导;教学科研能力薄弱,参加学术会议和培训机会相对较少。针对此种状况提出了促进小学科学教师专业发展的若干建议。%A survey is conducted to investigate the professional development status of elementary school backbone science teachers who participated in the“National training program for primary and secondary school teachers”in Hebei province. The results show that these teachers are young and energetic. Their seniority is long but that of science is short. Most of the teachers are lack of professional discipline background and their professional knowledge and ability structure are defective. Their ways of professional development are not perfect enough as they need guidance on professional development planning. Their teaching and scientific research abilities are weak, and they don’t have enough opportunities to participate in academic conferences and training. Finally, suggestions are proposed to promote the professional development of the elementary school science teachers.

  18. Post-translational heterocyclic backbone modifications in the 43-peptide antibiotic microcin B17. Structure elucidation and NMR study of a 13C,15N-labelled gyrase inhibitor.

    Science.gov (United States)

    Bayer, A; Freund, S; Jung, G

    1995-12-01

    Microcin B17 (McB17), the first known gyrase inhibitor of peptidic nature, is produced by ribosomal synthesis and post-translational modification of the 69-residue precursor protein by an Escherichia coli strain. To elucidate the chemical structure of the mature 43-residue peptide antibiotic, fermentation and purification protocols were established and optimized which allowed the isolation and purification of substantial amounts of highly pure McB17 (non-labelled, 15N-labelled and 13C/15N-labelled peptide. By ultraviolet-absorption spectroscopy. HPLC-electrospray mass spectrometry and GC-mass spectrometry, amino acid analysis, protein sequencing, and, in particular, multidimensional NMR, we could demonstrate and unequivocally prove that the enzymic modification of the precursor backbone at Gly-Cys and Gly-Ser segments leads to the formation of 2-aminomethylthiazole-4-carboxylic acid and 2-aminomethyloxazole-4-carboxylic acid, respectively. In addition, two bicyclic modifications 2-(2-aminomethyloxazolyl)thiazole-4-carboxylic acid and 2-(2-aminomethylthiazolyl)oxazole-4-carboxylic acid were found that consist of directly linked thiazole and oxazole rings derived from one Gly-Ser-Cys and one Gly-Cys-Ser segment. Analogous to the thiazole and oxazole rings found in antitumor peptides of microbial and marine origin, these heteroaromatic ring systems of McB17 presumably play an important role in its gyrase-inhibiting activity, e.g. interacting with the DNA to trap the covalent protein-DNA intermediate of the breakage-reunion reaction of the gyrase.

  19. Enhanced binding affinity, remarkable selectivity, and high capacity of CO 2 by dual functionalization of a rht-type metal-organic framework

    KAUST Repository

    Li, Baiyan

    2011-12-23

    Open and friendly: The smallest member of the rht-type metal-organic frameworks (MOFs, see picture) constructed by a hexacarboxylate ligand with a nitrogen-rich imino triazine backbone shows a significantly enhanced gas binding affinity relative to all other isoreticular rht-type MOFs. The high adsorption capacity and remarkable selectivity of CO 2 are attributed to the high density of open metal and Lewis basic sites in the framework. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Inserting CO2 into Aryl C-H Bonds of Metal-Organic Frameworks: CO2 Utilization for Direct Heterogeneous C-H Activation.

    Science.gov (United States)

    Gao, Wen-Yang; Wu, Haifan; Leng, Kunyue; Sun, Yinyong; Ma, Shengqian

    2016-04-25

    Described for the first time is that carbon dioxide (CO2 ) can be successfully inserted into aryl C-H bonds of the backbone of a metal-organic framework (MOF) to generate free carboxylate groups, which serve as Brønsted acid sites for efficiently catalyzing the methanolysis of epoxides. The work delineates the very first example of utilizing CO2 for heterogeneous C-H activation and carboxylation reactions on MOFs, and opens a new avenue for CO2 chemical transformations under mild reaction conditions.

  1. Why won’t talents return home? : a case study of contract breach by graduates of the Program of Training High-Caliber Backbone Personnel from the Ethnic Minorities = ¿Por qué el talento no vuelve a casa? : un estudio de caso sobre la brecha contractual entre graduados de Grupos Minoritarios del Programa para la Formación de Alto Nivel de Personal Backbone

    Directory of Open Access Journals (Sweden)

    Zhiyong Zhu

    2014-01-01

    Full Text Available In 2004, the Ministry of Education, National Development and Reform Commission, State Ethnic Affairs Commission, Ministry of Finance, Ministry of Human Resources and Social Security jointly released a special document On Training High-Caliber Backbone Personnel from the Ethnic Minorities, as a supporting measure for the strategy of human resources in western development of China. The central government takes it as an important force in thriving and developing the western region, especially the region where ethnic minority groups reside in the west. However, more and more graduates through the Program have breached or intend to break the contract of the Program. Why do they not abide by the contract and return to their hometown province for the work after they have enjoyed the preferential Program? This case study focused on three graduates who broke the employment contract through the Program, traced the origin and development of their minds and action, and demonstrated more about what hid behind the phenomenon. According to the deep interaction with these ethnic minority students, the research found that the social background under which high education policies for the ethnic minorities had greatly changed. The changes have challenged the implementation of the Program. Furthermore, under the socialistic market economy system, the employment contract of the Program couldn’t be processed and secured as the involved actors have expected. Last but not the least, the graduates benefited from the Program have become more and more individualistic and diversified in their career development due to different micro and macro reasons.En el año 2004 y de manera conjunta, el Ministerio de Educación, la Comisión Nacional para el Desarrollo y las Reformas, la Comisión Estatal de Asuntos Étnicos, el Ministerio de Economía, el Ministerio de Recursos Humanos y la Seguridad Social, publicaron una normativa especial para la Formación de Alto Nivel de

  2. Colour and Organization Studies

    DEFF Research Database (Denmark)

    Beyes, Timon

    2016-01-01

    of colour as aesthetic force and medium of transformation, the essay presents a montage of scenes that set up encounters with what colour does: how it affects organization, and how it is affected by organization; how it organizes what is given to perception, knowledge and organization itself, and how...

  3. Organizing design work

    DEFF Research Database (Denmark)

    Scheuer, John Damm

    2016-01-01

    The aim of this paper is to demonstrate the importance of the kind of understanding of organizing that is implied by design theories for project managers' understanding and organizing of design work. Five theories and their organizing consequences for project managers organizing of design work...... are analyzed. The paper contributes to design research and organization studies by putting the organizing of design projects on the research agenda. It also contributes by demonstrating the importance of being aware of the ontological and epistemological assumptions and organizing consequences of different...

  4. Growing Self-organized Design of Efficient and Robust Complex Networks

    CERN Document Server

    Hayashi, Yukio

    2014-01-01

    A self-organization of efficient and robust networks is important for a future design of communication or transportation systems, however both characteristics are incompatible in many real networks. Recently, it has been found that the robustness of onion-like structure with positive degree-degree correlations is optimal against intentional attacks. We show that, by biologically inspired copying, an onion-like network emerges in the incremental growth with functions of proxy access and reinforced connectivity on a space. The proposed network consists of the backbone of tree-like structure by copyings and the periphery by adding shortcut links between low degree nodes to enhance the connectivity. It has the fine properties of the statistically self-averaging unlike the conventional duplication-divergence model, exponential-like degree distribution without overloaded hubs, strong robustness against both malicious attacks and random failures, and the efficiency with short paths counted by the number of hops as m...

  5. Cyclic peptides-assisted trans- port of metal ions across liquid-organic membrane

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The formation of alkali and alkaline-earth metal picrate complexes with cyclo(Pro-Gly)n ionophores (1, n = 3; 2, n = 4) can facilitate the migration of metal ions across a bulk liquid CH2Cl2 membrane. The migration behavior was studied by measuring the solution absorption at 356 nm, using a UV/Vis spectrophotometer, and the rates can be determined by comparing the initial absorption of donor solutions with the absorption of the corresponding receiver solutions as the function of time. It was found that cyclic peptide 1 shows higher transport activity for the studied alkali and alkaline-earth metal ions than compound 2, which is related to the backbone flexibility of the cyclic peptides. The findings in this work suggest that the rate of ionophore-facilitated ion transport depends not only on the ability of complex forma-tion in aqueous phase, but also on the ability of complex dissociation in organic phase.

  6. Organic food processing

    DEFF Research Database (Denmark)

    Kahl, Johannes; Alborzi, Farnaz; Beck, Alexander

    2014-01-01

    In 2007 EU Regulation (EC) 834/2007 introduced principles and criteria for organic food processing. These regulations have been analysed and discussed in several scientific publications and research project reports. Recently, organic food quality was described by principles, aspects and criteria....... These principles from organic agriculture were verified and adapted for organic food processing. Different levels for evaluation were suggested. In another document, underlying paradigms and consumer perception of organic food were reviewed against functional food, resulting in identifying integral product...... to evaluate processing methods. Therefore the goal of this paper is to describe and discuss the topic of organic food processing to make it operational. A conceptual background for organic food processing is given by verifying the underlying paradigms and principles of organic farming and organic food as well...

  7. 面向骨干网NIDS的细粒度并行多模式匹配方法%Fine-grained Parallel Multi-pattern Matching for Backbone Network NIDS

    Institute of Scientific and Technical Information of China (English)

    邵宗有; 刘兴奎; 刘新春; 孙凝晖

    2013-01-01

    As the network bandwidth continuously increases, the network security has been seriously threatened by malicious behaviors and risks. Network intrusion detection system (NIDS) is one of the efficient measures to cope with intrusion threats and protect information security, which employs pattern matching techniques to analyze incoming packets and detect potential threats. However,pattern matching is such a compute-intensive task that most current techniques can't meet the demand of NIDS for backbone networks over lOGbps speed. We proposed a novel Bloom filter based approach for pattern matching,called PBPM (Parallel-Bloom-filter-based multi-Pattern Matching). PBPM employs multiple copies of the same Bloom filter to carry out parallel matching on different positions of the input text at the same time. The fine-grained parallel approach is able to skip multiple characters per clock when implemented on FPGAs,dramatically improving pattern matching performance. Experimental results on the rule set from Snort 2. 9 show that the throughput of PBPM exceeds more than 20Gbps.%随着网络带宽的快速增长,互联网正面临着日益严重的安全威胁.网络入侵检测系统(NIDS)利用模式匹配等技术对网络报文进行分析和检测,是防范网络威胁、保护网络安全的一种有效手段.但模式匹配消耗巨大的计算量,现有的技术难以满足10Gbps以上骨干网络NIDS的需求.提出了基于Bloom filter的细粒度并行模式匹配技术PBPM(Parallel-Bloom-filter-based multi-Pattern Matching),PBPM利用多个相同的Bloom filter分别从输入文本的不同位置处并行匹配,每个周期可完成多个字符的匹配,显著提高了匹配速率.详细讨论了在FPGA上的实现方式,在Snort 2.9规则集上的测试结果表明,PBPM能够提供超过20Gbps的模式匹配需求.

  8. A Cooperative Game Based Data Center Backbone Network Bandwidth Allocation Policy%基于合作博弈的数据中心骨干网带宽分配策略

    Institute of Scientific and Technical Information of China (English)

    孟飞; 兰巨龙; 胡宇翔

    2016-01-01

    数据中心(data center ,DC)之间通过部署流量工程来提高连接各个数据中心骨干网的利用率,虽然效率提升显著,但对不同类型汇聚流的带宽分配的公平性没有考虑。将多个汇聚流对带宽分配的竞争行为建模为一个合作博弈,通过寻求此博弈的纳什谈判解(Nash bargaining solution ,NBS)来确定优化的带宽分配策略 CGBA(cooperation game based bandwidth allocation ),权衡各汇聚流的最小带宽保证与带宽分配的公平性。在 Mininet 平台上进行实验仿真并和典型的带宽分配策略对比,结果表明CGBA 不但可保证各汇聚流的最小带宽需求,还确保了各类流对带宽资源竞争的公平性。%Currently ,traffic engineering is typically deployed to improve the utilization of data centers (DC) backbone networks ,which usually belongs to the same online service providers .Although the efficiency is remarkable ,the bandwidth allocation fairness of different aggregate flow isn’t considered . Hence ,the QoS guarantee is restricted .Because the bandwidth resource is expensive and packet loss is typically thought unacceptable ,the bandwidth utilization should be maximized ,at the same time , the QoS guarantee of different flow should be improved .In this paper ,the problem of contending the share bandwidth is modeled as a cooperative game ,and different aggregate flow compets the share bandwidth and maximizes the overall bandwidth resource utilization simultaneously ,and the optimal bandwidth allocation policy ,called cooperation game based bandwidth allocation (CGBA) ,is obtained through searching the Nash bargaining solution (NBS) of the game and balancing the tradeoff between minimum bandwidth guarantee and bandwidth allocation fairness .Simulation on a Mininet testbed shows that the proposed policy can effectively guarantee minimum bandwidth of each aggregate flow while ensuring the allocation fairness , compared with three

  9. Entrepreneurship and Organizations' Development

    Institute of Scientific and Technical Information of China (English)

    李慧

    2013-01-01

    In modern society, the competition has become increasingly fierce. Organizations pay close attention to their manage-ment in order to gain the priority. Under this context, entrepreneurship has been attached great importance to. Entrepreneurship has played an indispensable role in organizations. Compare to those short-lived companies, powerful organizations, such as Google, IBM and P&G has gain great progress in the last decades. Therefore, it is essential to study how the powerful organiza-tion could always be innovative. This paper aims to study the role that entrepreneurship plays in the organizations and take Google as an example. It provides some previous lessons that Chinese organizations could draw from.

  10. Interface Modifications for Applications in Organic and Hybrid Photovoltaics

    Science.gov (United States)

    Mazzio, Katherine A.

    Considerable research has been conducted in the area of organic photovoltaics due to several intrinsic advantages, including their high throughput solution processability, light weight, and their applicability on flexible substrates. Product development has been limited, however, due to the low mobilities and short exciton diffusion lengths of organic materials relative to inorganic materials used for photovoltaics. In this dissertation, we look at interfacial phenomena in attempt to control the charge transport dynamics in different parts of photovoltaic systems. The first chapter provides an overview of the field of organic photovoltaics, including their benefits, operating procedures, and a brief history of materials and device development. Chapter 2 examines some donor-acceptor small molecules as the electron donors in all organic bulk heterojunction solar cells with soluble fullerene derivatives as the electron acceptors. The donor-acceptor small molecules are unique because their energy levels agree well with the theoretical optimal HOMO and LUMO energy levels required for high efficiency organic photovoltaics. Even with energy level matching, however, we found that we were only able to obtain modest device efficiencies due to the formation of large domains that are greater than the exciton diffusion length and result in large interfacial areas. In chapter 3 we examine some of the optical, physical, and charge transport properties of a series of fully conjugated brush copolymers that are comprised of a carbazole-diketopyrrolorpyrrole donor-acceptor backbone copolymerized with different lengths of poly(3-hexylthiophene) pendant chains. It was found that there was a sufficient break in conjugation between the two copolymers such that the absorbance characteristics of both could be realized independently. In addition, the physical and charge transport properties could be tuned to primarily show influence from either the ambipolar low band gap backbone or the p

  11. The Visual Dimension in Organizing, Organization and Organization Research

    DEFF Research Database (Denmark)

    van Leeuwen, Theo; Meyer, Renate; Hollerer, Markus

    2013-01-01

    With the unprecedented rise in the use of visuals, and its undeniable omnipresence in organizational contexts, as well as in the individual's everyday life, organization and management science has recently started to pay closer attention to the to date under-theorized "visual mode" of discourse...... and meaning constriction, Building primarily on insights from the phenomenological tradition in organization theory and from social semiotics, this article sets out to consolidate previous scholarly efforts and to sketch a fertile future research agenda, After briefly exploring the working of visuals, we...... introduce the methodological and theoretical roots of visual studies in a number of disciplines that have a long-standing tradition of incorporating the visual. We then continue by extensively reviewing work in the field of organization and management studies: More specifically, we present five distinct...

  12. The Visual Dimension in Organizing, Organization, and Organization Research

    DEFF Research Database (Denmark)

    Meyer, Renate E.; Höllerer, Markus A.; Jancsary, Dennis

    2013-01-01

    With the unprecedented rise in the use of visuals, and its undeniable omnipresence in organizational contexts, as well as in the individual's everyday life, organization and management science has recently started to pay closer attention to the to date under-theorized “visual mode” of discourse...... and meaning construction. Building primarily on insights from the phenomenological tradition in organization theory and from social semiotics, this article sets out to consolidate previous scholarly efforts and to sketch a fertile future research agenda. After briefly exploring the workings of visuals, we...... introduce the methodological and theoretical “roots” of visual studies in a number of disciplines that have a long-standing tradition of incorporating the visual. We then continue by extensively reviewing work in the field of organization and management studies: More specifically, we present five distinct...

  13. Volatile Organic Compounds (VOCs)

    Science.gov (United States)

    ... Share Facebook Twitter Google+ Pinterest Contact Us Volatile Organic Compounds' Impact on Indoor Air Quality On this ... Exposure Standards or Guidelines Additional Resources Introduction Volatile organic compounds (VOCs) are emitted as gases from certain ...

  14. Soil Organic Carbon Stock

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — Soil organic carbon (SOC) is the carbon held within soil organic constituents (i.e., products produced as dead plants and animals decompose and the soil microbial...

  15. Organization theory. Analyzing health care organizations.

    Science.gov (United States)

    Cors, W K

    1997-02-01

    Organization theory (OT) is a tool that can be applied to analyze and understand health care organizations. Transaction cost theory is used to explain, in a unifying fashion, the myriad changes being undertaken by different groups of constituencies in health care. Agency theory is applied to aligning economic incentives needed to ensure Integrated Delivery System (IDS) success. By using tools such as OT, a clearer understanding of organizational changes is possible.

  16. Transparency in Organizing

    DEFF Research Database (Denmark)

    Albu, Oana Brindusa

    This dissertation provides a critical analysis of transparency in the context of organizing. The empirical material is based on qualitative studies of international cooperative organizations. The dissertation seeks to contribute to transparency and organizing scholarship by adopting a communication...... to being a solution for efficiency and democratic organizing, is a communicatively contested process which may lead to unintended consequences. The dissertation shows that transparency is performative: it can impact authority by de/legitimating action, shape the processes of organizational identity co...

  17. The Matrix Organization Revisited

    DEFF Research Database (Denmark)

    Gattiker, Urs E.; Ulhøi, John Parm

    1999-01-01

    This paper gives a short overview of matrix structure and technology management. It outlines some of the characteristics and also points out that many organizations may actualy be hybrids (i.e. mix several ways of organizing to allocate resorces effectively).......This paper gives a short overview of matrix structure and technology management. It outlines some of the characteristics and also points out that many organizations may actualy be hybrids (i.e. mix several ways of organizing to allocate resorces effectively)....

  18. Focus on Organic Conductors

    OpenAIRE

    Shinya Uji, Takehiko Mori and Toshihiro Takahashi

    2009-01-01

    Organic materials are usually thought of as electrical insulators. Progress in chemical synthesis, however, has brought us a rich variety of conducting organic materials, which can be classified into conducting polymers and molecular crystals. Researchers can realize highly conducting molecular crystals in charge-transfer complexes, where suitable combinations of organic electron donor or acceptor molecules with counter ions or other organic molecules provide charge carriers. By means of a ki...

  19. What is organic certification?

    Science.gov (United States)

    Certified organic crop production is a holistic approach to sustainable and healthy food production to enhance the well being of the consumer, while protecting natural resources. Organic certification was implemented by the National Organic Program (NOP) in 2002 in recognition of the necessity for c...

  20. Inverted organic photosensitive devices

    Energy Technology Data Exchange (ETDEWEB)

    Forrest, Stephen R.; Bailey-Salzman, Rhonda F.

    2016-12-06

    The present disclosure relates to organic photosensitive optoelectronic devices grown in an inverted manner. An inverted organic photosensitive optoelectronic device of the present disclosure comprises a reflective electrode, an organic donor-acceptor heterojunction over the reflective electrode, and a transparent electrode on top of the donor-acceptor heterojunction.

  1. Values in Organic Farming

    DEFF Research Database (Denmark)

    Kjærgård, Bente; Pedersen, Kirsten Bransholm; Land, Birgit

    The study focuses on the recent debate about what is, or what constitutes, organic farming and what is the right path for organic farming in the future. The study is based on a critical discourse analysis of the controversy about suspending the private standard for organic farming adopted...

  2. Nanostructured Organic Solar Cells

    DEFF Research Database (Denmark)

    Radziwon, Michal Jędrzej; Rubahn, Horst-Günter; Madsen, Morten

    Recent forecasts for alternative energy generation predict emerging importance of supporting state of art photovoltaic solar cells with their organic equivalents. Despite their significantly lower efficiency, number of application niches are suitable for organic solar cells. This work reveals...... the principles of bulk heterojunction organic solar cells fabrication as well as summarises major differences in physics of their operation....

  3. Organics go hybrid

    Science.gov (United States)

    Lanzani, Guglielmo; Petrozza, Annamaria; Caironi, Mario

    2017-01-01

    From displays to solar cells, the field of organic optoelectronics has come a long way over the past 50 years, but the realization of an electrically pumped organic laser remains elusive. The answer may lie with hybrid organic-inorganic materials called perovskites.

  4. Organ Harvesting and Transplants

    Science.gov (United States)

    Baskette, Kimberly G.; Ritz, John M.

    2010-01-01

    Humans and animals need healthy organs to live. Due to medical conditions and accidents, some organs fail to function properly. For these reasons, the medical community has experimented and can now perform successful organ transplants, allowing patients to continue to live their lives. Many countries have medical programs where individuals can…

  5. Organic chemistry in space

    Science.gov (United States)

    Johnson, R. D.

    1977-01-01

    Organic cosmochemistry, organic materials in space exploration, and biochemistry of man in space are briefly surveyed. A model of Jupiter's atmosphere is considered, and the search for organic molecules in the solar system and in interstellar space is discussed. Materials and analytical techniques relevant to space exploration are indicated, and the blood and urine analyses performed on Skylab are described.

  6. Multiple organ procurement

    Directory of Open Access Journals (Sweden)

    Vuković Milivoje

    2007-01-01

    Full Text Available Introduction. Liver transplantation is the most demanding of all solid organ transplantations. It requires perfect organization and motivation of health care professionals, patients and their families. This article deals with the procedure for multiple organ procurement, reviews criteria for organ donation and describes the surgical technique for multiple organ procurement. Discussion. Adequate selection and evaluation of cadaveric donors and of organs for transplantation should include early identification of potential donors, and early diagnosis of brain death. The procurement of the highest number of viable organs for transplantation requires excellence in each of the phases. Early and aggressive physiologic support in the maintenance of potential donors can reduce organ donor loss due to irreversible asystole or multiorgan failure (it is almost always possible to maintain organ perfusion pressure and increase the number of organs without increasing post-transplant morbidity or mortality. The ideal donor is a young, previously healthy, brain dead, victim of an accident. Conclusion. The surgical procedure for multiple organ procurement from brain death donors must be performed without intraopertive organ damage. .

  7. The Semantic Learning Organization

    Science.gov (United States)

    Sicilia, Miguel-Angel; Lytras, Miltiadis D.

    2005-01-01

    Purpose: The aim of this paper is introducing the concept of a "semantic learning organization" (SLO) as an extension of the concept of "learning organization" in the technological domain. Design/methodology/approach: The paper takes existing definitions and conceptualizations of both learning organizations and Semantic Web technology to develop…

  8. Organic photosensitive devices

    Science.gov (United States)

    Rand, Barry P; Forrest, Stephen R

    2013-11-26

    The present invention generally relates to organic photosensitive optoelectronic devices. More specifically, it is directed to organic photosensitive optoelectronic devices having a photoactive organic region containing encapsulated nanoparticles that exhibit plasmon resonances. An enhancement of the incident optical field is achieved via surface plasmon polariton resonances. This enhancement increases the absorption of incident light, leading to a more efficient device.

  9. Development of Polymer Acceptors for Organic Photovoltaic Cells

    Directory of Open Access Journals (Sweden)

    Yujeong Kim

    2014-02-01

    Full Text Available This review provides a current status report of the various n-type polymer acceptors for use as active materials in organic photovoltaic cells (OPVs. The polymer acceptors are divided into four categories. The first section of this review focuses on rylene diimide-based polymers, including perylene diimide, naphthalene diimide, and dithienocoronene diimide-based polymers. The high electron mobility and good stability of rylene diimides make them suitable for use as polymer acceptors in OPVs. The second section deals with fluorene and benzothiadiazole-based polymers such as poly(9,9’-dioctylfluorene-co-benzothiadiazole, and the ensuing section focuses on the cyano-substituted polymer acceptors. Cyano-poly(phenylenevinylene and poly(3-cyano-4-hexylthiophene have been used as acceptors in OPVs and exhibit high electron affinity arising from the electron-withdrawing cyano groups in the vinylene group of poly(phenylenevinylene or the thiophene ring of polythiophene. Lastly, a number of other electron-deficient groups such as thiazole, diketopyrrolopyrrole, and oxadiazole have also been introduced onto polymer backbones to induce n-type characteristics in the polymer. Since the first report on all-polymer solar cells in 1995, the best power conversion efficiency obtained with these devices to date has been 3.45%. The overall trend in the development of n-type polymer acceptors is presented in this review.

  10. Supramolecular organization in organic-inorganic heterogeneous hybrid catalysts formed from polyoxometalate and poly(ampholyte) polymer.

    Science.gov (United States)

    Raj, Gijo; Swalus, Colas; Guillet, Alain; Devillers, Michel; Nysten, Bernard; Gaigneaux, Eric M

    2013-04-01

    Hybridization of polyoxometalates (POMs) via the formation of an organic-inorganic association constitutes a new route to develop a heterogeneous POM catalyst with tunable functionality imparted through supramolecular assembly. Herein, we report on strategies to obtain tunable well-defined supramolecular architectures of an organic-inorganic heterogeneous hybrid catalyst formed by the association of a hydrophobically substituted polyampholyte copolymer (poly N, N-diallyl-N-hexylamine-alt-maleic acid) and phosphotungstic acid (H3PW12O40) POMs. The self-assembling property of the initial polyampholyte copolymer matrix is modulated by controlling the pH of the hybridization solution. When deposited on a mica surface, isolated, long and extended polymer chains are formed under basic conditions (pH 7.9), while globular or coiled structures are formed under acidic conditions (pH 2). The supramolecular assembly of the POM-polymer hybrid is found to be directed by the type and quantities of charges present on the polyampholyte copolymer, which themselves depend on the pH conditions. The hypothesis is that the Keggin type [PW12O40](3-) anions, which have a size of ~1 nm, electrostatically bind to the positive charge sites of the polymer backbone. The hybrid material stabilized at pH 5.3 consists of POM-decorated polymer chains. Statistical analysis of distances between pairs of POM entities show narrow density distributions, suggesting that POM entities are attached to the polymer chains with a high level of order. Conversely, under acidic conditions (pH 2), the hybrid shows the formation of a core-shell type of structure. The strategies reported here, to tune the supramolecular assembly of organic-inorganic hybrid materials, are highly valuable for the design and a more rational utilization of POM heterogeneous catalysts in several chemical transformations.

  11. Conjugated Polymer Zwitterions: Efficient Interlayer Materials in Organic Electronics.

    Science.gov (United States)

    Liu, Yao; Duzhko, Volodimyr V; Page, Zachariah A; Emrick, Todd; Russell, Thomas P

    2016-11-15

    quenching, possess optimal electron affinity that neither limits the work function reduction nor impedes the charge extraction, transport electrons selectively, and exhibit long-term stability. Our recent discoveries show that CPZs achieve many of these attributes, and are poised for further expansion and development in the interfacial science of organic electronics. This Account reviews a recent collaboration that began with the synthesis of CPZs and a study of their structural and electronic properties on metals, then extended to their application as interlayer materials for OPVs. We discuss CPZ structure-property relationships based on several material platforms, ranging from homopolymers to copolymers, and from materials with intrinsic p-type conjugated backbones to those with intrinsic n-type conjugated backbones. We discuss key components of such interlayers, including (i) the origin of work function reduction of CPZ interlayers on metals; (ii) the role of the frontier molecular orbital energy levels and their trade-offs in optimizing electronic and device properties; and (iii) the role of polymer conductivity type and the magnitude of charge carrier mobility. Our motivation is to present our prior use and current understanding of CPZs as interlayer materials in organic electronics, and describe outstanding issues and future potential directions.

  12. Challenges in organ transplantation.

    Science.gov (United States)

    Beyar, Rafael

    2011-04-01

    Organ transplantation has progressed tremendously with improvements in surgical methods, organ preservation, and pharmaco-immunologic therapies and has become a critical pathway in the management of severe organ failure worldwide. The major sources of organs are deceased donors after brain death; however, a substantial number of organs come from live donations, and a significant number can also be obtained from non-heart-beating donors. Yet, despite progress in medical, pharmacologic, and surgical techniques, the shortage of organs is a worldwide problem that needs to be addressed internationally at the highest possible levels. This particular field involves medical ethics, religion, and society behavior and beliefs. Some of the critical ethical issues that require aggressive interference are organ trafficking, payments for organs, and the delicate balance in live donations between the benefit to the recipient and the possible harm to the donor and others. A major issue in organ transplantation is the definition of death and particularly brain death. Another major critical factor is the internal tendency of a specific society to donate organs. In the review below, we will discuss the various challenges that face organ donation worldwide, and particularly in Israel, and some proposed mechanisms to overcome this difficulty.

  13. Immunity of international organizations

    CERN Document Server

    Schrijver, Nico

    2015-01-01

    Immunity rules are part and parcel of the law of international organizations. It has long been accepted that international organizations and their staff need to enjoy immunity from the jurisdiction of national courts. However, it is the application of these rules in practice that increasingly causes controversy. Claims against international organizations are brought before national courts by those who allegedly suffer from their activities. These can be both natural and legal persons such as companies. National courts, in particular lower courts, have often been less willing to recognize the immunity of the organization concerned than the organization s founding fathers. Likewise, public opinion and legal writings frequently criticize international organizations for invoking their immunity and for the lack of adequate means of redress for claimants. It is against this background that an international conference was organized at Leiden University in June 2013. A number of highly qualified academics and practit...

  14. Organs as inheritable property?

    Science.gov (United States)

    Voo, Teck Chuan; Holm, Soren

    2014-01-01

    It has been argued that organs should be treated as individual tradable property like other material possessions and assets, on the basis that this would promote individual freedom and increase efficiency in addressing the shortage of organs for transplantation. If organs are to be treated as property, should they be inheritable? This paper seeks to contribute to the idea of organs as inheritable property by providing a defence of a default of the family of a dead person as inheritors of transplantable organs. In the course of discussion, various succession rules for organs and their justifications will be suggested. We then consider two objections to organs as inheritable property. Our intention here is to provoke further thought on whether ownership of one's body parts should be assimilated to property ownership.

  15. Focus on Organic Conductors

    Directory of Open Access Journals (Sweden)

    Shinya Uji, Takehiko Mori and Toshihiro Takahashi

    2009-01-01

    Full Text Available Organic materials are usually thought of as electrical insulators. Progress in chemical synthesis, however, has brought us a rich variety of conducting organic materials, which can be classified into conducting polymers and molecular crystals. Researchers can realize highly conducting molecular crystals in charge-transfer complexes, where suitable combinations of organic electron donor or acceptor molecules with counter ions or other organic molecules provide charge carriers. By means of a kind of chemical doping, the charge-transfer complexes exhibit high electrical conductivity and, thanks to their highly crystalline nature, even superconductivity has been observed. This focus issue of Science and Technology of Advanced Materials is devoted to the research into such 'organic conductors'The first organic metal was (TTF(TCNQ, which was found in 1973 to have high conductivity at room temperature and a metal–insulator transition at low temperatures. The first organic superconductor was (TMTSF2PF6, whose superconductivity under high pressures was reported by J´erome in 1980. After these findings, the research on organic conductors exploded. Hundreds of organic conductors have been reported, among which more than one hundred exhibit superconductivity. Recently, a single-component organic conductor has been found with metallic conductivity down to low temperatures.In these organic conductors, in spite of their simple electronic structures, much new physics has arisen from the low dimensionality. Examples are charge and spin density waves, characteristic metal–insulator transitions, charge order, unconventional superconductivity, superconductor–insulator transitions, and zero-gap conductors with Dirac cones. The discovery of this new physics is undoubtedly derived from the development of many intriguing novel organic conductors. High quality single crystals are indispensable to the precise measurement of electronic states.This focus issue

  16. Evolution of genetic organization in digital organisms

    CERN Document Server

    Ofria, C A; Ofria, Charles; Adami, Christoph

    1999-01-01

    We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed ancestor, we witness the development of complex, parallel secondary expression patterns. Using principles from information theory, we demonstrate an evolutionary pressure towards overlapping expressions causing variation (and hence further evolution) to sharply drop. Finally, we compare the overlapping sections of dominant genomes to those portions which are singly expressed and observe a significant difference in the entropy of their encoding.

  17. The Expressive Organization

    DEFF Research Database (Denmark)

    This text challenges beliefs about organizational identity, reputation, and branding. It contains a wealth of new ideas for finding the elusive answers to questions troubling contemporary organizations. How does an organization create a strong reputation? What are the implications of corporate...... branding on organizational structures and processes? How do organizations discover their identities? These are some of the vexing problems addressed in this book by a diverse international team of contributors. According to the authors, the future lies with "the expressive organization". Such organizations...... not only understand their distinct identity and their brands, but are also able to express these externally and internally. In order to thrive in an era of transparency and customer choice, the authors argue, organizations will have to be expressive. This book is intended for undergraduate and postgraduate...

  18. Theology and Organization

    DEFF Research Database (Denmark)

    Meier Sørensen, Bent; Spoelstra, Sverre; Höpfl, Heather

    2012-01-01

    of religious practices in organizations. Instead, theology of organization recognizes that the way we think about and act in organizations is profoundly structured by theological concepts. In this editorial to the special issue we have three aims: to outline what theology of organization is, to show how...... it builds upon Carl Schmitt’s ‘political theology’ and Giorgio Agamben’s ‘economic theology’ and finally to propose three different forms that theology of organization can take. These forms of theology of organization respectively (1) analyse organizational concepts as secularized theological concepts, (2......) show how theological concepts have survived unaltered in organizational contexts and (3) show how theological concepts have been corrupted or lost their original meaning when deployed in organizational contexts. In the final section of this editorial, we introduce the five contributions to this issue...

  19. Evolving Procurement Organizations

    DEFF Research Database (Denmark)

    Bals, Lydia; Laiho, Aki; Laine, Jari

    Procurement has to find further levers and advance its contribution to corporate goals continuously. This places pressure on its organization in order to facilitate its performance. Therefore, Procurement organizations constantly have to evolve in order to match these demands. A conceptual model...... is presented and results of a first case study discussed. The findings highlight the importance of taking a contingency perspective on Procurement organization, understanding the internal and internal contingency factors. From a theoretical perspective, it opens up insights that can be furthermore leveraged...... in future studies in the fields of hybrid procurement organizations, global sourcing organizations as well as international procurement offices (IPOs). From a practical standpoint, an assessment of external and internal contingencies provides the opportunity to consciously match organization to its...

  20. Organic matter in meteorites.

    Science.gov (United States)

    Llorca, Jordi

    2004-12-01

    Some primitive meteorites are carbon-rich objects containing a variety of organic molecules that constitute a valuable record of organic chemical evolution in the universe prior to the appearance of microorganisms. Families of compounds include hydrocarbons, alcohols, aldehydes, ketones, carboxylic acids, amino acids, amines, amides, heterocycles, phosphonic acids, sulfonic acids, sugar-related compounds and poorly defined high-molecular weight macromolecules. A variety of environments are required in order to explain this organic inventory, including interstellar processes, gas-grain reactions operating in the solar nebula, and hydrothermal alteration of parent bodies. Most likely, substantial amounts of such organic materials were delivered to the Earth via a late accretion, thereby providing organic compounds important for the emergence of life itself, or that served as a feedstock for further chemical evolution. This review discusses the organic content of primitive meteorites and their relevance to the build up of biomolecules.