Science.gov

Sample records for complex fibre architecture

  1. Resolving complex fibre architecture by means of sparse spherical deconvolution in the presence of isotropic diffusion

    NASA Astrophysics Data System (ADS)

    Zhou, Q.; Michailovich, O.; Rathi, Y.

    2014-03-01

    High angular resolution diffusion imaging (HARDI) improves upon more traditional diffusion tensor imaging (DTI) in its ability to resolve the orientations of crossing and branching neural fibre tracts. The HARDI signals are measured over a spherical shell in q-space, and are usually used as an input to q-ball imaging (QBI) which allows estimation of the diffusion orientation distribution functions (ODFs) associated with a given region-of interest. Unfortunately, the partial nature of single-shell sampling imposes limits on the estimation accuracy. As a result, the recovered ODFs may not possess sufficient resolution to reveal the orientations of fibre tracts which cross each other at acute angles. A possible solution to the problem of limited resolution of QBI is provided by means of spherical deconvolution, a particular instance of which is sparse deconvolution. However, while capable of yielding high-resolution reconstructions over spacial locations corresponding to white matter, such methods tend to become unstable when applied to anatomical regions with a substantial content of isotropic diffusion. To resolve this problem, a new deconvolution approach is proposed in this paper. Apart from being uniformly stable across the whole brain, the proposed method allows one to quantify the isotropic component of cerebral diffusion, which is known to be a useful diagnostic measure by itself.

  2. A unique cross section through the skin of the dinosaur Psittacosaurus from China showing a complex fibre architecture.

    PubMed

    Lingham-Soliar, Theagarten

    2008-04-07

    This paper reports on a unique preservation of soft tissues in the ventrolateral region of the plant-eating dinosaur Psittacosaurus from the Jehol biota of China. The preservation is of a deep cross section through the dermis, which includes multiple layers of collagenous fibres in excess of 25, among the highest recorded in vertebrates, with a further 15 more layers (poorly preserved) estimated for the entire height of the section. Also, for the first time in a dinosaur two fibre layers parallel to the skin surface are preserved deep within the dermis at the base of the cross section. These fibre layers comprise regularly disposed fibres arranged in left- and right-handed geodesic helices, matching the pattern at the surface and reasonably inferred for the entire section. As noted from the studies on modern-day animals, this fibre structure plays a critical part in the stresses and strains the skin may be subjected to and is ideally suited to providing support and protection. Psittacosaurus gives a remarkable, unprecedented understanding of the dinosaur skin.

  3. Quantification of the collagen fibre architecture of human cranial dura mater

    PubMed Central

    JIMENEZ HAMANN, MARIA C.; SACKS, MICHAEL S.; MALININ, THEODORE I.

    1998-01-01

    The purpose of this study was to quantify and map the gross fibre architecture of the cranial dura mater (CDM) using small angle light scattering (SALS). In SALS, HeNe laser light is passed through the tissue, and the resultant scattering pattern is analysed to determine the preferred fibre direction and degree of orientation. The dura mater was found to be a complex structure with fibre orientations ranging from highly aligned to nearly random. In the temporal region, 80% of the samples (n=20) were found to have regions composed of highly oriented fibres with a mean fibre direction of 6.3°±0.8° with respect to the sagittal plane (i.e. almost parallel to the superior sagittal sinus). These highly aligned regions were found in symmetric anatomical locations about the median sagittal sinus and had similar fibre orientations over both hemispheres. Although our sample size was small, we found that the size of the symmetric regions, which covered 14.4±1.6% of the total CDM area, was not influenced by subject's age or sex. The presence of these highly oriented fibre regions in CDM may be due to mechanical forces exerted on dura mater during its development. These forces may have induced realignment of the collagen fibres in the direction of tensile pull, although the exact basis for the unique gross fibre architecture of CDM remains unknown. PMID:9568565

  4. Simulation of complex phenomena in optical fibres

    NASA Astrophysics Data System (ADS)

    Allington-Smith, Jeremy; Murray, Graham; Lemke, Ulrike

    2012-12-01

    Optical fibres are essential for many types of highly multiplexed and precision spectroscopy. The success of the new generation of multifibre instruments under construction to investigate fundamental problems in cosmology, such as the nature of dark energy, requires accurate modellization of the fibre system to achieve their signal-to-noise ratio (SNR) goals. Despite their simple construction, fibres exhibit unexpected behaviour including non-conservation of etendue (focal ratio degradation, FRD) and modal noise. Furthermore, new fibre geometries (non-circular or tapered) have become available to improve the scrambling properties that, together with modal noise, limit the achievable SNR in precision spectroscopy. These issues have often been addressed by extensive tests on candidate fibres and their terminations, but these are difficult and time-consuming. Modelling by ray tracing and wave analysis is possible with commercial software packages, but these do not address the more complex features, in particular FRD. We use a phase-tracking ray-tracing method to provide a practical description of FRD derived from our previous experimental work on circular fibres and apply it to non-standard fibres. This allows the relationship between scrambling and FRD to be quantified for the first time. We find that scrambling primarily affects the shape of the near-field pattern but has negligible effect on the barycentre. FRD helps to homogenize the near-field pattern but does not make it completely uniform. Fibres with polygonal cross-section improve scrambling without amplifying the FRD. Elliptical fibres, in conjunction with tapering, may offer an efficient means of image slicing to improve the product of resolving power and throughput, but the result is sensitive to the details of illumination. We also investigated the performance of fibres close to the limiting numerical aperture since this may affect the uniformity of the SNR for some prime focus fibre instrumentation.

  5. Superhydrophobic bio-fibre surfaces via tailored grafting architecture.

    PubMed

    Nyström, Daniel; Lindqvist, Josefina; Ostmark, Emma; Hult, Anders; Malmström, Eva

    2006-09-14

    Superhydrophobic bio-fibre surfaces with a micro-nano-binary surface structure have been achieved via the surface-confined grafting of glycidyl methacrylate, using a branched "graft-on-graft" architecture, followed by post-functionalisation to obtain fluorinated brushes.

  6. Complex Event Recognition Architecture

    NASA Technical Reports Server (NTRS)

    Fitzgerald, William A.; Firby, R. James

    2009-01-01

    Complex Event Recognition Architecture (CERA) is the name of a computational architecture, and software that implements the architecture, for recognizing complex event patterns that may be spread across multiple streams of input data. One of the main components of CERA is an intuitive event pattern language that simplifies what would otherwise be the complex, difficult tasks of creating logical descriptions of combinations of temporal events and defining rules for combining information from different sources over time. In this language, recognition patterns are defined in simple, declarative statements that combine point events from given input streams with those from other streams, using conjunction, disjunction, and negation. Patterns can be built on one another recursively to describe very rich, temporally extended combinations of events. Thereafter, a run-time matching algorithm in CERA efficiently matches these patterns against input data and signals when patterns are recognized. CERA can be used to monitor complex systems and to signal operators or initiate corrective actions when anomalous conditions are recognized. CERA can be run as a stand-alone monitoring system, or it can be integrated into a larger system to automatically trigger responses to changing environments or problematic situations.

  7. A viscoelastic-viscoplastic model for short-fibre reinforced polymers with complex fibre orientations

    NASA Astrophysics Data System (ADS)

    Nciri, M.; Notta-Cuvier, D.; Lauro, F.; Chaari, F.; Zouari, B.; Maalej, Y.

    2015-09-01

    This paper presents an innovative approach for the modelling of viscous behaviour of short-fibre reinforced composites (SFRC) with complex distributions of fibre orientations and for a wide range of strain rates. As an alternative to more complex homogenisation methods, the model is based on an additive decomposition of the state potential for the computation of composite's macroscopic behaviour. Thus, the composite material is seen as the assembly of a matrix medium and several linear elastic fibre media. The division of short fibres into several families means that complex distributions of orientation or random orientation can be easily modelled. The matrix behaviour is strain-rate sensitive, i.e. viscoelastic and/or viscoplastic. Viscoelastic constitutive laws are based on a generalised linear Maxwell model and the modelling of the viscoplasticity is based on an overstress approach. The model is tested for the case of a polypropylene reinforced with short-glass fibres with distributed orientations and subjected to uniaxial tensile tests, in different loading directions and under different strain rates. Results demonstrate the efficiency of the model over a wide range of strain rates.

  8. Composites for bone repair: phosphate glass fibre reinforced PLA with varying fibre architecture.

    PubMed

    Ahmed, I; Jones, I A; Parsons, A J; Bernard, J; Farmer, J; Scotchford, C A; Walker, G S; Rudd, C D

    2011-08-01

    Internal fixation for bone fractures with rigid metallic plates, screws and pins is a proven operative technique. However, refracture's have been observed after rigid internal fixation with metal plates and plate fixation has been known to cause localised osteopenia under and near the plate. In the present study, resorbable composites comprising a PLA matrix reinforced with iron doped phosphate glass fibres were investigated. Non-woven random mat laminates of approximately 30% and 45% fibre volume fraction (V(f)) were produced, along with unidirectional and 0°-90° samples of approximately 20% V(f). The non-woven composite laminates achieved maximum values of 10 GPa modulus and 120 MPa strength. The 0-90º samples showed unexpectedly low strengths close to matrix value (~50 MPa) although with a modulus of 7 GPa. The UD specimens exhibited values of 130 MPa and 11.5 GPa for strength and modulus respectively. All the modulus values observed were close to that expected from the rule of mixtures. Samples immersed in deionised water at 37°C revealed rapid mechanical property loss, more so for the UD and 0-90º samples. It was suggested that continuous fibres wicked the degradation media into the composite plates which sped up the deterioration of the fibre-matrix interface. The effect was less pronounced in the non-woven random mat laminates due to the discontinuous arrangement of fibres within the composite, making it less prone to wicking. Random mat composites revealed a higher mass loss than the UD and 0°-90° specimens, it was suggested this was due to the higher fibre volume fractions of these composites and SEM studies revealed voidage around the fibres by day 3. Studies of pH of the degradation media showed similar profiles for all the composites investigated. An initial decrease in pH was attributed to the release of phosphate ions into solution followed by a gradual return back to neutral.

  9. Fibre architecture and song activation rates of syringeal muscles are not lateralized in the European starling

    PubMed Central

    Uchida, A. M.; Meyers, R. A.; Cooper, B. G.; Goller, F.

    2010-01-01

    The songbird vocal organ, the syrinx, is composed of two sound generators, which are independently controlled by sets of two extrinsic and four intrinsic muscles. These muscles rank among the fastest vertebrate muscles, but the molecular and morphological foundations of this rapid physiological performance are unknown. Here we show that the four intrinsic muscles in the syrinx of male European starlings (Sturnus vulgaris) are composed of fast oxidative and superfast fibres. Dorsal and ventral tracheobronchialis muscles contain slightly more superfast fibres relative to the number of fast oxidative fibres than dorsal and ventral syringealis muscles. This morphological difference is not reflected in the highest, burst-like activation rate of the two muscle groups during song as assessed with electromyographic recordings. No difference in fibre type ratio was found between the corresponding muscles of the left and right sound generators. Airflow and electromyographic measurements during song indicate that maximal activation rate and speed of airflow regulation do not differ between the two sound sources. Whereas the potential for high-speed muscular control exists on both sides, the two sound generators are used differentially for modulation of acoustic parameters. These results show that large numbers of superfast fibre types are present in intrinsic syringeal muscles of a songbird, providing further confirmation of rapid contraction kinetics. However, syringeal muscles are composed of two fibre types which raises questions about the neuromuscular control of this heterogeneous muscle architecture. PMID:20228343

  10. Fibre architecture and song activation rates of syringeal muscles are not lateralized in the European starling.

    PubMed

    Uchida, A M; Meyers, R A; Cooper, B G; Goller, F

    2010-04-01

    The songbird vocal organ, the syrinx, is composed of two sound generators, which are independently controlled by sets of two extrinsic and four intrinsic muscles. These muscles rank among the fastest vertebrate muscles, but the molecular and morphological foundations of this rapid physiological performance are unknown. Here we show that the four intrinsic muscles in the syrinx of male European starlings (Sturnus vulgaris) are composed of fast oxidative and superfast fibres. Dorsal and ventral tracheobronchialis muscles contain slightly more superfast fibres relative to the number of fast oxidative fibres than dorsal and ventral syringealis muscles. This morphological difference is not reflected in the highest, burst-like activation rate of the two muscle groups during song as assessed with electromyographic recordings. No difference in fibre type ratio was found between the corresponding muscles of the left and right sound generators. Airflow and electromyographic measurements during song indicate that maximal activation rate and speed of airflow regulation do not differ between the two sound sources. Whereas the potential for high-speed muscular control exists on both sides, the two sound generators are used differentially for modulation of acoustic parameters. These results show that large numbers of superfast fibre types are present in intrinsic syringeal muscles of a songbird, providing further confirmation of rapid contraction kinetics. However, syringeal muscles are composed of two fibre types which raises questions about the neuromuscular control of this heterogeneous muscle architecture.

  11. In-plane mechanics of soft architectured fibre-reinforced silicone rubber membranes.

    PubMed

    Bailly, L; Toungara, M; Orgéas, L; Bertrand, E; Deplano, V; Geindreau, C

    2014-12-01

    Silicone rubber membranes reinforced with architectured fibre networks were processed with a dedicated apparatus, allowing a control of the fibre content and orientation. The membranes were subjected to tensile loadings combined with continuous and discrete kinematical field measurements (DIC and particle tracking). These tests show that the mechanical behaviour of the membranes is hyperelastic at the first order. They highlight the influence of the fibre content and orientation on both the membrane in-plane deformation and stress levels. They also prove that for the considered fibrous architectures and mechanical loadings, the motion and deformation of fibres is an affine function of the macroscale transformation. These trends are fairly well described by the micromechanical model proposed recently in Bailly et al. (JMBBM, 2012). This result proves that these materials are very good candidates for new biomimetic membranes, e.g. to improve aortic analogues used for in vitro experiments, or existing textiles used for vascular (endo)prostheses. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Cellulose fibre networks reinforced with carboxymethyl cellulose/chitosan complex layer-by-layer.

    PubMed

    Wu, Tongfei; Farnood, Ramin

    2014-12-19

    An eco-friendly and full-polysaccharide polyelectrolyte complex system was developed to enhance the wet and dry tensile strength of cellulose fibre networks. Cellulose fibres were treated by carboxymethyl cellulose (CMC) in pulp suspension. Paper sheets made from CMC-treated fibres were further modified via the layer-by-layer (LbL) deposition of CMC/chitosan (CS) complex. The effect of number of CMC/CS layers on the strength properties of cellulose fibre networks (both under wet and dry conditions) was studied and sample structure was investigated by scanning electron microscopy (SEM). Water vapour transmission rate (WVTR) of CMC/CS-treated samples was also examined. The observed changes in the strength properties of treated samples were explained based on the competition between the rate of diffusion of CS to the fibre-fibre bond areas and the rate of disassociation of fibre-fibre interactions during the LbL deposition process.

  13. Spider wrapping silk fibre architecture arising from its modular soluble protein precursor

    PubMed Central

    Tremblay, Marie-Laurence; Xu, Lingling; Lefèvre, Thierry; Sarker, Muzaddid; Orrell, Kathleen E.; Leclerc, Jérémie; Meng, Qing; Pézolet, Michel; Auger, Michèle; Liu, Xiang-Qin; Rainey, Jan K.

    2015-01-01

    Spiders store spidroins in their silk glands as high concentration aqueous solutions, spinning these dopes into fibres with outstanding mechanical properties. Aciniform (or wrapping) silk is the toughest spider silk and is devoid of the short amino acid sequence motifs characteristic of the other spidroins. Using solution-state NMR spectroscopy, we demonstrate that the 200 amino acid Argiope trifasciata AcSp1 repeat unit contrasts with previously characterized spidroins, adopting a globular 5-helix bundle flanked by intrinsically disordered N- and C-terminal tails. Split-intein-mediated segmental NMR-active isotope-enrichment allowed unambiguous demonstration of modular and malleable “beads-on-a-string” concatemeric behaviour. Concatemers form fibres upon manual drawing with silk-like morphology and mechanical properties, alongside secondary structuring and orientation consistent with native AcSp1 fibres. AcSp1 structural stability varies locally, with the fifth helix denaturing most readily. The structural transition of aciniform spidroin from a mostly α-helical dope to a mixed α-helix/β-sheet-containing fibre can be directly related to spidroin architecture and stability. PMID:26112753

  14. Spider wrapping silk fibre architecture arising from its modular soluble protein precursor.

    PubMed

    Tremblay, Marie-Laurence; Xu, Lingling; Lefèvre, Thierry; Sarker, Muzaddid; Orrell, Kathleen E; Leclerc, Jérémie; Meng, Qing; Pézolet, Michel; Auger, Michèle; Liu, Xiang-Qin; Rainey, Jan K

    2015-06-26

    Spiders store spidroins in their silk glands as high concentration aqueous solutions, spinning these dopes into fibres with outstanding mechanical properties. Aciniform (or wrapping) silk is the toughest spider silk and is devoid of the short amino acid sequence motifs characteristic of the other spidroins. Using solution-state NMR spectroscopy, we demonstrate that the 200 amino acid Argiope trifasciata AcSp1 repeat unit contrasts with previously characterized spidroins, adopting a globular 5-helix bundle flanked by intrinsically disordered N- and C-terminal tails. Split-intein-mediated segmental NMR-active isotope-enrichment allowed unambiguous demonstration of modular and malleable "beads-on-a-string" concatemeric behaviour. Concatemers form fibres upon manual drawing with silk-like morphology and mechanical properties, alongside secondary structuring and orientation consistent with native AcSp1 fibres. AcSp1 structural stability varies locally, with the fifth helix denaturing most readily. The structural transition of aciniform spidroin from a mostly α-helical dope to a mixed α-helix/β-sheet-containing fibre can be directly related to spidroin architecture and stability.

  15. Spider wrapping silk fibre architecture arising from its modular soluble protein precursor

    NASA Astrophysics Data System (ADS)

    Tremblay, Marie-Laurence; Xu, Lingling; Lefèvre, Thierry; Sarker, Muzaddid; Orrell, Kathleen E.; Leclerc, Jérémie; Meng, Qing; Pézolet, Michel; Auger, Michèle; Liu, Xiang-Qin; Rainey, Jan K.

    2015-06-01

    Spiders store spidroins in their silk glands as high concentration aqueous solutions, spinning these dopes into fibres with outstanding mechanical properties. Aciniform (or wrapping) silk is the toughest spider silk and is devoid of the short amino acid sequence motifs characteristic of the other spidroins. Using solution-state NMR spectroscopy, we demonstrate that the 200 amino acid Argiope trifasciata AcSp1 repeat unit contrasts with previously characterized spidroins, adopting a globular 5-helix bundle flanked by intrinsically disordered N- and C-terminal tails. Split-intein-mediated segmental NMR-active isotope-enrichment allowed unambiguous demonstration of modular and malleable “beads-on-a-string” concatemeric behaviour. Concatemers form fibres upon manual drawing with silk-like morphology and mechanical properties, alongside secondary structuring and orientation consistent with native AcSp1 fibres. AcSp1 structural stability varies locally, with the fifth helix denaturing most readily. The structural transition of aciniform spidroin from a mostly α-helical dope to a mixed α-helix/β-sheet-containing fibre can be directly related to spidroin architecture and stability.

  16. Adaptive functional specialisation of architectural design and fibre type characteristics in agonist shoulder flexor muscles of the llama, Lama glama

    PubMed Central

    Graziotti, Guillermo H; Chamizo, Verónica E; Ríos, Clara; Acevedo, Luz M; Rodríguez-Menéndez, J M; Victorica, C; Rivero, José-Luis L

    2012-01-01

    Like other camelids, llamas (Lama glama) have the natural ability to pace (moving ipsilateral limbs in near synchronicity). But unlike the Old World camelids (bactrian and dromedary camels), they are well adapted for pacing at slower or moderate speeds in high-altitude habitats, having been described as good climbers and used as pack animals for centuries. In order to gain insight into skeletal muscle design and to ascertain its relationship with the llama’s characteristic locomotor behaviour, this study examined the correspondence between architecture and fibre types in two agonist muscles involved in shoulder flexion (M. teres major – TM and M. deltoideus, pars scapularis – DS and pars acromialis – DA). Architectural properties were found to be correlated with fibre-type characteristics both in DS (long fibres, low pinnation angle, fast-glycolytic fibre phenotype with abundant IIB fibres, small fibre size, reduced number of capillaries per fibre and low oxidative capacity) and in DA (short fibres, high pinnation angle, slow-oxidative fibre phenotype with numerous type I fibres, very sparse IIB fibres, and larger fibre size, abundant capillaries and high oxidative capacity). This correlation suggests a clear division of labour within the M. deltoideus of the llama, DS being involved in rapid flexion of the shoulder joint during the swing phase of the gait, and DA in joint stabilisation during the stance phase. However, the architectural design of the TM muscle (longer fibres and lower fibre pinnation angle) was not strictly matched with its fibre-type characteristics (very similar to those of the postural DA muscle). This unusual design suggests a dual function of the TM muscle both in active flexion of the shoulder and in passive support of the limb during the stance phase, pulling the forelimb to the trunk. This functional specialisation seems to be well suited to a quadruped species that needs to increase ipsilateral stability of the limb during the

  17. Adaptive functional specialisation of architectural design and fibre type characteristics in agonist shoulder flexor muscles of the llama, Lama glama.

    PubMed

    Graziotti, Guillermo H; Chamizo, Verónica E; Ríos, Clara; Acevedo, Luz M; Rodríguez-Menéndez, J M; Victorica, C; Rivero, José-Luis L

    2012-08-01

    Like other camelids, llamas (Lama glama) have the natural ability to pace (moving ipsilateral limbs in near synchronicity). But unlike the Old World camelids (bactrian and dromedary camels), they are well adapted for pacing at slower or moderate speeds in high-altitude habitats, having been described as good climbers and used as pack animals for centuries. In order to gain insight into skeletal muscle design and to ascertain its relationship with the llama's characteristic locomotor behaviour, this study examined the correspondence between architecture and fibre types in two agonist muscles involved in shoulder flexion (M. teres major - TM and M. deltoideus, pars scapularis - DS and pars acromialis - DA). Architectural properties were found to be correlated with fibre-type characteristics both in DS (long fibres, low pinnation angle, fast-glycolytic fibre phenotype with abundant IIB fibres, small fibre size, reduced number of capillaries per fibre and low oxidative capacity) and in DA (short fibres, high pinnation angle, slow-oxidative fibre phenotype with numerous type I fibres, very sparse IIB fibres, and larger fibre size, abundant capillaries and high oxidative capacity). This correlation suggests a clear division of labour within the M. deltoideus of the llama, DS being involved in rapid flexion of the shoulder joint during the swing phase of the gait, and DA in joint stabilisation during the stance phase. However, the architectural design of the TM muscle (longer fibres and lower fibre pinnation angle) was not strictly matched with its fibre-type characteristics (very similar to those of the postural DA muscle). This unusual design suggests a dual function of the TM muscle both in active flexion of the shoulder and in passive support of the limb during the stance phase, pulling the forelimb to the trunk. This functional specialisation seems to be well suited to a quadruped species that needs to increase ipsilateral stability of the limb during the support

  18. Kernel methods for phenotyping complex plant architecture.

    PubMed

    Kawamura, Koji; Hibrand-Saint Oyant, Laurence; Foucher, Fabrice; Thouroude, Tatiana; Loustau, Sébastien

    2014-02-07

    The Quantitative Trait Loci (QTL) mapping of plant architecture is a critical step for understanding the genetic determinism of plant architecture. Previous studies adopted simple measurements, such as plant-height, stem-diameter and branching-intensity for QTL mapping of plant architecture. Many of these quantitative traits were generally correlated to each other, which give rise to statistical problem in the detection of QTL. We aim to test the applicability of kernel methods to phenotyping inflorescence architecture and its QTL mapping. We first test Kernel Principal Component Analysis (KPCA) and Support Vector Machines (SVM) over an artificial dataset of simulated inflorescences with different types of flower distribution, which is coded as a sequence of flower-number per node along a shoot. The ability of discriminating the different inflorescence types by SVM and KPCA is illustrated. We then apply the KPCA representation to the real dataset of rose inflorescence shoots (n=1460) obtained from a 98 F1 hybrid mapping population. We find kernel principal components with high heritability (>0.7), and the QTL analysis identifies a new QTL, which was not detected by a trait-by-trait analysis of simple architectural measurements. The main tools developed in this paper could be use to tackle the general problem of QTL mapping of complex (sequences, 3D structure, graphs) phenotypic traits.

  19. Architecture of the yeast Elongator complex.

    PubMed

    Dauden, Maria I; Kosinski, Jan; Kolaj-Robin, Olga; Desfosses, Ambroise; Ori, Alessandro; Faux, Celine; Hoffmann, Niklas A; Onuma, Osita F; Breunig, Karin D; Beck, Martin; Sachse, Carsten; Séraphin, Bertrand; Glatt, Sebastian; Müller, Christoph W

    2017-02-01

    The highly conserved eukaryotic Elongator complex performs specific chemical modifications on wobble base uridines of tRNAs, which are essential for proteome stability and homeostasis. The complex is formed by six individual subunits (Elp1-6) that are all equally important for its tRNA modification activity. However, its overall architecture and the detailed reaction mechanism remain elusive. Here, we report the structures of the fully assembled yeast Elongator and the Elp123 sub-complex solved by an integrative structure determination approach showing that two copies of the Elp1, Elp2, and Elp3 subunits form a two-lobed scaffold, which binds Elp456 asymmetrically. Our topological models are consistent with previous studies on individual subunits and further validated by complementary biochemical analyses. Our study provides a structural framework on how the tRNA modification activity is carried out by Elongator.

  20. Molecular Architecture of the Yeast Monopolin Complex

    SciTech Connect

    Corbett, Kevin D.; Harrison, Stephen C.

    2012-07-30

    The Saccharomyces cerevisiae monopolin complex directs proper chromosome segregation in meiosis I by mediating co-orientation of sister kinetochores on the meiosis I spindle. The monopolin subunits Csm1 and Lrs4 form a V-shaped complex that may directly crosslink sister kinetochores. We report here biochemical characterization of the monopolin complex subunits Mam1 and Hrr25 and of the complete four-protein monopolin complex. By purifying monopolin subcomplexes with different subunit combinations, we have determined the stoichiometry and overall architecture of the full monopolin complex. We have determined the crystal structure of Csm1 bound to a Mam1 fragment, showing how Mam1 wraps around the Csm1 dimer and alters the stoichiometry of kinetochore-protein binding by Csm1. We further show that the kinase activity of Hrr25 is altered by Mam1 binding, and we identify Hrr25 phosphorylation sites on Mam1 that may affect monopolin complex stability and/or kinetochore binding in meiosis.

  1. Architecture of mammalian respiratory complex I.

    PubMed

    Vinothkumar, Kutti R; Zhu, Jiapeng; Hirst, Judy

    2014-11-06

    Complex I (NADH:ubiquinone oxidoreductase) is essential for oxidative phosphorylation in mammalian mitochondria. It couples electron transfer from NADH to ubiquinone with proton translocation across the energy-transducing inner membrane, providing electrons for respiration and driving ATP synthesis. Mammalian complex I contains 44 different nuclear- and mitochondrial-encoded subunits, with a combined mass of 1 MDa. The 14 conserved 'core' subunits have been structurally defined in the minimal, bacterial complex, but the structures and arrangement of the 30 'supernumerary' subunits are unknown. Here we describe a 5 Å resolution structure of complex I from Bos taurus heart mitochondria, a close relative of the human enzyme, determined by single-particle electron cryo-microscopy. We present the structures of the mammalian core subunits that contain eight iron-sulphur clusters and 60 transmembrane helices, identify 18 supernumerary transmembrane helices, and assign and model 14 supernumerary subunits. Thus, we considerably advance knowledge of the structure of mammalian complex I and the architecture of its supernumerary ensemble around the core domains. Our structure provides insights into the roles of the supernumerary subunits in regulation, assembly and homeostasis, and a basis for understanding the effects of mutations that cause a diverse range of human diseases.

  2. Architecture of mammalian respiratory complex I

    PubMed Central

    Hirst, Judy

    2014-01-01

    Complex I (NADH:ubiquinone oxidoreductase) is essential for oxidative phosphorylation in mammalian mitochondria. It couples electron transfer from NADH to ubiquinone with proton translocation across the energy-transducing inner membrane, providing electrons for respiration and driving ATP synthesis. Mammalian complex I contains 44 different nuclear- and mitochondrial-encoded subunits, with a combined mass of 1 MDa. The fourteen conserved ‘core’ subunits have been structurally defined in the minimal, bacterial complex, but the structures and arrangement of the 30 ‘supernumerary’ subunits are unknown. Here, we describe a 5 Å resolution structure of complex I from Bos taurus heart mitochondria, a close relative of the human enzyme, determined by single-particle electron cryo-microscopy. We present the structures of the mammalian core subunits that contain eight iron-sulphur clusters and 60 transmembrane helices, identify 18 supernumerary transmembrane helices, and assign and model 14 supernumerary subunits. Thus, we significantly advance knowledge of the structure of mammalian complex I and the architecture of its supernumerary ensemble around the core domains. Our structure provides insights into the roles of the supernumerary subunits in regulation, assembly and homeostasis, and a basis for understanding the effects of mutations that cause a diverse range of human diseases. PMID:25209663

  3. Influence of Fibre Architecture on Impact Damage Tolerance in 3D Woven Composites

    NASA Astrophysics Data System (ADS)

    Potluri, P.; Hogg, P.; Arshad, M.; Jetavat, D.; Jamshidi, P.

    2012-10-01

    3D woven composites, due to the presence of through-thickness fibre-bridging, have the potential to improve damage tolerance and at the same time to reduce the manufacturing costs. However, ability to withstand damage depends on weave topology as well as geometry of individual tows. There is an extensive literature on damage tolerance of 2D prepreg laminates but limited work is reported on the damage tolerance of 3D weaves. In view of the recent interest in 3D woven composites from aerospace as well as non-aerospace sectors, this paper aims to provide an understanding of the impact damage resistance as well as damage tolerance of 3D woven composites. Four different 3D woven architectures, orthogonal, angle interlocked, layer-to-layer and modified layer-to-layer structures, have been produced under identical weaving conditions. Two additional structures, Unidirectional (UD) cross-ply and 2D plain weave, have been developed for comparison with 3D weaves. All the four 3D woven laminates have similar order of magnitude of damage area and damage width, but significantly lower than UD and 2D woven laminates. Damage Resistance, calculated as impact energy per unit damage area, has been shown to be significantly higher for 3D woven laminates. Rate of change of CAI strength with impact energy appears to be similar for all four 3D woven laminates as well as UD laminate; 2D woven laminate has higher rate of degradation with respect to impact energy. Undamaged compression strength has been shown to be a function of average tow waviness angle. Additionally, 3D weaves exhibit a critical damage size; below this size there is no appreciable reduction in compression strength. 3D woven laminates have also exhibited a degree of plasticity during compression whereas UD laminates fail instantly. The experimental work reported in this paper forms a foundation for systematic development of computational models for 3D woven architectures for damage tolerance.

  4. GhMCS1, the Cotton Orthologue of Human GRIM-19, Is a Subunit of Mitochondrial Complex I and Associated with Cotton Fibre Growth

    PubMed Central

    Dong, Chun-Juan; Wu, Ai-Min; Du, Shao-Jun; Tang, Kai; Wang, Yun; Liu, Jin-Yuan

    2016-01-01

    GRIM-19 (Gene associated with Retinoid-Interferon-induced Mortality 19) is a subunit of mitochondrial respiratory complex I in mammalian systems, and it has been demonstrated to be a multifunctional protein involved in the cell cycle, cell motility and innate immunity. However, little is known about the molecular functions of its homologues in plants. Here, we characterised GhMCS1, an orthologue of human GRIM-19 from cotton (Gossypium hirsutum L.), and found that it was essential for maintaining complex integrity and mitochondrial function in cotton. GhMCS1 was detected in various cotton tissues, with high levels expressed in developing fibres and flowers and lower levels in leaves, roots and ovules. In fibres at different developmental stages, GhMCS1 expression peaked at 5–15 days post anthesis (dpa) and then decreased at 20 dpa and diminished at 25 dpa. By Western blot analysis, GhMCS1 was observed to be localised to the mitochondria of cotton leaves and to colocalise with complex I. In Arabidopsis, GhMCS1 overexpression enhanced the assembly of complex I and thus respiratory activity, whereas the GhMCS1 homologue (At1g04630) knockdown mutants showed significantly decreased respiratory activities. Furthermore, the mutants presented with some phenotypic changes, such as smaller whole-plant architecture, poorly developed seeds and fewer trichomes. More importantly, in the cotton fibres, both the GhMCS1 transcript and protein levels were correlated with respiratory activity and fibre developmental phase. Our results suggest that GhMCS1, a functional ortholog of the human GRIM-19, is an essential subunit of mitochondrial complex I and is involved in cotton fibre development. The present data may deepen our knowledge on the potential roles of mitochondria in fibre morphogenesis. PMID:27632161

  5. Automatic reconstruction of the muscle architecture from the superficial layer fibres data.

    PubMed

    Kohout, Josef; Cholt, David

    2017-10-01

    Physiological cross-sectional area (PCSA) of a muscle plays a significant role in determining the force contribution of muscle fascicles to skeletal movement. This parameter is typically calculated from the lengths of muscle fibres selectively sampled from the superficial layer of the muscle. However, recent studies have found that the length of fibres in the superficial layer often differs significantly (p < 0.5) from the length of fibres in the deep layer. As a result, PCSA estimation is inaccurate. In this paper, we propose a method to automatically reconstruct fibres in the whole volume of a muscle from those selectively sampled on the superficial layer. The method performs a centripetal Catmull-Rom interpolation of the input fibres within the volume of a muscle represented by its 3D surface model, automatically distributing the fibres among multiple heads of the muscle and shortening the deep fibres to support large attachment areas with extremely acute angles. Our C++ implementation runs in a couple of seconds on commodity hardware providing realistic results for both artificial and real data sets we tested. The fibres produced by the method can be used directly to determine the personalised mechanical muscle functioning. Our implementation is publicly available for the researchers at https://mi.kiv.zcu.cz/. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Orbital Architectures of Dynamically Complex Exoplanet Systems

    NASA Astrophysics Data System (ADS)

    Nelson, Benjamin E.

    2015-01-01

    The most powerful constraints on planet formation will come from characterizing the dynamical state of complex multi-planet systems. Unfortunately, with that complexity comes a number of factors that make analyzing these systems a computationally challenging endeavor: the sheer number of model parameters, a wonky shaped posterior distribution, and hundreds to thousands of time series measurements. We develop a differential evolution Markov chain Monte Carlo (RUN DMC) to tackle these difficult aspects of data analysis. We apply RUN DMC to two classic multi-planet systems from radial velocity surveys, 55 Cancri and GJ 876. For 55 Cancri, we find the inner-most planet "e" must be coplanar to within 40 degrees of the outer planets, otherwise Kozai-like perturbations will cause the planet's orbit to cross the stellar surface. We find the orbits of planets "b" and "c" are apsidally aligned and librating with low to median amplitude (50±610 degrees), but they are not orbiting in a mean-motion resonance. For GJ 876, we can meaningfully constrain the three-dimensional orbital architecture of all the planets based on the radial velocity data alone. By demanding orbital stability, we find the resonant planets have low mutual inclinations (Φ) so they must be roughly coplanar (Φcb = 1.41±0.620.57 degrees and Φbe = 3.87±1.991.86 degrees). The three-dimensional Laplace argument librates with an amplitude of 50.5±7.910.0 degrees, indicating significant past disk migration and ensuring long-term stability. These empirically derived models will provide new challenges for planet formation models and motivate the need for more sophisticated algorithms to analyze exoplanet data.

  7. Neuromuscular organization of avian flight muscle: architecture of single muscle fibres in muscle units of the pectoralis (pars thoracicus) of pigeon (Columba livia)

    PubMed Central

    Sokoloff, A. J.

    1999-01-01

    The M. pectoralis (pars thoracicus) of pigeons (Columba livia) is comprised of short muscle fibres that do not extend from muscle origin to insertion but overlap 'in-series'. Individual pectoralis motor units are limited in territory to a portion of muscle length and are comprised of either fast twitch, oxidative and glycolytic fibres (FOG) or fast twitch and glycolytic fibres (FG). FOG fibres make up 88 to 90% of the total muscle population and have a mean diameter one-half of that of the relatively large FG fibres. Here we report on the organization of individual fibres identified in six muscle units depleted of glycogen, three comprised of FOG fibres and three comprised of FG fibres. For each motor unit, fibre counts revealed unequal numbers of depleted fibres in different unit cross-sections. We traced individual fibres in one unit comprised of FOG fibres and a second comprised of FG fibres. Six fibres from a FOG unit (total length 15.45 mm) ranged from 10.11 to 11.82 mm in length and averaged (± s.d.) 10.74 ± 0.79 mm. All originated bluntly (en mass) from a fascicle near the proximal end of the muscle unit and all terminated intramuscularly. Five of these ended in a taper and one ended bluntly. Fibres coursed on average for 70% of the muscle unit length. Six fibres from a FG unit (total length 34.76 mm) ranged from 8.97 to 18.38 mm in length and averaged 15.32 ± 3.75 mm. All originated bluntly and terminated intramuscularly; one of these ended in a taper and five ended bluntly. Fibres coursed on average for 44% of the muscle unit length. Because fibres of individual muscle units do not extend the whole muscle unit territory, the effective cross-sectional area changes along the motor unit length. These non-uniformities in the distribution of fibres within a muscle unit emphasize that the functional interactions within and between motor units are complex.

  8. Dietary fibre.

    PubMed

    Escudero Alvarez, E; González Sánchez, P

    2006-05-01

    Currently and after 30 years of research, dietary fibre is part of what is considered a healthy diet. There is no single definition yet comprising the different components of dietary fibre and its functions. The main factors of fibre are complex carbohydrates and lignin, although new products may be included in the future within the concept of fibre. Dietary fibres reach the large bowel and are attacked by colonic microflora, yielding short chain fatty acids, hydrogen, carbon dioxide, and methane as fermentation products. Short chain fatty acids represent a way of recovering energy and they are also implicated in other beneficial functions for the human organism. Although there are no yet conclusive data on recommendations of different types of fibre, it is still appropriate to indicate a diet providing 20-35 g/day of fibre from different sources. There is a consensus to recommend a mixture of fibres or fibre like soybean polysaccharide for constipation. There are few conclusive data, still, on the benefit of fibre on prevention of colorectal cancer and cardiovascular disease. However, a fibre-rich diet is recommended from early years of life since it is often associated to a lifestyle that in the long term helps controlling other risk factors.

  9. Rapid self-assembly of complex biomolecular architectures during mussel byssus biofabrication

    PubMed Central

    Priemel, Tobias; Degtyar, Elena; Dean, Mason N.; Harrington, Matthew J.

    2017-01-01

    Protein-based biogenic materials provide important inspiration for the development of high-performance polymers. The fibrous mussel byssus, for instance, exhibits exceptional wet adhesion, abrasion resistance, toughness and self-healing capacity–properties that arise from an intricate hierarchical organization formed in minutes from a fluid secretion of over 10 different protein precursors. However, a poor understanding of this dynamic biofabrication process has hindered effective translation of byssus design principles into synthetic materials. Here, we explore mussel byssus assembly in Mytilus edulis using a synergistic combination of histological staining and confocal Raman microspectroscopy, enabling in situ tracking of specific proteins during induced thread formation from soluble precursors to solid fibres. Our findings reveal critical insights into this complex biological manufacturing process, showing that protein precursors spontaneously self-assemble into complex architectures, while maturation proceeds in subsequent regulated steps. Beyond their biological importance, these findings may guide development of advanced materials with biomedical and industrial relevance. PMID:28262668

  10. Rapid self-assembly of complex biomolecular architectures during mussel byssus biofabrication.

    PubMed

    Priemel, Tobias; Degtyar, Elena; Dean, Mason N; Harrington, Matthew J

    2017-03-06

    Protein-based biogenic materials provide important inspiration for the development of high-performance polymers. The fibrous mussel byssus, for instance, exhibits exceptional wet adhesion, abrasion resistance, toughness and self-healing capacity-properties that arise from an intricate hierarchical organization formed in minutes from a fluid secretion of over 10 different protein precursors. However, a poor understanding of this dynamic biofabrication process has hindered effective translation of byssus design principles into synthetic materials. Here, we explore mussel byssus assembly in Mytilus edulis using a synergistic combination of histological staining and confocal Raman microspectroscopy, enabling in situ tracking of specific proteins during induced thread formation from soluble precursors to solid fibres. Our findings reveal critical insights into this complex biological manufacturing process, showing that protein precursors spontaneously self-assemble into complex architectures, while maturation proceeds in subsequent regulated steps. Beyond their biological importance, these findings may guide development of advanced materials with biomedical and industrial relevance.

  11. Rapid self-assembly of complex biomolecular architectures during mussel byssus biofabrication

    NASA Astrophysics Data System (ADS)

    Priemel, Tobias; Degtyar, Elena; Dean, Mason N.; Harrington, Matthew J.

    2017-03-01

    Protein-based biogenic materials provide important inspiration for the development of high-performance polymers. The fibrous mussel byssus, for instance, exhibits exceptional wet adhesion, abrasion resistance, toughness and self-healing capacity-properties that arise from an intricate hierarchical organization formed in minutes from a fluid secretion of over 10 different protein precursors. However, a poor understanding of this dynamic biofabrication process has hindered effective translation of byssus design principles into synthetic materials. Here, we explore mussel byssus assembly in Mytilus edulis using a synergistic combination of histological staining and confocal Raman microspectroscopy, enabling in situ tracking of specific proteins during induced thread formation from soluble precursors to solid fibres. Our findings reveal critical insights into this complex biological manufacturing process, showing that protein precursors spontaneously self-assemble into complex architectures, while maturation proceeds in subsequent regulated steps. Beyond their biological importance, these findings may guide development of advanced materials with biomedical and industrial relevance.

  12. The complex Young's modulus of skeletal muscle fibre segments in the high frequency range determined from tension transients.

    PubMed

    De Winkel, M E; Blangé, T; Treijtel, B W

    1993-06-01

    Stiffness measurements of muscle fibres are often based on application of a length change at one end of the muscle fibre and recording of the following tension change at the other end. In this study a method is developed to determine in the high frequency range (up to 40 kHz) the complex Young's modulus of skeletal muscle fibre as a function of frequency from the tension transient, following a rapid stepwise length change completed within 40 microseconds. For this purpose both a new mechanical moving part of the displacement generating system and a force transducer with a high natural frequency (70 kHz) had to be developed. In addition to stiffness measurements of a silk fibre to test the displacement generating system and the method of analysis, stiffness of skeletal muscle fibres in relaxed and rigor state have been measured. The complex Young's moduli of relaxed muscle fibres as well as muscle fibres in rigor state are frequency dependent. In both cases the complex Young's modulus increases smoothly with increasing frequency over a range of 250 Hz up to 40 kHz. The phase angles of the responses remained almost constant at a value of 0.3 radians for a fibre in rigor and 0.6 radians for a relaxed fibre. This leads to the conclusion that for muscle fibres in rigor state the recovery in the tension response to a step length change shows a continuous distribution of relaxation times rather than a few discrete ones. Results of our stiffness measurements are compared with results obtained from current viscoelastic models used to describe stiffness of muscle fibre in this frequency range.(ABSTRACT TRUNCATED AT 250 WORDS)

  13. Coral identity underpins architectural complexity on Caribbean reefs.

    PubMed

    Alvarez-Filip, Lorenzo; Dulvy, Nicholas K; Côte, Isabelle M; Watkinson, Andrew R; Gill, Jennifer A

    2011-09-01

    The architectural complexity of ecosystems can greatly influence their capacity to support biodiversity and deliver ecosystem services. Understanding the components underlying this complexity can aid the development of effective strategies for ecosystem conservation. Caribbean coral reefs support and protect millions of livelihoods, but recent anthropogenic change is shifting communities toward reefs dominated by stress-resistant coral species, which are often less architecturally complex. With the regionwide decline in reef fish abundance, it is becoming increasingly important to understand changes in coral reef community structure and function. We quantify the influence of coral composition, diversity, and morpho-functional traits on the architectural complexity of reefs across 91 sites at Cozumel, Mexico. Although reef architectural complexity increases with coral cover and species richness, it is highest on sites that are low in taxonomic evenness and dominated by morpho-functionally important, reef-building coral genera, particularly Montastraea. Sites with similar coral community composition also tend to occur on reefs with very similar architectural complexity, suggesting that reef structure tends to be determined by the same key species across sites. Our findings provide support for prioritizing and protecting particular reef types, especially those dominated by key reef-building corals, in order to enhance reef complexity.

  14. Towards a trustworthy distributed architecture for complex sensing networks

    NASA Astrophysics Data System (ADS)

    Schubert, Heidi; Luke, Jahn A.

    2012-06-01

    Fast, efficient distributed computing enables much more capable sensing systems for defense and commercial applications. However, distributed systems face distributed threats. These threats can be countered with a distributed trustworthiness architecture that measures and enforces trust across a network. Currently, there are no designs for distributed trust architectures suitable for complex systems. We present such an architecture, which measures nodes' trustworthiness before they join the network and while they are operational. In order to facilitate the computation and enforcement of trust, a distributed sensing network has to integrate a new type of component. We define the trust agents in terms of capabilities that support trustworthiness measurements.

  15. Nanoparticle Optics of Complex Nanorod Architectures

    SciTech Connect

    Shuford, Kevin L; Park, Sungho

    2009-01-01

    Computational studies on the optical properties of nanorods with unique compositions and exotic surface structure are presented. The distinctive architectures investigated-and compared to smooth Au rods-include Ni/Au multiblock rods and nanoporous Au rods. The surface plasmon resonances are extremely dependent upon the morphology and makeup of the nanorods. For a rod with a given aspect ratio, the resonance structure is sensitive to attributes such as the size of Ni sections of multiblock rods and pore structure of nanoporous rods. These studies indicate that control of the optical properties of nanorods is possible via characteristics other than the aspect ratio and suggest that a broader range of tunability is attainable.

  16. Molecular architecture of the complete COG tethering complex

    PubMed Central

    Ha, Jun Yong; Chou, Hui-Ting; Ungar, Daniel; Yip, Calvin K.; Walz, Thomas; Hughson, Frederick M.

    2016-01-01

    The conserved oligomeric Golgi (COG) complex orchestrates vesicular trafficking to and within the Golgi apparatus. Here, we use negative-stain electron microscopy to elucidate the architecture of the hetero-octameric COG complex from Saccharomyces cerevisiae. Intact COG has an intricate shape, with four (or possibly five) flexible legs, that differs strikingly from the exocyst complex and appears well-suited for vesicle capture and fusion. PMID:27428773

  17. The elastic fibre network of the human lumbar anulus fibrosus: architecture, mechanical function and potential role in the progression of intervertebral disc degeneration

    PubMed Central

    Fazzalari, Nicola L.

    2009-01-01

    Elastic fibres are critical constituents of dynamic biological structures that functionally require elasticity and resilience. The network of elastic fibres in the anulus fibrosus of the intervertebral disc is extensive, however until recently, the majority of histological, biochemical and biomechanical studies have focussed on the roles of other extracellular matrix constituents such as collagens and proteoglycans. The resulting lack of detailed descriptions of elastic fibre network architecture and mechanical function has limited understanding of the potentially important contribution made by elastic fibres to healthy disc function and their possible roles in the progression of disc degeneration. In addition, it has made it difficult to postulate what the consequences of elastic fibre related disorders would be for intervertebral disc behaviour, and to develop treatments accordingly. In this paper, we review recent and historical studies which have examined both the structure and the function of the human lumbar anulus fibrosus elastic fibre network, provide a synergistic discussion in an attempt to clarify its potentially critical contribution both to normal intervertebral disc behaviour and the processes relating to its degeneration, and recommend critical areas for future research. PMID:19263091

  18. Plant Fibre: Molecular Structure and Biomechanical Properties, of a Complex Living Material, Influencing Its Deconstruction towards a Biobased Composite

    PubMed Central

    Sorieul, Mathias; Dickson, Alan; Hill, Stefan J.; Pearson, Hamish

    2016-01-01

    Plant cell walls form an organic complex composite material that fulfils various functions. The hierarchical structure of this material is generated from the integration of its elementary components. This review provides an overview of wood as a composite material followed by its deconstruction into fibres that can then be incorporated into biobased composites. Firstly, the fibres are defined, and their various origins are discussed. Then, the organisation of cell walls and their components are described. The emphasis is on the molecular interactions of the cellulose microfibrils, lignin and hemicelluloses in planta. Hemicelluloses of diverse species and cell walls are described. Details of their organisation in the primary cell wall are provided, as understanding of the role of hemicellulose has recently evolved and is likely to affect our perception and future study of their secondary cell wall homologs. The importance of the presence of water on wood mechanical properties is also discussed. These sections provide the basis for understanding the molecular arrangements and interactions of the components and how they influence changes in fibre properties once isolated. A range of pulping processes can be used to individualise wood fibres, but these can cause damage to the fibres. Therefore, issues relating to fibre production are discussed along with the dispersion of wood fibres during extrusion. The final section explores various ways to improve fibres obtained from wood. PMID:28773739

  19. Molecular architecture of a multifunctional MCM complex

    PubMed Central

    Sanchez-Berrondo, June; Mesa, Pablo; Ibarra, Arkaitz; Martínez-Jiménez, Maria I.; Blanco, Luis; Méndez, Juan; Boskovic, Jasminka; Montoya, Guillermo

    2012-01-01

    DNA replication is strictly regulated through a sequence of steps that involve many macromolecular protein complexes. One of them is the replicative helicase, which is required for initiation and elongation phases. A MCM helicase found as a prophage in the genome of Bacillus cereus is fused with a primase domain constituting an integrative arrangement of two essential activities for replication. We have isolated this helicase–primase complex (BcMCM) showing that it can bind DNA and displays not only helicase and primase but also DNA polymerase activity. Using single-particle electron microscopy and 3D reconstruction, we obtained structures of BcMCM using ATPγS or ADP in the absence and presence of DNA. The complex depicts the typical hexameric ring shape. The dissection of the unwinding mechanism using site-directed mutagenesis in the Walker A, Walker B, arginine finger and the helicase channels, suggests that the BcMCM complex unwinds DNA following the extrusion model similarly to the E1 helicase from papillomavirus. PMID:21984415

  20. Molecular architecture of the yeast Mediator complex

    PubMed Central

    Robinson, Philip J; Trnka, Michael J; Pellarin, Riccardo; Greenberg, Charles H; Bushnell, David A; Davis, Ralph; Burlingame, Alma L; Sali, Andrej; Kornberg, Roger D

    2015-01-01

    The 21-subunit Mediator complex transduces regulatory information from enhancers to promoters, and performs an essential role in the initiation of transcription in all eukaryotes. Structural information on two-thirds of the complex has been limited to coarse subunit mapping onto 2-D images from electron micrographs. We have performed chemical cross-linking and mass spectrometry, and combined the results with information from X-ray crystallography, homology modeling, and cryo-electron microscopy by an integrative modeling approach to determine a 3-D model of the entire Mediator complex. The approach is validated by the use of X-ray crystal structures as internal controls and by consistency with previous results from electron microscopy and yeast two-hybrid screens. The model shows the locations and orientations of all Mediator subunits, as well as subunit interfaces and some secondary structural elements. Segments of 20–40 amino acid residues are placed with an average precision of 20 Å. The model reveals roles of individual subunits in the organization of the complex. DOI: http://dx.doi.org/10.7554/eLife.08719.001 PMID:26402457

  1. Molecular architecture of polycomb repressive complexes

    PubMed Central

    Chittock, Emily C.; Latwiel, Sebastian; Miller, Thomas C.R.

    2017-01-01

    The polycomb group (PcG) proteins are a large and diverse family that epigenetically repress the transcription of key developmental genes. They form three broad groups of polycomb repressive complexes (PRCs) known as PRC1, PRC2 and Polycomb Repressive DeUBiquitinase, each of which modifies and/or remodels chromatin by distinct mechanisms that are tuned by having variable compositions of core and accessory subunits. Until recently, relatively little was known about how the various PcG proteins assemble to form the PRCs; however, studies by several groups have now allowed us to start piecing together the PcG puzzle. Here, we discuss some highlights of recent PcG structures and the insights they have given us into how these complexes regulate transcription through chromatin. PMID:28202673

  2. Lasercom system architecture with reduced complexity

    NASA Technical Reports Server (NTRS)

    Lesh, James R. (Inventor); Chen, Chien-Chung (Inventor); Ansari, Homayoon (Inventor)

    1994-01-01

    Spatial acquisition and precision beam pointing functions are critical to spaceborne laser communication systems. In the present invention, a single high bandwidth CCD detector is used to perform both spatial acquisition and tracking functions. Compared to previous lasercom hardware design, the array tracking concept offers reduced system complexity by reducing the number of optical elements in the design. Specifically, the design requires only one detector and one beam steering mechanism. It also provides the means to optically close the point-ahead control loop. The technology required for high bandwidth array tracking was examined and shown to be consistent with current state of the art. The single detector design can lead to a significantly reduced system complexity and a lower system cost.

  3. Ultrasound detection of damage in complex carbon fibre/metal structures

    NASA Astrophysics Data System (ADS)

    Thursby, G. J.; MacLean, A.; Hogg, H.; Culshaw, B.

    2006-03-01

    We describe work carried out to monitor the structural health of a complex structure comprising both carbon fibre and metal components using ultrasound techniques. The work is designed to be used in a high performance car, but could find applications in other areas such as the aerospace industry. There are two different types of potential problem that need to be examined; the first is damage (e.g. holes, delaminations) to carbon fibre structure, and the second is damage to joints either between two carbon fibre components or between a carbon fibre component and a metallic one. The techniques used are based around the use of PZT transducers for both the generation and detection of ultrasonic Lamb waves. To date we have been carrying out experiments on mock-up samples, but are due to conduct tests on an actual vehicle. Lamb waves propagate in modes whose order is determined by the frequency thickness product. Their properties, such as phase and amplitude can be modified by the presence of damage, such as holes and delaminations. If we record the response of a healthy structure, we can then compare it with signals obtained on subsequent occasions to determine if any significant change has taken place. It is essential, however, to be able to differentiate between the effects of damage and those of environmental changes such as temperature. For this reason we have monitored the response of a sample at different temperatures both before and after drilling a hole in it to simulate damage. Depending on the positions of the transducers with respect to the damaged area, it is possible to detect either attenuation of the entire signal or changes in a specific portion of the signal produced by reflections. Results from these experiments will be presented at the conference. Signal processing techniques for separating damage from the effects of temperature will also be discussed. We also look at the deterioration of joints, which can either be epoxy bonded (carbon fibre to

  4. Porous ceramic scaffolds with complex architectures

    SciTech Connect

    Saiz, Eduardo; Munch, Etienne; Franco, Jaime; Deville, Sylvain; Hunger, Phillip; Saiz, Eduardo; Tomsia, Antoni P.

    2008-03-15

    This work compares two novel techniques for the fabrication of ceramic scaffolds for bone tissue engineering with complex porosity: robocasting and freeze casting. Both techniques are based on the preparation of concentrated ceramic suspensions with suitable properties for the process. In robocasting, the computer-guided deposition of the suspensions is used to build porous materials with designed three dimensional (3-D) geometries and microstructures. Freeze casting uses ice crystals as a template to form porous lamellar ceramic materials. Preliminary results on the compressive strengths of the materials are also reported.

  5. Complex Processes from Dynamical Architectures with Time-Scale Hierarchy

    PubMed Central

    Perdikis, Dionysios; Huys, Raoul; Jirsa, Viktor

    2011-01-01

    The idea that complex motor, perceptual, and cognitive behaviors are composed of smaller units, which are somehow brought into a meaningful relation, permeates the biological and life sciences. However, no principled framework defining the constituent elementary processes has been developed to this date. Consequently, functional configurations (or architectures) relating elementary processes and external influences are mostly piecemeal formulations suitable to particular instances only. Here, we develop a general dynamical framework for distinct functional architectures characterized by the time-scale separation of their constituents and evaluate their efficiency. Thereto, we build on the (phase) flow of a system, which prescribes the temporal evolution of its state variables. The phase flow topology allows for the unambiguous classification of qualitatively distinct processes, which we consider to represent the functional units or modes within the dynamical architecture. Using the example of a composite movement we illustrate how different architectures can be characterized by their degree of time scale separation between the internal elements of the architecture (i.e. the functional modes) and external interventions. We reveal a tradeoff of the interactions between internal and external influences, which offers a theoretical justification for the efficient composition of complex processes out of non-trivial elementary processes or functional modes. PMID:21347363

  6. Complex processes from dynamical architectures with time-scale hierarchy.

    PubMed

    Perdikis, Dionysios; Huys, Raoul; Jirsa, Viktor

    2011-02-10

    The idea that complex motor, perceptual, and cognitive behaviors are composed of smaller units, which are somehow brought into a meaningful relation, permeates the biological and life sciences. However, no principled framework defining the constituent elementary processes has been developed to this date. Consequently, functional configurations (or architectures) relating elementary processes and external influences are mostly piecemeal formulations suitable to particular instances only. Here, we develop a general dynamical framework for distinct functional architectures characterized by the time-scale separation of their constituents and evaluate their efficiency. Thereto, we build on the (phase) flow of a system, which prescribes the temporal evolution of its state variables. The phase flow topology allows for the unambiguous classification of qualitatively distinct processes, which we consider to represent the functional units or modes within the dynamical architecture. Using the example of a composite movement we illustrate how different architectures can be characterized by their degree of time scale separation between the internal elements of the architecture (i.e. the functional modes) and external interventions. We reveal a tradeoff of the interactions between internal and external influences, which offers a theoretical justification for the efficient composition of complex processes out of non-trivial elementary processes or functional modes.

  7. Europium complex-based thermochromic sensor for integration in plastic optical fibres

    NASA Astrophysics Data System (ADS)

    Lopez, Inma Suarez; Luisa Mendonça, A.; Fernandes, Mariana; Bermudez, Verónica de Zea; Morgado, Jorge; Del Pozo, G.; Romero, B.; Cabanillas-Gonzalez, Juan

    2012-06-01

    We report on a new thermochromic material containing a europium complex for thermal sensing through its fluorescence response to temperature. The ratio between the strong luminescence peak of europium (III) and a side band emission is employed as a new probe for optical sensing of temperature. The ratio is observed to follow an Arrhenius-type dependence with temperature. Based on these results we developed a thermal probe based on a segment of luminescent thermometer optically cemented to the tip of a PMMA fibre.

  8. Fibre typing of intrafusal fibres

    PubMed Central

    Thornell, Lars-Eric; Carlsson, Lena; Eriksson, Per-Olof; Liu, Jing-Xia; Österlund, Catharina; Stål, Per; Pedrosa-Domellöf, Fatima

    2015-01-01

    The first descriptions of muscle spindles with intrafusal fibres containing striated myofibrils and nervous elements were given approximately 150 years ago. It took, however, another 100 years to establish the presence of two types of intrafusal muscle fibres: nuclear bag and nuclear chain fibres. The present paper highlights primarily the contribution of Robert Banks in fibre typing of intrafusal fibres: the confirmation of the principle of two types of nuclear bag fibres in mammalian spindles and the variation in occurrence of a dense M-band along the fibres. Furthermore, this paper summarizes how studies from the Umeå University group (Laboratory of Muscle Biology in the Department of Integrative Medical Biology) on fibre typing and the structure and composition of M-bands have contributed to the current understanding of muscle spindle complexity in adult humans as well as to muscle spindle development and effects of ageing. The variable molecular composition of the intrafusal sarcomeres with respect to myosin heavy chains and M-band proteins gives new perspectives on the role of the intrafusal myofibrils as stretch-activated sensors influencing tension/stiffness and signalling to nuclei. PMID:26179023

  9. Purification and architecture of the ubiquitous Wave complex

    PubMed Central

    Gautreau, Alexis; Ho, Hsin-yi H.; Li, Jiaxu; Steen, Hanno; Gygi, Steven P.; Kirschner, Marc W.

    2004-01-01

    The Wave proteins are major activators of the Arp2/3 complex. The ubiquitous Wave-2 is required for actin polymerization at the leading edge of migrating cells. Here we purify Wave-2 from HeLa cells. Five proteins, Sra, Nap, Wave-2, Abi, and Hspc, are copurified, indicating that they form a tight complex. These proteins are only present in the complexed form, with the exception of Hspc, which displays a free pool. We reconstitute the Wave-2 complex by cotranslating in vitro the five subunits and use this system together with specific immunoprecipitations to study the molecular architecture of the complex. The complex is organized around a core of Nap and Abi. Sra is a peripheral subunit recruited on the Nap side, whereas the Wave and Hspc subunits are recruited on the Abi side of the core. PMID:15070726

  10. Development of the nuclear weapons complex EP architecture

    SciTech Connect

    Murray, C.; Halbleib, L.

    1996-07-01

    The Nuclear Weapons Guidance Team is an interagency committee led by Earl Whiteman, DOE that chartered the generation of EP40100, Concurrent Qualification and its successor EP401099, Concurrent Engineering and Qualification. As this new philosophy of concurrent operations has evolved and as implementation has been initiated, conflicts and insufficiencies in the remaining Engineering Procedures (EPs) have become more apparent. At the Guidance Team meeting in November 1995, this issue was explored and several approaches were considered. It was concluded at this meeting, that a smaller set of interagency EPs described in a hierarchical system could provide the necessary interagency direction to support complex-wide implementation. This set consolidates many existing EP processes where consistency and commonality are critical to success of the extended enterprise. The Guidance Team subsequently chartered an interagency team to initiate development activity associated with the envisioned new EP set. This team had participation from seven Nuclear Weapons Complex (NWC) sites as well as DOE/AL and DP-14 (team members are acknowledged later in this report). Per the Guidance Team, this team, referred to as the Architecture Subcommittee, was to map out and define an EP Architecture for the interagency EPs, make recommendations regarding a more agile process for EP approval and suggest an aggressive timeline to develop the combined EPs. The Architecture Subcommittee was asked to brief their output at the February Guidance Team meeting. This SAND report documents the results of the Architecture Subcommittee`s recommendations.

  11. The effect of comb architecture on complex coacervation.

    PubMed

    Johnston, Brandon M; Johnston, Cameron W; Letteri, Rachel A; Lytle, Tyler K; Sing, Charles E; Emrick, Todd; Perry, Sarah L

    2017-09-20

    Complex coacervation is a widely utilized technique for effecting phase separation, though predictive understanding of molecular-level details remains underdeveloped. Here, we couple coarse-grained Monte Carlo simulations with experimental efforts using a polypeptide-based model system to investigate how a comb-like architecture affects complex coacervation and coacervate stability. Specifically, the phase separation behavior of linear polycation-linear polyanion pairs was compared to that of comb polycation-linear polyanion and comb polycation-comb polyanion pairs. The comb architecture was found to mitigate cooperative interactions between oppositely charged polymers, as no discernible phase separation was observed for comb-comb pairs and complex coacervation of linear-linear pairs yielded stable coacervates at higher salt concentration than linear-comb pairs. This behavior was attributed to differences in counterion release by linear vs. comb polymers during polyeletrolyte complexation. Additionally, the comb polycation formed coacervates with both stereoregular poly(l-glutamate) and racemic poly(d,l-glutamate), whereas the linear polycation formed coacervates only with the racemic polyanion. In contrast, solid precipitates were obtained from mixtures of stereoregular poly(l-lysine) and poly(l-glutamate). Moreover, the formation of coacervates from cationic comb polymers incorporating up to ∼90% pendant zwitterionic groups demonstrated the potential for inclusion of comonomers to modulate the hydrophilicity and/or other properties of a coacervate-forming polymer. These results provide the first detailed investigation into the role of polymer architecture on complex coacervation using a chemically and architecturally well-defined model system, and highlight the need for additional research on this topic.

  12. Pectin impacts cellulose fibre architecture and hydrogel mechanics in the absence of calcium.

    PubMed

    Lopez-Sanchez, Patricia; Martinez-Sanz, Marta; Bonilla, Mauricio R; Wang, Dongjie; Walsh, Cherie T; Gilbert, Elliot P; Stokes, Jason R; Gidley, Michael J

    2016-11-20

    Pectin is a major polysaccharide in many plant cell walls and recent advances indicate that its role in wall mechanics is more important than previously thought. In this work cellulose hydrogels were synthesised in pectin solutions, as a biomimetic tool to investigate the influence of pectin on cellulose assembly and hydrogel mechanical properties. Most of the pectin (60-80%) did not interact at the molecular level with cellulose, as judged by small angle scattering techniques (SAXS and SANS). Despite the lack of strong interactions with cellulose, this pectin fraction impacted the mechanical properties of the hydrogels through poroelastic effects. The other 20-40% of pectin (containing neutral sugar sidechains) was able to interact intimately with cellulose microfibrils at the point of assembly. These results support the need to revise the role of pectin in cell wall architecture and mechanics, and; furthermore they assist the design of cellulose-based products through controlling the viscoelasticity of the fluid phase.

  13. Facile synthesis of complex shaped Pt-Cu alloy architectures

    NASA Astrophysics Data System (ADS)

    Nosheen, Farhat; Ni, Bing; Xu, Xiaobin; Yang, Haozhou; Zhang, Zhicheng; Wang, Xun

    2016-07-01

    Several intricate Pt-Cu alloy architectures have been synthesized including hexapod backbones with stretchers and caved octahedron like hexapods, as well as some other intermediates with complex structures. The mechanistic study indicates that the shape is realized via a competitive effect between etching and growth induced by different chemicals.Several intricate Pt-Cu alloy architectures have been synthesized including hexapod backbones with stretchers and caved octahedron like hexapods, as well as some other intermediates with complex structures. The mechanistic study indicates that the shape is realized via a competitive effect between etching and growth induced by different chemicals. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr03511f

  14. Complex Microfluidic Systems Architectures and Applications to Micropower Generation

    DTIC Science & Technology

    2010-07-07

    Complex Microfluidic Systems Architectures and Applications to Micropower Generation” AFOSR grant FA9550-08-1-0345 Integrated Fluidics, Santa...reliability of components and the size of the system built up from such components. We advanced a novel microfluidic concept, named µfCPU, the Microfluidic ...Central Processing Unit, where the key microfluidic operations are performed within a single enclosure, using active, software-based inputs rather

  15. Low complexity 1D IDCT for 16-bit parallel architectures

    NASA Astrophysics Data System (ADS)

    Bivolarski, Lazar

    2007-09-01

    This paper shows that using the Loeffler, Ligtenberg, and Moschytz factorization of 8-point IDCT [2] one-dimensional (1-D) algorithm as a fast approximation of the Discrete Cosine Transform (DCT) and using only 16 bit numbers, it is possible to create in an IEEE 1180-1990 compliant and multiplierless algorithm with low computational complexity. This algorithm as characterized by its structure is efficiently implemented on parallel high performance architectures as well as due to its low complexity is sufficient for wide range of other architectures. Additional constraint on this work was the requirement of compliance with the existing MPEG standards. The hardware implementation complexity and low resources where also part of the design criteria for this algorithm. This implementation is also compliant with the precision requirements described in MPEG IDCT precision specification ISO/IEC 23002-1. Complexity analysis is performed as an extension to the simple measure of shifts and adds for the multiplierless algorithm as additional operations are included in the complexity measure to better describe the actual transform implementation complexity.

  16. Some fast elliptic solvers on parallel architectures and their complexities

    NASA Technical Reports Server (NTRS)

    Gallopoulos, E.; Saad, Youcef

    1989-01-01

    The discretization of separable elliptic partial differential equations leads to linear systems with special block triangular matrices. Several methods are known to solve these systems, the most general of which is the Block Cyclic Reduction (BCR) algorithm which handles equations with nonconsistant coefficients. A method was recently proposed to parallelize and vectorize BCR. Here, the mapping of BCR on distributed memory architectures is discussed, and its complexity is compared with that of other approaches, including the Alternating-Direction method. A fast parallel solver is also described, based on an explicit formula for the solution, which has parallel computational complexity lower than that of parallel BCR.

  17. Fibre Optics In Automobiles

    NASA Astrophysics Data System (ADS)

    Harmer, A. L.

    1984-08-01

    Optical fibres are used in three application areas in automobiles. Illumination of the dashboard is done with a single lamp and monofilament fibres or woven tapes which illuminate the front panel. Fibre-optic multiplexing can replace the conventional wiring harness. Different trial systems (two-fibre links, bidirectional transmission, star-coupled architecture) are reviewed. Problems still exist in component performance, high costs and unknown reliability of optoelectronic systems. Fibre-optics are also used in sensors; for headlight monitoring, liquid-level sensing and other applications.

  18. The architecture of the management system of complex steganographic information

    NASA Astrophysics Data System (ADS)

    Evsutin, O. O.; Meshcheryakov, R. V.; Kozlova, A. S.; Solovyev, T. M.

    2017-01-01

    The aim of the study is to create a wide area information system that allows one to control processes of generation, embedding, extraction, and detection of steganographic information. In this paper, the following problems are considered: the definition of the system scope and the development of its architecture. For creation of algorithmic maintenance of the system, classic methods of steganography are used to embed information. Methods of mathematical statistics and computational intelligence are used to identify the embedded information. The main result of the paper is the development of the architecture of the management system of complex steganographic information. The suggested architecture utilizes cloud technology in order to provide service using the web-service via the Internet. It is meant to provide streams of multimedia data processing that are streams with many sources of different types. The information system, built in accordance with the proposed architecture, will be used in the following areas: hidden transfer of documents protected by medical secrecy in telemedicine systems; copyright protection of online content in public networks; prevention of information leakage caused by insiders.

  19. Complexes of xylan and synthetic polyelectrolytes. Characterization and adsorption onto high quality unbleached fibres.

    PubMed

    Mocchiutti, Paulina; Galván, María V; Peresin, María S; Schnell, Carla N; Zanuttini, Miguel A

    2015-02-13

    In this work, polyelectrolyte complexes (PECs) were formed by adding polyacrylic acid (PAA) or 4-O-methylglucuronoxylan (Xyl) on poly(allylamine hydrochloride) (PAH) solutions, at different ionic strength and neutral pH. Turbidity curves, charge densities of the cationic complexes determined by polyelectrolyte titration method, and z-potential values showed clear differences between both complexes. Stirring favourably reverses the effects of sedimentation of Xyl/PAH complexes, as demonstrated by colloidal stability tests. Adsorption studies on silica surfaces, performed by Quartz Crystal Microbalance with Dissipation (QCM-D) showed that PAA/PAH adsorbed complexes layers were rigid, while the corresponding Xyl/PAH layers were viscoelastic. Despite the different conformations, both complexes were adsorbed as spherical particles, as observed by Atomic Force Microscopy (AFM). Adsorption isotherms performed on fibre suspensions showed that the ionic strength of the liquid medium determines the amount of PEC retained. Finally, it was found that the papermaking properties were significantly increased due to the addition of these PECs.

  20. A modeling process to understand complex system architectures

    NASA Astrophysics Data System (ADS)

    Robinson, Santiago Balestrini

    2009-12-01

    In recent decades, several tools have been developed by the armed forces, and their contractors, to test the capability of a force. These campaign level analysis tools, often times characterized as constructive simulations are generally expensive to create and execute, and at best they are extremely difficult to verify and validate. This central observation, that the analysts are relying more and more on constructive simulations to predict the performance of future networks of systems, leads to the two central objectives of this thesis: (1) to enable the quantitative comparison of architectures in terms of their ability to satisfy a capability without resorting to constructive simulations, and (2) when constructive simulations must be created, to quantitatively determine how to spend the modeling effort amongst the different system classes. The first objective led to Hypothesis A, the first main hypotheses, which states that by studying the relationships between the entities that compose an architecture, one can infer how well it will perform a given capability. The method used to test the hypothesis is based on two assumptions: (1) the capability can be defined as a cycle of functions, and that it (2) must be possible to estimate the probability that a function-based relationship occurs between any two types of entities. If these two requirements are met, then by creating random functional networks, different architectures can be compared in terms of their ability to satisfy a capability. In order to test this hypothesis, a novel process for creating representative functional networks of large-scale system architectures was developed. The process, named the Digraph Modeling for Architectures (DiMA), was tested by comparing its results to those of complex constructive simulations. Results indicate that if the inputs assigned to DiMA are correct (in the tests they were based on time-averaged data obtained from the ABM), DiMA is able to identify which of any two

  1. Multilayered and complex nanoparticle architectures through plasma synthesis

    SciTech Connect

    Phillips, Jonathan; Wakeland, Stephen; Cui, Yuehua; Knapp, Angela; Richard, Monique; Luhrs, Claudia

    2009-01-01

    Using the Aerosol Through Plasma (ATP) method in conjunction with simple chemical techniques a variety of complex and novel nanoparticle architectures were created. A TP was used to make metal-core/carbon shell nanoparticles (ca. 50 nm diameter) of SnlCarbon and AI/Carbon. These have, respectively, potential for application as battery anode (for hybrid and electric vehicles) and high energy fuel In one example of post processing, the Sn-core/carbon-shell material is treated in acidic solution and yields a true nano-sized hollow carbon shell. These shells have potential application as catalyst supports, gas storage, a neutral buoyancy material for applications as varied as proppants, and slow release capsules for pharmaceutical or agricultural applications. A different set of post-A-T-P processes were used to make three layer nanoparticles with a metal core, graphite inner shell and ceramic outer shell. This method extends the range of achievable nanoparticles architectures, hence enabling new applications.

  2. The Ccr4-Not Complex: Architecture and Structural Insights.

    PubMed

    Collart, Martine A; Panasenko, Olesya O

    2017-01-01

    The Ccr4-Not complex is an essential multi-subunit protein complex that plays a fundamental role in eukaryotic mRNA metabolism and has a multitude of different roles that impact eukaryotic gene expression . It has a conserved core of three Not proteins, the Ccr4 protein, and two Ccr4 associated factors, Caf1 and Caf40. A fourth Not protein, Not4, is conserved, but is only a stable subunit of the complex in yeast. Certain subunits have been duplicated during evolution, with functional divergence, such as Not3 in yeast, and Ccr4 or Caf1 in human. However the complex includes only one homolog for each protein. In addition, species-specific subunits are part of the complex, such as Caf130 in yeast or Not10 and Not11 in human. Two conserved catalytic functions are associated with the complex, deadenylation and ubiquitination . The complex adopts an L-shaped structure, in which different modules are bound to a large Not1 scaffold protein. In this chapter we will summarize our current knowledge of the architecture of the complex and of the structure of its constituents.

  3. The mitochondrial contact site complex, a determinant of mitochondrial architecture

    PubMed Central

    Harner, Max; Körner, Christian; Walther, Dirk; Mokranjac, Dejana; Kaesmacher, Johannes; Welsch, Ulrich; Griffith, Janice; Mann, Matthias; Reggiori, Fulvio; Neupert, Walter

    2011-01-01

    Mitochondria are organelles with a complex architecture. They are bounded by an envelope consisting of the outer membrane and the inner boundary membrane (IBM). Narrow crista junctions (CJs) link the IBM to the cristae. OMs and IBMs are firmly connected by contact sites (CS). The molecular nature of the CS remained unknown. Using quantitative high-resolution mass spectrometry we identified a novel complex, the mitochondrial contact site (MICOS) complex, formed by a set of mitochondrial membrane proteins that is essential for the formation of CS. MICOS is preferentially located at the CJs. Upon loss of one of the MICOS subunits, CJs disappear completely or are impaired, showing that CJs require the presence of CS to form a superstructure that links the IBM to the cristae. Loss of MICOS subunits results in loss of respiratory competence and altered inheritance of mitochondrial DNA. PMID:22009199

  4. An ICAI architecture for troubleshooting in complex, dynamic systems

    NASA Technical Reports Server (NTRS)

    Fath, Janet L.; Mitchell, Christine M.; Govindaraj, T.

    1990-01-01

    Ahab, an intelligent computer-aided instruction (ICAI) program, illustrates an architecture for simulator-based ICAI programs to teach troubleshooting in complex, dynamic environments. The architecture posits three elements of a computerized instructor: the task model, the student model, and the instructional module. The task model is a prescriptive model of expert performance that uses symptomatic and topographic search strategies to provide students with directed problem-solving aids. The student model is a descriptive model of student performance in the context of the task model. This student model compares the student and task models, critiques student performance, and provides interactive performance feedback. The instructional module coordinates information presented by the instructional media, the task model, and the student model so that each student receives individualized instruction. Concept and metaconcept knowledge that supports these elements is contained in frames and production rules, respectively. The results of an experimental evaluation are discussed. They support the hypothesis that training with an adaptive online system built using the Ahab architecture produces better performance than training using simulator practice alone, at least with unfamiliar problems. It is not sufficient to develop an expert strategy and present it to students using offline materials. The training is most effective if it adapts to individual student needs.

  5. An ICAI architecture for troubleshooting in complex, dynamic systems

    NASA Technical Reports Server (NTRS)

    Fath, Janet L.; Mitchell, Christine M.; Govindaraj, T.

    1990-01-01

    Ahab, an intelligent computer-aided instruction (ICAI) program, illustrates an architecture for simulator-based ICAI programs to teach troubleshooting in complex, dynamic environments. The architecture posits three elements of a computerized instructor: the task model, the student model, and the instructional module. The task model is a prescriptive model of expert performance that uses symptomatic and topographic search strategies to provide students with directed problem-solving aids. The student model is a descriptive model of student performance in the context of the task model. This student model compares the student and task models, critiques student performance, and provides interactive performance feedback. The instructional module coordinates information presented by the instructional media, the task model, and the student model so that each student receives individualized instruction. Concept and metaconcept knowledge that supports these elements is contained in frames and production rules, respectively. The results of an experimental evaluation are discussed. They support the hypothesis that training with an adaptive online system built using the Ahab architecture produces better performance than training using simulator practice alone, at least with unfamiliar problems. It is not sufficient to develop an expert strategy and present it to students using offline materials. The training is most effective if it adapts to individual student needs.

  6. Some fast elliptic solvers on parallel architectures and their complexities

    NASA Technical Reports Server (NTRS)

    Gallopoulos, E.; Saad, Y.

    1989-01-01

    The discretization of separable elliptic partial differential equations leads to linear systems with special block tridiagonal matrices. Several methods are known to solve these systems, the most general of which is the Block Cyclic Reduction (BCR) algorithm which handles equations with nonconstant coefficients. A method was recently proposed to parallelize and vectorize BCR. In this paper, the mapping of BCR on distributed memory architectures is discussed, and its complexity is compared with that of other approaches including the Alternating-Direction method. A fast parallel solver is also described, based on an explicit formula for the solution, which has parallel computational compelxity lower than that of parallel BCR.

  7. Precise Regulation of Gene Expression Dynamics Favors Complex Promoter Architectures

    PubMed Central

    Müller, Dirk; Stelling, Jörg

    2009-01-01

    Promoters process signals through recruitment of transcription factors and RNA polymerase, and dynamic changes in promoter activity constitute a major noise source in gene expression. However, it is barely understood how complex promoter architectures determine key features of promoter dynamics. Here, we employ prototypical promoters of yeast ribosomal protein genes as well as simplified versions thereof to analyze the relations among promoter design, complexity, and function. These promoters combine the action of a general regulatory factor with that of specific transcription factors, a common motif of many eukaryotic promoters. By comprehensively analyzing stationary and dynamic promoter properties, this model-based approach enables us to pinpoint the structural characteristics underlying the observed behavior. Functional tradeoffs impose constraints on the promoter architecture of ribosomal protein genes. We find that a stable scaffold in the natural design results in low transcriptional noise and strong co-regulation of target genes in the presence of gene silencing. This configuration also exhibits superior shut-off properties, and it can serve as a tunable switch in living cells. Model validation with independent experimental data suggests that the models are sufficiently realistic. When combined, our results offer a mechanistic explanation for why specific factors are associated with low protein noise in vivo. Many of these findings hold for a broad range of model parameters and likely apply to other eukaryotic promoters of similar structure. PMID:19180182

  8. Architecture of the fungal nuclear pore inner ring complex.

    PubMed

    Stuwe, Tobias; Bley, Christopher J; Thierbach, Karsten; Petrovic, Stefan; Schilbach, Sandra; Mayo, Daniel J; Perriches, Thibaud; Rundlet, Emily J; Jeon, Young E; Collins, Leslie N; Huber, Ferdinand M; Lin, Daniel H; Paduch, Marcin; Koide, Akiko; Lu, Vincent; Fischer, Jessica; Hurt, Ed; Koide, Shohei; Kossiakoff, Anthony A; Hoelz, André

    2015-10-02

    The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. We present the reconstitution and interdisciplinary analyses of the ~425-kilodalton inner ring complex (IRC), which forms the central transport channel and diffusion barrier of the NPC, revealing its interaction network and equimolar stoichiometry. The Nsp1•Nup49•Nup57 channel nucleoporin heterotrimer (CNT) attaches to the IRC solely through the adaptor nucleoporin Nic96. The CNT•Nic96 structure reveals that Nic96 functions as an assembly sensor that recognizes the three-dimensional architecture of the CNT, thereby mediating the incorporation of a defined CNT state into the NPC. We propose that the IRC adopts a relatively rigid scaffold that recruits the CNT to primarily form the diffusion barrier of the NPC, rather than enabling channel dilation.

  9. Sex differences in genetic architecture of complex phenotypes?

    PubMed

    Vink, Jacqueline M; Bartels, Meike; van Beijsterveldt, Toos C E M; van Dongen, Jenny; van Beek, Jenny H D A; Distel, Marijn A; de Moor, Marleen H M; Smit, Dirk J A; Minica, Camelia C; Ligthart, Lannie; Geels, Lot M; Abdellaoui, Abdel; Middeldorp, Christel M; Hottenga, Jouke Jan; Willemsen, Gonneke; de Geus, Eco J C; Boomsma, Dorret I

    2012-01-01

    We examined sex differences in familial resemblance for a broad range of behavioral, psychiatric and health related phenotypes (122 complex traits) in children and adults. There is a renewed interest in the importance of genotype by sex interaction in, for example, genome-wide association (GWA) studies of complex phenotypes. If different genes play a role across sex, GWA studies should consider the effect of genetic variants separately in men and women, which affects statistical power. Twin and family studies offer an opportunity to compare resemblance between opposite-sex family members to the resemblance between same-sex relatives, thereby presenting a test of quantitative and qualitative sex differences in the genetic architecture of complex traits. We analyzed data on lifestyle, personality, psychiatric disorder, health, growth, development and metabolic traits in dizygotic (DZ) same-sex and opposite-sex twins, as these siblings are perfectly matched for age and prenatal exposures. Sample size varied from slightly over 300 subjects for measures of brain function such as EEG power to over 30,000 subjects for childhood psychopathology and birth weight. For most phenotypes, sample sizes were large, with an average sample size of 9027 individuals. By testing whether the resemblance in DZ opposite-sex pairs is the same as in DZ same-sex pairs, we obtain evidence for genetic qualitative sex-differences in the genetic architecture of complex traits for 4% of phenotypes. We conclude that for most traits that were examined, the current evidence is that same the genes are operating in men and women.

  10. Development of the Neurochemical Architecture of the Central Complex

    PubMed Central

    Boyan, George S.; Liu, Yu

    2016-01-01

    The central complex represents one of the most conspicuous neuroarchitectures to be found in the insect brain and regulates a wide repertoire of behaviors including locomotion, stridulation, spatial orientation and spatial memory. In this review article, we show that in the grasshopper, a model insect system, the intricate wiring of the fan-shaped body (FB) begins early in embryogenesis when axons from the first progeny of four protocerebral stem cells (called W, X, Y, Z, respectively) in each brain hemisphere establish a set of tracts to the primary commissural system. Decussation of subsets of commissural neurons at stereotypic locations across the brain midline then establishes a columnar neuroarchitecture in the FB which is completed during embryogenesis. Examination of the expression patterns of various neurochemicals in the central complex including neuropeptides, a neurotransmitter and the gas nitric oxide (NO), show that these appear progressively and in a substance-specific manner during embryogenesis. Each neuroactive substance is expressed by neurons located at stereotypic locations in a given central complex lineage, confirming that the stem cells are biochemically multipotent. The organization of axons expressing the various neurochemicals within the central complex is topologically related to the location, and hence birthdate, of the neurons within the lineages. The neurochemical expression patterns within the FB are layered, and so reflect the temporal topology present in the lineages. This principle relates the neuroanatomical to the neurochemical architecture of the central complex and so may provide insights into the development of adaptive behaviors. PMID:27630548

  11. Cribellate thread production in spiders: Complex processing of nano-fibres into a functional capture thread.

    PubMed

    Joel, Anna-Christin; Kappel, Peter; Adamova, Hana; Baumgartner, Werner; Scholz, Ingo

    2015-11-01

    Spider silk production has been studied intensively in the last years. However, capture threads of cribellate spiders employ an until now often unnoticed alternative of thread production. This thread in general is highly interesting, as it not only involves a controlled arrangement of three types of threads with one being nano-scale fibres (cribellate fibres), but also a special comb-like structure on the metatarsus of the fourth leg (calamistrum) for its production. We found the cribellate fibres organized as a mat, enclosing two parallel larger fibres (axial fibres) and forming the typical puffy structure of cribellate threads. Mat and axial fibres are punctiform connected to each other between two puffs, presumably by the action of the median spinnerets. However, this connection alone does not lead to the typical puffy shape of a cribellate thread. Removing the calamistrum, we found a functional capture thread still being produced, but the puffy shape of the thread was lost. Therefore, the calamistrum is not necessary for the extraction or combination of fibres, but for further processing of the nano-scale cribellate fibres. Using data from Uloborus plumipes we were able to develop a model of the cribellate thread production, probably universally valid for cribellate spiders.

  12. Shaping the light transmission through a multimode optical fibre: complex transformation analysis and applications in biophotonics.

    PubMed

    Čižmár, Tomáš; Dholakia, Kishan

    2011-09-26

    We present a powerful approach towards full understanding of laser light propagation through multimode optical fibres and control of the light at the fibre output. Transmission of light within a multimode fibre introduces randomization of laser beam amplitude, phase and polarization. We discuss the importance of each of these factors and introduce an experimental geometry allowing full analysis of the light transmission through the multimode fibre and subsequent beam-shaping using a single spatial light modulator. We show that using this approach one can generate an arbitrary output optical field within the accessible field of view and range of spatial frequencies given by fibre core diameter and numerical aperture, respectively, that contains over 80% of the total available power. We also show that this technology has applications in biophotonics. As an example, we demonstrate the manipulation of colloidal microparticles. © 2011 Optical Society of America

  13. Mandibular gnathobases of marine planktonic copepods - feeding tools with complex micro- and nanoscale composite architectures.

    PubMed

    Michels, Jan; Gorb, Stanislav N

    2015-01-01

    Copepods are dominant members of the marine zooplankton. Their diets often comprise large proportions of diatom taxa whose silicified frustules are mechanically stable and offer protection against grazers. Despite of this protection, many copepod species are able to efficiently break even the most stable frustule types. This ability requires specific feeding tools with mechanically adapted architectures, compositions and properties. When ingesting food, the copepods use the gnathobases of their mandibles to grab and, if necessary, crush and mince the food items. The morphology of these gnathobases is related to the diets of the copepods. Gnathobases of copepod species that mainly feed on phytoplankton feature compact and stable tooth-like structures, so-called teeth. In several copepod species these gnathobase teeth have been found to contain silica. Recent studies revealed that the siliceous teeth are complex microscale composites with silica-containing cap-like structures located on chitinous exoskeleton sockets that are connected with rubber-like bearings formed by structures with high proportions of the soft and elastic protein resilin. In addition, the silica-containing cap-like structures exhibit a nanoscale composite architecture. They contain some amorphous silica and large proportions of the crystalline silica type α-cristobalite and are pervaded by a fine chitinous fibre network that very likely serves as a scaffold during the silicification process. All these intricate composite structures are assumed to be the result of a coevolution between the copepod gnathobases and diatom frustules in an evolutionary arms race. The composites very likely increase both the performance of the siliceous teeth and their resistance to mechanical damage, and it is conceivable that their development has favoured the copepods' dominance of the marine zooplankton observed today.

  14. Architecture and dynamics of the autophagic phosphatidylinositol 3-kinase complex

    PubMed Central

    Baskaran, Sulochanadevi; Carlson, Lars-Anders; Stjepanovic, Goran; Young, Lindsey N; Kim, Do Jin; Grob, Patricia; Stanley, Robin E; Nogales, Eva; Hurley, James H

    2014-01-01

    The class III phosphatidylinositol 3-kinase complex I (PI3KC3-C1) that functions in early autophagy consists of the lipid kinase VPS34, the scaffolding protein VPS15, the tumor suppressor BECN1, and the autophagy-specific subunit ATG14. The structure of the ATG14-containing PI3KC3-C1 was determined by single-particle EM, revealing a V-shaped architecture. All of the ordered domains of VPS34, VPS15, and BECN1 were mapped by MBP tagging. The dynamics of the complex were defined using hydrogen–deuterium exchange, revealing a novel 20-residue ordered region C-terminal to the VPS34 C2 domain. VPS15 organizes the complex and serves as a bridge between VPS34 and the ATG14:BECN1 subcomplex. Dynamic transitions occur in which the lipid kinase domain is ejected from the complex and VPS15 pivots at the base of the V. The N-terminus of BECN1, the target for signaling inputs, resides near the pivot point. These observations provide a framework for understanding the allosteric regulation of lipid kinase activity. DOI: http://dx.doi.org/10.7554/eLife.05115.001 PMID:25490155

  15. Architecture and function of IFT complex proteins in ciliogenesis.

    PubMed

    Taschner, Michael; Bhogaraju, Sagar; Lorentzen, Esben

    2012-02-01

    Cilia and flagella (interchangeable terms) are evolutionarily conserved organelles found on many different types of eukaryotic cells where they fulfill important functions in motility, sensory reception and signaling. The process of Intraflagellar Transport (IFT) is of central importance for both the assembly and maintenance of cilia, as it delivers building blocks from their site of synthesis in the cell body to the ciliary assembly site at the tip of the cilium. A key player in this process is the multi-subunit IFT-complex, which acts as an adapter between the motor proteins required for movement and the ciliary cargo proteins. Since the discovery of IFT more than 15 years ago, considerable effort has gone into the purification and characterization of the IFT complex proteins. Even though this has led to very interesting findings and has greatly improved our knowledge of the IFT process, we still know very little about the overall architecture of the IFT complex and the specific functions of the various subunits. In this review we will give an update on the knowledge of the structure and function of individual IFT proteins, and the way these proteins interact to form the complex that facilitates IFT.

  16. RootNav: navigating images of complex root architectures.

    PubMed

    Pound, Michael P; French, Andrew P; Atkinson, Jonathan A; Wells, Darren M; Bennett, Malcolm J; Pridmore, Tony

    2013-08-01

    We present a novel image analysis tool that allows the semiautomated quantification of complex root system architectures in a range of plant species grown and imaged in a variety of ways. The automatic component of RootNav takes a top-down approach, utilizing the powerful expectation maximization classification algorithm to examine regions of the input image, calculating the likelihood that given pixels correspond to roots. This information is used as the basis for an optimization approach to root detection and quantification, which effectively fits a root model to the image data. The resulting user experience is akin to defining routes on a motorist's satellite navigation system: RootNav makes an initial optimized estimate of paths from the seed point to root apices, and the user is able to easily and intuitively refine the results using a visual approach. The proposed method is evaluated on winter wheat (Triticum aestivum) images (and demonstrated on Arabidopsis [Arabidopsis thaliana], Brassica napus, and rice [Oryza sativa]), and results are compared with manual analysis. Four exemplar traits are calculated and show clear illustrative differences between some of the wheat accessions. RootNav, however, provides the structural information needed to support extraction of a wider variety of biologically relevant measures. A separate viewer tool is provided to recover a rich set of architectural traits from RootNav's core representation.

  17. Complex Product Architecture Analysis using an Integrated Approach

    NASA Astrophysics Data System (ADS)

    Uddin, Amad; Felician Campean, Ioan; Khurshid Khan, Mohammed

    2014-07-01

    Product design decomposition and synthesis is a constant challenge with its continuously increasing complexity at each level of abstraction. Currently, design decomposition and synthesis analytical tasks are mostly accomplished via functional and structural methods. These methods are useful in different phases of design process for product definition and architecture but limited in a way that they tend to focus more on 'what' and less on 'how' and vice versa. This paper combines a functional representation tool known as System State Flow Diagram (a solution independent approach), a solution search tool referred as Morphology Table, and Design Structure Matrix (mainly a solution dependent tool). The proposed approach incorporates Multiple Domain Matrix (MDM) to integrate the knowledge of both solution independent and dependent analyses. The approach is illustrated with a case study of solar robot toy, followed by its limitations, future work and discussion.

  18. Genetic Architecture Of Declarative Memory: Implications for Complex Illnesses

    PubMed Central

    Bearden, Carrie E.; Karlsgodt, Katherine H.; Bachman, Peter; van Erp, Theo G.M.; Winkler, Anderson M.; Glahn, David C.

    2013-01-01

    Why do memory abilities vary so greatly across individuals and cognitive domains? Although memory functions are highly heritable, what exactly is being genetically transmitted? Here we review evidence for the contribution of both common and partially independent inheritance of distinct aspects of memory function. We begin by discussing the assessment of long-term memory and its underlying neural and molecular basis. We then consider evidence for both specialist and generalist genes underlying individual variability in memory, indicating that carving memory into distinct subcomponents may yield important information regarding its genetic architecture. And finally we review evidence from both complex and single-gene disorders, which provide insight into the molecular mechanisms underlying the genetic basis of human memory function. PMID:21832260

  19. Structural Architecture of SNP Effects on Complex Traits

    PubMed Central

    Gamazon, Eric R.; Cox, Nancy J.; Davis, Lea K.

    2014-01-01

    Despite the discovery of copy-number variation (CNV) across the genome nearly 10 years ago, current SNP-based analysis methodologies continue to collapse the homozygous (i.e., A/A), hemizygous (i.e., A/0), and duplicative (i.e., A/A/A) genotype states, treating the genotype variable as irreducible or unaltered by other colocalizing forms of genetic (e.g., structural) variation. Our understanding of common, genome-wide CNVs suggests that the canonical genotype construct might belie the enormous complexity of the genome. Here we present multiple analyses of several phenotypes and provide methods supporting a conceptual shift that embraces the structural dimension of genotype. We comprehensively investigate the impact of the structural dimension of genotype on (1) GWAS methods, (2) interpretation of rare LOF variants, (3) characterization of genomic architecture, and (4) implications for mapping loci involved in complex disease. Taken together, these results argue for the inclusion of a structural dimension and suggest that some portion of the “missing” heritability might be recovered through integration of the structural dimension of SNP effects on complex traits. PMID:25307299

  20. Insight into the Architecture of the NuRD Complex

    PubMed Central

    Alqarni, Saad S. M.; Murthy, Andal; Zhang, Wei; Przewloka, Marcin R.; Silva, Ana P. G.; Watson, Aleksandra A.; Lejon, Sara; Pei, Xue Y.; Smits, Arne H.; Kloet, Susan L.; Wang, Hongxin; Shepherd, Nicholas E.; Stokes, Philippa H.; Blobel, Gerd A.; Vermeulen, Michiel; Glover, David M.; Mackay, Joel P.; Laue, Ernest D.

    2014-01-01

    The nucleosome remodeling and deacetylase (NuRD) complex is a widely conserved transcriptional co-regulator that harbors both nucleosome remodeling and histone deacetylase activities. It plays a critical role in the early stages of ES cell differentiation and the reprogramming of somatic to induced pluripotent stem cells. Abnormalities in several NuRD proteins are associated with cancer and aging. We have investigated the architecture of NuRD by determining the structure of a subcomplex comprising RbAp48 and MTA1. Surprisingly, RbAp48 recognizes MTA1 using the same site that it uses to bind histone H4, showing that assembly into NuRD modulates RbAp46/48 interactions with histones. Taken together with other results, our data show that the MTA proteins act as scaffolds for NuRD complex assembly. We further show that the RbAp48-MTA1 interaction is essential for the in vivo integration of RbAp46/48 into the NuRD complex. PMID:24920672

  1. Molecular architecture and mechanism of the anaphase-promoting complex

    PubMed Central

    Yang, Jing; McLaughlin, Stephen H.; Barford, David

    2015-01-01

    The ubiquitination of cell cycle regulatory proteins by the anaphase-promoting complex/cyclosome (APC/C) controls sister chromatid segregation, cytokinesis and the establishment of G1. The APC/C is an unusually large multimeric cullin-RING ligase. Its activity is strictly dependent on regulatory coactivator subunits that promote APC/C – substrate interactions and stimulate its catalytic reaction. Because the structures of many APC/C subunits and their organization within the assembly are unknown, the molecular basis for these processes is poorly understood. Here, from a cryo-EM reconstruction of a human APC/C-coactivator-substrate complex at 7.4 Å resolution, we have determined the complete secondary structural architecture of the complex. With this information we identified protein folds for structurally uncharacterized subunits, and the definitive location of all 20 APC/C subunits within the 1.2 MDa assembly. Comparison with apo APC/C shows that coactivator promotes a profound allosteric transition involving displacement of the cullin-RING catalytic subunits relative to the degron recognition module of coactivator and Apc10. This transition is accompanied by increased flexibility of the cullin-RING subunits and enhanced affinity for UbcH10~ubiquitin, changes which may contribute to coactivator-mediated stimulation of APC/C E3 ligase activity. PMID:25043029

  2. Fibre Optics Distributed Temperature Sensing for EcoHydrological Characterization of a Complex Terrain

    NASA Astrophysics Data System (ADS)

    Ciocca, Francesco; Krause, Stefan; Chalari, Athena; Mondanos, Michael

    2015-04-01

    Being able to properly monitor the heat and water dynamics in the soil vadose zone is crucial to the ecohydrological characterization of any field site. Point sensors may provide accurate measurements of temperature and soil moisture but offering a spatial footprint limited to few centimeters, dramatically reducing the amount of information that can be obtained, in particular about the spatial variability and directions of the soil heat and water fluxes. Fibre Optics Distributed Temperature Sensing (FO-DTS) demonstrated to be a very promising, cost effective and non invasive technique for heat and moisture distributed monitoring from small (centimeters) to large (kilometers) spatial scales. A permanent installation aiming at monitoring the long time and large space-scale soil moisture and temperature variations in the shallow soil is going to be realized in two areas presenting different vegetation (trees and low grass, respectively) and inclined transects in a forest close to the Birmingham area. FO cable is going to be buried at different depths by mean of a plow and both active (monitor cooling rates of a heated cable) and passive (e.g. Fourier or Dynamic Harmonic Regression analysis to diurnal and seasonal temperature trends) FO-DTS techniques will be used to constantly monitor and quantify the soil water and heat traces. The ability of FO-DTS to provide reliable information about moisture and heat dynamics in this complex environment affected by the variability of many natural factors (e.g. precipitation, presence or absence of deep vegetation, diurnal/seasonal atmospheric forcing, orography) will be exploited. A detailed description of this complex and unique installation will be provided, along with a presentation of the preliminary results of the FO-DTS measurements. Particular emphasis to the comparison between both the initial state and the differences in diurnal moisture and temperature regimes between the two areas (due to the difference in vegetation

  3. Polygonal Shapes Detection in 3d Models of Complex Architectures

    NASA Astrophysics Data System (ADS)

    Benciolini, G. B.; Vitti, A.

    2015-02-01

    A sequential application of two global models defined on a variational framework is proposed for the detection of polygonal shapes in 3D models of complex architectures. As a first step, the procedure involves the use of the Mumford and Shah (1989) 1st-order variational model in dimension two (gridded height data are processed). In the Mumford-Shah model an auxiliary function detects the sharp changes, i.e., the discontinuities, of a piecewise smooth approximation of the data. The Mumford-Shah model requires the global minimization of a specific functional to simultaneously produce both the smooth approximation and its discontinuities. In the proposed procedure, the edges of the smooth approximation derived by a specific processing of the auxiliary function are then processed using the Blake and Zisserman (1987) 2nd-order variational model in dimension one (edges are processed in the plane). This second step permits to describe the edges of an object by means of piecewise almost-linear approximation of the input edges themselves and to detects sharp changes of the first-derivative of the edges so to detect corners. The Mumford-Shah variational model is used in two dimensions accepting the original data as primary input. The Blake-Zisserman variational model is used in one dimension for the refinement of the description of the edges. The selection among all the boundaries detected by the Mumford-Shah model of those that present a shape close to a polygon is performed by considering only those boundaries for which the Blake-Zisserman model identified discontinuities in their first derivative. The output of the procedure are hence shapes, coming from 3D geometric data, that can be considered as polygons. The application of the procedure is suitable for, but not limited to, the detection of objects such as foot-print of polygonal buildings, building facade boundaries or windows contours. v The procedure is applied to a height model of the building of the Engineering

  4. Dilated cardiomyopathy: the complexity of a diverse genetic architecture.

    PubMed

    Hershberger, Ray E; Hedges, Dale J; Morales, Ana

    2013-09-01

    Remarkable progress has been made in understanding the genetic basis of dilated cardiomyopathy (DCM). Rare variants in >30 genes, some also involved in other cardiomyopathies, muscular dystrophy, or syndromic disease, perturb a diverse set of important myocardial proteins to produce a final DCM phenotype. Large, publicly available datasets have provided the opportunity to evaluate previously identified DCM-causing mutations, and to examine the population frequency of sequence variants similar to those that have been observed to cause DCM. The frequency of these variants, whether associated with dilated or hypertrophic cardiomyopathy, is greater than estimates of disease prevalence. This mismatch might be explained by one or more of the following possibilities: that the penetrance of DCM-causing mutations is lower than previously thought, that some variants are noncausal, that DCM prevalence is higher than previously estimated, or that other more-complex genomics underlie DCM. Reassessment of our assumptions about the complexity of the genomic and phenomic architecture of DCM is warranted. Much about the genomic basis of DCM remains to be investigated, which will require comprehensive genomic studies in much larger cohorts of rigorously phenotyped probands and family members than previously examined.

  5. Evidence for Complex Molecular Architectures for Solvent-Extracted Lignins

    SciTech Connect

    Rials, Timothy G; Urban, Volker S; Langan, Paul

    2012-01-01

    Lignin, an abundant, naturally occurring biopolymer, is often considered 'waste' and used as a simple fuel source in the paper-making process. However, lignin has emerged as a promising renewable resource for engineering materials, such as carbon fibers. Unfortunately, the molecular architecture of lignin (in vivo and extracted) is still elusive, with numerous conflicting reports in the literature, and knowledge of this structure is extremely important, not only for materials technologies, but also for production of biofuels such as cellulosic ethanol due to biomass recalcitrance. As such, the molecular structures of solvent-extracted (sulfur-free) lignins, which have been modified using various acyl chlorides, have been probed using small-angle X-ray (SAXS) and neutron (SANS) scattering in tetrahydrofuran (THF) solution along with hydrodynamic characterization using dilute solution viscometry and gel permeation chromatography (GPC) in THF. Mass spectrometry shows an absolute molecular weight {approx}18-30 kDa ({approx}80-140 monomers), while GPC shows a relative molecular weight {approx}3 kDa. A linear styrene oligomer (2.5 kDa) was also analyzed in THF using SANS. Results clearly show that lignin molecular architectures are somewhat rigid and complex, ranging from nanogels to hyperbranched macromolecules, not linear oligomers or physical assemblies of oligomers, which is consistent with previously proposed delignification (extraction) mechanisms. Future characterization using the methods discussed here can be used to guide extraction processes as well as genetic engineering technologies to convert lignin into value added materials with the potential for high positive impact on global sustainability.

  6. Correlation of Utrophin Levels with the Dystrophin Protein Complex and Muscle Fibre Regeneration in Duchenne and Becker Muscular Dystrophy Muscle Biopsies.

    PubMed

    Janghra, Narinder; Morgan, Jennifer E; Sewry, Caroline A; Wilson, Francis X; Davies, Kay E; Muntoni, Francesco; Tinsley, Jonathon

    2016-01-01

    Duchenne muscular dystrophy is a severe and currently incurable progressive neuromuscular condition, caused by mutations in the DMD gene that result in the inability to produce dystrophin. Lack of dystrophin leads to loss of muscle fibres and a reduction in muscle mass and function. There is evidence from dystrophin-deficient mouse models that increasing levels of utrophin at the muscle fibre sarcolemma by genetic or pharmacological means significantly reduces the muscular dystrophy pathology. In order to determine the efficacy of utrophin modulators in clinical trials, it is necessary to accurately measure utrophin levels and other biomarkers on a fibre by fibre basis within a biopsy section. Our aim was to develop robust and reproducible staining and imaging protocols to quantify sarcolemmal utrophin levels, sarcolemmal dystrophin complex members and numbers of regenerating fibres within a biopsy section. We quantified sarcolemmal utrophin in mature and regenerating fibres and the percentage of regenerating muscle fibres, in muscle biopsies from Duchenne, the milder Becker muscular dystrophy and controls. Fluorescent immunostaining followed by image analysis was performed to quantify utrophin intensity and β-dystrogylcan and ɣ -sarcoglycan intensity at the sarcolemma. Antibodies to fetal and developmental myosins were used to identify regenerating muscle fibres allowing the accurate calculation of percentage regeneration fibres in the biopsy. Our results indicate that muscle biopsies from Becker muscular dystrophy patients have fewer numbers of regenerating fibres and reduced utrophin intensity compared to muscle biopsies from Duchenne muscular dystrophy patients. Of particular interest, we show for the first time that the percentage of regenerating muscle fibres within the muscle biopsy correlate with the clinical severity of Becker and Duchenne muscular dystrophy patients from whom the biopsy was taken. The ongoing development of these tools to quantify

  7. Correlation of Utrophin Levels with the Dystrophin Protein Complex and Muscle Fibre Regeneration in Duchenne and Becker Muscular Dystrophy Muscle Biopsies

    PubMed Central

    Janghra, Narinder; Morgan, Jennifer E.; Sewry, Caroline A.; Wilson, Francis X.; Davies, Kay E.; Muntoni, Francesco; Tinsley, Jonathon

    2016-01-01

    Duchenne muscular dystrophy is a severe and currently incurable progressive neuromuscular condition, caused by mutations in the DMD gene that result in the inability to produce dystrophin. Lack of dystrophin leads to loss of muscle fibres and a reduction in muscle mass and function. There is evidence from dystrophin-deficient mouse models that increasing levels of utrophin at the muscle fibre sarcolemma by genetic or pharmacological means significantly reduces the muscular dystrophy pathology. In order to determine the efficacy of utrophin modulators in clinical trials, it is necessary to accurately measure utrophin levels and other biomarkers on a fibre by fibre basis within a biopsy section. Our aim was to develop robust and reproducible staining and imaging protocols to quantify sarcolemmal utrophin levels, sarcolemmal dystrophin complex members and numbers of regenerating fibres within a biopsy section. We quantified sarcolemmal utrophin in mature and regenerating fibres and the percentage of regenerating muscle fibres, in muscle biopsies from Duchenne, the milder Becker muscular dystrophy and controls. Fluorescent immunostaining followed by image analysis was performed to quantify utrophin intensity and β-dystrogylcan and ɣ –sarcoglycan intensity at the sarcolemma. Antibodies to fetal and developmental myosins were used to identify regenerating muscle fibres allowing the accurate calculation of percentage regeneration fibres in the biopsy. Our results indicate that muscle biopsies from Becker muscular dystrophy patients have fewer numbers of regenerating fibres and reduced utrophin intensity compared to muscle biopsies from Duchenne muscular dystrophy patients. Of particular interest, we show for the first time that the percentage of regenerating muscle fibres within the muscle biopsy correlate with the clinical severity of Becker and Duchenne muscular dystrophy patients from whom the biopsy was taken. The ongoing development of these tools to quantify

  8. Planification de trajectoires pour placement automatise de fibres sur surfaces de geometries complexes

    NASA Astrophysics Data System (ADS)

    Hely, Clement

    During the past 50 years, the use of composite materials drastically increase, mainly thanks to the interest of aeronautical industries for these strong and lightweight materials. To improve the productivity of composite materials manufacturing some of the largest aeronautics companies began to develop automated processes such as Automated Fibre Placement (AFP). The AFP workcells currently used by the industry were mainly developed for production of large, nearly flat, plates with low curvatures such as aircraft fuselages. However, the fields of aeronautics and sport goods production begin nowadays to show an interest for manufacturing of smaller and more complex parts. The aim of the project in which this research takes place is to design a new AFP workcell and to develop new techniques allowing production of parts with small size and complex geometry. The work presented in this thesis focuses on the path planning on multi-axial revolution surfaces, e.g. Y-shaped tubes of constant circular cross section. Several path planning algorithms will be presented aiming at the exhaustive coverage of a mandrel with pre-impregnated (prepreg) composite tape. The methodology used in two of these algorithms is to individually cover each branch of the Y-shaped part with paths deriving from a helix. In the first one, the helix will be cut at the boundary between a branch and the junction region (algorithm HD) while in the second (algorithm HA) the pseudo-helix path can be adjusted to follow this boundary. These two methods were shown to have some drawbacks compromising their practical use and possibly leading to parts with diminished mechanical properties. To avoid these drawbacks, two others algorithms were developed with a new methodology. With them, the aim is to cover two branches of the Y-shape with a continuous course (i.e. without cut). The first one uses a well known strategy which defines plies with a constant fibre orientation. Parallel paths are then computed to

  9. Drivers of region-wide declines in architectural complexity on Caribbean reefs

    NASA Astrophysics Data System (ADS)

    Alvarez-Filip, Lorenzo; Gill, J. A.; Dulvy, N. K.; Perry, A. L.; Watkinson, A. R.; Côté, I. M.

    2011-12-01

    Severe declines in the cover of live hard coral on reefs have been reported worldwide, and in the Caribbean region, the architectural complexity of coral reefs has also declined markedly. While the drivers of coral cover loss are relatively well understood, little is known about the drivers of regional-scale declines in architectural complexity. We have used a dataset of 49 time series reporting reef architectural complexity to explore the effect of hurricanes, coral bleaching and fishing on Caribbean-wide annual rates of change in reef complexity. Hurricane impacts greatly influence reef complexity, with the most rapid rates of decline in complexity occurring at sites impacted during their survey period, and with lower rates of loss occurring at unimpacted sites. Reef architectural complexity did not change significantly following mass bleaching events (in a time frame of <5 years) or positive thermal anomalies. Although the rates of change in architectural complexity were similar in and out of marine protected areas (MPAs), significant declines in complexity were observed inside but not outside of MPAs, possibly because reductions in fishing can lead to increased bioerosion by herbivores within MPAs. Our findings suggest that major drivers of coral mortality, such as coral bleaching, do not influence reef architectural complexity in the short term (<5 years). Instead, direct physical impacts and reef bioerosion appear to be important drivers of the widespread loss of architecturally complex reefs in the Caribbean.

  10. Architecture of the Florida Power Grid as a Complex Network

    NASA Astrophysics Data System (ADS)

    Xu, Yan; Gurfinkel, Aleks Jacob; Rikvold, Per Arne

    2014-03-01

    Power grids are the largest engineered systems ever built. Our work presents a simple and self-consistent graph-theoretic analysis of the Florida high-voltage power grid as a technological network embedded in two-dimensional space. We take a new perspective on the mixing patterns of generators and loads in power grids, pointing out that the real grid is usually intermediate between the random mixing and semi-bipartite case (in which generator-generator power transmission lines are disallowed). We propose spatial network models for power grids, which are obtained via a Monte Carlo cooling optimization process. Our results suggest some possible design principles behind the complex architecture of the Florida grid, viz. balancing low construction cost (measured by the total length of transmission lines) and an indispensable redundancy (measured by the clustering coefficient and edge multiplicity) responsible for the robustness of the grid. We also study community structures (modularity) of the real and modeled power-grid networks. Such communities can be electrically separated from each other to limit cascading power failures, a technique known as intentional islanding. Supported by NSF Grant No. DMR-1104829.

  11. Architecture of the Florida power grid as a complex network

    NASA Astrophysics Data System (ADS)

    Xu, Yan; Gurfinkel, Aleks Jacob; Rikvold, Per Arne

    2014-05-01

    We study the Florida high-voltage power grid as a technological network embedded in space. Measurements of geographical lengths of transmission lines, the mixing of generators and loads, the weighted clustering coefficient, as well as the organization of edge conductance weights show a complex architecture quite different from random-graph models usually considered. In particular, we introduce a parametrized mixing matrix to characterize the mixing pattern of generators and loads in the Florida Grid, which is intermediate between the random mixing case and the semi-bipartite case where generator-generator transmission lines are forbidden. Our observations motivate an investigation of optimization (design) principles leading to the structural organization of power grids. We thus propose two network optimization models for the Florida Grid as a case study. Our results show that the Florida Grid is optimized not only by reducing the construction cost (measured by the total length of power lines), but also through reducing the total pairwise edge resistance in the grid, which increases the robustness of power transmission between generators and loads against random line failures. We then embed our models in spatial areas of different aspect ratios and study how this geometric factor affects the network structure, as well as the box-counting fractal dimension of the grids generated by our models.

  12. RAINBOW: Architecture-Based Adaptation of Complex Systems

    DTIC Science & Technology

    2005-04-01

    2 This is the core architectural representation scheme adopted by a number of ADLs, including Acme [8], xArch [3], xADL [5], ADML [15], and SADL...International, Mar. 1997. 15. The OpenGroup. Architecture Description Markup Language ( ADML ) Version 1. Apr. 2000. Available at http

  13. Flattening of Caribbean coral reefs: region-wide declines in architectural complexity

    PubMed Central

    Alvarez-Filip, Lorenzo; Dulvy, Nicholas K.; Gill, Jennifer A.; Côté, Isabelle M.; Watkinson, Andrew R.

    2009-01-01

    Coral reefs are rich in biodiversity, in large part because their highly complex architecture provides shelter and resources for a wide range of organisms. Recent rapid declines in hard coral cover have occurred across the Caribbean region, but the concomitant consequences for reef architecture have not been quantified on a large scale to date. We provide, to our knowledge, the first region-wide analysis of changes in reef architectural complexity, using nearly 500 surveys across 200 reefs, between 1969 and 2008. The architectural complexity of Caribbean reefs has declined nonlinearly with the near disappearance of the most complex reefs over the last 40 years. The flattening of Caribbean reefs was apparent by the early 1980s, followed by a period of stasis between 1985 and 1998 and then a resumption of the decline in complexity to the present. Rates of loss are similar on shallow (<6 m), mid-water (6–20 m) and deep (>20 m) reefs and are consistent across all five subregions. The temporal pattern of declining architecture coincides with key events in recent Caribbean ecological history: the loss of structurally complex Acropora corals, the mass mortality of the grazing urchin Diadema antillarum and the 1998 El Nino Southern Oscillation-induced worldwide coral bleaching event. The consistently low estimates of current architectural complexity suggest regional-scale degradation and homogenization of reef structure. The widespread loss of architectural complexity is likely to have serious consequences for reef biodiversity, ecosystem functioning and associated environmental services. PMID:19515663

  14. Flattening of Caribbean coral reefs: region-wide declines in architectural complexity.

    PubMed

    Alvarez-Filip, Lorenzo; Dulvy, Nicholas K; Gill, Jennifer A; Côté, Isabelle M; Watkinson, Andrew R

    2009-08-22

    Coral reefs are rich in biodiversity, in large part because their highly complex architecture provides shelter and resources for a wide range of organisms. Recent rapid declines in hard coral cover have occurred across the Caribbean region, but the concomitant consequences for reef architecture have not been quantified on a large scale to date. We provide, to our knowledge, the first region-wide analysis of changes in reef architectural complexity, using nearly 500 surveys across 200 reefs, between 1969 and 2008. The architectural complexity of Caribbean reefs has declined nonlinearly with the near disappearance of the most complex reefs over the last 40 years. The flattening of Caribbean reefs was apparent by the early 1980s, followed by a period of stasis between 1985 and 1998 and then a resumption of the decline in complexity to the present. Rates of loss are similar on shallow (<6 m), mid-water (6-20 m) and deep (>20 m) reefs and are consistent across all five subregions. The temporal pattern of declining architecture coincides with key events in recent Caribbean ecological history: the loss of structurally complex Acropora corals, the mass mortality of the grazing urchin Diadema antillarum and the 1998 El Nino Southern Oscillation-induced worldwide coral bleaching event. The consistently low estimates of current architectural complexity suggest regional-scale degradation and homogenization of reef structure. The widespread loss of architectural complexity is likely to have serious consequences for reef biodiversity, ecosystem functioning and associated environmental services.

  15. Does plant architectural complexity increase with increasing habitat complexity? A test with a pioneer shrub in the Brazilian Cerrado.

    PubMed

    Silveira, F A O; Oliveira, E G

    2013-05-01

    Understanding variation in plant traits in heterogeneous habitats is important to predict responses to changing environments, but trait-environment associations are poorly known along ecological gradients. We tested the hypothesis that plant architectural complexity increases with habitat complexity along a soil fertility gradient in a Cerrado (Neotropical savanna) area in southeastern Brazil. Plant architecture and productivity (estimated as the total number of healthy infructescences) of Miconia albicans (SW.) Triana were examined in three types of vegetation which together form a natural gradient of increasing soil fertility, tree density and canopy cover: grasslands (campo sujo, CS), shrublands (cerrado sensu strico, CE) and woodlands (cerradão, CD). As expected, plants growing at the CS were shorter and had a lower branching pattern, whereas plants at the CD were the tallest. Unexpectedly, however, CD plants did not show higher architectural complexity compared to CE plants. Higher architectural similarity between CE and CD plants compared to similarity between CS and CE plants suggests reduced expression of functional architectural traits under shade. Plants growing at the CE produced more quaternary shoots, leading to a larger number of infructescences. This higher plant productivity in CE indicates that trait variation in ecological gradients is more complex than previously thought. Nematode-induced galls accounted for fruit destruction in 76.5% infructescences across physiognomies, but percentage of attack was poorly related to architectural variables. Our data suggest shade-induced limitation in M. albicans architecture, and point to complex phenotypic variation in heterogeneous habitats in Neotropical savannas.

  16. An Optical Fibre Sensor Array For The Measurement Of Displacements Of Complex Engineering Structures

    NASA Astrophysics Data System (ADS)

    Petrie, G. R.; Jones, K. W.; Jones, R.

    1986-08-01

    The system described in this paper has been developed in response to a need to measure components of the dynamic displacement of a railway track relative to the sleeper. It embodies an array of two-wavelength optical fibre displacement sensors based on the Cambridge Consultants Ltd moving shutter principle. The sensors have been designed to operate over the frequency range DC to 3.5kHz with a resolution of lom over the displacement range 0-2mm. The distribution of the sensors over the track and sleeper enables combinations of orthogonal displacement components and linear tilts to be measured. The paper describes the detailed optical, mechanical and electronic design together with experimental results which demonstrate the immunity of the system to fibre noise, differential coupling losses, etc. Furthermore, preliminary structural displacement measurements are also presented.

  17. The infectious particle of insect-borne totivirus-like Omono River virus has raised ridges and lacks fibre complexes

    PubMed Central

    Okamoto, Kenta; Miyazaki, Naoyuki; Larsson, Daniel S. D.; Kobayashi, Daisuke; Svenda, Martin; Mühlig, Kerstin; Maia, Filipe R. N. C.; Gunn, Laura H.; Isawa, Haruhiko; Kobayashi, Mutsuo; Sawabe, Kyoko; Murata, Kazuyoshi; Hajdu, Janos

    2016-01-01

    Omono River virus (OmRV) is a double-stranded RNA virus isolated from Culex mosquitos, and it belongs to a group of unassigned insect viruses that appear to be related to Totiviridae. This paper describes electron cryo-microscopy (cryoEM) structures for the intact OmRV virion to 8.9 Å resolution and the structure of the empty virus-like-particle, that lacks RNA, to 8.3 Å resolution. The icosahedral capsid contains 120-subunits and resembles another closely related arthropod-borne totivirus-like virus, the infectious myonecrosis virus (IMNV) from shrimps. Both viruses have an elevated plateau around their icosahedral 5-fold axes, surrounded by a deep canyon. Sequence and structural analysis suggests that this plateau region is mainly composed of the extended C-terminal region of the capsid proteins. In contrast to IMNV, the infectious form of OmRV lacks extensive fibre complexes at its 5-fold axes as directly confirmed by a contrast-enhancement technique, using Zernike phase-contrast cryo-EM. Instead, these fibre complexes are replaced by a short “plug” structure at the five-fold axes of OmRV. OmRV and IMNV have acquired an extracellular phase, and the structures at the five-fold axes may be significant in adaptation to cell-to-cell transmission in metazoan hosts. PMID:27616740

  18. Evaluating empirical bounds on complex disease genetic architecture

    PubMed Central

    Agarwala, Vineeta; Flannick, Jason; Sunyaev, Shamil; Altshuler, David

    2014-01-01

    The genetic architecture of human diseases governs the success of genetic mapping and the future of personalized medicine. Although numerous studies have queried the genetic basis of common disease, contradictory hypotheses have been advocated about features of genetic architecture (e.g., the contribution of rare vs. common variants). We developed an integrated simulation framework, calibrated to empirical data, to enable systematic evaluation of such hypotheses. For type 2 diabetes (T2D), two simple parameters – (a) the target size for causal mutation and (b) the coupling between selection and phenotypic effect – define a broad space of architectures. While extreme models are excluded, many models remain consistent with epidemiology, linkage, and genome-wide association studies for T2D, including those where rare variants explain little (<25%) or most (>80%) of heritability. Ongoing sequencing and genotyping studies will further constrain architecture, but very large samples (e.g., >250K unselected individuals) will be required to localize most of the heritability underlying traits like T2D. PMID:24141362

  19. Designing bioinspired composite reinforcement architectures via 3D magnetic printing

    PubMed Central

    Martin, Joshua J.; Fiore, Brad E.; Erb, Randall M.

    2015-01-01

    Discontinuous fibre composites represent a class of materials that are strong, lightweight and have remarkable fracture toughness. These advantages partially explain the abundance and variety of discontinuous fibre composites that have evolved in the natural world. Many natural structures out-perform the conventional synthetic counterparts due, in part, to the more elaborate reinforcement architectures that occur in natural composites. Here we present an additive manufacturing approach that combines real-time colloidal assembly with existing additive manufacturing technologies to create highly programmable discontinuous fibre composites. This technology, termed as ‘3D magnetic printing', has enabled us to recreate complex bioinspired reinforcement architectures that deliver enhanced material performance compared with monolithic structures. Further, we demonstrate that we can now design and evolve elaborate reinforcement architectures that are not found in nature, demonstrating a high level of possible customization in discontinuous fibre composites with arbitrary geometries. PMID:26494282

  20. Designing bioinspired composite reinforcement architectures via 3D magnetic printing

    NASA Astrophysics Data System (ADS)

    Martin, Joshua J.; Fiore, Brad E.; Erb, Randall M.

    2015-10-01

    Discontinuous fibre composites represent a class of materials that are strong, lightweight and have remarkable fracture toughness. These advantages partially explain the abundance and variety of discontinuous fibre composites that have evolved in the natural world. Many natural structures out-perform the conventional synthetic counterparts due, in part, to the more elaborate reinforcement architectures that occur in natural composites. Here we present an additive manufacturing approach that combines real-time colloidal assembly with existing additive manufacturing technologies to create highly programmable discontinuous fibre composites. This technology, termed as `3D magnetic printing', has enabled us to recreate complex bioinspired reinforcement architectures that deliver enhanced material performance compared with monolithic structures. Further, we demonstrate that we can now design and evolve elaborate reinforcement architectures that are not found in nature, demonstrating a high level of possible customization in discontinuous fibre composites with arbitrary geometries.

  1. A NEW LEVEL OF ARCHITECTURAL COMPLEXITY IN THE HUMAN PYRUVATE DEHYDROGENASE COMPLEX

    PubMed Central

    Smolle, Michaela; Prior, Alison Elizabeth; Brown, Audrey Elaine; Cooper, Alan; Byron, Olwyn; Lindsay, John Gordon

    2006-01-01

    SUMMARY Mammalian pyruvate dehydrogenase multi-enzyme complex (PDC) is a key metabolic assembly comprising a 60- meric pentagonal dodecahedral E2 core attached to which are 30 E1 heterotetramers and 6 E3 homodimers at maximal occupancy. Stable E3 integration is mediated by an accessory E3 binding protein (E3BP) located on each of the 12 E2 icosahedral faces. Here, we present evidence for a novel subunit organisation in which dihydrolipoamide dehydrogenase (E3) and E3BP form subcomplexes with a 1:2 stoichiometry implying the existence of a network of E3 ‘cross-bridges’ linking pairs of E3BPs across the surface of the E2 core assembly. We have also determined a low resolution structure for a truncated E3BP/E3 subcomplex using small angle xray scattering showing one of the E3BP lipoyl domains docked into the E3 active site. This new level of architectural complexity in mammalian PDC contrasts with the recently published crystal structure of human E3 complexed with its cognate subunit binding domain and provides important new insights into subunit organisation, its catalytic mechanism and regulation by the intrinsic PDC kinase. PMID:16679318

  2. The Molecular Architecture for the Intermediate Filaments of Hard α -Keratin Based on the Superlattice Data Obtained from a Study of Mammals Using Synchrotron Fibre Diffraction

    DOE PAGES

    James, Veronica

    2011-01-01

    High- and low-angle X-ray diffraction studies of hard α -keratin have been studied, and various models have been proposed over the last 70 years. Most of these studies have been confined to one or two forms of alpha keratin. This high- and low-angle synchrotron fibre diffraction study extends the study to cover all available data for all known forms of hard α -keratin including hairs, fingernails, hooves, horn, and quills from mammals, marsupials, and a monotreme, and it confirms that the model proposed is universally acceptable for all mammals. A complete Bragg analysis of the meridional diffraction patterns, includingmore » multiple-time exposures to verify any weak reflections, verified the existence of a superlattice consisting of two infinite lattices and three finite lattices. An analysis of the equatorial patterns establishes the radii of the oligomeric levels of dimers, tetramers, and intermediate filaments (IFs) together with the centre to centre distance for the IFs, thus confirming the proposed helices within helices molecular architecture for hard α -keratin. The results verify that the structure proposed by Feughelman and James meets the criteria for a valid α -keratin structure.« less

  3. The Molecular Architecture for the Intermediate Filaments of Hard α-Keratin Based on the Superlattice Data Obtained from a Study of Mammals Using Synchrotron Fibre Diffraction.

    PubMed

    James, Veronica

    2011-01-01

    High- and low-angle X-ray diffraction studies of hard α-keratin have been studied, and various models have been proposed over the last 70 years. Most of these studies have been confined to one or two forms of alpha keratin. This high- and low-angle synchrotron fibre diffraction study extends the study to cover all available data for all known forms of hard α-keratin including hairs, fingernails, hooves, horn, and quills from mammals, marsupials, and a monotreme, and it confirms that the model proposed is universally acceptable for all mammals. A complete Bragg analysis of the meridional diffraction patterns, including multiple-time exposures to verify any weak reflections, verified the existence of a superlattice consisting of two infinite lattices and three finite lattices. An analysis of the equatorial patterns establishes the radii of the oligomeric levels of dimers, tetramers, and intermediate filaments (IFs) together with the centre to centre distance for the IFs, thus confirming the proposed helices within helices molecular architecture for hard α-keratin. The results verify that the structure proposed by Feughelman and James meets the criteria for a valid α-keratin structure.

  4. The Molecular Architecture for the Intermediate Filaments of Hard α-Keratin Based on the Superlattice Data Obtained from a Study of Mammals Using Synchrotron Fibre Diffraction

    PubMed Central

    James, Veronica

    2011-01-01

    High- and low-angle X-ray diffraction studies of hard α-keratin have been studied, and various models have been proposed over the last 70 years. Most of these studies have been confined to one or two forms of alpha keratin. This high- and low-angle synchrotron fibre diffraction study extends the study to cover all available data for all known forms of hard α-keratin including hairs, fingernails, hooves, horn, and quills from mammals, marsupials, and a monotreme, and it confirms that the model proposed is universally acceptable for all mammals. A complete Bragg analysis of the meridional diffraction patterns, including multiple-time exposures to verify any weak reflections, verified the existence of a superlattice consisting of two infinite lattices and three finite lattices. An analysis of the equatorial patterns establishes the radii of the oligomeric levels of dimers, tetramers, and intermediate filaments (IFs) together with the centre to centre distance for the IFs, thus confirming the proposed helices within helices molecular architecture for hard α-keratin. The results verify that the structure proposed by Feughelman and James meets the criteria for a valid α-keratin structure. PMID:22028970

  5. The Molecular Architecture for the Intermediate Filaments of Hard [alpha]-Keratin Based on the Superlattice Data Obtained from a Study ofMammals Using Synchrotron Fibre Diffraction

    SciTech Connect

    James, Veronica

    2014-09-24

    High- and low-angle X-ray diffraction studies of hard {alpha}-keratin have been studied, and various models have been proposed over the last 70 years. Most of these studies have been confined to one or two forms of alpha keratin. This high- and low-angle synchrotron fibre diffraction study extends the study to cover all available data for all known forms of hard {alpha}-keratin including hairs, fingernails, hooves, horn, and quills from mammals, marsupials, and a monotreme, and it confirms that the model proposed is universally acceptable for all mammals. A complete Bragg analysis of the meridional diffraction patterns, including multiple-time exposures to verify any weak reflections, verified the existence of a superlattice consisting of two infinite lattices and three finite lattices. An analysis of the equatorial patterns establishes the radii of the oligomeric levels of dimers, tetramers, and intermediate filaments (IFs) together with the centre to centre distance for the IFs, thus confirming the proposed helices within helices molecular architecture for hard {alpha}-keratin. The results verify that the structure proposed by Feughelman and James meets the criteria for a valid {alpha}-keratin structure.

  6. Tandem riboswitch architectures exhibit complex gene control functions.

    PubMed

    Sudarsan, Narasimhan; Hammond, Ming C; Block, Kirsten F; Welz, Rüdiger; Barrick, Jeffrey E; Roth, Adam; Breaker, Ronald R

    2006-10-13

    Riboswitches are structured RNAs typically located in the 5' untranslated regions of bacterial mRNAs that bind metabolites and control gene expression. Most riboswitches sense one metabolite and function as simple genetic switches. However, we found that the 5' region of the Bacillus clausii metE messenger RNA includes two riboswitches that respond to S-adenosylmethionine and coenzyme B12. This tandem arrangement yields a composite gene control system that functions as a two-input Boolean NOR logic gate. These findings and the discovery of additional tandem riboswitch architectures reveal how simple RNA elements can be assembled to make sophisticated genetic decisions without involving protein factors.

  7. Designing polyethylenes of complex chain architectures via Pd-diimine-catalyzed "living" ethylene polymerization.

    PubMed

    Ye, Zhibin; Xu, Lixin; Dong, Zhongmin; Xiang, Peng

    2013-07-18

    Polymer chain architecture is a critically important chain parameter governing intrinsically the properties and applications of polymers. The rapid developments in "living"/controlled polymerization techniques, particularly the controlled radical polymerization techniques, in the past two decades have enabled the precision synthesis of novel polymers having a great variety of complex yet well-defined chain architectures from various monomer stocks. For polyolefins synthesized via catalytic coordination polymerization, the design of complex chain architectures, however, has only started recently because of the relatively limited advancements in the catalytic "living" olefin polymerization technique. In this regard, the versatile Pd-diimine catalysts have provided some unprecedented opportunities, due to their outstanding features, in rendering successfully a novel class of polyethylenes of various new complex chain architectures through the "living" ethylene polymerization protocol. The complex chain architectures designed to date have included hyperbranched, hybrid hyperbranched-linear, block, gradient and block-gradient, star, telechelic, graft and comb, and surface-tethered polymer brushes. This Feature Article attempts to summarize the recent developments achieved in the area, with an emphasis on the synthetic strategies for the architectural design. These developments demonstrate the great potential for further advancements of this new exciting research area.

  8. Complex multi-enhancer contacts captured by genome architecture mapping.

    PubMed

    Beagrie, Robert A; Scialdone, Antonio; Schueler, Markus; Kraemer, Dorothee C A; Chotalia, Mita; Xie, Sheila Q; Barbieri, Mariano; de Santiago, Inês; Lavitas, Liron-Mark; Branco, Miguel R; Fraser, James; Dostie, Josée; Game, Laurence; Dillon, Niall; Edwards, Paul A W; Nicodemi, Mario; Pombo, Ana

    2017-03-23

    The organization of the genome in the nucleus and the interactions of genes with their regulatory elements are key features of transcriptional control and their disruption can cause disease. Here we report a genome-wide method, genome architecture mapping (GAM), for measuring chromatin contacts and other features of three-dimensional chromatin topology on the basis of sequencing DNA from a large collection of thin nuclear sections. We apply GAM to mouse embryonic stem cells and identify enrichment for specific interactions between active genes and enhancers across very large genomic distances using a mathematical model termed SLICE (statistical inference of co-segregation). GAM also reveals an abundance of three-way contacts across the genome, especially between regions that are highly transcribed or contain super-enhancers, providing a level of insight into genome architecture that, owing to the technical limitations of current technologies, has previously remained unattainable. Furthermore, GAM highlights a role for gene-expression-specific contacts in organizing the genome in mammalian nuclei.

  9. The complexity of bone architecture: A tool to differentiate bone diseases

    NASA Astrophysics Data System (ADS)

    Saparin, Peter I.; Gowin, Wolfgang; Kurths, Jürgen; Felsenberg, Dieter

    2000-02-01

    We introduce a generalization of symbolic dynamics to analyze two-dimensional objects and propose measures of complexity to quantify the structure of symbol encoded images. This technique is applied to evaluate the architecture of human cancellous bone by analyzing computed tomography images of vertebrae acquired from specimens and in vivo. The pixels of the preprocessed images are encoded using a mixture of static and dynamic encoding. The architecture of encoded cancellous bone is evaluated as a whole using measures of complexity. A set of new parameters are introduced to quantify the different aspects of structure: complexity and degree of disorder of the architecture as a whole, or spatial arrangements of hard or soft elements of the bone separately. It is found that the complexity of the bone structure relates to its density exponentially. Normal bone has a complex ordered structure, while the architecture during the initial stage of bone loss is characterized by lower complexity and a maximal level of disorder. Increased bone loss leads again to ordered structure, however, its complexity is minimal. This phenomenon was observed in a series of osteoporotic specimens as well as in vivo in patients treated with fluor, and hormone replacement therapy. We found that different bone diseases demonstrate distinctive features captured by the measurements of complexity of the bone's structural composition. It is shown that the application of the proposed technique leads to new insights for understanding of the bone's response on medical treatment and provide important additional information for the diagnostics of bone diseases.

  10. An architecture for intelligent interfaces - Outline of an approach to supporting operators of complex systems

    NASA Technical Reports Server (NTRS)

    Rouse, W. B.; Geddes, N. D.; Curry, R. E.

    1986-01-01

    The conceptual design of a comprehensive support system for operators of complex systems is presented. Key functions within the support system architecture include information management, error monitoring, and adaptive aiding. One of the central knowledge bases underlying this functionality is an operator model that involves a 'matrix' of algorithmic and symbolic models for assessing and predicting an operator's activities, awareness resources, intentions, and performance. Functional block diagrams are presented for the overall architecture as well as the key elements within this architecture. A variety of difficult design issues are discussed and ongoing efforts aimed at resolving these issues are noted.

  11. Linear and nonlinear rheology of architecturally complex polymers

    NASA Astrophysics Data System (ADS)

    Kapnistos, Michail

    We investigated the linear and nonlinear rheology of several model polymeric materials ranging from combs with linear or star-like backbone to third generation dendrimers and cyclic polymers (with no free ends or branches). These systems are governed by topological interactions, which influence their mechanical properties. We combined experiments with theoretical models in order to identify the factors that affect the mechanical response of polymers of various architectures. All polymeric materials exhibited some universal features that were assigned to their microscopic motions. The tube model and the concept of hierarchy of motions along with the dynamic tube dilation (DTD) were the key elements to understand the rheology of branched polymer melts and solutions. We also performed nonlinear experiments in solutions of branched polymers obtaining an extensive dataset of damping functions in combs. We found evidence that the above ideas and mainly DTD, are also present during nonlinear deformations. Apart for the experiments, we modified the existent tube model, improving several shortcomings. The topological free ends of combs were treated simultaneously with the branches and included the effect of polydispersity in a direct manner. The equations were integrated with a user-friendly computer interface for modeling the linear viscoelastic data of several polymer architectures. We explored the role of polymer topology in rheology with the use of model polymers. We found universal principles that govern the mechanical response and linked the microstructure with macroscopic experiments. The extended experimental data have revealed some issues not explained by current theoretical model that need to be addressed in the future.

  12. Effect of collagen fibre orientation on intervertebral disc torsion mechanics.

    PubMed

    Yang, Bo; O'Connell, Grace D

    2017-07-21

    The intervertebral disc is a complex fibro-cartilaginous material, consisting of a pressurized nucleus pulposus surrounded by the annulus fibrosus, which has an angle-ply structure. Disc injury and degeneration are noted by significant changes in tissue structure and function, which significantly alters stress distribution and disc joint stiffness. Differences in fibre orientation are thought to contribute to changes in disc torsion mechanics. Therefore, the objective of this study was to evaluate the effect of collagen fibre orientation on internal disc mechanics under compression combined with axial rotation. We developed and validated a finite element model (FEM) to delineate changes in disc mechanics due to fibre orientation from differences in material properties. FEM simulations were performed with fibres oriented at [Formula: see text] throughout the disc (uniform by region and fibre layer). The initial model was validated by published experimental results for two load conditions, including [Formula: see text] axial compression and [Formula: see text] axial rotation. Once validated, fibre orientation was rotated by [Formula: see text] or [Formula: see text] towards the horizontal plane, resulting in a decrease in disc joint torsional stiffness. Furthermore, we observed that axial rotation caused a sinusoidal change in disc height and radial bulge, which may be beneficial for nutrient transport. In conclusion, including anatomically relevant fibre angles in disc joint FEMs is important for understanding stress distribution throughout the disc and will be important for understanding potential causes for disc injury. Future models will include regional differences in fibre orientation to better represent the fibre architecture of the native disc.

  13. Evaluation of the retinal nerve fibre layer and ganglion cell complex thickness in pituitary macroadenomas without optic chiasmal compression

    PubMed Central

    Cennamo, G; Auriemma, R S; Cardone, D; Grasso, L F S; Velotti, N; Simeoli, C; Di Somma, C; Pivonello, R; Colao, A; de Crecchio, G

    2015-01-01

    Purpose The aim of this prospective study was to measure the thickness of the circumpapillary retinal nerve fibre layer (cpRNFL) and the ganglion cell complex (GCC) using spectral domain optical coherence tomography (SD-OCT) in a cohort of consecutive de novo patients with pituitary macroadenomas without chiasmal compression. Patients and methods Twenty-two consecutive patients with pituitary macroadenoma without chiasmal compression (16 men, 6 women, aged 45.2±14.6 years, 43 eyes) entered the study between September 2011 and June 2013. Among them, 31.8% harboured a growth hormone-secreting pituitary adenoma, 27.3% a prolactin-secreting pituitary adenoma, 27.3% a corticotrophin-secreting pituitary adenoma, and 13.6% a non-secreting pituitary tumour. Eighteen subjects (nine females, nine males, mean age 36.47±6.37 years; 33 eyes) without pituitary adenoma, with normal ophthalmic examination, served as controls. In both patients and controls, cpRNFL and GCC thicknesses were measured by SD-OCT. Results Patients were significantly older (P=0.02) than controls. Best corrected visual acuity, intraocular pressure, colour fundus photography, and automatic perimetry test were within the normal range in patients and controls. Conversely, cpRNFL (P=0.009) and GCC (P<0.0001) were significantly thinner in patients than in controls. The average GCC (r=0.306, P=0.046) significantly correlated with the presence of arterial hypertension. OCT parameters did not differ significantly between patients with a tumour volume above the median and those with a tumour volume below the median. Conclusion Pituitary macroadenomas, even in the absence of chiasmal compression, may induce GCC and retinal nerve fibre layer thinning. SD-OCT may have a role in the early diagnosis and management of patients with pituitary tumours. PMID:25853400

  14. Architecture of a Serine Recombinase-DNA Regulatory Complex

    SciTech Connect

    Mouw, Kent W.; Rowland, Sally-J.; Gajjar, Mark M.; Boocock, Martin R.; Stark, W. Marshall; Rice, Phoebe A.

    2008-04-29

    An essential feature of many site-specific recombination systems is their ability to regulate the direction and topology of recombination. Resolvases from the serine recombinase family assemble an interwound synaptic complex that harnesses negative supercoiling to drive the forward reaction and promote recombination between properly oriented sites. To better understand the interplay of catalytic and regulatory functions within these synaptic complexes, we have solved the structure of the regulatory site synapse in the Sin resolvase system. It reveals an unexpected synaptic interface between helix-turn-helix DNA-binding domains that is also highlighted in a screen for synapsis mutants. The tetramer defined by this interface provides the foundation for a robust model of the synaptic complex, assembled entirely from available crystal structures, that gives insight into how the catalytic activity of Sin and other serine recombinases may be regulated.

  15. Exploiting sparsity and equation-free architectures in complex systems

    NASA Astrophysics Data System (ADS)

    Proctor, J. L.; Brunton, S. L.; Brunton, B. W.; Kutz, J. N.

    2014-12-01

    Complex systems exhibit dynamics that typically evolve on low-dimensional attractors and may have sparse representation in some optimal basis. Recently developed compressive sensing techniques exploit this sparsity for state reconstruction and/or categorical identification from limited measurements. We argue that data-driven dimensionality reduction methods integrate naturally with sparse sensing in the context of complex systems. This framework works equally well with a physical model or in an equation-free context, where data is available but the governing equations may be unknown. We demonstrate the advantages of combining these methods on three prototypical examples: classification of dynamical regimes, optimal sensor placement, and equation-free dynamic model reduction. These examples motivate the potentially transformative role that state-of-the-art data methods and machine learning can play in the analysis of complex systems.

  16. Brain architecture and social complexity in modern and ancient birds.

    PubMed

    Burish, Mark J; Kueh, Hao Yuan; Wang, Samuel S-H

    2004-01-01

    Vertebrate brains vary tremendously in size, but differences in form are more subtle. To bring out functional contrasts that are independent of absolute size, we have normalized brain component sizes to whole brain volume. The set of such volume fractions is the cerebrotype of a species. Using this approach in mammals we previously identified specific associations between cerebrotype and behavioral specializations. Among primates, cerebrotypes are linked principally to enlargement of the cerebral cortex and are associated with increases in the complexity of social structure. Here we extend this analysis to include a second major vertebrate group, the birds. In birds the telencephalic volume fraction is strongly correlated with social complexity. This correlation accounts for almost half of the observed variation in telencephalic size, more than any other behavioral specialization examined, including the ability to learn song. A prominent exception to this pattern is owls, which are not social but still have very large forebrains. Interpolating the overall correlation for Archaeopteryx, an ancient bird, suggests that its social complexity was likely to have been on a par with modern domesticated chickens. Telencephalic volume fraction outperforms residuals-based measures of brain size at separating birds by social structure. Telencephalic volume fraction may be an anatomical substrate for social complexity, and perhaps cognitive ability, that can be generalized across a range of vertebrate brains, including dinosaurs. Copyright 2004 S. Karger AG, Basel

  17. Functional architecture of the retromer cargo-recognition complex

    PubMed Central

    Hierro, Aitor; Rojas, Adriana L.; Rojas, Raul; Murthy, Namita; Effantin, Grégory; Kajava, Andrey V.; Steven, Alasdair C.; Bonifacino, Juan S.; Hurley, James H.

    2008-01-01

    The retromer complex 1, 2 is required for the sorting of acid hydrolases to lysosomes 3-7, transcytosis of the polymeric Ig receptor 8, Wnt gradient formation 9, 10, iron transporter recycling 11, and processing of the amyloid precursor protein 12. Human retromer consists of two smaller complexes, the cargo recognition Vps26:Vps29:Vps35 heterotrimer, and a membrane-targeting heterodimer or homodimer of SNX1 and/or SNX2 13. The crystal structure of a Vps29:Vps35 subcomplex shows how the metallophosphoesterase-fold subunit Vps29 14, 15 acts as a scaffold for the C-terminal half of Vps35. Vps35 forms a horseshoe-shaped right-handed α-helical solenoid whose concave face completely covers the metal-binding site of Vps29 and whose convex face exposes a series of hydrophobic interhelical grooves. Electron microscopy shows that the intact Vps26:Vps29:Vps35 complex is a stick-shaped, somewhat flexible, structure, ∼ 21 nm long. A hybrid structural model derived from crystal structures, electron microscopy, interaction studies, and bioinformatics shows that the α-solenoid fold extends the full length of Vps35, and that Vps26 is bound at the opposite end from Vps29. This extended structure presents multiple binding sites for the SNX complex and receptor cargo, and appears capable of flexing to conform to curved vesicular membranes. PMID:17891154

  18. Functional architecture of the retromer cargo-recognition complex.

    PubMed

    Hierro, Aitor; Rojas, Adriana L; Rojas, Raul; Murthy, Namita; Effantin, Grégory; Kajava, Andrey V; Steven, Alasdair C; Bonifacino, Juan S; Hurley, James H

    2007-10-25

    The retromer complex is required for the sorting of acid hydrolases to lysosomes, transcytosis of the polymeric immunoglobulin receptor, Wnt gradient formation, iron transporter recycling and processing of the amyloid precursor protein. Human retromer consists of two smaller complexes: the cargo recognition VPS26-VPS29-VPS35 heterotrimer and a membrane-targeting heterodimer or homodimer of SNX1 and/or SNX2 (ref. 13). Here we report the crystal structure of a VPS29-VPS35 subcomplex showing how the metallophosphoesterase-fold subunit VPS29 (refs 14, 15) acts as a scaffold for the carboxy-terminal half of VPS35. VPS35 forms a horseshoe-shaped, right-handed, alpha-helical solenoid, the concave face of which completely covers the metal-binding site of VPS29, whereas the convex face exposes a series of hydrophobic interhelical grooves. Electron microscopy shows that the intact VPS26-VPS29-VPS35 complex is a stick-shaped, flexible structure, approximately 21 nm long. A hybrid structural model derived from crystal structures, electron microscopy, interaction studies and bioinformatics shows that the alpha-solenoid fold extends the full length of VPS35, and that VPS26 is bound at the opposite end from VPS29. This extended structure presents multiple binding sites for the SNX complex and receptor cargo, and appears capable of flexing to conform to curved vesicular membranes.

  19. LaserCom System Architecture With Reduced Complexity

    NASA Technical Reports Server (NTRS)

    Lesh, James R. (Inventor); Chen, Chien-Chung (Inventor); Ansari, Homa-Yoon (Inventor)

    1996-01-01

    Spatial acquisition and precision beam pointing functions are critical to spaceborne laser communication systems. In the present invention a single high bandwidth CCD detector is used to perform both spatial acquisition and tracking functions. Compared to previous lasercom hardware design, the array tracking concept offers reduced system complexity by reducing the number of optical elements in the design. Specifically, the design requires only one detector and one beam steering mechanism. It also provides means to optically close the point-ahead control loop. The technology required for high bandwidth array tracking was examined and shown to be consistent with current state of the art. The single detector design can lead to a significantly reduced system complexity and a lower system cost.

  20. Probing nuclear pore complex architecture with proximity-dependent biotinylation.

    PubMed

    Kim, Dae In; Birendra, K C; Zhu, Wenhong; Motamedchaboki, Khatereh; Doye, Valérie; Roux, Kyle J

    2014-06-17

    Proximity-dependent biotin identification (BioID) is a method for identifying protein associations that occur in vivo. By fusing a promiscuous biotin ligase to a protein of interest expressed in living cells, BioID permits the labeling of proximate proteins during a defined labeling period. In this study we used BioID to study the human nuclear pore complex (NPC), one of the largest macromolecular assemblies in eukaryotes. Anchored within the nuclear envelope, NPCs mediate the nucleocytoplasmic trafficking of numerous cellular components. We applied BioID to constituents of the Nup107-160 complex and the Nup93 complex, two conserved NPC subcomplexes. A strikingly different set of NPC constituents was detected depending on the position of these BioID-fusion proteins within the NPC. By applying BioID to several constituents located throughout the extremely stable Nup107-160 subcomplex, we refined our understanding of this highly conserved subcomplex, in part by demonstrating a direct interaction of Nup43 with Nup85. Furthermore, by using the extremely stable Nup107-160 structure as a molecular ruler, we defined the practical labeling radius of BioID. These studies further our understanding of human NPC organization and demonstrate that BioID is a valuable tool for exploring the constituency and organization of large protein assemblies in living cells.

  1. Noise-Coupled Image Rejection Architecture of Complex Bandpass ΔΣAD Modulator

    NASA Astrophysics Data System (ADS)

    San, Hao; Kobayashi, Haruo

    This paper proposes a new realization technique of image rejection function by noise-coupling architecture, which is used for a complex bandpass ΔΣAD modulator. The complex bandpass ΔΣAD modulator processes just input I and Q signals, not image signals, and the AD conversion can be realized with low power dissipation. It realizes an asymmetric noise-shaped spectra, which is desirable for such low-IF receiver applications. However, the performance of the complex bandpass ΔΣAD modulator suffers from the mismatch between internal analog I and Q paths. I/Q path mismatch causes an image signal, and the quantization noise of the mirror image band aliases into the desired signal band, which degrades the SQNDR (Signal to Quantization Noise and Distortion Ratio) of the modulator. In our proposed modulator architecture, an extra notch for image rejection is realized by noise-coupled topology. We just add some passive capacitors and switches to the modulator; the additional integrator circuit composed of an operational amplifier in the conventional image rejection realization is not necessary. Therefore, the performance of the complex modulator can be effectively raised without additional power dissipation. We have performed simulation with MATLAB to confirm the validity of the proposed architecture. The simulation results show that the proposed architecture can achieve the realization of image-rejection effectively, and improve the SQNDR of the complex bandpass ΔΣAD modulator.

  2. Complex Polymeric Architectures Synthesized and Functionalized using Robust Chemistries

    NASA Astrophysics Data System (ADS)

    Killops, Kathryn L.

    Niche applications for polymeric materials put stringent requirements on their properties and architecture. Although polymer synthesis techniques have improved significantly to produce well-defined materials with narrow molecular weight distributions from a variety of monomeric precursors, the final materials often require fine-tuning of the structure or functionality to achieve the properties necessary for a given high performance application. The ability to modify and synthesize soft materials in precise and predictable manner requires the use of robust, efficient, and orthogonal chemistries. The highly branched structure of dendrimers provides an ideal platform to rigorously evaluate the ability of a reaction to proceed with quantitative conversion and high specificity. In order to achieve a macromolecular structure having a monodisperse molecular weight of over 10,000 Da, highly efficient reactions must be used. The synthesis of dendrimers up to the fourth generation was accomplished using successive iterations of thiol--ene 'click' chemistry and esterification reactions. The high molecular weight dendrimers were subsequently derivitized at the periphery using a variety of functional groups to demonstrate the orthogonality of the thiol--ene reaction. An extension of this work provided direct comparison of the thermally- and photochemically-initiated thiol--ene reactions, as applied to the functionalization of polymers both along the backbone and at the chain ends. With block copolymers, access to nanoscale features is afforded by the propensity of two chemically-distinct, covalently-linked polymer chains phase separate into discrete domains. These nanoscopic features have important implications for high performance applications like microelectronics and water purification. Precise modification of these structures expands the number of applications that could benefit from their implementation. In the search for a poly(ethylene oxide)-based nanoparticle with

  3. Strategies for concurrent processing of complex algorithms in data driven architectures

    NASA Technical Reports Server (NTRS)

    Stoughton, John W.; Mielke, Roland R.

    1988-01-01

    The purpose is to document research to develop strategies for concurrent processing of complex algorithms in data driven architectures. The problem domain consists of decision-free algorithms having large-grained, computationally complex primitive operations. Such are often found in signal processing and control applications. The anticipated multiprocessor environment is a data flow architecture containing between two and twenty computing elements. Each computing element is a processor having local program memory, and which communicates with a common global data memory. A new graph theoretic model called ATAMM which establishes rules for relating a decomposed algorithm to its execution in a data flow architecture is presented. The ATAMM model is used to determine strategies to achieve optimum time performance and to develop a system diagnostic software tool. In addition, preliminary work on a new multiprocessor operating system based on the ATAMM specifications is described.

  4. Three-dimensional representation of complex muscle architectures and geometries.

    PubMed

    Blemker, Silvia S; Delp, Scott L

    2005-05-01

    Almost all computer models of the musculoskeletal system represent muscle geometry using a series of line segments. This simplification (i) limits the ability of models to accurately represent the paths of muscles with complex geometry and (ii) assumes that moment arms are equivalent for all fibers within a muscle (or muscle compartment). The goal of this work was to develop and evaluate a new method for creating three-dimensional (3D) finite-element models that represent complex muscle geometry and the variation in moment arms across fibers within a muscle. We created 3D models of the psoas, iliacus, gluteus maximus, and gluteus medius muscles from magnetic resonance (MR) images. Peak fiber moment arms varied substantially among fibers within each muscle (e.g., for the psoas the peak fiber hip flexion moment arms varied from 2 to 3 cm, and for the gluteus maximus the peak fiber hip extension moment arms varied from 1 to 7 cm). Moment arms from the literature were generally within the range of fiber moment arms predicted by the 3D models. The models accurately predicted changes in muscle surface geometry over a 55 degrees range of hip flexion, as compared to changes in shape predicted from MR images (average errors between the model and measured surfaces were between 1.7 and 5.2 mm). This new framework for representing muscle will enhance the accuracy of computer models of the musculoskeletal system.

  5. A high throughput architecture for a low complexity soft-output demapping algorithm

    NASA Astrophysics Data System (ADS)

    Ali, I.; Wasenmüller, U.; Wehn, N.

    2015-11-01

    Iterative channel decoders such as Turbo-Code and LDPC decoders show exceptional performance and therefore they are a part of many wireless communication receivers nowadays. These decoders require a soft input, i.e., the logarithmic likelihood ratio (LLR) of the received bits with a typical quantization of 4 to 6 bits. For computing the LLR values from a received complex symbol, a soft demapper is employed in the receiver. The implementation cost of traditional soft-output demapping methods is relatively large in high order modulation systems, and therefore low complexity demapping algorithms are indispensable in low power receivers. In the presence of multiple wireless communication standards where each standard defines multiple modulation schemes, there is a need to have an efficient demapper architecture covering all the flexibility requirements of these standards. Another challenge associated with hardware implementation of the demapper is to achieve a very high throughput in double iterative systems, for instance, MIMO and Code-Aided Synchronization. In this paper, we present a comprehensive communication and hardware performance evaluation of low complexity soft-output demapping algorithms to select the best algorithm for implementation. The main goal of this work is to design a high throughput, flexible, and area efficient architecture. We describe architectures to execute the investigated algorithms. We implement these architectures on a FPGA device to evaluate their hardware performance. The work has resulted in a hardware architecture based on the figured out best low complexity algorithm delivering a high throughput of 166 Msymbols/second for Gray mapped 16-QAM modulation on Virtex-5. This efficient architecture occupies only 127 slice registers, 248 slice LUTs and 2 DSP48Es.

  6. Architectural Analysis of Complex Evolving Systems of Systems

    NASA Technical Reports Server (NTRS)

    Lindvall, Mikael; Stratton, William C.; Sibol, Deane E.; Ray, Arnab; Ackemann, Chris; Yonkwa, Lyly; Ganesan, Dharma

    2009-01-01

    The goal of this collaborative project between FC-MD, APL, and GSFC and supported by NASA IV&V Software Assurance Research Program (SARP), was to develop a tool, Dynamic SAVE, or Dyn-SAVE for short, for analyzing architectures of systems of systems. The project team was comprised of the principal investigator (PI) from FC-MD and four other FC-MD scientists (part time) and several FC-MD students (full time), as well as, two APL software architects (part time), and one NASA POC (part time). The PI and FC-MD scientists together with APL architects were responsible for requirements analysis, and for applying and evaluating the Dyn-SAVE tool and method. The PI and a group of FC-MD scientists were responsible for improving the method and conducting outreach activities, while another group of FC-MD scientists were responsible for development and improvement of the tool. Oversight and reporting was conducted by the PI and NASA POC. The project team produced many results including several prototypes of the Dyn-SAVE tool and method, several case studies documenting how the tool and method was applied to APL s software systems, and several published papers in highly respected conferences and journals. Dyn-SAVE as developed and enhanced throughout this research period, is a software tool intended for software developers and architects, software integration testers, and persons who need to analyze software systems from the point of view of how it communicates with other systems. Using the tool, the user specifies the planned communication behavior of the system modeled as a sequence diagram. The user then captures and imports the actual communication behavior of the system, which is then converted and visualized as a sequence diagram by Dyn-SAVE. After mapping the planned to the actual and specifying parameter and timing constraints, Dyn-SAVE detects and highlights deviations between the planned and the actual behavior. Requirements based on the need to analyze two inter

  7. Architectures for Distributed and Complex M-Learning Systems: Applying Intelligent Technologies

    ERIC Educational Resources Information Center

    Caballe, Santi, Ed.; Xhafa, Fatos, Ed.; Daradoumis, Thanasis, Ed.; Juan, Angel A., Ed.

    2009-01-01

    Over the last decade, the needs of educational organizations have been changing in accordance with increasingly complex pedagogical models and with the technological evolution of e-learning environments with very dynamic teaching and learning requirements. This book explores state-of-the-art software architectures and platforms used to support…

  8. Architectures for Distributed and Complex M-Learning Systems: Applying Intelligent Technologies

    ERIC Educational Resources Information Center

    Caballe, Santi, Ed.; Xhafa, Fatos, Ed.; Daradoumis, Thanasis, Ed.; Juan, Angel A., Ed.

    2009-01-01

    Over the last decade, the needs of educational organizations have been changing in accordance with increasingly complex pedagogical models and with the technological evolution of e-learning environments with very dynamic teaching and learning requirements. This book explores state-of-the-art software architectures and platforms used to support…

  9. Assessment of the integration capability of system architectures from a complex and distributed software systems perspective

    NASA Astrophysics Data System (ADS)

    Leuchter, S.; Reinert, F.; Müller, W.

    2014-06-01

    Procurement and design of system architectures capable of network centric operations demand for an assessment scheme in order to compare different alternative realizations. In this contribution an assessment method for system architectures targeted at the C4ISR domain is presented. The method addresses the integration capability of software systems from a complex and distributed software system perspective focusing communication, interfaces and software. The aim is to evaluate the capability to integrate a system or its functions within a system-of-systems network. This method uses approaches from software architecture quality assessment and applies them on the system architecture level. It features a specific goal tree of several dimensions that are relevant for enterprise integration. These dimensions have to be weighed against each other and totalized using methods from the normative decision theory in order to reflect the intention of the particular enterprise integration effort. The indicators and measurements for many of the considered quality features rely on a model based view on systems, networks, and the enterprise. That means it is applicable to System-of-System specifications based on enterprise architectural frameworks relying on defined meta-models or domain ontologies for defining views and viewpoints. In the defense context we use the NATO Architecture Framework (NAF) to ground respective system models. The proposed assessment method allows evaluating and comparing competing system designs regarding their future integration potential. It is a contribution to the system-of-systems engineering methodology.

  10. Localization of Pathology on Complex Architecture Building Surfaces

    NASA Astrophysics Data System (ADS)

    Sidiropoulos, A. A.; Lakakis, K. N.; Mouza, V. K.

    2017-02-01

    The technology of 3D laser scanning is considered as one of the most common methods for heritage documentation. The point clouds that are being produced provide information of high detail, both geometric and thematic. There are various studies that examine techniques of the best exploitation of this information. In this study, an algorithm of pathology localization, such as cracks and fissures, on complex building surfaces is being tested. The algorithm makes use of the points' position in the point cloud and tries to distinguish them in two groups-patterns; pathology and non-pathology. The extraction of the geometric information that is being used for recognizing the pattern of the points is being accomplished via Principal Component Analysis (PCA) in user-specified neighborhoods in the whole point cloud. The implementation of PCA leads to the definition of the normal vector at each point of the cloud. Two tests that operate separately examine both local and global geometric criteria among the points and conclude which of them should be categorized as pathology. The proposed algorithm was tested on parts of the Gazi Evrenos Baths masonry, which are located at the city of Giannitsa at Northern Greece.

  11. Architecture of the Yeast RNA Polymerase II Open Complex and Regulation of Activity by TFIIF

    PubMed Central

    Fishburn, James

    2012-01-01

    To investigate the function and architecture of the open complex state of RNA polymerase II (Pol II), Saccharomyces cerevisiae minimal open complexes were assembled by using a series of heteroduplex HIS4 promoters, TATA binding protein (TBP), TFIIB, and Pol II. The yeast system demonstrates great flexibility in the position of active open complexes, spanning 30 to 80 bp downstream from TATA, consistent with the transcription start site scanning behavior of yeast Pol II. TFIIF unexpectedly modulates the activity of the open complexes, either repressing or stimulating initiation. The response to TFIIF was dependent on the sequence of the template strand within the single-stranded bubble. Mutations in the TFIIB reader and linker region, which were inactive on duplex DNA, were suppressed by the heteroduplex templates, showing that a major function of the TFIIB reader and linker is in the initiation or stabilization of single-stranded DNA. Probing of the architecture of the minimal open complexes with TFIIB-FeBABE [TFIIB–p-bromoacetamidobenzyl–EDTA-iron(III)] derivatives showed that the TFIIB core domain is surprisingly positioned away from Pol II, and the addition of TFIIF repositions the TFIIB core domain to the Pol II wall domain. Together, our results show an unexpected architecture of minimal open complexes and the regulation of activity by TFIIF and the TFIIB core domain. PMID:22025674

  12. Architecture of ribonucleoprotein complexes in influenza A virus particles.

    PubMed

    Noda, Takeshi; Sagara, Hiroshi; Yen, Albert; Takada, Ayato; Kida, Hiroshi; Cheng, R Holland; Kawaoka, Yoshihiro

    2006-01-26

    In viruses, as in eukaryotes, elaborate mechanisms have evolved to protect the genome and to ensure its timely replication and reliable transmission to progeny. Influenza A viruses are enveloped, spherical or filamentous structures, ranging from 80 to 120 nm in diameter. Inside each envelope is a viral genome consisting of eight single-stranded negative-sense RNA segments of 890 to 2,341 nucleotides each. These segments are associated with nucleoprotein and three polymerase subunits, designated PA, PB1 and PB2; the resultant ribonucleoprotein complexes (RNPs) resemble a twisted rod (10-15 nm in width and 30-120 nm in length) that is folded back and coiled on itself. Late in viral infection, newly synthesized RNPs are transported from the nucleus to the plasma membrane, where they are incorporated into progeny virions capable of infecting other cells. Here we show, by transmission electron microscopy of serially sectioned virions, that the RNPs of influenza A virus are organized in a distinct pattern (seven segments of different lengths surrounding a central segment). The individual RNPs are suspended from the interior of the viral envelope at the distal end of the budding virion and are oriented perpendicular to the budding tip. This finding argues against random incorporation of RNPs into virions, supporting instead a model in which each segment contains specific incorporation signals that enable the RNPs to be recruited and packaged as a complete set. A selective mechanism of RNP incorporation into virions and the unique organization of the eight RNP segments may be crucial to maintaining the integrity of the viral genome during repeated cycles of replication.

  13. Optical fibre gas detections systems

    NASA Astrophysics Data System (ADS)

    Culshaw, Brian

    2016-05-01

    This tutorial review covers the principles of and prospects for fibre optic sensor technology in gas detection. Many of the potential benefits common to fibre sensor technology also apply in the context of gas sensing - notably long distance - many km - access to multiple remote measurement points; invariably intrinsic safety; access to numerous important gas species and often uniquely high levels of selectivity and/or sensitivity. Furthermore, the range of fibre sensor network architectures - single point, multiple point and distributed - enable unprecedented flexibility in system implementation. Additionally, competitive technologies and regulatory issues contribute to final application potential.

  14. Outer nuclear membrane protein Kuduk modulates the LINC complex and nuclear envelope architecture.

    PubMed

    Ding, Zhao-Ying; Wang, Ying-Hsuan; Huang, Yu-Cheng; Lee, Myong-Chol; Tseng, Min-Jen; Chi, Ya-Hui; Huang, Min-Lang

    2017-09-04

    Linker of nucleoskeleton and cytoskeleton (LINC) complexes spanning the nuclear envelope (NE) contribute to nucleocytoskeletal force transduction. A few NE proteins have been found to regulate the LINC complex. In this study, we identify one, Kuduk (Kud), which can reside at the outer nuclear membrane and is required for the development of Drosophila melanogaster ovarian follicles and NE morphology of myonuclei. Kud associates with LINC complex components in an evolutionarily conserved manner. Loss of Kud increases the level but impairs functioning of the LINC complex. Overexpression of Kud suppresses NE targeting of cytoskeleton-free LINC complexes. Thus, Kud acts as a quality control mechanism for LINC-mediated nucleocytoskeletal connections. Genetic data indicate that Kud also functions independently of the LINC complex. Overexpression of the human orthologue TMEM258 in Drosophila proved functional conservation. These findings expand our understanding of the regulation of LINC complexes and NE architecture. © 2017 Ding et al.

  15. Polysiloxane optical fibres and fibre structures

    NASA Astrophysics Data System (ADS)

    Martincek, Ivan; Pudis, Dusan

    2016-12-01

    The polysiloxane fibres made of polysiloxanes such as polydimethylsiloxane (PDMS) and poly(dimethyl)(diphenil)siloxane (PDMDPS) can be attractive for different fibre applications and fibre structures. In this paper we describe the fabrication technological process of polysiloxane fibres and fibre structures integrated with conventional single-mode optical fibres. We present two-modes interferometer prepared from PDMS biconical optical fibre taper, PDMDPS optical fibre microloop interferometer and liquid microdroplet optical fibre interferometer. We achieved interesting optical properties all these fibre structures as was confirmed from the transmission characteristics what may be attractive for utilisation in various types of optical fibre sensors.

  16. Reconfiguration of Brain Network Architectures between Resting-State and Complexity-Dependent Cognitive Reasoning.

    PubMed

    Hearne, Luke J; Cocchi, Luca; Zalesky, Andrew; Mattingley, Jason B

    2017-08-30

    Our capacity for higher cognitive reasoning has a measurable limit. This limit is thought to arise from the brain's capacity to flexibly reconfigure interactions between spatially distributed networks. Recent work, however, has suggested that reconfigurations of task-related networks are modest when compared with intrinsic "resting-state" network architecture. Here we combined resting-state and task-driven functional magnetic resonance imaging to examine how flexible, task-specific reconfigurations associated with increasing reasoning demands are integrated within a stable intrinsic brain topology. Human participants (21 males and 28 females) underwent an initial resting-state scan, followed by a cognitive reasoning task involving different levels of complexity, followed by a second resting-state scan. The reasoning task required participants to deduce the identity of a missing element in a 4 × 4 matrix, and item difficulty was scaled parametrically as determined by relational complexity theory. Analyses revealed that external task engagement was characterized by a significant change in functional brain modules. Specifically, resting-state and null-task demand conditions were associated with more segregated brain-network topology, whereas increases in reasoning complexity resulted in merging of resting-state modules. Further increments in task complexity did not change the established modular architecture, but affected selective patterns of connectivity between frontoparietal, subcortical, cingulo-opercular, and default-mode networks. Larger increases in network efficiency within the newly established task modules were associated with higher reasoning accuracy. Our results shed light on the network architectures that underlie external task engagement, and highlight selective changes in brain connectivity supporting increases in task complexity.SIGNIFICANCE STATEMENT Humans have clear limits in their ability to solve complex reasoning problems. It is thought that

  17. Contrasting genetic architectures in different mouse reference populations used for studying complex traits

    PubMed Central

    Buchner, David A.; Nadeau, Joseph H.

    2015-01-01

    Quantitative trait loci (QTLs) are being used to study genetic networks, protein functions, and systems properties that underlie phenotypic variation and disease risk in humans, model organisms, agricultural species, and natural populations. The challenges are many, beginning with the seemingly simple tasks of mapping QTLs and identifying their underlying genetic determinants. Various specialized resources have been developed to study complex traits in many model organisms. In the mouse, remarkably different pictures of genetic architectures are emerging. Chromosome Substitution Strains (CSSs) reveal many QTLs, large phenotypic effects, pervasive epistasis, and readily identified genetic variants. In contrast, other resources as well as genome-wide association studies (GWAS) in humans and other species reveal genetic architectures dominated with a relatively modest number of QTLs that have small individual and combined phenotypic effects. These contrasting architectures are the result of intrinsic differences in the study designs underlying different resources. The CSSs examine context-dependent phenotypic effects independently among individual genotypes, whereas with GWAS and other mouse resources, the average effect of each QTL is assessed among many individuals with heterogeneous genetic backgrounds. We argue that variation of genetic architectures among individuals is as important as population averages. Each of these important resources has particular merits and specific applications for these individual and population perspectives. Collectively, these resources together with high-throughput genotyping, sequencing and genetic engineering technologies, and information repositories highlight the power of the mouse for genetic, functional, and systems studies of complex traits and disease models. PMID:25953951

  18. Fibre Models

    NASA Astrophysics Data System (ADS)

    Herrmann, H. J.; Kun, F.

    2007-12-01

    Fibre models have been introduced as simple models to describe failure. They are based on the probability distribution of broken fibres. The load redistribution after a fibre yields can be global or local and the first case can often be solved analytically. We will present an interpolation between these the local and the global case and apply it to experimental situations like the compression of granular packings. Introducing viscoelastic fibres allows to describe the creep of wood. It is even possible to deal analytically with a gradual degradation of fibres and consider damage as well as healing. In this way Basquin's law of fatigue can be reproduced and new universalities concerning the histograms of bursts and waiting times can be uncovered.

  19. Numerical and Experimental Investigation of the Hydrostatic Performance of Fibre Reinforced Tubes

    NASA Astrophysics Data System (ADS)

    Pavlopoulou, S.; Roy, S. S.; Gautam, M.; Bradshaw, L.; Potluri, P.

    2016-12-01

    The increasing demands in subsea industry such as oil and gas, led to a rapidly growing need for the use of advanced, high performance, lightweight materials such as composite materials. E-glass fibre laminated pre-preg, filament wound and braided tubes were tested to destruction under hydrostatic external pressure in order to study their buckling and crushing behaviour. Different fibre architectures and wind angles were tested at a range of wall thicknesses highlighting the advantage that hoop reinforcement offers. The experimental results were compared with theoretical predictions obtained from classic laminate theory and finite element analysis (ABAQUS) based on the principal that the predominant failure mode was buckling. SEM analysis was further performed to investigate the resulting failure mechanisms, indicating that the failure mechanisms can be more complex with a variety of observed modes taking place such as fibre fracture, delamination and fibre-matrix interface failure.

  20. Numerical and Experimental Investigation of the Hydrostatic Performance of Fibre Reinforced Tubes

    NASA Astrophysics Data System (ADS)

    Pavlopoulou, S.; Roy, S. S.; Gautam, M.; Bradshaw, L.; Potluri, P.

    2017-04-01

    The increasing demands in subsea industry such as oil and gas, led to a rapidly growing need for the use of advanced, high performance, lightweight materials such as composite materials. E-glass fibre laminated pre-preg, filament wound and braided tubes were tested to destruction under hydrostatic external pressure in order to study their buckling and crushing behaviour. Different fibre architectures and wind angles were tested at a range of wall thicknesses highlighting the advantage that hoop reinforcement offers. The experimental results were compared with theoretical predictions obtained from classic laminate theory and finite element analysis (ABAQUS) based on the principal that the predominant failure mode was buckling. SEM analysis was further performed to investigate the resulting failure mechanisms, indicating that the failure mechanisms can be more complex with a variety of observed modes taking place such as fibre fracture, delamination and fibre-matrix interface failure.

  1. Control of cell fate by the formation of an architecturally complex bacterial community

    PubMed Central

    Vlamakis, Hera; Aguilar, Claudio; Losick, Richard; Kolter, Roberto

    2008-01-01

    Bacteria form architecturally complex communities known as biofilms in which cells are held together by an extracellular matrix. Biofilms harbor multiple cell types, and it has been proposed that within biofilms individual cells follow different developmental pathways, resulting in heterogeneous populations. Here we demonstrate cellular differentiation within biofilms of the spore-forming bacterium Bacillus subtilis, and present evidence that formation of the biofilm governs differentiation. We show that motile, matrix-producing, and sporulating cells localize to distinct regions within the biofilm, and that the localization and percentage of each cell type is dynamic throughout development of the community. Importantly, mutants that do not produce extracellular matrix form unstructured biofilms that are deficient in sporulation. We propose that sporulation is a culminating feature of biofilm formation, and that spore formation is coupled to the formation of an architecturally complex community of cells. PMID:18381896

  2. Towards understanding nuclear pore complex architecture and dynamics in the age of integrative structural analysis.

    PubMed

    Hurt, Ed; Beck, Martin

    2015-06-01

    Determining the functional architecture of the nuclear pore complex, that remains only partially understood, requires bridging across different length scales. Recent technological advances in quantitative and cross-linking mass spectrometry, super-resolution fluorescence microscopy and electron microscopy have enormously accelerated the integration of different types of data into coherent structural models. Moreover, high-resolution structural analysis of nucleoporins and their in vitro reconstitution into complexes is now facilitated by the use of thermostable orthologs. In this review we highlight how the application of such technologies has led to novel insights into nuclear pore architecture and to a paradigm shift. Today nuclear pores are not anymore seen as static facilitators of nucleocytoplasmic transport but ensembles of multiple overlaying functional states that are involved in various cellular processes.

  3. The dynamics of architectural complexity on coral reefs under climate change.

    PubMed

    Bozec, Yves-Marie; Alvarez-Filip, Lorenzo; Mumby, Peter J

    2015-01-01

    One striking feature of coral reef ecosystems is the complex benthic architecture which supports diverse and abundant fauna, particularly of reef fish. Reef-building corals are in decline worldwide, with a corresponding loss of live coral cover resulting in a loss of architectural complexity. Understanding the dynamics of the reef architecture is therefore important to envision the ability of corals to maintain functional habitats in an era of climate change. Here, we develop a mechanistic model of reef topographical complexity for contemporary Caribbean reefs. The model describes the dynamics of corals and other benthic taxa under climate-driven disturbances (hurricanes and coral bleaching). Corals have a simplified shape with explicit diameter and height, allowing species-specific calculation of their colony surface and volume. Growth and the mechanical (hurricanes) and biological erosion (parrotfish) of carbonate skeletons are important in driving the pace of extension/reduction in the upper reef surface, the net outcome being quantified by a simple surface roughness index (reef rugosity). The model accurately simulated the decadal changes of coral cover observed in Cozumel (Mexico) between 1984 and 2008, and provided a realistic hindcast of coral colony-scale (1-10 m) changing rugosity over the same period. We then projected future changes of Caribbean reef rugosity in response to global warming. Under severe and frequent thermal stress, the model predicted a dramatic loss of rugosity over the next two or three decades. Critically, reefs with managed parrotfish populations were able to delay the general loss of architectural complexity, as the benefits of grazing in maintaining living coral outweighed the bioerosion of dead coral skeletons. Overall, this model provides the first explicit projections of reef rugosity in a warming climate, and highlights the need of combining local (protecting and restoring high grazing) to global (mitigation of greenhouse gas

  4. Genetic architecture of cancer and other complex diseases: lessons learned and future directions

    PubMed Central

    Hindorff, Lucia A.; Gillanders, Elizabeth M.; Manolio, Teri A.

    2011-01-01

    Genome-wide association studies have broadened our understanding of the genetic architecture of cancer to include common variants, in addition to the rare variants previously identified by linkage analysis. We review current knowledge on the genetic architecture of four cancers—breast, lung, prostate and colorectal—for which the balance of common and rare alleles identified ranges from fewer common alleles (lung cancer) to more common alleles (prostate cancer). Although most variants are cancer specific, pleiotropy has been observed for several variants, for example, variants at the 8q24 locus and breast, ovarian and prostate cancers or variants in KITLG in relation to hair color and testicular cancer. Although few studies have been adequately powered to investigate heterogeneity among ancestry groups, effect sizes associated with common variants have been reported to be fairly homogenous among ethnic groups. Some associations appear to be ancestry specific, such as HNF1B, which is associated with prostate cancer in European Americans and Latinos but not in African-Americans. Studies of cancer and other complex diseases suggest that a simple dichotomy between rare and common allelic architectures may be too simplistic and that future research is needed to characterize a fuller spectrum of allele frequency (common (>5%), uncommon (1–5%) and rare (<<1%) alleles) and effect size. In addition, a broadening of the concept of genetic architecture to encompass both population architecture, which reflects differences in exposures, genetic factors and population level risk among diverse groups of people, and genomic architecture, which includes structural, epigenomic and somatic variation, is envisioned. PMID:21459759

  5. On the complexity of neural network classifiers: a comparison between shallow and deep architectures.

    PubMed

    Bianchini, Monica; Scarselli, Franco

    2014-08-01

    Recently, researchers in the artificial neural network field have focused their attention on connectionist models composed by several hidden layers. In fact, experimental results and heuristic considerations suggest that deep architectures are more suitable than shallow ones for modern applications, facing very complex problems, e.g., vision and human language understanding. However, the actual theoretical results supporting such a claim are still few and incomplete. In this paper, we propose a new approach to study how the depth of feedforward neural networks impacts on their ability in implementing high complexity functions. First, a new measure based on topological concepts is introduced, aimed at evaluating the complexity of the function implemented by a neural network, used for classification purposes. Then, deep and shallow neural architectures with common sigmoidal activation functions are compared, by deriving upper and lower bounds on their complexity, and studying how the complexity depends on the number of hidden units and the used activation function. The obtained results seem to support the idea that deep networks actually implements functions of higher complexity, so that they are able, with the same number of resources, to address more difficult problems.

  6. Subunit connectivity, assembly determinants, and architecture of the yeast exocyst complex

    PubMed Central

    Heider, Margaret R.; Gu, Mingyu; Duffy, Caroline M.; Mirza, Anne M.; Marcotte, Laura L.; Walls, Alexandra C.; Farrall, Nicholas; Hakhverdyan, Zhanna; Field, Mark C.; Rout, Michael P.; Frost, Adam; Munson, Mary

    2016-01-01

    The exocyst is a hetero-octameric complex proposed to serve as the tethering complex for exocytosis, although it remains poorly understood at the molecular level. Here, we purified endogenous exocyst from Saccharomyces cerevisiae, and show that the purified complexes are stable and consist of all eight subunits with equal stoichiometry. Using a combination of biochemical and auxin-induced degradation experiments in yeast, we mapped the subunit connectivity, identified two stable four-subunit modules within the octamer, and demonstrated that several known exocyst binding partners are not necessary for exocyst assembly and stability. Furthermore, we visualized the structure of the yeast complex using negative stain electron microscopy; our results indicate that exocyst exists predominantly as a stable, octameric complex with an elongated architecture that suggests the subunits are contiguous helical bundles packed together into a bundle of long rods. PMID:26656853

  7. An unusual 3D interdigitated architecture assembled from Keggin polyoxometalates and dinuclear copper(II) complexes

    SciTech Connect

    Pang, Haijun; Yang, Ming; Kang, Lu; Ma, Huiyuan; Liu, Bo; Li, Shaobin; Liu, Heng

    2013-02-15

    A novel organic-inorganic hybrid compound, [Cu{sub 2}(bipy){sub 3}({mu}{sub 1}-H{sub 2}O){sub 2}({mu}{sub 2}-H{sub 2}O)({mu}{sub 2}-OH)(H{sub 2}BW{sub 12}O{sub 40})]{center_dot}4 H{sub 2}O (1) (bipy=4,4 Prime -bipy), has been synthesized in hydrothermal condition and characterized by elemental analysis, IR spectrum, TG analysis and single-crystal X-ray diffraction. Compound 1 possesses poly-pendant layered motifs composed of 12-tungstoborates and dinuclear copper(II) complexes, in which the mono-coordinated bipy molecules are orderly appended to both sides of the layer, respectively. Adjacent layers mutually engage in a zipper-like pattern to result in a novel 3D interdigitated architecture. The variable-temperature magnetic susceptibility of 1 showed that there existed weak antiferromagnetic interaction in 1. Toward the reduction of hydrogen peroxide, 1 has good electrocatalytic activity and remarkable stability. - A new compound has been obtained, which represents the first interdigitated architecture assembled by POMs and dinuclear copper(II) complexes. Highlights: Black-Right-Pointing-Pointer The first example of interdigitated architecture assembled by POMs and dinuclear copper(II) complexes is observed. Black-Right-Pointing-Pointer A zipper-like pattern is observed in the structure. Black-Right-Pointing-Pointer The IR, TG, XRPD, magnetism and electrochemical property of the title compound were studied.

  8. Assessing the complex architecture of polygenic traits in diverged yeast populations.

    PubMed

    Cubillos, Francisco A; Billi, Eleonora; Zörgö, Enikö; Parts, Leopold; Fargier, Patrick; Omholt, Stig; Blomberg, Anders; Warringer, Jonas; Louis, Edward J; Liti, Gianni

    2011-04-01

    Phenotypic variation arising from populations adapting to different niches has a complex underlying genetic architecture. A major challenge in modern biology is to identify the causative variants driving phenotypic variation. Recently, the baker's yeast, Saccharomyces cerevisiae has emerged as a powerful model for dissecting complex traits. However, past studies using a laboratory strain were unable to reveal the complete architecture of polygenic traits. Here, we present a linkage study using 576 recombinant strains obtained from crosses of isolates representative of the major lineages. The meiotic recombinational landscape appears largely conserved between populations; however, strain-specific hotspots were also detected. Quantitative measurements of growth in 23 distinct ecologically relevant environments show that our recombinant population recapitulates most of the standing phenotypic variation described in the species. Linkage analysis detected an average of 6.3 distinct QTLs for each condition tested in all crosses, explaining on average 39% of the phenotypic variation. The QTLs detected are not constrained to a small number of loci, and the majority are specific to a single cross-combination and to a specific environment. Moreover, crosses between strains of similar phenotypes generate greater variation in the offspring, suggesting the presence of many antagonistic alleles and epistatic interactions. We found that subtelomeric regions play a key role in defining individual quantitative variation, emphasizing the importance of the adaptive nature of these regions in natural populations. This set of recombinant strains is a powerful tool for investigating the complex architecture of polygenic traits. © 2011 Blackwell Publishing Ltd.

  9. Capacitating epistasis--detection and role in the genetic architecture of complex traits.

    PubMed

    Pettersson, Mats E; Carlborg, Orjan

    2015-01-01

    Here, we discuss the potential role of capacitating epistasis in the genetic architecture of complex traits. Two alternative methods for identifying such gene-gene interactions in genetic association studies-mapping of variance controlling loci and the variance plane ratio (VPR) method-are introduced. An overview of the theoretical foundation of the methods is presented together with a discussion on their implementation and available software for performing these analyses. We conclude by highlighting a few examples of capacitating epistasis described in the literature and its potential impacts on the genetics of complex traits.

  10. Architectural elements of fan-delta complex in Pennsylvanian Taos Trough, New Mexico

    SciTech Connect

    Soegaard, K.

    1989-03-01

    Identification of architectural elements within alluvial-fan and subaqueous fan-delta gravel units is fundamental to resolving depositional processes within fan-delta complexes of the Pennsylvanian Taos trough, New Mexico. Subaqueous fan-delta deposits consist of lenticular gravel-body complexes encased by black, basinal shales. Gravel-body complexes are composed of a series of stacked gravel lenses, each of which is enveloped by fifth-order bounding surfaces. The central portion of individual gravel lenses contains a channel complex. Channels are outlined by third- and fourth-order bounding surfaces and are infilled by high-density gravity flow deposits. The fringe of submarine gravel lenses consists of stacked, laterally continuous Bouma sequences separated by second-order bounding surfaces. Bouma sequences were deposited by dilute turbidity flows during evacuation of submarine channels. Subaqueous channel complexes within gravel lenses represent midfan channels, whereas the fringe of lenticular gravel lenses represent outer-fan lobes. Recognition of depositional processes and architectural elements of fan deltas in the Sandia Formation enables distinction between these and other types of coarse-grained deltas in the Taos trough. This, in turn, has implications for resolving evolution of the trough.

  11. Genetics of complex traits: prediction of phenotype, identification of causal polymorphisms and genetic architecture

    PubMed Central

    Goddard, M. E.; Kemper, K. E.; MacLeod, I. M.; Chamberlain, A. J.; Hayes, B. J.

    2016-01-01

    Complex or quantitative traits are important in medicine, agriculture and evolution, yet, until recently, few of the polymorphisms that cause variation in these traits were known. Genome-wide association studies (GWAS), based on the ability to assay thousands of single nucleotide polymorphisms (SNPs), have revolutionized our understanding of the genetics of complex traits. We advocate the analysis of GWAS data by a statistical method that fits all SNP effects simultaneously, assuming that these effects are drawn from a prior distribution. We illustrate how this method can be used to predict future phenotypes, to map and identify the causal mutations, and to study the genetic architecture of complex traits. The genetic architecture of complex traits is even more complex than previously thought: in almost every trait studied there are thousands of polymorphisms that explain genetic variation. Methods of predicting future phenotypes, collectively known as genomic selection or genomic prediction, have been widely adopted in livestock and crop breeding, leading to increased rates of genetic improvement. PMID:27440663

  12. Contrasting genetic architectures of schizophrenia and other complex diseases using fast variance-components analysis.

    PubMed

    Loh, Po-Ru; Bhatia, Gaurav; Gusev, Alexander; Finucane, Hilary K; Bulik-Sullivan, Brendan K; Pollack, Samuela J; de Candia, Teresa R; Lee, Sang Hong; Wray, Naomi R; Kendler, Kenneth S; O'Donovan, Michael C; Neale, Benjamin M; Patterson, Nick; Price, Alkes L

    2015-12-01

    Heritability analyses of genome-wide association study (GWAS) cohorts have yielded important insights into complex disease architecture, and increasing sample sizes hold the promise of further discoveries. Here we analyze the genetic architectures of schizophrenia in 49,806 samples from the PGC and nine complex diseases in 54,734 samples from the GERA cohort. For schizophrenia, we infer an overwhelmingly polygenic disease architecture in which ≥71% of 1-Mb genomic regions harbor ≥1 variant influencing schizophrenia risk. We also observe significant enrichment of heritability in GC-rich regions and in higher-frequency SNPs for both schizophrenia and GERA diseases. In bivariate analyses, we observe significant genetic correlations (ranging from 0.18 to 0.85) for several pairs of GERA diseases; genetic correlations were on average 1.3 tunes stronger than the correlations of overall disease liabilities. To accomplish these analyses, we developed a fast algorithm for multicomponent, multi-trait variance-components analysis that overcomes prior computational barriers that made such analyses intractable at this scale.

  13. Beyond 'furballs' and 'dumpling soups' - towards a molecular architecture of signaling complexes and networks.

    PubMed

    Lewitzky, Marc; Simister, Philip C; Feller, Stephan M

    2012-08-14

    The molecular architectures of intracellular signaling networks are largely unknown. Understanding their design principles and mechanisms of processing information is essential to grasp the molecular basis of virtually all biological processes. This is particularly challenging for human pathologies like cancers, as essentially each tumor is a unique disease with vastly deranged signaling networks. However, even in normal cells we know almost nothing. A few 'signalosomes', like the COP9 and the TCR signaling complexes have been described, but detailed structural information on their architectures is largely lacking. Similarly, many growth factor receptors, for example EGF receptor, insulin receptor and c-Met, signal via huge protein complexes built on large platform proteins (Gab, Irs/Dok, p130Cas[BCAR1], Frs families etc.), which are structurally not well understood. Subsequent higher order processing events remain even more enigmatic. We discuss here methods that can be employed to study signaling architectures, and the importance of too often neglected features like macromolecular crowding, intrinsic disorder in proteins and the sophisticated cellular infrastructures, which need to be carefully considered in order to develop a more mature understanding of cellular signal processing.

  14. Synthesis and Functional Reconstitution of Light-Harvesting Complex II into Polymeric Membrane Architectures.

    PubMed

    Zapf, Thomas; Tan, Cherng-Wen Darren; Reinelt, Tobias; Huber, Christoph; Shaohua, Ding; Geifman-Shochat, Susana; Paulsen, Harald; Sinner, Eva-Kathrin

    2015-12-01

    One of most important processes in nature is the harvesting and dissipation of solar energy with the help of light-harvesting complex II (LHCII). This protein, along with its associated pigments, is the main solar-energy collector in higher plants. We aimed to generate stable, highly controllable, and sustainable polymer-based membrane systems containing LHCII-pigment complexes ready for light harvesting. LHCII was produced by cell-free protein synthesis based on wheat-germ extract, and the successful integration of LHCII and its pigments into different membrane architectures was monitored. The unidirectionality of LHCII insertion was investigated by protease digestion assays. Fluorescence measurements indicated chlorophyll integration in the presence of LHCII in spherical as well as planar bilayer architectures. Surface plasmon enhanced fluorescence spectroscopy (SPFS) was used to reveal energy transfer from chlorophyll b to chlorophyll a, which indicates native folding of the LHCII proteins.

  15. Complex multi-enhancer contacts captured by Genome Architecture Mapping (GAM)

    PubMed Central

    Beagrie, Robert A.; Scialdone, Antonio; Schueler, Markus; Kraemer, Dorothee C.A.; Chotalia, Mita; Xie, Sheila Q.; Barbieri, Mariano; de Santiago, Inês; Lavitas, Liron-Mark; Branco, Miguel R.; Fraser, James; Dostie, Josée; Game, Laurence; Dillon, Niall; Edwards, Paul A.W.; Nicodemi, Mario; Pombo, Ana

    2017-01-01

    Summary The organization of the genome in the nucleus and the interactions of genes with their regulatory elements are key features of transcriptional control and their disruption can cause disease. We developed a novel genome-wide method, Genome Architecture Mapping (GAM), for measuring chromatin contacts, and other features of three-dimensional chromatin topology, based on sequencing DNA from a large collection of thin nuclear sections. We apply GAM to mouse embryonic stem cells and identify an enrichment for specific interactions between active genes and enhancers across very large genomic distances, using a mathematical model ‘SLICE’ (Statistical Inference of Co-segregation). GAM also reveals an abundance of three-way contacts genome-wide, especially between regions that are highly transcribed or contain super-enhancers, highlighting a previously inaccessible complexity in genome architecture and a major role for gene-expression specific contacts in organizing the genome in mammalian nuclei. PMID:28273065

  16. The bacterial chromosome: architecture and action of bacterial SMC and SMC-like complexes.

    PubMed

    Nolivos, Sophie; Sherratt, David

    2014-05-01

    Structural Maintenance of Chromosomes (SMC) protein complexes are found in all three domains of life. They are characterized by a distinctive and conserved architecture in which a globular ATPase 'head' domain is formed by the N- and C-terminal regions of the SMC protein coming together, with a c. 50-nm-long antiparallel coiled-coil separating the head from a dimerization 'hinge'. Dimerization gives both V- and O-shaped SMC dimers. The distinctive architecture points to a conserved biochemical mechanism of action. However, the details of this mechanism are incomplete, and the precise ways in which this mechanism leads to the biological functions of these complexes in chromosome organization and processing remain unclear. In this review, we introduce the properties of bacterial SMC complexes, compare them with eukaryotic complexes and discuss how their likely biochemical action relates to their roles in chromosome organization and segregation. © 2013 The Authors. FEMS Microbiology Reviews published by John Wiley & Sons Ltd on behalf of the Federation of European Microbiological Societies.

  17. Dynamics and architecture of the NRBF2-containing phosphatidylinositol 3-kinase complex I of autophagy

    PubMed Central

    Young, Lindsey N.; Cho, Kelvin; Lawrence, Rosalie; Zoncu, Roberto; Hurley, James H.

    2016-01-01

    The class III phosphatidylinositol 3-kinase complex I (PI3KC3-C1) is central to autophagy initiation. We previously reported the V-shaped architecture of the four-subunit version of PI3KC3-C1 consisting of VPS (vacuolar protein sorting) 34, VPS15, BECN1 (Beclin 1), and ATG (autophagy-related) 14. Here we show that a putative fifth subunit, nuclear receptor binding factor 2 (NRBF2), is a tightly bound component of the complex that profoundly affects its activity and architecture. NRBF2 enhances the lipid kinase activity of the catalytic subunit, VPS34, by roughly 10-fold. We used hydrogen–deuterium exchange coupled to mass spectrometry and negative-stain electron microscopy to map NRBF2 to the base of the V-shaped complex. NRBF2 interacts primarily with the N termini of ATG14 and BECN1. We show that NRBF2 is a homodimer and drives the dimerization of the larger PI3KC3-C1 complex, with implications for the higher-order organization of the preautophagosomal structure. PMID:27385829

  18. The molecular architecture of dihydropyrindine receptor/L-type Ca2+ channel complex

    PubMed Central

    Hu, Hongli; Wang, Zhao; Wei, Risheng; Fan, Guizhen; Wang, Qiongling; Zhang, Kaiming; Yin, Chang-Cheng

    2015-01-01

    Dihydropyridine receptor (DHPR), an L-type Ca2+ channel complex, plays an essential role in muscle contraction, secretion, integration of synaptic input in neurons and synaptic transmission. The molecular architecture of DHPR complex remains elusive. Here we present a 15-Å resolution cryo-electron microscopy structure of the skeletal DHPR/L-type Ca2+ channel complex. The DHPR has an asymmetrical main body joined by a hook-like extension. The main body is composed of a “trapezoid” and a “tetrahedroid”. Homologous crystal structure docking and site-specific antibody labelling revealed that the α1 and α2 subunits are located in the “trapezoid” and the β subunit is located in the “tetrahedroid”. This structure revealed the molecular architecture of a eukaryotic Ca2+ channel complex. Furthermore, this structure provides structural insights into the key elements of DHPR involved in physical coupling with the RyR/Ca2+ release channel and shed light onto the mechanism of excitation-contraction coupling. PMID:25667046

  19. Contrasting genetic architectures in different mouse reference populations used for studying complex traits.

    PubMed

    Buchner, David A; Nadeau, Joseph H

    2015-06-01

    Quantitative trait loci (QTLs) are being used to study genetic networks, protein functions, and systems properties that underlie phenotypic variation and disease risk in humans, model organisms, agricultural species, and natural populations. The challenges are many, beginning with the seemingly simple tasks of mapping QTLs and identifying their underlying genetic determinants. Various specialized resources have been developed to study complex traits in many model organisms. In the mouse, remarkably different pictures of genetic architectures are emerging. Chromosome Substitution Strains (CSSs) reveal many QTLs, large phenotypic effects, pervasive epistasis, and readily identified genetic variants. In contrast, other resources as well as genome-wide association studies (GWAS) in humans and other species reveal genetic architectures dominated with a relatively modest number of QTLs that have small individual and combined phenotypic effects. These contrasting architectures are the result of intrinsic differences in the study designs underlying different resources. The CSSs examine context-dependent phenotypic effects independently among individual genotypes, whereas with GWAS and other mouse resources, the average effect of each QTL is assessed among many individuals with heterogeneous genetic backgrounds. We argue that variation of genetic architectures among individuals is as important as population averages. Each of these important resources has particular merits and specific applications for these individual and population perspectives. Collectively, these resources together with high-throughput genotyping, sequencing and genetic engineering technologies, and information repositories highlight the power of the mouse for genetic, functional, and systems studies of complex traits and disease models. © 2015 Buchner and Nadeau; Published by Cold Spring Harbor Laboratory Press.

  20. Acoustical model of a Shoddy fibre absorber

    NASA Astrophysics Data System (ADS)

    Manning, John Peter

    Shoddy fibres or "Shoddies" are a mixture of post-consumer and post-industrial fibres diverted from textile waste streams and recycled into their raw fibre form. They have found widespread use as a raw material for manufacturing sound absorbers that include, but are not limited to: automotive, architectural and home appliance applications. The purpose of this project is to develop a simple acoustic model to describe the acoustic behaviour of sound absorbers composed primarily of Shoddy fibres. The model requires knowledge of the material's bulk density only. To date, these materials have not been the focus of much published research and acoustical designers must rely on models that were developed for other materials or are overly complex. For modelling purposes, an equivalent fluid approach is chosen to balance complexity and accuracy. In deriving the proposed model, several popular equivalent fluid models are selected and the required input parameters for each model identified. The models are: the model of Delaney and Bazley, two models by Miki, the model of Johnson in conjunction with the model of Champoux and Allard and the model of Johnson in conjunction with the model of Lafarge. Characterization testing is carried out on sets of Shoddy absorbers produced using three different manufacturing methods. The measured properties are open porosity, tortuosity, airflow resistivity, the viscous and thermal characteristic lengths and the static thermal permeability. Empirical relationships between model parameters and bulk density are then derived and used to populate the selected models. This yields several 'simplified' models with bulk density as the only parameter. The most accurate model is then selected by comparing each model's prediction to the results of normal incidence sound absorption tests. The model of Johnson-Lafarge populated with the empirical relations is the most accurate model over the range of frequencies considered (approx. 300 Hz - 4000 Hz

  1. Architecture and ssDNA interaction of the Timeless-Tipin-RPA complex

    PubMed Central

    Witosch, Justine; Wolf, Eva; Mizuno, Naoko

    2014-01-01

    The Timeless-Tipin (Tim-Tipin) complex, also referred to as the fork protection complex, is involved in coordination of DNA replication. Tim-Tipin is suggested to be recruited to replication forks via Replication Protein A (RPA) but details of the interaction are unknown. Here, using cryo-EM and biochemical methods, we characterized complex formation of Tim-Tipin, RPA and single-stranded DNA (ssDNA). Tim-Tipin and RPA form a 258 kDa complex with a 1:1:1 stoichiometry. The cryo-EM 3D reconstruction revealed a globular architecture of the Tim-Tipin-RPA complex with a ring-like and a U-shaped domain covered by a RPA lid. Interestingly, RPA in the complex adopts a horse shoe-like shape resembling its conformation in the presence of long ssDNA (>30 nucleotides). Furthermore, the recruitment of the Tim-Tipin-RPA complex to ssDNA is modulated by the RPA conformation and requires RPA to be in the more compact 30 nt ssDNA binding mode. The dynamic formation and disruption of the Tim-Tipin-RPA-ssDNA complex implicates the RPA-based recruitment of Tim-Tipin to the replication fork. PMID:25348395

  2. BECLIN 1-VPS34 COMPLEX ARCHITECTURE: UNDERSTANDING THE NUTS AND BOLTS OF THERAPEUTIC TARGETS

    PubMed Central

    Morris, Deanna H.; Yip, Calvin K.; Shi, Yi; Chait, Brian T.; Wang, Qing Jun

    2015-01-01

    Autophagy is an important lysosomal degradation pathway that aids in the maintenance of cellular homeostasis by breaking down and recycling intracellular contents. Dysregulation of autophagy is linked to a growing number of human diseases. The Beclin 1-Vps34 protein-protein interaction network is critical for autophagy regulation and is therefore essential to cellular integrity. Manipulation of autophagy, in particular via modulation of the action of the Beclin 1-Vps34 complexes, is considered a promising route to combat autophagy-related diseases. Here we summarize recent findings on the core components and structural architecture of the Beclin 1-Vps34 complexes, and how these findings provide valuable insights into the molecular mechanisms that underlie the multiple functions of these complexes and for devising therapeutic strategies. PMID:26692106

  3. Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes.

    PubMed

    Lee, Kenneth K; Sardiu, Mihaela E; Swanson, Selene K; Gilmore, Joshua M; Torok, Michael; Grant, Patrick A; Florens, Laurence; Workman, Jerry L; Washburn, Michael P

    2011-07-05

    Despite the availability of several large-scale proteomics studies aiming to identify protein interactions on a global scale, little is known about how proteins interact and are organized within macromolecular complexes. Here, we describe a technique that consists of a combination of biochemistry approaches, quantitative proteomics and computational methods using wild-type and deletion strains to investigate the organization of proteins within macromolecular protein complexes. We applied this technique to determine the organization of two well-studied complexes, Spt-Ada-Gcn5 histone acetyltransferase (SAGA) and ADA, for which no comprehensive high-resolution structures exist. This approach revealed that SAGA/ADA is composed of five distinct functional modules, which can persist separately. Furthermore, we identified a novel subunit of the ADA complex, termed Ahc2, and characterized Sgf29 as an ADA family protein present in all Gcn5 histone acetyltransferase complexes. Finally, we propose a model for the architecture of the SAGA and ADA complexes, which predicts novel functional associations within the SAGA complex and provides mechanistic insights into phenotypical observations in SAGA mutants.

  4. Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes

    PubMed Central

    Lee, Kenneth K; Sardiu, Mihaela E; Swanson, Selene K; Gilmore, Joshua M; Torok, Michael; Grant, Patrick A; Florens, Laurence; Workman, Jerry L; Washburn, Michael P

    2011-01-01

    Despite the availability of several large-scale proteomics studies aiming to identify protein interactions on a global scale, little is known about how proteins interact and are organized within macromolecular complexes. Here, we describe a technique that consists of a combination of biochemistry approaches, quantitative proteomics and computational methods using wild-type and deletion strains to investigate the organization of proteins within macromolecular protein complexes. We applied this technique to determine the organization of two well-studied complexes, Spt–Ada–Gcn5 histone acetyltransferase (SAGA) and ADA, for which no comprehensive high-resolution structures exist. This approach revealed that SAGA/ADA is composed of five distinct functional modules, which can persist separately. Furthermore, we identified a novel subunit of the ADA complex, termed Ahc2, and characterized Sgf29 as an ADA family protein present in all Gcn5 histone acetyltransferase complexes. Finally, we propose a model for the architecture of the SAGA and ADA complexes, which predicts novel functional associations within the SAGA complex and provides mechanistic insights into phenotypical observations in SAGA mutants. PMID:21734642

  5. Tension vein arrays in progressive strain: complex but predictable architecture, and major hosts of ore deposits

    NASA Astrophysics Data System (ADS)

    Laing, W. P.

    2004-06-01

    Most en échelon vein arrays are extensional and can be termed tension vein arrays (TVAs). TVAs in major fault and shear zones (FSZs) are subject to progressive deformation. This deforms the initial TVA (whose geometry is well documented in the literature), via discrete stages; first into progressively more complex architecture, involving folding of the tension veins, then into progressively more simple architecture, ultimately forming pipes. During this progression the TVA axis (new definition) rotates within the shear plane from normal, to parallel, to the displacement vector. The deforming TVA axis has simpler geometry than the complex tension veins, and it can be employed to precisely track the deformation state of the FSZ, its displacement vector, and shear sense, through all the strain stages. Five structural-metasomatic stages are defined by discrete steps in the strain evolution. TVAs are difficult to recognise, and are under-recognised, in ore systems for a number of inherent geological reasons. Orebodies founded on dilation form parallel to the TVA axis, which is also parallel to dilational jogs in the parent FSZ. Orebodies formed early in the FSZ history are normal to the displacement vector, and in progressive shear rotate with the TVA axis toward the displacement vector; orebodies formed late in the FSZ history overprint apparently complex to 'chaotic' vein stockwork, which nevertheless has analysable geometry. TVA-hosted orebodies are not necessarily parallel to the displacement vector of the host FSZ, but occupy elongate orientations over a 90° range within the FSZ. Large orebodies are favourably developed in TVAs in unfoliated FSZs (type 1 shear zones), which may form fluid 'superhighways'. Type 1 shear zones form in predictable circumstances involving particularly host rocktype and crustal position. Strike-slip FSZs possess a downdip TVA axis and are especially able to tap deep crustal fluid. TVA-hosted orebodies form a major deposit style

  6. Speciality optical fibres for astronomy

    NASA Astrophysics Data System (ADS)

    Ellis, S. C.; Bland-Hawthorn, J.

    2015-05-01

    Astrophotonics is a rapidly developing area of research which applies photonic technology to astronomical instrumentation. Such technology has the capability of significantly improving the sensitivity, calibration and stability of astronomical instruments, or indeed providing novel capabilities which are not possible using classical optics. We review the development and application of speciality fibres for astronomy, including multi-mode to single-mode converters, notch filters and frequency combs.In particular we focus on our development of instruments designed to filter atmospheric emission lines to enable much deeper spectroscopic observations in the near-infrared. These instruments employ two novel photonic technologies. First, we have developed complex aperiodic fibre Bragg gratings which filter over 100 irregularly spaced wavelengths in a single device, covering a bandwidth of over 200 nm. However, astronomical instruments require highly multi-mode fibres to enable sufficient coupling into the fibre, since atmospheric turbulence heavily distorts the wavefront. But photonic technologies such as fibre Bragg gratings, require single mode fibres. This problem is solved by the photonic lantern, which enables efficient coupling from a multi-mode fibre to an array of single-mode fibres and vice versa. We present the results of laboratory tests of these technologies and of on-sky experiments made using the first instruments to deploy these technologies on a telescope. These tests show that the fibre Bragg gratings suppress the night sky background by a factor of 9. Current instruments are limited by thermal and detector emission. Planned instruments should improve the background suppression even further, by optimising the design of the spectrograph for the properties of the photonic components. Finally we review ongoing research in astrophotonics, including multi-moded multicore fibre Bragg gratings, which enable multiple gratings to be written into the same device

  7. The development of advanced cellulosic fibres.

    PubMed

    Woodings, C R

    1995-12-01

    For the majority of the last century, commercial routes to regenerated cellulose fibres have coped with the difficulties of making a good cellulose solution by using an easy to dissolve derivative (e.g. xanthate in the case of viscose rayon) or complex (e.g. cuprammonium rayon). For the purposes of this paper, advanced cellulosic fibres are defined as those made from a process involving direct dissolution of cellulose. The first examples of such fibres have now been generically designated as lyocell fibres to distinguish them from rayons, and the first commercial lyocell fibre is Courtaulds' Tencel.

  8. Causal architecture, complexity and self-organization in time series and cellular automata

    NASA Astrophysics Data System (ADS)

    Shalizi, Cosma Rohilla

    2001-10-01

    All self-respecting nonlinear scientists know self- organization when they see it: except when we disagree. For this reason, if no other, it is important to put some mathematical spine into our floppy intuitive notion of self-organization. Only a few measures of self- organization have been proposed; none can be adopted in good intellectual conscience. To find a decent formalization of self-organization, we need to pin down what we mean by organization. The best answer is that the organization of a process is its causal architecture-its internal, possibly hidden, causal states and their interconnections. Computational mechanics is a method for inferring causal architecture-represented by a mathematical object called the ɛ-machine-from observed behavior. The ɛ-machine captures all patterns in the process which have any predictive power, so computational mechanics is also a method for pattern discovery. In this work, I develop computational mechanics for four increasingly sophisticated types of process-memoryless transducers, time series, transducers with memory, and cellular automata. In each case I prove the optimality and uniqueness of the ɛ-machine's representation of the causal architecture, and give reliable algorithms for pattern discovery. The ɛ-machine is the organization of the process, or at least of the part of it which is relevant to our measurements. It leads to a natural measure of the statistical complexity of processes, namely the amount of information needed to specify the state of the E-machine. Self-organization is a self- generated increase in statistical complexity. This fulfills various hunches which have been advanced in the literature, seems to accord with people's intuitions, and is both mathematically precise and operational.

  9. From Tls to Hbim. High Quality Semantically-Aware 3d Modeling of Complex Architecture

    NASA Astrophysics Data System (ADS)

    Quattrini, R.; Malinverni, E. S.; Clini, P.; Nespeca, R.; Orlietti, E.

    2015-02-01

    In order to improve the framework for 3D modeling, a great challenge is to obtain the suitability of Building Information Model (BIM) platform for historical architecture. A specific challenge in HBIM is to guarantee appropriateness of geometrical accuracy. The present work demonstrates the feasibility of a whole HBIM approach for complex architectural shapes, starting from TLS point clouds. A novelty of our method is to work in a 3D environment throughout the process and to develop semantics during the construction phase. This last feature of HBIM was analyzed in the present work verifying the studied ontologies, enabling the data enrichment of the model with non-geometrical information, such as historical notes, decay or deformation evidence, decorative elements etc. The case study is the Church of Santa Maria at Portonovo, an abbey from the Romanesque period. Irregular or complex historical architecture, such as Romanesque, needs the construction of shared libraries starting from the survey of its already existing elements. This is another key aspect in delivering Building Information Modeling standards. In particular, we focus on the quality assessment of the obtained model, using an open-source sw and the point cloud as reference. The proposed work shows how it is possible to develop a high quality 3D model semantic-aware, capable of connecting geometrical-historical survey with descriptive thematic databases. In this way, a centralized HBIM will serve as comprehensive dataset of information about all disciplines, particularly for restoration and conservation. Moreover, the geometric accuracy will ensure also reliable visualization outputs.

  10. Non-covalent synthesis of supermicelles with complex architectures using spatially confined hydrogen-bonding interactions

    NASA Astrophysics Data System (ADS)

    Li, Xiaoyu; Gao, Yang; Boott, Charlotte E.; Winnik, Mitchell A.; Manners, Ian

    2015-09-01

    Nature uses orthogonal interactions over different length scales to construct structures with hierarchical levels of order and provides an important source of inspiration for the creation of synthetic functional materials. Here, we report the programmed assembly of monodisperse cylindrical block comicelle building blocks with crystalline cores to create supermicelles using spatially confined hydrogen-bonding interactions. We also demonstrate that it is possible to further program the self-assembly of these synthetic building blocks into structures of increased complexity by combining hydrogen-bonding interactions with segment solvophobicity. The overall approach offers an efficient, non-covalent synthesis method for the solution-phase fabrication of a range of complex and potentially functional supermicelle architectures in which the crystallization, hydrogen-bonding and solvophobic interactions are combined in an orthogonal manner.

  11. Functional interplay between Mediator and TFIIB in preinitiation complex assembly in relation to promoter architecture

    PubMed Central

    Eychenne, Thomas; Novikova, Elizaveta; Barrault, Marie-Bénédicte; Alibert, Olivier; Boschiero, Claire; Peixeiro, Nuno; Cornu, David; Redeker, Virginie; Kuras, Laurent; Nicolas, Pierre; Werner, Michel; Soutourina, Julie

    2016-01-01

    Mediator is a large coregulator complex conserved from yeast to humans and involved in many human diseases, including cancers. Together with general transcription factors, it stimulates preinitiation complex (PIC) formation and activates RNA polymerase II (Pol II) transcription. In this study, we analyzed how Mediator acts in PIC assembly using in vivo, in vitro, and in silico approaches. We revealed an essential function of the Mediator middle module exerted through its Med10 subunit, implicating a key interaction between Mediator and TFIIB. We showed that this Mediator–TFIIB link has a global role on PIC assembly genome-wide. Moreover, the amplitude of Mediator's effect on PIC formation is gene-dependent and is related to the promoter architecture in terms of TATA elements, nucleosome occupancy, and dynamics. This study thus provides mechanistic insights into the coordinated function of Mediator and TFIIB in PIC assembly in different chromatin contexts. PMID:27688401

  12. Non-covalent synthesis of supermicelles with complex architectures using spatially confined hydrogen-bonding interactions

    PubMed Central

    Li, Xiaoyu; Gao, Yang; Boott, Charlotte E.; Winnik, Mitchell A.; Manners, Ian

    2015-01-01

    Nature uses orthogonal interactions over different length scales to construct structures with hierarchical levels of order and provides an important source of inspiration for the creation of synthetic functional materials. Here, we report the programmed assembly of monodisperse cylindrical block comicelle building blocks with crystalline cores to create supermicelles using spatially confined hydrogen-bonding interactions. We also demonstrate that it is possible to further program the self-assembly of these synthetic building blocks into structures of increased complexity by combining hydrogen-bonding interactions with segment solvophobicity. The overall approach offers an efficient, non-covalent synthesis method for the solution-phase fabrication of a range of complex and potentially functional supermicelle architectures in which the crystallization, hydrogen-bonding and solvophobic interactions are combined in an orthogonal manner. PMID:26337527

  13. Complexity reduction of chromatin architecture in macula densa cells during mouse postnatal development.

    PubMed

    Pantic, Igor; Basta-Jovanovic, Gordana; Starcevic, Vesna; Paunovic, Jovana; Suzic, Slavica; Kojic, Zvezdana; Pantic, Senka

    2013-02-01

    To determine whether complexity of chromatin structure in kidney macula densa cells (MDC) decreases during postnatal development in mice. The levels of chromatin structural complexity were measured by determining fractal dimension of MDC nuclei. Kidney tissue was obtained from the total of 32 male Swiss albino mice divided into four age groups (n = 8): newborn (0 days), 10 days old, 20 days old and 30 days old. For a total of 640 MDC chromatin structures, fractal dimension, lacunarity, as well as parameters of Grey level co-occurrence matrix (GLCM) texture were determined. Chromatin fractal dimension in animals aged 10 days, 20 days and 30 days was significantly lower (P < 0.05, P < 0.01 and P < 0.001, respectively), compared with newborn mice. This complexity reduction of chromatin architecture is in accordance with previously published studies, which detected generalized and sustained loss of both tissue and cell complexity during aging. The loss of complexity was texture-independent, since there was no statistically significant difference (P > 0.05) in both chromatin angular second moment and inverse difference moment between the age groups. Our results indicate that age-related nuclear intrinsic factors which do not influence chromatin texture may have an important role in MDC postnatal development. © 2012 The Authors. Nephrology © 2012 Asian Pacific Society of Nephrology.

  14. Conversion of Highly Complex Faulted Hydrostratigraphic Architectures into MODFLOW Grid for Groundwater Modeling

    NASA Astrophysics Data System (ADS)

    Pham, H. V.; Tsai, F. T.

    2013-12-01

    The USGS MODFLOW is widely used for groundwater modeling. Because of using structured grid, all layers have to be continuous throughout the model domain. This makes it difficult to generate computational grid for complex hydrostratigraphic architectures including thin and discontinuous layers, interconnections of sand units, pinch-outs, and faults. In this study, we present a technique for automatically generating MODFLOW grid for complex aquifer systems of strongly sand-clay binary heterogeneity. To do so, an indicator geostatistical method is adopted to interpolate sand and clay distributions in a gridded two-dimensional plane along the structural dip for every one-foot vertical interval. A three-dimensional gridded binary geological architecture is reconstructed by assembling all two-dimensional planes. Then, the geological architecture is converted to MODFLOW computational grid by the procedures as follows. First, we determine bed boundary elevation of sand and clay units for each vertical column. Then, we determine the total number of bed boundaries for a vertical column by projecting the bed boundaries of its adjacent four vertical columns to the column. This step is of importance to preserve flow pathways, especially for narrow connections between sand units. Finally, we determine the number of MODFLOW layers and assign layer indices to bed boundaries. A MATLAB code was developed to implement the technique. The inputs for the code are bed boundary data from well logs, a structural dip, minimal layer thickness, and the number of layers. The outputs are MODFLOW grid of sand and clay indicators. The technique is able to generate grid that preserves fault features in the geological architecture. Moreover, the code is very efficient for regenerating MODFLOW grid with different grid resolutions. The technique was applied to MODFLOW grid generation for the fluvial aquifer system in Baton Rouge, Louisiana. The study area consists of the '1,200-foot' sand, the '1

  15. Ageing alters the supramolecular architecture of OxPhos complexes in rat brain cortex.

    PubMed

    Frenzel, Monika; Rommelspacher, Hans; Sugawa, Michiru D; Dencher, Norbert A

    2010-08-01

    Activity and stability of life-supporting proteins are determined not only by their abundance and by post-translational modifications, but also by specific protein-protein interactions. This holds true both for signal-transduction and energy-converting cascades. For vital processes such as life-span control and senescence, to date predominantly age-dependent alterations in abundance and to lesser extent in post-translational modifications of proteins are examined to elucidate the cause of ageing at the molecular level. In mitochondria of rat cortex, we quantified profound changes in the proportion of supramolecular assemblies (supercomplexes) of the respiratory chain complexes I, III(2), IV as well as of the MF(o)F(1) ATP synthase (complex V) by 2D-native/SDS electrophoresis and fluorescent staining. Complex I was present solely in supercomplexes and those lacking complex IV were least stable in aged animals (2.4-fold decline). The ATP synthase was confirmed as a prominent target of age-associated degradation by an overall decline in abundance of 1.5-fold for the monomer and an 2.8-fold increase of unbound F(1). Oligomerisation of the ATP synthase increases during ageing and might modulate the cristae architecture. These data could explain the link between ageing and respiratory control as well as ROS generation.

  16. Including inputs and control within equation-free architectures for complex systems

    NASA Astrophysics Data System (ADS)

    Proctor, Joshua L.; Brunton, Steven L.; Kutz, J. Nathan

    2016-11-01

    The increasing ubiquity of complex systems that require control is a challenge for existing methodologies in characterization and controller design when the system is high-dimensional, nonlinear, and without physics-based governing equations. We review standard model reduction techniques such as Proper Orthogonal Decomposition (POD) with Galerkin projection and Balanced POD (BPOD). Further, we discuss the link between these equation-based methods and recently developed equation-free methods such as the Dynamic Mode Decomposition and Koopman operator theory. These data-driven methods can mitigate the challenge of not having a well-characterized set of governing equations. We illustrate that this equation-free approach that is being applied to measurement data from complex systems can be extended to include inputs and control. Three specific research examples are presented that extend current equation-free architectures toward the characterization and control of complex systems. These examples motivate a potentially revolutionary shift in the characterization of complex systems and subsequent design of objective-based controllers for data-driven models.

  17. Changes in architecture of the Golgi complex and other subcellular organelles during myogenesis

    PubMed Central

    1993-01-01

    Myogenesis involves changes in both gene expression and cellular architecture. Little is known of the organization, in muscle in vivo, of the subcellular organelles involved in protein synthesis despite the potential importance of targeted protein synthesis for formation and maintenance of functional domains such as the neuromuscular junction. A panel of antibodies to markers of the ER, the Golgi complex, and the centrosome were used to localize these organelles by immunofluorescence in myoblasts and myotubes of the mouse muscle cell line C2 in vitro, and in intact single muscle fibers from the rat flexor digitorum brevis. Antibodies to the ER stained structures throughout the cytoplasm of both C2 myoblasts and myotubes. In contrast, the spatial relationship between nucleus, centrosome, and Golgi complex was dramatically altered. These changes could also be observed in a low- calcium medium that allowed differentiation while preventing myoblast fusion. Muscle fibers in vivo resembled myotubes except that the ER occupied a smaller volume of cytoplasm and no staining was found for one of the Golgi complex markers, the enzyme alpha-mannosidase II. Electron microscopy, however, clearly showed the presence of stacks of Golgi cisternae in both junctional and extrajunctional regions of muscle fibers. The perinuclear distribution of the Golgi complex was also observed in live muscle fibers stained with a fluorescent lipid. Thus, the distribution of subcellular organelles of the secretory pathway was found to be similar in myotubes and muscle fibers, and all organelles were found in both junctional and extrajunctional areas of muscle. PMID:7678420

  18. Age-related reduction of structural complexity in spleen hematopoietic tissue architecture in mice.

    PubMed

    Pantic, Igor; Paunovic, Jovana; Basta-Jovanovic, Gordana; Perovic, Milan; Pantic, Senka; Milosevic, Nebojsa T

    2013-09-01

    The effects of aging on structural complexity in hematopoietic tissue are unknown. In this work, in a mouse experimental model, we report the age-related reduction of spleen hematopoietic tissue (SHT) complexity. Spleen tissue was obtained from the total of 64 male Swiss albino mice divided into 8 age groups: newborns (0 days old), 10 days, 20 days, 30 days, 120 days, 210 days, 300 and 390 days old. SHT was stained using conventional hematoxylin/eosin, and DNA-binding toluidine blue dyes. Fractal dimension as an indicator of cellular complexity, and lacunarity as indicator of tissue heterogeneity were determined based on the binarized SHT micrographs. Results indicate that fractal dimension of mice spleen hematopoietic tissue decreases with age, while lacunarity increases. These changes/trends have been detected in SHT stained both with toluidine blue and conventional hematoxylin/eosin. Fractal dimension was negatively correlated with lacunarity. The detected reduction in complexity suggests that age-related structural changes are present in mouse SHT both in general tissue architecture and progenitor cell DNA.

  19. Modelling fibre laydown and web uniformity in nonwoven fabric

    NASA Astrophysics Data System (ADS)

    Battocchio, F.; Sutcliffe, M. P. F.

    2017-04-01

    The mechanical and functional performance of nonwoven fabric critically depends on the fibre architecture. The fibre laydown process plays a key role in controlling this architecture. The fibre dynamic behaviour during laydown is studied through a finite element model which describes the role of the parameters in defining the area covered by a single fibre when deposited on the conveyor belt. The path taken by a fibre is described in terms of the radius of gyration, which characterises the area covered by the fibre in the textile, and the spectrum of curvature, which describes the degree of fibre looping as a function of the arc length. Starting from deterministic and idealised fibre curvature spectra, stochastic Monte Carlo simulations are undertaken to generate full nonwoven web samples and reproduce the uniformity of fibre density. A novel image analysis technique that allows measurement of the uniformity of real spunbonded nonwoven samples from images of textiles is used to confirm the validity of the model. It is shown that the main parameter that governs the fibre density uniformity is the ratio of the fibre spinning velocity to the velocity of conveyor belt, while fibre oscillations prior to deposition play a secondary role.

  20. Screw dislocation-driven growth of nanoplates and complex multidimensional architectures

    NASA Astrophysics Data System (ADS)

    Forticaux, Audrey

    Structures are essential to function, and for crystals, structure also determines properties despite a similar chemical composition. Nanoscale materials of various dimensionalities have demonstrated great promise in many applications. Controlling the bottom-up synthesis of high quality nanomaterials with specific dimensions relies on the understanding of crystal growth. I describe more specifically the screw dislocation-driven growth of nanomaterials prevalent in low supersaturation conditions, since this mechanism offers the unique advantage of breaking the symmetry of crystal growth and driving anisotropic crystal growth and enables the formation of a variety of nanostructures, from one-dimensional (1D) nanowires (NWs) and nanotubes, to two-dimensional (2D) nanoplates, and three-dimensional (3D) nanostructures of any class of materials. Several examples of 2D nanoplates are presented, especially layered compounds, such as cobalt hydroxide, zinc hydroxyl sulfate (ZHS), and several layered double hydroxides (LDHs). 2D nanoplates are of special interest, not only for their diverse properties and applications, but also to study the screw dislocation-driven growth by various microscopy techniques due to their convenient planar morphology. Moreover, 2D nanoplates can be used as platforms to devise strategies for synthesizing complex 3D material architectures, which is still a challenge for chemists and materials scientists. For example, here I use CuGaO2 nanoplates as individual nanosubstrates onto which ZnO NWs arrays are epitaxially grown to produce individual 3D mesoscale p-n junction diodes. Organic molecules are often used to modify and control crystal morphology, but inorganic ions can also enable dramatic changes in crystal growth. In this thesis, I also investigate inorganic nanoclusters as a new class of crystal growth modifiers. I show that polyoxometalate nanoclusters of 1 nm in size control the dimensionality of ZHS crystal growth between its screw

  1. Simple fold composition and modular architecture of the nuclear pore complex

    PubMed Central

    Devos, Damien; Dokudovskaya, Svetlana; Williams, Rosemary; Alber, Frank; Eswar, Narayanan; Chait, Brian T.; Rout, Michael P.; Sali, Andrej

    2006-01-01

    The nuclear pore complex (NPC) consists of multiple copies of ≈30 different proteins [nucleoporins (nups)], forming a channel in the nuclear envelope that mediates macromolecular transport between the cytosol and the nucleus. With <5% of the nup residues currently available in experimentally determined structures, little is known about the detailed structure of the NPC. Here, we use a combined computational and biochemical approach to assign folds for ≈95% of the residues in the yeast and vertebrate nups. These fold assignments suggest an underlying simplicity in the composition and modularity in the architecture of all eukaryotic NPCs. The simplicity in NPC composition is reflected in the presence of only eight fold types, with the three most frequent folds accounting for ≈85% of the residues. The modularity in NPC architecture is reflected in its hierarchical and symmetrical organization that partitions the predicted nup folds into three groups: the transmembrane group containing transmembrane helices and a cadherin fold, the central scaffold group containing β-propeller and α-solenoid folds, and the peripheral FG group containing predominantly the FG repeats and the coiled-coil fold. Moreover, similarities between structures in coated vesicles and those in the NPC support our prior hypothesis for their common evolutionary origin in a progenitor protocoatomer. The small number of predicted fold types in the NPC and their internal symmetries suggest that the bulk of the NPC structure has evolved through extensive motif and gene duplication from a simple precursor set of only a few proteins. PMID:16461911

  2. RootNav: Navigating Images of Complex Root Architectures1[C][W

    PubMed Central

    Pound, Michael P.; French, Andrew P.; Atkinson, Jonathan A.; Wells, Darren M.; Bennett, Malcolm J.; Pridmore, Tony

    2013-01-01

    We present a novel image analysis tool that allows the semiautomated quantification of complex root system architectures in a range of plant species grown and imaged in a variety of ways. The automatic component of RootNav takes a top-down approach, utilizing the powerful expectation maximization classification algorithm to examine regions of the input image, calculating the likelihood that given pixels correspond to roots. This information is used as the basis for an optimization approach to root detection and quantification, which effectively fits a root model to the image data. The resulting user experience is akin to defining routes on a motorist’s satellite navigation system: RootNav makes an initial optimized estimate of paths from the seed point to root apices, and the user is able to easily and intuitively refine the results using a visual approach. The proposed method is evaluated on winter wheat (Triticum aestivum) images (and demonstrated on Arabidopsis [Arabidopsis thaliana], Brassica napus, and rice [Oryza sativa]), and results are compared with manual analysis. Four exemplar traits are calculated and show clear illustrative differences between some of the wheat accessions. RootNav, however, provides the structural information needed to support extraction of a wider variety of biologically relevant measures. A separate viewer tool is provided to recover a rich set of architectural traits from RootNav’s core representation. PMID:23766367

  3. Complex bud architecture and cell-specific chemical patterns enable supercooling of Picea abies bud primordia.

    PubMed

    Kuprian, Edith; Munkler, Caspar; Resnyak, Anna; Zimmermann, Sonja; Tuong, Tan D; Gierlinger, Notburga; Müller, Thomas; Livingston, David P; Neuner, Gilbert

    2017-09-29

    Bud primordia of Picea abies, despite a frozen shoot, stay ice free down to -50°C by a mechanism termed supercooling whose biophysical and biochemical requirements are poorly understood. Bud architecture was assessed by 3D-reconstruction, supercooling and freezing patterns by infrared video thermography, freeze dehydration and extra-organ freezing by water potential measurements and cell-specific chemical patterns by RAMAN microscopy and Mass Spectrometry Imaging. A bowl-like ice barrier tissue insulates primordia from entrance by intrinsic ice. Water repellent and densely packed bud scales prevent extrinsic ice penetration. At -18°C break-down of supercooling was triggered by intrinsic ice nucleators while the ice barrier remained active. Temperature-dependent freeze dehydration (-0.1 MPa/K) caused accumulation of extra-organ ice masses that by rupture of the shoot pith tissue are accommodated in large voids. The barrier tissue has exceptionally pectin-rich cell walls and intercellular spaces and the cell lumina were lined or filled with proteins, especially near the primordium. Primordial cells close to the barrier accumulate di-, tri- and tetrasaccharides. Bud architecture efficiently prevents ice penetration but ice nucleators become active inside the primordium below a temperature threshold. Biochemical patterns indicate a complex cellular interplay enabling supercooling and the necessity for cell-specific biochemical analysis. This article is protected by copyright. All rights reserved.

  4. Code generator for implementing dual tree complex wavelet transform on reconfigurable architectures for mobile applications

    PubMed Central

    Canbay, Ferhat; Levent, Vecdi Emre; Serbes, Gorkem; Ugurdag, H. Fatih; Goren, Sezer

    2016-01-01

    The authors aimed to develop an application for producing different architectures to implement dual tree complex wavelet transform (DTCWT) having near shift-invariance property. To obtain a low-cost and portable solution for implementing the DTCWT in multi-channel real-time applications, various embedded-system approaches are realised. For comparison, the DTCWT was implemented in C language on a personal computer and on a PIC microcontroller. However, in the former approach portability and in the latter desired speed performance properties cannot be achieved. Hence, implementation of the DTCWT on a reconfigurable platform such as field programmable gate array, which provides portable, low-cost, low-power, and high-performance computing, is considered as the most feasible solution. At first, they used the system generator DSP design tool of Xilinx for algorithm design. However, the design implemented by using such tools is not optimised in terms of area and power. To overcome all these drawbacks mentioned above, they implemented the DTCWT algorithm by using Verilog Hardware Description Language, which has its own difficulties. To overcome these difficulties, simplify the usage of proposed algorithms and the adaptation procedures, a code generator program that can produce different architectures is proposed. PMID:27733925

  5. Code generator for implementing dual tree complex wavelet transform on reconfigurable architectures for mobile applications.

    PubMed

    Canbay, Ferhat; Levent, Vecdi Emre; Serbes, Gorkem; Ugurdag, H Fatih; Goren, Sezer; Aydin, Nizamettin

    2016-09-01

    The authors aimed to develop an application for producing different architectures to implement dual tree complex wavelet transform (DTCWT) having near shift-invariance property. To obtain a low-cost and portable solution for implementing the DTCWT in multi-channel real-time applications, various embedded-system approaches are realised. For comparison, the DTCWT was implemented in C language on a personal computer and on a PIC microcontroller. However, in the former approach portability and in the latter desired speed performance properties cannot be achieved. Hence, implementation of the DTCWT on a reconfigurable platform such as field programmable gate array, which provides portable, low-cost, low-power, and high-performance computing, is considered as the most feasible solution. At first, they used the system generator DSP design tool of Xilinx for algorithm design. However, the design implemented by using such tools is not optimised in terms of area and power. To overcome all these drawbacks mentioned above, they implemented the DTCWT algorithm by using Verilog Hardware Description Language, which has its own difficulties. To overcome these difficulties, simplify the usage of proposed algorithms and the adaptation procedures, a code generator program that can produce different architectures is proposed.

  6. Molecular architecture of the yeast Elongator complex reveals an unexpected asymmetric subunit arrangement.

    PubMed

    Setiaputra, Dheva T; Cheng, Derrick Th; Lu, Shan; Hansen, Jesse M; Dalwadi, Udit; Lam, Cindy Hy; To, Jeffrey L; Dong, Meng-Qiu; Yip, Calvin K

    2017-02-01

    Elongator is a ~850 kDa protein complex involved in multiple processes from transcription to tRNA modification. Conserved from yeast to humans, Elongator is assembled from two copies of six unique subunits (Elp1 to Elp6). Despite the wealth of structural data on the individual subunits, the overall architecture and subunit organization of the full Elongator and the molecular mechanisms of how it exerts its multiple activities remain unclear. Using single-particle electron microscopy (EM), we revealed that yeast Elongator adopts a bilobal architecture and an unexpected asymmetric subunit arrangement resulting from the hexameric Elp456 subassembly anchored to one of the two Elp123 lobes that form the structural scaffold. By integrating the EM data with available subunit crystal structures and restraints generated from cross-linking coupled to mass spectrometry, we constructed a multiscale molecular model that showed the two Elp3, the main catalytic subunit, are located in two distinct environments. This work provides the first structural insights into Elongator and a framework to understand the molecular basis of its multifunctionality.

  7. Assembly and Architecture of the EBV B Cell Entry Triggering Complex

    PubMed Central

    Sathiyamoorthy, Karthik; Jiang, Jiansen; Hu, Yao Xiong; Rowe, Cynthia L.; Möhl, Britta S.; Chen, Jia; Jiang, Wei; Mellins, Elizabeth D.; Longnecker, Richard; Zhou, Z. Hong; Jardetzky, Theodore S.

    2014-01-01

    Epstein-Barr Virus (EBV) is an enveloped double-stranded DNA virus of the gammaherpesvirinae sub-family that predominantly infects humans through epithelial cells and B cells. Three EBV glycoproteins, gH, gL and gp42, form a complex that targets EBV infection of B cells. Human leukocyte antigen (HLA) class II molecules expressed on B cells serve as the receptor for gp42, triggering membrane fusion and virus entry. The mechanistic role of gHgL in herpesvirus entry has been largely unresolved, but it is thought to regulate the activation of the virally-encoded gB protein, which acts as the primary fusogen. Here we study the assembly and function of the reconstituted B cell entry complex comprised of gHgL, gp42 and HLA class II. The structure from negative-stain electron microscopy provides a detailed snapshot of an intermediate state in EBV entry and highlights the potential for the triggering complex to bring the two membrane bilayers into proximity. Furthermore, gHgL interacts with a previously identified, functionally important hydrophobic pocket on gp42, defining the overall architecture of the complex and playing a critical role in membrane fusion activation. We propose a macroscopic model of the initiating events in EBV B cell fusion centered on the formation of the triggering complex in the context of both viral and host membranes. This model suggests how the triggering complex may bridge the two membrane bilayers, orienting critical regions of the N- and C- terminal ends of gHgL to promote the activation of gB and efficient membrane fusion. PMID:25144748

  8. Heteroscorpionate aluminium complexes as chiral building blocks to engineer helical architectures.

    PubMed

    Castro-Osma, Jose A; Alonso-Moreno, Carlos; Gómez, M Victoria; Márquez-Segovia, Isabel; Otero, Antonio; Lara-Sánchez, Agustín; Fernández-Baeza, Juan; Sánchez-Barba, Luis F; Rodríguez, Ana M

    2013-10-21

    Treatment of heteroscorpionate ligand precursors pbptamH, pbpamH, sbpamH and (S)-mbpamH with 2 equivalents of AlR3 (R = Et, Me) yielded the corresponding binuclear organoaluminium complexes [Al2R4(μ-pbptam)] (R = Me 1, Et 2), [Al2R4(μ-pbpam)] (R = Me 3, Et 4), [Al2R4(μ-sbpam)] (R = Me 5, Et 6) and [Al2R4{μ-(S)-mbpam}] (R = Me 7, Et 8). These complexes have helical chirality due to the demands of the fixed pyrazole rings. The stereoisomerism and the self-assembly processes of these helicates have been studied in some detail in solution by NMR and in the solid state by X-ray diffraction. Mixtures of M- and P-handed enantiomers and mixtures of M- and P-handed diastereoisomers were obtained when achiral (1–4) and chiral (5–8) heteroscorpionate ligands were used as scaffolds, respectively. Re-crystallization from hexane allowed us to obtain M-homochiral architectures in the solid state for the helical complexes [Al2Et4(μ-sbpam)] (6) and [Al2Et4{μ-(S)-mbpam}] (8). The reaction of heteroscorpionate ligands with 3 equivalents of AlR3 (R = Me, Et) led to the corresponding trinuclear organoaluminium complexes [Al3R7(μ3-pbptam)] (R = Me 9, Et 10), [Al3R7(μ3-pbpam)] (R = Me 11, Et 12), [Al3R7(μ3-sbpam)] (R = Me 13, Et 14) and [Al3R7{μ3-(S)-mbpam}] (R = Me 15, Et 16). The extra AlR3 molecule contributes to the formation of a diastereomeric excess of the PS helicate for complexes 15 and 16. X-ray determination of some of the helical complexes allowed us to witness a versatile and efficient self-assembly process of the building blocks (heteroscorpionate aluminium complexes) directed by noncovalent intermolecular CH–π interactions. The structures of these complexes have been determined by spectroscopic methods and the X-ray crystal structures of 2, 6, 8, and 16 have also been established. Concentration-dependent 1H pulsed field-gradient spin echo (PFGSE) NMR experiments provided evidence for the self-assembly of the single molecular species of complex 2 in

  9. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa

    PubMed Central

    Zhao, Keyan; Tung, Chih-Wei; Eizenga, Georgia C.; Wright, Mark H.; Ali, M. Liakat; Price, Adam H.; Norton, Gareth J.; Islam, M. Rafiqul; Reynolds, Andy; Mezey, Jason; McClung, Anna M.; Bustamante, Carlos D.; McCouch, Susan R.

    2011-01-01

    Asian rice, Oryza sativa is a cultivated, inbreeding species that feeds over half of the world's population. Understanding the genetic basis of diverse physiological, developmental, and morphological traits provides the basis for improving yield, quality and sustainability of rice. Here we show the results of a genome-wide association study based on genotyping 44,100 SNP variants across 413 diverse accessions of O. sativa collected from 82 countries that were systematically phenotyped for 34 traits. Using cross-population-based mapping strategies, we identified dozens of common variants influencing numerous complex traits. Significant heterogeneity was observed in the genetic architecture associated with subpopulation structure and response to environment. This work establishes an open-source translational research platform for genome-wide association studies in rice that directly links molecular variation in genes and metabolic pathways with the germplasm resources needed to accelerate varietal development and crop improvement. PMID:21915109

  10. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa.

    PubMed

    Zhao, Keyan; Tung, Chih-Wei; Eizenga, Georgia C; Wright, Mark H; Ali, M Liakat; Price, Adam H; Norton, Gareth J; Islam, M Rafiqul; Reynolds, Andy; Mezey, Jason; McClung, Anna M; Bustamante, Carlos D; McCouch, Susan R

    2011-09-13

    Asian rice, Oryza sativa is a cultivated, inbreeding species that feeds over half of the world's population. Understanding the genetic basis of diverse physiological, developmental, and morphological traits provides the basis for improving yield, quality and sustainability of rice. Here we show the results of a genome-wide association study based on genotyping 44,100 SNP variants across 413 diverse accessions of O. sativa collected from 82 countries that were systematically phenotyped for 34 traits. Using cross-population-based mapping strategies, we identified dozens of common variants influencing numerous complex traits. Significant heterogeneity was observed in the genetic architecture associated with subpopulation structure and response to environment. This work establishes an open-source translational research platform for genome-wide association studies in rice that directly links molecular variation in genes and metabolic pathways with the germplasm resources needed to accelerate varietal development and crop improvement.

  11. Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex.

    PubMed

    Upla, Paula; Kim, Seung Joong; Sampathkumar, Parthasarathy; Dutta, Kaushik; Cahill, Sean M; Chemmama, Ilan E; Williams, Rosemary; Bonanno, Jeffrey B; Rice, William J; Stokes, David L; Cowburn, David; Almo, Steven C; Sali, Andrej; Rout, Michael P; Fernandez-Martinez, Javier

    2017-03-07

    The membrane ring that equatorially circumscribes the nuclear pore complex (NPC) in the perinuclear lumen of the nuclear envelope is composed largely of Pom152 in yeast and its ortholog Nup210 (or Gp210) in vertebrates. Here, we have used a combination of negative-stain electron microscopy, nuclear magnetic resonance, and small-angle X-ray scattering methods to determine an integrative structure of the ∼120 kDa luminal domain of Pom152. Our structural analysis reveals that the luminal domain is formed by a flexible string-of-pearls arrangement of nine repetitive cadherin-like Ig-like domains, indicating an evolutionary connection between NPCs and the cell adhesion machinery. The 16 copies of Pom152 known to be present in the yeast NPC are long enough to form the observed membrane ring, suggesting how interactions between Pom152 molecules help establish and maintain the NPC architecture.

  12. Materials science. Assembly of micro/nanomaterials into complex, three-dimensional architectures by compressive buckling.

    PubMed

    Xu, Sheng; Yan, Zheng; Jang, Kyung-In; Huang, Wen; Fu, Haoran; Kim, Jeonghyun; Wei, Zijun; Flavin, Matthew; McCracken, Joselle; Wang, Renhan; Badea, Adina; Liu, Yuhao; Xiao, Dongqing; Zhou, Guoyan; Lee, Jungwoo; Chung, Ha Uk; Cheng, Huanyu; Ren, Wen; Banks, Anthony; Li, Xiuling; Paik, Ungyu; Nuzzo, Ralph G; Huang, Yonggang; Zhang, Yihui; Rogers, John A

    2015-01-09

    Complex three-dimensional (3D) structures in biology (e.g., cytoskeletal webs, neural circuits, and vasculature networks) form naturally to provide essential functions in even the most basic forms of life. Compelling opportunities exist for analogous 3D architectures in human-made devices, but design options are constrained by existing capabilities in materials growth and assembly. We report routes to previously inaccessible classes of 3D constructs in advanced materials, including device-grade silicon. The schemes involve geometric transformation of 2D micro/nanostructures into extended 3D layouts by compressive buckling. Demonstrations include experimental and theoretical studies of more than 40 representative geometries, from single and multiple helices, toroids, and conical spirals to structures that resemble spherical baskets, cuboid cages, starbursts, flowers, scaffolds, fences, and frameworks, each with single- and/or multiple-level configurations. Copyright © 2015, American Association for the Advancement of Science.

  13. Assembly of micro/nanomaterials into complex, three-dimensional architectures by compressive buckling

    NASA Astrophysics Data System (ADS)

    Xu, Sheng; Yan, Zheng; Jang, Kyung-In; Huang, Wen; Fu, Haoran; Kim, Jeonghyun; Wei, Zijun; Flavin, Matthew; McCracken, Joselle; Wang, Renhan; Badea, Adina; Liu, Yuhao; Xiao, Dongqing; Zhou, Guoyan; Lee, Jungwoo; Chung, Ha Uk; Cheng, Huanyu; Ren, Wen; Banks, Anthony; Li, Xiuling; Paik, Ungyu; Nuzzo, Ralph G.; Huang, Yonggang; Zhang, Yihui; Rogers, John A.

    2015-01-01

    Complex three-dimensional (3D) structures in biology (e.g., cytoskeletal webs, neural circuits, and vasculature networks) form naturally to provide essential functions in even the most basic forms of life. Compelling opportunities exist for analogous 3D architectures in human-made devices, but design options are constrained by existing capabilities in materials growth and assembly. We report routes to previously inaccessible classes of 3D constructs in advanced materials, including device-grade silicon. The schemes involve geometric transformation of 2D micro/nanostructures into extended 3D layouts by compressive buckling. Demonstrations include experimental and theoretical studies of more than 40 representative geometries, from single and multiple helices, toroids, and conical spirals to structures that resemble spherical baskets, cuboid cages, starbursts, flowers, scaffolds, fences, and frameworks, each with single- and/or multiple-level configurations.

  14. An integration architecture for the automation of a continuous production complex.

    PubMed

    Chacón, Edgar; Besembel, Isabel; Narciso, Flor; Montilva, Jonás; Colina, Eliezer

    2002-01-01

    The development of integrated automation systems for continuous production plants is a very complicated process. A variety of factors must be taken into account, such as their different components (e.g., production units control systems, planning systems, financial systems, etc.), the interaction among them, and their different behavior (continuous or discrete). Moreover, the difficulty of this process is increased by the fact that each component can be viewed in a different way depending on the kind of decisions to be made, and its specific behavior. Modeling continuous production complexes as a composition of components, where, in turn, each component may also be a composite, appears to be the simplest and safest way to develop integrated automation systems. In order to provide the most versatile way to develop this kind of system, this work proposes a new approach for designing and building them, where process behavior, operation conditions and equipment conditions are integrated into a hierarchical automation architecture.

  15. Complex Genetic Architecture of Cardiac Disease in a Wild Type Inbred Strain of Drosophila melanogaster

    PubMed Central

    Zhang, Zhi; Hsieh, Benjamin; Poe, Amy; Anderson, Julie; Ocorr, Karen; Gibson, Greg; Bodmer, Rolf

    2013-01-01

    Natural populations of the fruit fly, Drosophila melanogaster, segregate genetic variation that leads to cardiac disease phenotypes. One nearly isogenic line from a North Carolina peach orchard, WE70, is shown to harbor two genetically distinct heart phenotypes: elevated incidence of arrhythmias, and a dramatically constricted heart diameter in both diastole and systole, with resemblance to restrictive cardiomyopathy in humans. Assuming the source to be rare variants of large effect, we performed Bulked Segregant Analysis using genomic DNA hybridization to Affymetrix chips to detect single feature polymorphisms, but found that the mutant phenotypes are more likely to have a polygenic basis. Further mapping efforts revealed a complex architecture wherein the constricted cardiomyopathy phenotype was observed in individual whole chromosome substitution lines, implying that variants on both major autosomes are sufficient to produce the phenotype. A panel of 170 Recombinant Inbred Lines (RIL) was generated, and a small subset of mutant lines selected, but these each complemented both whole chromosome substitutions, implying a non-additive (epistatic) contribution to the “disease” phenotype. Low coverage whole genome sequencing was also used to attempt to map chromosomal regions contributing to both the cardiomyopathy and arrhythmia, but a polygenic architecture had to be again inferred to be most likely. These results show that an apparently simple rare phenotype can have a complex genetic basis that would be refractory to mapping by deep sequencing in pedigrees. We present this as a cautionary tale regarding assumptions related to attempts to map new disease mutations on the assumption that probands carry a single causal mutation. PMID:23638165

  16. Architecture of Amylose Supramolecules in Form of Inclusion Complexes by Phosphorylase-Catalyzed Enzymatic Polymerization

    PubMed Central

    Kadokawa, Jun-ichi

    2013-01-01

    This paper reviews the architecture of amylose supramolecules in form of inclusion complexes with synthetic polymers by phosphorylase-catalyzed enzymatic polymerization. Amylose is known to be synthesized by enzymatic polymerization using α-d-glucose 1-phosphate as a monomer, by phosphorylase catalysis. When the phosphorylase-catalyzed enzymatic polymerization was conducted in the presence of various hydrophobic polymers, such as polyethers, polyesters, poly(ester-ether), and polycarbonates as a guest polymer, such inclusion supramolecules were formed by the hydrophobic interaction in the progress of polymerization. Because the representation of propagation in the polymerization is similar to the way that a vine of a plant grows, twining around a rod, this polymerization method for the formation of amylose-polymer inclusion complexes was proposed to be named “vine-twining polymerization”. To yield an inclusion complex from a strongly hydrophobic polyester, the parallel enzymatic polymerization system was extensively developed. The author found that amylose selectively included one side of the guest polymer from a mixture of two resemblant guest polymers, as well as a specific range in molecular weights of the guest polymers poly(tetrahydrofuran) (PTHF) in the vine-twining polymerization. Selective inclusion behavior of amylose toward stereoisomers of chiral polyesters, poly(lactide)s, also appeared in the vine-twining polymerization. PMID:24970172

  17. Functional and architectural complexity within and between muscles: regional variation and intermuscular force transmission.

    PubMed

    Higham, Timothy E; Biewener, Andrew A

    2011-05-27

    Over the past 30 years, studies of single muscles have revealed complex patterns of regional variation in muscle architecture, activation, strain and force. In addition, muscles are often functionally integrated with other muscles in parallel or in series. Understanding the extent of this complexity and the interactions between muscles will profoundly influence how we think of muscles in relation to organismal function, and will allow us to address questions regarding the functional benefits (or lack thereof) and dynamics of this complexity under in vivo conditions. This paper has two main objectives. First, we present a cohesive and integrative review of regional variation in function within muscles, and discuss the functional ramifications that can stem from this variation. This involves splitting regional variation into passive and active components. Second, we assess the functional integration of muscles between different limb segments by presenting new data involving in vivo measurements of activation and strain from the medial gastrocnemius, iliotibialis cranialis and iliotibialis lateralis pars preacetabularis of the helmeted guinea fowl (Numida meleagris) during level running on a motorized treadmill. Future research directions for both of these objectives are presented.

  18. Functional and architectural complexity within and between muscles: regional variation and intermuscular force transmission

    PubMed Central

    Higham, Timothy E.; Biewener, Andrew A.

    2011-01-01

    Over the past 30 years, studies of single muscles have revealed complex patterns of regional variation in muscle architecture, activation, strain and force. In addition, muscles are often functionally integrated with other muscles in parallel or in series. Understanding the extent of this complexity and the interactions between muscles will profoundly influence how we think of muscles in relation to organismal function, and will allow us to address questions regarding the functional benefits (or lack thereof) and dynamics of this complexity under in vivo conditions. This paper has two main objectives. First, we present a cohesive and integrative review of regional variation in function within muscles, and discuss the functional ramifications that can stem from this variation. This involves splitting regional variation into passive and active components. Second, we assess the functional integration of muscles between different limb segments by presenting new data involving in vivo measurements of activation and strain from the medial gastrocnemius, iliotibialis cranialis and iliotibialis lateralis pars preacetabularis of the helmeted guinea fowl (Numida meleagris) during level running on a motorized treadmill. Future research directions for both of these objectives are presented. PMID:21502119

  19. Architecture of coatomer: molecular characterization of delta-COP and protein interactions within the complex

    PubMed Central

    1996-01-01

    Coatomer is a cytosolic protein complex that forms the coat of COP I- coated transport vesicles. In our attempt to analyze the physical and functional interactions between its seven subunits (coat proteins, [COPs] alpha-zeta), we engaged in a program to clone and characterize the individual coatomer subunits. We have now cloned, sequenced, and overexpressed bovine alpha-COP, the 135-kD subunit of coatomer as well as delta-COP, the 57-kD subunit and have identified a yeast homolog of delta-COP by cDNA sequence comparison and by NH2-terminal peptide sequencing. delta-COP shows homologies to subunits of the clathrin adaptor complexes AP1 and AP2. We show that in Golgi-enriched membrane fractions, the protein is predominantly found in COP I-coated transport vesicles and in the budding regions of the Golgi membranes. A knock-out of the delta-COP gene in yeast is lethal. Immunoprecipitation, as well as analysis exploiting the two-hybrid system in a complete COP screen, showed physical interactions between alpha- and epsilon-COPs and between beta- and delta-COPs. Moreover, the two-hybrid system indicates interactions between gamma- and zeta-COPs as well as between alpha- and beta' COPs. We propose that these interactions reflect in vivo associations of those subunits and thus play a functional role in the assembly of coatomer and/or serve to maintain the molecular architecture of the complex. PMID:8858162

  20. Random distributed feedback fibre lasers

    NASA Astrophysics Data System (ADS)

    Turitsyn, Sergei K.; Babin, Sergey A.; Churkin, Dmitry V.; Vatnik, Ilya D.; Nikulin, Maxim; Podivilov, Evgenii V.

    2014-09-01

    The concept of random lasers exploiting multiple scattering of photons in an amplifying disordered medium in order to generate coherent light without a traditional laser resonator has attracted a great deal of attention in recent years. This research area lies at the interface of the fundamental theory of disordered systems and laser science. The idea was originally proposed in the context of astrophysics in the 1960s by V.S. Letokhov, who studied scattering with “negative absorption” of the interstellar molecular clouds. Research on random lasers has since developed into a mature experimental and theoretical field. A simple design of such lasers would be promising for potential applications. However, in traditional random lasers the properties of the output radiation are typically characterized by complex features in the spatial, spectral and time domains, making them less attractive than standard laser systems in terms of practical applications. Recently, an interesting and novel type of one-dimensional random laser that operates in a conventional telecommunication fibre without any pre-designed resonator mirrors-random distributed feedback fibre laser-was demonstrated. The positive feedback required for laser generation in random fibre lasers is provided by the Rayleigh scattering from the inhomogeneities of the refractive index that are naturally present in silica glass. In the proposed laser concept, the randomly backscattered light is amplified through the Raman effect, providing distributed gain over distances up to 100 km. Although an effective reflection due to the Rayleigh scattering is extremely small (˜0.1%), the lasing threshold may be exceeded when a sufficiently large distributed Raman gain is provided. Such a random distributed feedback fibre laser has a number of interesting and attractive features. The fibre waveguide geometry provides transverse confinement, and effectively one-dimensional random distributed feedback leads to the generation

  1. ARC-VM: An architecture real options complexity-based valuation methodology for military systems-of-systems acquisitions

    NASA Astrophysics Data System (ADS)

    Domercant, Jean Charles

    The combination of today's national security environment and mandated acquisition policies makes it necessary for military systems to interoperate with each other to greater degrees. This growing interdependency results in complex Systems-of-Systems (SoS) that only continue to grow in complexity to meet evolving capability needs. Thus, timely and affordable acquisition becomes more difficult, especially in the face of mounting budgetary pressures. To counter this, architecting principles must be applied to SoS design. The research objective is to develop an Architecture Real Options Complexity-Based Valuation Methodology (ARC-VM) suitable for acquisition-level decision making, where there is a stated desire for more informed tradeoffs between cost, schedule, and performance during the early phases of design. First, a framework is introduced to measure architecture complexity as it directly relates to military SoS. Development of the framework draws upon a diverse set of disciplines, including Complexity Science, software architecting, measurement theory, and utility theory. Next, a Real Options based valuation strategy is developed using techniques established for financial stock options that have recently been adapted for use in business and engineering decisions. The derived complexity measure provides architects with an objective measure of complexity that focuses on relevant complex system attributes. These attributes are related to the organization and distribution of SoS functionality and the sharing and processing of resources. The use of Real Options provides the necessary conceptual and visual framework to quantifiably and traceably combine measured architecture complexity, time-valued performance levels, as well as programmatic risks and uncertainties. An example suppression of enemy air defenses (SEAD) capability demonstrates the development and usefulness of the resulting architecture complexity & Real Options based valuation methodology. Different

  2. Hierarchical structures made of proteins. The complex architecture of spider webs and their constituent silk proteins.

    PubMed

    Heim, Markus; Römer, Lin; Scheibel, Thomas

    2010-01-01

    Biopolymers fulfil a variety of different functions in nature. They conduct various processes inside and outside cells and organisms, with a functionality ranging from storage of information to stabilization, protection, shaping, transport, cellular division, or movement of whole organisms. Within the plethora of biopolymers, the most sophisticated group is of proteinaceous origin: the cytoskeleton of a cell is made of protein filaments that aid in pivotal processes like intracellular transport, movement, and cell division; geckos use a distinct arrangement of keratin-like filaments on their toes which enable them to walk up smooth surfaces, such as walls, and even upside down across ceilings; and spiders spin silks that are extra-corporally used for protection of offspring and construction of complex prey traps. The following tutorial review describes the hierarchical organization of protein fibers, using spider dragline silk as an example. The properties of a dragline silk thread originate from the strictly controlled assembly of the underlying protein chains. The assembly procedure leads to protein fibers showing a complex hierarchical organization comprising three different structural phases. This structural organization is responsible for the outstanding mechanical properties of individual fibers, which out-compete even those of high-performance artificial fibers like Kevlar. Web-weaving spiders produce, in addition to dragline silk, other silks with distinct properties, based on slightly variant constituent proteins--a feature that allows construction of highly sophisticated spider webs with well designed architectures and with optimal mechanical properties for catching prey.

  3. Proteins with complex architecture as potential targets for drug design: a case study of Mycobacterium tuberculosis.

    PubMed

    Mészáros, Bálint; Tóth, Judit; Vértessy, Beáta G; Dosztányi, Zsuzsanna; Simon, István

    2011-07-01

    Lengthy co-evolution of Homo sapiens and Mycobacterium tuberculosis, the main causative agent of tuberculosis, resulted in a dramatically successful pathogen species that presents considerable challenge for modern medicine. The continuous and ever increasing appearance of multi-drug resistant mycobacteria necessitates the identification of novel drug targets and drugs with new mechanisms of action. However, further insights are needed to establish automated protocols for target selection based on the available complete genome sequences. In the present study, we perform complete proteome level comparisons between M. tuberculosis, mycobacteria, other prokaryotes and available eukaryotes based on protein domains, local sequence similarities and protein disorder. We show that the enrichment of certain domains in the genome can indicate an important function specific to M. tuberculosis. We identified two families, termed pkn and PE/PPE that stand out in this respect. The common property of these two protein families is a complex domain organization that combines species-specific regions, commonly occurring domains and disordered segments. Besides highlighting promising novel drug target candidates in M. tuberculosis, the presented analysis can also be viewed as a general protocol to identify proteins involved in species-specific functions in a given organism. We conclude that target selection protocols should be extended to include proteins with complex domain architectures instead of focusing on sequentially unique and essential proteins only.

  4. Architecture of TFIIIC and its role in RNA polymerase III pre-initiation complex assembly

    NASA Astrophysics Data System (ADS)

    Male, Gary; von Appen, Alexander; Glatt, Sebastian; Taylor, Nicholas M. I.; Cristovao, Michele; Groetsch, Helga; Beck, Martin; Müller, Christoph W.

    2015-06-01

    In eukaryotes, RNA Polymerase III (Pol III) is specifically responsible for transcribing genes encoding tRNAs and other short non-coding RNAs. The recruitment of Pol III to tRNA-encoding genes requires the transcription factors (TF) IIIB and IIIC. TFIIIC has been described as a conserved, multi-subunit protein complex composed of two subcomplexes, called τA and τB. How these two subcomplexes are linked and how their interaction affects the formation of the Pol III pre-initiation complex (PIC) is poorly understood. Here we use chemical crosslinking mass spectrometry and determine the molecular architecture of TFIIIC. We further report the crystal structure of the essential TPR array from τA subunit τ131 and characterize its interaction with a central region of τB subunit τ138. The identified τ131-τ138 interacting region is essential in vivo and overlaps with TFIIIB-binding sites, revealing a crucial interaction platform for the regulation of tRNA transcription initiation.

  5. A reciprocal cross design to map the genetic architecture of complex traits in apomictic plants.

    PubMed

    Yin, Danni; Zhu, Xuli; Jiang, Libo; Zhang, Jian; Zeng, Yanru; Wu, Rongling

    2015-02-01

    Many higher plants of economic and biological importance undergo apomixis in which the maternal tissue of the ovule forms a seed, without experiencing meiosis and fertilization. This feature of apomixis has made it difficult to perform linkage mapping which relies on meiotic recombination. Here, we describe a computational model for mapping quantitative trait loci (QTLs) that control complex traits in apomictic plants. The model is founded on the mixture model-based likelihood in which maternal genotypes are dissolved into two possible components generated by meiotic and apomictic processes, respectively. The EM algorithm was implemented to discern meiotic and apomictic genotypes and, therefore, allow the marker-QTL linkage relationship to be estimated. By capitalizing on reciprocal crosses, the model is renovated to estimate and test imprinting effects of QTLs, providing a better gateway to characterize the genetic architecture of complex traits. The model was validated through computer simulation and further demonstrated for its usefulness by analyzing a real data for an apomictic woody plant. The model has for the first time provided a unique tool for genetic mapping in apomictic plants.

  6. Using cognitive architectures to study issues in team cognition in a complex task environment

    NASA Astrophysics Data System (ADS)

    Smart, Paul R.; Sycara, Katia; Tang, Yuqing

    2014-05-01

    Cognitive social simulation is a computer simulation technique that aims to improve our understanding of the dynamics of socially-situated and socially-distributed cognition. This makes cognitive social simulation techniques particularly appealing as a means to undertake experiments into team cognition. The current paper reports on the results of an ongoing effort to develop a cognitive social simulation capability that can be used to undertake studies into team cognition using the ACT-R cognitive architecture. This capability is intended to support simulation experiments using a team-based problem solving task, which has been used to explore the effect of different organizational environments on collective problem solving performance. The functionality of the ACT-R-based cognitive social simulation capability is presented and a number of areas of future development work are outlined. The paper also describes the motivation for adopting cognitive architectures in the context of social simulation experiments and presents a number of research areas where cognitive social simulation may be useful in developing a better understanding of the dynamics of team cognition. These include the use of cognitive social simulation to study the role of cognitive processes in determining aspects of communicative behavior, as well as the impact of communicative behavior on the shaping of task-relevant cognitive processes (e.g., the social shaping of individual and collective memory as a result of communicative exchanges). We suggest that the ability to perform cognitive social simulation experiments in these areas will help to elucidate some of the complex interactions that exist between cognitive, social, technological and informational factors in the context of team-based problem-solving activities.

  7. Human skeletal muscle architecture studied in vivo by non-invasive imaging techniques: functional significance and applications.

    PubMed

    Narici, M

    1999-04-01

    The internal architecture plays an essential role in determining the functional features of skeletal muscle. Both length-force and force-velocity relationships depend on the spatial arrangement of muscle fibres in skeletal muscle. The degree of muscle pennation determines both the amount of contractile tissue packed along the tendons and fibre length, and is reflected by the force-generating capacity and shortening velocity of the muscle and by the elastic properties of the muscle-tendon complex. Until recently, knowledge on human muscle architecture was based on measurements performed on cadavers, whose muscle fibres were often shrunk by the preserving medium and by age. With the introduction of non-invasive imaging techniques, it has become possible to study muscle architecture in vivo at rest and the changes thereof upon contraction. This paper discusses the applications of these techniques, namely ultrasonography and nuclear magnetic resonance imaging, and their relevance in physiology and biomechanics.

  8. Exploring architecture of xyloglucan cellulose nanocrystal complexes through enzyme susceptibility at different adsorption regimes.

    PubMed

    Dammak, Abir; Quémener, Bernard; Bonnin, Estelle; Alvarado, Camille; Bouchet, Brigitte; Villares, Ana; Moreau, Céline; Cathala, Bernard

    2015-02-09

    Xyloglucan (XG) is believed to act as a cementing material that contributes to the cross-linking and mechanical properties of the cellulose framework in plant cell walls. XG can adsorb to the cellulose nanocrystal (CNC) surface in vitro in order to simulate this in vivo relationship. The target of our work was to investigate the sorption behavior of tamarind seed XG on CNC extracted from cotton linters at different XG/CNC concentration ratios, that is, different adsorption regimes regarding the XG-CNC complex organization and the enzymatic susceptibility of XG. First, we determined the adsorption isotherm. Second, XG-CNC complexes were enzymatically hydrolyzed using a xyloglucan-specific endoglucanase in order to quantify the different XG fractions involved in binding to CNC and to determine adsorption regimes, that is, presence of loops, tails, and trains. Finally, the architecture of the XG-CNC complex was investigated by transmission electron microscopy imaging of negatively stained XG-CNC suspensions and XG immunolabeled suspensions at different XG/CNC concentration ratios, both before and after xyloglucanase hydrolysis process. This study revealed that an increasing XG/CNC concentration ratio led to a change in the XG binding organization to CNC. At low XG/CNC concentration ratios, almost all XG chains were bound as trains to the CNC surface. In contrast, at increasing XG/CNC concentration ratios, the proportion of loops and tails increases. The organization change induces CNC aggregation to form a cellulose/XG network at low XG/CNC regimes, whereas CNC remains in the form of individual particles at higher XG/CNC regimes. Results are discussed both regarding the biological role of XG in plant cell walls and in the perspective of designing new biobased materials.

  9. A Low-Complexity Euclidean Orthogonal LDPC Architecture for Low Power Applications

    PubMed Central

    Revathy, M.; Saravanan, R.

    2015-01-01

    Low-density parity-check (LDPC) codes have been implemented in latest digital video broadcasting, broadband wireless access (WiMax), and fourth generation of wireless standards. In this paper, we have proposed a high efficient low-density parity-check code (LDPC) decoder architecture for low power applications. This study also considers the design and analysis of check node and variable node units and Euclidean orthogonal generator in LDPC decoder architecture. The Euclidean orthogonal generator is used to reduce the error rate of the proposed LDPC architecture, which can be incorporated between check and variable node architecture. This proposed decoder design is synthesized on Xilinx 9.2i platform and simulated using Modelsim, which is targeted to 45 nm devices. Synthesis report proves that the proposed architecture greatly reduces the power consumption and hardware utilizations on comparing with different conventional architectures. PMID:26065017

  10. A Low-Complexity Euclidean Orthogonal LDPC Architecture for Low Power Applications.

    PubMed

    Revathy, M; Saravanan, R

    2015-01-01

    Low-density parity-check (LDPC) codes have been implemented in latest digital video broadcasting, broadband wireless access (WiMax), and fourth generation of wireless standards. In this paper, we have proposed a high efficient low-density parity-check code (LDPC) decoder architecture for low power applications. This study also considers the design and analysis of check node and variable node units and Euclidean orthogonal generator in LDPC decoder architecture. The Euclidean orthogonal generator is used to reduce the error rate of the proposed LDPC architecture, which can be incorporated between check and variable node architecture. This proposed decoder design is synthesized on Xilinx 9.2i platform and simulated using Modelsim, which is targeted to 45 nm devices. Synthesis report proves that the proposed architecture greatly reduces the power consumption and hardware utilizations on comparing with different conventional architectures.

  11. Obesity and genomics: role of technology in unraveling the complex genetic architecture of obesity.

    PubMed

    Apalasamy, Yamunah Devi; Mohamed, Zahurin

    2015-04-01

    Obesity is a complex and multifactorial disease that occurs as a result of the interaction between "obesogenic" environmental factors and genetic components. Although the genetic component of obesity is clear from the heritability studies, the genetic basis remains largely elusive. Successes have been achieved in identifying the causal genes for monogenic obesity using animal models and linkage studies, but these approaches are not fruitful for polygenic obesity. The developments of genome-wide association approach have brought breakthrough discovery of genetic variants for polygenic obesity where tens of new susceptibility loci were identified. However, the common SNPs only accounted for a proportion of heritability. The arrival of NGS technologies and completion of 1000 Genomes Project have brought other new methods to dissect the genetic architecture of obesity, for example, the use of exome genotyping arrays and deep sequencing of candidate loci identified from GWAS to study rare variants. In this review, we summarize and discuss the developments of these genetic approaches in human obesity.

  12. Architecture of the nasal complex in neanderthals: comparison with other hominids and phylogenetic significance.

    PubMed

    Schwartz, Jeffrey H; Tattersall, Ian; Teschler-Nicola, Maria

    2008-11-01

    Although paranasal sinus configuration has occasionally been the focus in analyses of the phylogenetic relationships of various primates, other elements of the region of the nasal fossa--in particular, the turbinals--have received far less attention. A preliminary study of Neanderthal cranial morphology revealed the presence of an apparently unique configuration of the lateral wall of the nasal cavity: namely, in the region in which in Homo sapiens the anterior extremity of the maxilloturbinal (also referred to as the inferior nasal concha) articulates with the internal surface of the maxilla along a relatively anteroposteriorly long and essentially horizontally oriented conchal crest, there exists a vertically oriented thickening that protrudes medially into the nasal cavity (Schwartz and Tattersall, Proc Natl Acad Sci USA 1996; 93:10852-10854). Subsequent citations of this report either claimed that this "medial projection" in Neanderthals is merely an enlarged maxilloturbinal or mistakenly identified as this structure the base of a maxilloturbinal that had fused to the lateral wall of the nasal cavity and subsequently broken off. In light of the potential significance that any novel configuration of the nasal complex architecture may have for elucidating hominid evolution, we present here a comparative overview of this region in fossil and extant large-bodied hominoids, and demonstrate that Neanderthals do indeed possess a configuration that is unique among hominids. Copyright 2008 Wiley-Liss, Inc.

  13. Molecular architecture of the human sperm IZUMO1 and egg JUNO fertilization complex.

    PubMed

    Aydin, Halil; Sultana, Azmiri; Li, Sheng; Thavalingam, Annoj; Lee, Jeffrey E

    2016-06-23

    Fertilization is an essential biological process in sexual reproduction and comprises a series of molecular interactions between the sperm and egg. The fusion of the haploid spermatozoon and oocyte is the culminating event in mammalian fertilization, enabling the creation of a new, genetically distinct diploid organism. The merger of two gametes is achieved through a two-step mechanism in which the sperm protein IZUMO1 on the equatorial segment of the acrosome-reacted sperm recognizes its receptor, JUNO, on the egg surface. This recognition is followed by the fusion of the two plasma membranes. IZUMO1 and JUNO proteins are indispensable for fertilization, as constitutive knockdown of either protein results in mice that are healthy but infertile. Despite their central importance in reproductive medicine, the molecular architectures of these proteins and the details of their functional roles in fertilization are not known. Here we present the crystal structures of human IZUMO1 and JUNO in unbound and bound conformations. The human IZUMO1 structure exhibits a distinct boomerang shape and provides structural insights into the IZUMO family of proteins. Human IZUMO1 forms a high-affinity complex with JUNO and undergoes a major conformational change within its N-terminal domain upon binding to the egg-surface receptor. Our results provide insights into the molecular basis of sperm-egg recognition, cross-species fertilization, and the barrier to polyspermy, thereby promising benefits for the rational development of non-hormonal contraceptives and fertility treatments for humans and other mammals.

  14. Cigarette smoking reprograms apical junctional complex molecular architecture in the human airway epithelium in vivo.

    PubMed

    Shaykhiev, Renat; Otaki, Fouad; Bonsu, Prince; Dang, David T; Teater, Matthew; Strulovici-Barel, Yael; Salit, Jacqueline; Harvey, Ben-Gary; Crystal, Ronald G

    2011-03-01

    The apical junctional complex (AJC), composed of tight and adherens junctions, maintains epithelial barrier function. Since cigarette smoking and chronic obstructive pulmonary disease (COPD), the major smoking-induced disease, are associated with increased lung epithelial permeability, we hypothesized that smoking alters the transcriptional program regulating airway epithelial AJC integrity. Transcriptome analysis revealed global down-regulation of physiological AJC gene expression in the airway epithelium of healthy smokers (n = 59) compared to nonsmokers (n = 53) in association with changes in canonical epithelial differentiation pathways such as PTEN signaling accompanied by induction of cancer-related AJC components. The overall expression of AJC-related genes was further decreased in COPD smokers (n = 23). Exposure of airway epithelial cells to cigarette smoke extract in vitro resulted in down-regulation of several AJC genes paralleled by decreased transepithelial resistance. Thus, cigarette smoking induces transcriptional reprogramming of airway epithelial AJC architecture from its physiological pattern necessary for barrier function toward a disease-associated molecular phenotype.

  15. Continuous distribution model for the investigation of complex molecular architectures near interfaces with scattering techniques

    SciTech Connect

    Shekhar, Prabhanshu; Nanda, Hirsh; Heinrich, Frank; Loesche, Mathias

    2011-11-15

    Biological membranes are composed of a thermally disordered lipid matrix and therefore require non-crystallographic scattering approaches for structural characterization with x-rays or neutrons. Here we develop a continuous distribution (CD) model to refine neutron or x-ray reflectivity data from complex architectures of organic molecules. The new model is a flexible implementation of the composition-space refinement of interfacial structures to constrain the resulting scattering length density profiles. We show this model increases the precision with which molecular components may be localized within a sample, with a minimal use of free model parameters. We validate the new model by parameterizing all-atom molecular dynamics (MD) simulations of bilayers and by evaluating the neutron reflectivity of a phospholipid bilayer physisorbed to a solid support. The determination of the structural arrangement of a sparsely-tethered bilayer lipid membrane (stBLM) comprised of a multi-component phospholipid bilayer anchored to a gold substrate by a thiolated oligo(ethylene oxide) linker is also demonstrated. From the model we extract the bilayer composition and density of tether points, information which was previously inaccessible for stBLM systems. The new modeling strategy has been implemented into the ga lowbar refl reflectivity data evaluation suite, available through the National Institute of Standards and Technology (NIST) Center for Neutron Research (NCNR).

  16. The Cdc48-Vms1 complex maintains 26S proteasome architecture.

    PubMed

    Tran, Joseph R; Brodsky, Jeffrey L

    2014-03-15

    The 26S proteasome is responsible for most regulated protein turnover and for the degradation of aberrant proteins in eukaryotes. The assembly of this ~2.5 MDa multicatalytic protease requires several dedicated chaperones and, once assembled, substrate selectivity is mediated by ubiquitin conjugation. After modification with ubiquitin, substrates are escorted to the proteasome by myriad factors, including Cdc48 (cell-division cycle 48). Cdc48 also associates with numerous cofactors, but, to date, it is unclear whether each cofactor facilitates proteasome delivery. We discovered that yeast lacking a conserved Cdc48 cofactor, Vms1 [VCP (valosin-containing protein)/Cdc48-associated mitochondrial stress-responsive], accumulate proteasome-targeted ubiquitinated proteins. Vms1 mutant cells also contain elevated levels of unassembled 20S proteasome core particles and select 19S cap subunits. In addition, we found that the ability of Vms1 to support 26S proteasome assembly requires Cdc48 interaction, and that the loss of Vms1 reduced 26S proteasome levels and cell viability after prolonged culture in the stationary phase. The results of the present study highlight an unexpected link between the Cdc48-Vms1 complex and the preservation of proteasome architecture, and indicate how perturbed proteasome assembly affects the turnover of ubiquitinated proteins and maintains viability in aging cells.

  17. The Cdc48–Vms1 complex maintains 26S proteasome architecture

    PubMed Central

    Tran, Joseph R.; Brodsky, Jeffrey L.

    2014-01-01

    The 26S proteasome is responsible for most regulated protein turnover and for the degradation of aberrant proteins in eukaryotes. The assembly of this ~2.5 MDa multicatalytic protease requires several dedicated chaperones and, once assembled, substrate selectivity is mediated by ubiquitin conjugation. After modification with ubiquitin, substrates are escorted to the proteasome by myriad factors, including Cdc48 (cell-division cycle 48). Cdc48 also associates with numerous cofactors, but, to date, it is unclear whether each cofactor facilitates proteasome delivery. We discovered that yeast lacking a conserved Cdc48 cofactor, Vms1 [VCP (valosin-containing protein)/Cdc48-associated mitochondrial stress-responsive], accumulate proteasome-targeted ubiquitinated proteins. Vms1 mutant cells also contain elevated levels of unassembled 20S proteasome core particles and select 19S cap subunits. In addition, we found that the ability of Vms1 to support 26S proteasome assembly requires Cdc48 interaction, and that the loss of Vms1 reduced 26S proteasome levels and cell viability after prolonged culture in the stationary phase. The results of the present study highlight an unexpected link between the Cdc48–Vms1 complex and the preservation of proteasome architecture, and indicate how perturbed proteasome assembly affects the turnover of ubiquitinated proteins and maintains viability in aging cells. PMID:24351022

  18. Effects of ghrelin on the structural complexity of exocrine pancreas tissue architecture.

    PubMed

    Pantic, Igor; Nesic, Dejan; Stevanovic, Darko; Starcevic, Vesna; Pantic, Senka; Trajkovic, Vladimir

    2013-06-01

    Recent studies have shown that ghrelin increases pancreatic exocrine secretion. However, the potential effects of ghrelin on the morphology of exocrine pancreas (EP) remain unknown. In this work, using fractal analysis, we demonstrate that centrally administered ghrelin increases structural complexity and tissue disorder in rat EP. The study was carried out on a total of 40 male Wistar rats divided into four groups (n = 10): ghrelin-treated animals (average age, 1.5 months), ghrelin-treated animals (8.5 months), and controls (1.5 and 8.5 months). The pancreas tissue sections were stained with hematoxylin/eosin and visualized by light microscopy. For each animal, the average values of tissue fractal dimension, lacunarity, as well as parameters of co-occurrence matrix texture, were determined using tissue digital micrographs. The results indicate that ghrelin administration increases EP fractal dimension and textural entropy, and decreases lacunarity, regardless of the age. To our knowledge, this is the first study to investigate the effects of ghrelin on the morphological properties of pancreatic tissue, and also the first to apply fractal and textural analysis methods in quantification of EP tissue architecture.

  19. Continuous distribution model for the investigation of complex molecular architectures near interfaces with scattering techniques

    NASA Astrophysics Data System (ADS)

    Shekhar, Prabhanshu; Nanda, Hirsh; Lösche, Mathias; Heinrich, Frank

    2011-11-01

    Biological membranes are composed of a thermally disordered lipid matrix and therefore require non-crystallographic scattering approaches for structural characterization with x-rays or neutrons. Here we develop a continuous distribution (CD) model to refine neutron or x-ray reflectivity data from complex architectures of organic molecules. The new model is a flexible implementation of the composition-space refinement of interfacial structures to constrain the resulting scattering length density profiles. We show this model increases the precision with which molecular components may be localized within a sample, with a minimal use of free model parameters. We validate the new model by parameterizing all-atom molecular dynamics (MD) simulations of bilayers and by evaluating the neutron reflectivity of a phospholipid bilayer physisorbed to a solid support. The determination of the structural arrangement of a sparsely-tethered bilayer lipid membrane (stBLM) comprised of a multi-component phospholipid bilayer anchored to a gold substrate by a thiolated oligo(ethylene oxide) linker is also demonstrated. From the model we extract the bilayer composition and density of tether points, information which was previously inaccessible for stBLM systems. The new modeling strategy has been implemented into the ga_refl reflectivity data evaluation suite, available through the National Institute of Standards and Technology (NIST) Center for Neutron Research (NCNR).

  20. Molecular Architecture of the Transport Channel of the Nuclear Pore Complex

    PubMed Central

    Solmaz, Sozanne R.; Chauhan, Radha; Blobel, Günter; Melčák, Ivo

    2012-01-01

    SUMMARY The nuclear pore complex encloses a central channel for nucleocytoplasmic transport, which is thought to consist of three nucleoporins, Nup54, Nup58, and Nup62. However, the structure and composition of the channel are elusive. We determined the crystal structures of the interacting domains between these nucleoporins and pieced together the molecular architecture of the mammalian transport channel. Located in the channel midplane is a flexible Nup54·Nup58 ring that can undergo large rearrangements yielding diameter changes from ~20 to ~40 nm. Nup62·Nup54 triple helices project alternately up and down from either side of the midplane ring and form nucleoplasmic and cytoplasmic entries. The channel consists of as many as 224 copies of the three nucleoporins, amounting to a molar mass of 12.3 MDa and contributing 256 phenylalanine-glycine repeat regions. We propose that the occupancy of these repeat regions with transport receptors modulates ring diameter and transport activity. PMID:22036567

  1. 3D Printing of Photocurable Cellulose Nanocrystal Composite for Fabrication of Complex Architectures via Stereolithography.

    PubMed

    Palaganas, Napolabel B; Mangadlao, Joey Dacula; de Leon, Al Christopher C; Palaganas, Jerome O; Pangilinan, Katrina D; Lee, Yan Jie; Advincula, Rigoberto C

    2017-10-04

    The advantages of 3D printing on cost, speed, accuracy, and flexibility have attracted several new applications in various industries especially in the field of medicine where customized solutions are highly demanded. Although this modern fabrication technique offers several benefits, it also poses critical challenges in materials development suitable for industry use. Proliferation of polymers in biomedical application has been severely limited by their inherently weak mechanical properties despite their other excellent attributes. Earlier works on 3D printing of polymers focus mainly on biocompatibility and cellular viability and lack a close attention to produce robust specimens. Prized for superior mechanical strength and inherent stiffness, cellulose nanocrystal (CNC) from abaca plant is incorporated to provide the necessary toughness for 3D printable biopolymer. Hence, this work demonstrates 3D printing of CNC-filled biomaterial with significant improvement in mechanical and surface properties. These findings may potentially pave the way for an alternative option in providing innovative and cost-effective patient-specific solutions to various fields in medical industry. To the best of our knowledge, this work presents the first successful demonstration of 3D printing of CNC nanocomposite hydrogel via stereolithography (SL) forming a complex architecture with enhanced material properties potentially suited for tissue engineering.

  2. Electrospun curcumin-loaded cellulose acetate/polyvinylpyrrolidone fibrous materials with complex architecture and antibacterial activity.

    PubMed

    Tsekova, Petya B; Spasova, Mariya G; Manolova, Nevena E; Markova, Nadya D; Rashkov, Iliya B

    2017-04-01

    Novel fibrous materials from cellulose acetate (CA) and polyvinylpyrrolidone (PVP) containing curcumin (Curc) with original design were prepared by one-pot electrospinning or dual spinneret electrospinning. The electrospun materials were characterized by scanning electron microscopy (SEM), fluorescence microscopy, Fourier transform infrared spectroscopy (FTIR), ultraviolet-visible spectroscopy (UV-Vis), differential scanning calorimetry (DSC), water contact angle measurements, and microbiological tests. It was found that the incorporation of Curc into the CA and PVP solutions resulted in an increase of the solution viscosity and obtaining fibers with larger diameters (ca. 1.5μm) compared to the neat CA (ca. 800nm) and PVP fibers (ca. 500nm). The incorporation of PVP resulted in increased hydrophilicity of the fibers and in faster Curc release. Curc was found in the amorphous state in the Curc-containing fibers and these mats exhibited antibacterial activity against Staphylococcus aureus (S. aureus). The results suggest that, due to their complex architecture, the obtained new antibacterial materials are suitable for wound dressing applications, which necessitate diverse release behaviors of the bioactive compound.

  3. Molybdenum blue: binding to collagen fibres and microcrystal formation.

    PubMed

    Harris, J Robin; Reiber, Andreas; Therese, Helen Annal; Tremel, Wolfgang

    2005-01-01

    Collagen fibres have been shown by transmission electron microscopy to progressively bind the polyoxomolybdate ring-complex, termed molybdenum blue. Nucleation of cuboidal molybdenum blue microcrystals occurs on the surface of the collagen fibres, leading eventually to extensive coating of the fibres with microcrystals.

  4. Fibre-reinforced materials.

    PubMed

    Brown, D

    2000-11-01

    This paper considers the role of fibres in the reinforcement of composite materials, and the significance of the form the fibre takes and the material from which it is made. The current dental applications of fibre reinforcement, including dental cements and splints, fibres made into structures for use in composites, denture bases and the contemporary use of fibres in fixed partial dentures, are reviewed. Their role in biomedical implants is surveyed and their future forecast.

  5. Self-assembly of four new extended architectures based on reduced polyoxometalate clusters and cadmium complexes

    SciTech Connect

    Ma Ying; Li Yangguang; Wang Enbo . E-mail: wangenbo@public.cc.jl.cn; Lu Ying; Wang Xinlong; Xu Xinxin

    2006-08-15

    report four new extended architectures based on reduced polyoxometalate clusters and cadmium complexes. Compounds 1-4 are built of Cd[P{sub 4}Mo{sub 6}]{sub 2} dimers as the basic structural motif and Cd-4,4'-bpy, Cd-phen and Cd-2,2'-bpy complexes as the linkers to constructed novel 2D layer structure.

  6. Volcano-tectonic architecture of a Caldera Complex, Karthala volcano, Grande Comore: new field observations

    NASA Astrophysics Data System (ADS)

    Poppe, S.; Kervyn, M.; Soulé, H.; Cnudde, V.; De Kock, T.; Jacobs, P.

    2012-04-01

    fed small-scale eruptive cones, vertical degassing fissures and former caldera levels. Fissures with active fumaroles inside the two explosive craters and in the area between Choungou Chahalé and Changouméni are indicating a focus area in the hydrothermal activity. It is this hydrothermal system that is suggested to have controlled the phreatic nature of recent eruptions (1991, 2005 and 2007). Several pyroclastic beds and cones affected by block and bomb impacts inside the caldera complex and around the summit area testify the high explosive nature of these recent eruptions, in contrast with the effusive Hawaiian-style character generally associated with Karthala. The orientation of caldera-bounding structures, eruption and fumarolic fissures, dykes as well as the orientation of intra-caldera extensional faults indicate one minor (E-W) and two major volcano-tectonic directions (N-S and N135°S). The latter are concurring with previously identified regional stress orientations and rift zone's orientations on Karthala flanks. Upcoming field work will be dedicated to the exhaustive structural and stratigraphic mapping of Karthala caldera as it provides exceptional exposure to document the internal architecture of an alkali basalt shield volcano and a complex caldera subsidence chronology.

  7. MOLECULAR ARCHITECTURE OF THE HUMAN SPERM IZUMO1 AND EGG JUNO FERTILIZATION COMPLEX

    PubMed Central

    Aydin, Halil; Sultana, Azmiri; Li, Sheng; Thavalingam, Annoj; Lee, Jeffrey E.

    2017-01-01

    Fertilization is an essential biological process in sexual reproduction and comprises a series of molecular interactions between the sperm and egg1,2. The fusion of haploid spermatozoon and oocyte is the culminating event in mammalian fertilization, enabling the creation of a new genetically distinct diploid organism3,4. The merger of two gametes is achieved through a two-step mechanism where the sperm Izumo1 on the equatorial segment of the acrosome-reacted sperm recognizes its receptor Juno, on the egg surface4–6. This is followed by the fusion of two plasma membranes. Izumo1 and Juno proteins are indispensable for fertilization as constitutive knockout of either Izumo1 or Juno result in mice that are healthy but infertile5,6. Despite their central importance in reproductive medicine, the molecular architectures and the details of their functional roles in fertilization are not known. Here, we present the crystal structures of the human Izumo1 and Juno in unbound and bound conformations. The human Izumo1 structure exhibits a distinct boomerang shape and provides the first structural insights into the Izumo family of proteins7. Human Izumo1 forms a high-affinity complex with Juno and undergoes a major conformational change within its N-terminal domain upon binding to the egg-surface receptor. Our results provide new insights into the molecular basis of sperm-egg recognition, cross-species fertilization, and barrier to polyspermy, thus promising benefits for the rational development of novel non-hormonal contraceptives and fertility treatments for humans and other species of mammals. PMID:27309818

  8. Dynamics of the active site architecture in plant-type ferredoxin-NADP(+) reductases catalytic complexes.

    PubMed

    Sánchez-Azqueta, Ana; Catalano-Dupuy, Daniela L; López-Rivero, Arleth; Tondo, María Laura; Orellano, Elena G; Ceccarelli, Eduardo A; Medina, Milagros

    2014-10-01

    Kinetic isotope effects in reactions involving hydride transfer and their temperature dependence are powerful tools to explore dynamics of enzyme catalytic sites. In plant-type ferredoxin-NADP(+) reductases the FAD cofactor exchanges a hydride with the NADP(H) coenzyme. Rates for these processes are considerably faster for the plastidic members (FNR) of the family than for those belonging to the bacterial class (FPR). Hydride transfer (HT) and deuteride transfer (DT) rates for the NADP(+) coenzyme reduction of four plant-type FNRs (two representatives of the plastidic type FNRs and the other two from the bacterial class), and their temperature dependences are here examined applying a full tunnelling model with coupled environmental fluctuations. Parameters for the two plastidic FNRs confirm a tunnelling reaction with active dynamics contributions, but isotope effects on Arrhenius factors indicate a larger contribution for donor-acceptor distance (DAD) dynamics in the Pisum sativum FNR reaction than in the Anabaena FNR reaction. On the other hand, parameters for bacterial FPRs are consistent with passive environmental reorganisation movements dominating the HT coordinate and no contribution of DAD sampling or gating fluctuations. This indicates that active sites of FPRs are more organised and rigid than those of FNRs. These differences must be due to adaptation of the active sites and catalytic mechanisms to fulfil their particular metabolic roles, establishing a compromise between protein flexibility and functional optimisation. Analysis of site-directed mutants in plastidic enzymes additionally indicates the requirement of a minimal optimal architecture in the catalytic complex to provide a favourable gating contribution. Copyright © 2014 Elsevier B.V. All rights reserved.

  9. Linking the genetic architecture of cytosine modifications with human complex traits

    PubMed Central

    Zhang, Xu; Moen, Erika L.; Liu, Cong; Mu, Wenbo; Gamazon, Eric R.; Delaney, Shannon M.; Wing, Claudia; Godley, Lucy A.; Dolan, M. Eileen; Zhang, Wei

    2014-01-01

    Interindividual variation in cytosine modifications could contribute to heterogeneity in disease risks and other complex traits. We assessed the genetic architecture of cytosine modifications at 283 540 CpG sites in lymphoblastoid cell lines (LCLs) derived from independent samples of European and African descent. Our study suggests that cytosine modification variation was primarily controlled in local by single major modification quantitative trait locus (mQTL) and additional minor loci. Local genetic epistasis was detectable for a small proportion of CpG sites, which were enriched by more than 9-fold for CpG sites mapped to population-specific mQTL. Genetically dependent CpG sites whose modification levels negatively (repressive sites) or positively (facilitative sites) correlated with gene expression levels significantly co-localized with transcription factor binding, with the repressive sites predominantly associated with active promoters whereas the facilitative sites rarely at active promoters. Genetically independent repressive or facilitative sites preferentially modulated gene expression variation by influencing local chromatin accessibility, with the facilitative sites primarily antagonizing H3K27me3 and H3K9me3 deposition. In comparison with expression quantitative trait loci (eQTL), mQTL detected from LCLs were enriched in associations for a broader range of disease categories including chronic inflammatory, autoimmune and psychiatric disorders, suggesting that cytosine modification variation, while possesses a degree of cell linage specificity, is more stably inherited over development than gene expression variation. About 11% of unique single-nucleotide polymorphisms reported in the Genome-Wide Association Study Catalog were annotated, 78% as mQTL and 31% as eQTL in LCLs, which covered 37% of the investigated diseases/traits and provided insights to the biological mechanisms. PMID:24943591

  10. Genomic prediction of complex human traits: relatedness, trait architecture and predictive meta-models.

    PubMed

    Spiliopoulou, Athina; Nagy, Reka; Bermingham, Mairead L; Huffman, Jennifer E; Hayward, Caroline; Vitart, Veronique; Rudan, Igor; Campbell, Harry; Wright, Alan F; Wilson, James F; Pong-Wong, Ricardo; Agakov, Felix; Navarro, Pau; Haley, Chris S

    2015-07-15

    We explore the prediction of individuals' phenotypes for complex traits using genomic data. We compare several widely used prediction models, including Ridge Regression, LASSO and Elastic Nets estimated from cohort data, and polygenic risk scores constructed using published summary statistics from genome-wide association meta-analyses (GWAMA). We evaluate the interplay between relatedness, trait architecture and optimal marker density, by predicting height, body mass index (BMI) and high-density lipoprotein level (HDL) in two data cohorts, originating from Croatia and Scotland. We empirically demonstrate that dense models are better when all genetic effects are small (height and BMI) and target individuals are related to the training samples, while sparse models predict better in unrelated individuals and when some effects have moderate size (HDL). For HDL sparse models achieved good across-cohort prediction, performing similarly to the GWAMA risk score and to models trained within the same cohort, which indicates that, for predicting traits with moderately sized effects, large sample sizes and familial structure become less important, though still potentially useful. Finally, we propose a novel ensemble of whole-genome predictors with GWAMA risk scores and demonstrate that the resulting meta-model achieves higher prediction accuracy than either model on its own. We conclude that although current genomic predictors are not accurate enough for diagnostic purposes, performance can be improved without requiring access to large-scale individual-level data. Our methodologically simple meta-model is a means of performing predictive meta-analysis for optimizing genomic predictions and can be easily extended to incorporate multiple population-level summary statistics or other domain knowledge.

  11. Genomic prediction of complex human traits: relatedness, trait architecture and predictive meta-models

    PubMed Central

    Spiliopoulou, Athina; Nagy, Reka; Bermingham, Mairead L.; Huffman, Jennifer E.; Hayward, Caroline; Vitart, Veronique; Rudan, Igor; Campbell, Harry; Wright, Alan F.; Wilson, James F.; Pong-Wong, Ricardo; Agakov, Felix; Navarro, Pau; Haley, Chris S.

    2015-01-01

    We explore the prediction of individuals' phenotypes for complex traits using genomic data. We compare several widely used prediction models, including Ridge Regression, LASSO and Elastic Nets estimated from cohort data, and polygenic risk scores constructed using published summary statistics from genome-wide association meta-analyses (GWAMA). We evaluate the interplay between relatedness, trait architecture and optimal marker density, by predicting height, body mass index (BMI) and high-density lipoprotein level (HDL) in two data cohorts, originating from Croatia and Scotland. We empirically demonstrate that dense models are better when all genetic effects are small (height and BMI) and target individuals are related to the training samples, while sparse models predict better in unrelated individuals and when some effects have moderate size (HDL). For HDL sparse models achieved good across-cohort prediction, performing similarly to the GWAMA risk score and to models trained within the same cohort, which indicates that, for predicting traits with moderately sized effects, large sample sizes and familial structure become less important, though still potentially useful. Finally, we propose a novel ensemble of whole-genome predictors with GWAMA risk scores and demonstrate that the resulting meta-model achieves higher prediction accuracy than either model on its own. We conclude that although current genomic predictors are not accurate enough for diagnostic purposes, performance can be improved without requiring access to large-scale individual-level data. Our methodologically simple meta-model is a means of performing predictive meta-analysis for optimizing genomic predictions and can be easily extended to incorporate multiple population-level summary statistics or other domain knowledge. PMID:25918167

  12. Strategies for concurrent processing of complex algorithms in data driven architectures

    NASA Technical Reports Server (NTRS)

    Stoughton, John W.; Mielke, Roland R.

    1987-01-01

    The results of ongoing research directed at developing a graph theoretical model for describing data and control flow associated with the execution of large grained algorithms in a spatial distributed computer environment is presented. This model is identified by the acronym ATAMM (Algorithm/Architecture Mapping Model). The purpose of such a model is to provide a basis for establishing rules for relating an algorithm to its execution in a multiprocessor environment. Specifications derived from the model lead directly to the description of a data flow architecture which is a consequence of the inherent behavior of the data and control flow described by the model. The purpose of the ATAMM based architecture is to optimize computational concurrency in the multiprocessor environment and to provide an analytical basis for performance evaluation. The ATAMM model and architecture specifications are demonstrated on a prototype system for concept validation.

  13. Strategies for concurrent processing of complex algorithms in data driven architectures

    NASA Technical Reports Server (NTRS)

    Stoughton, John W.; Mielke, Roland R.

    1988-01-01

    Research directed at developing a graph theoretical model for describing data and control flow associated with the execution of large grained algorithms in a special distributed computer environment is presented. This model is identified by the acronym ATAMM which represents Algorithms To Architecture Mapping Model. The purpose of such a model is to provide a basis for establishing rules for relating an algorithm to its execution in a multiprocessor environment. Specifications derived from the model lead directly to the description of a data flow architecture which is a consequence of the inherent behavior of the data and control flow described by the model. The purpose of the ATAMM based architecture is to provide an analytical basis for performance evaluation. The ATAMM model and architecture specifications are demonstrated on a prototype system for concept validation.

  14. Early activation of quorum sensing in Pseudomonas aeruginosa reveals the architecture of a complex regulon

    PubMed Central

    Schuster, Martin; Greenberg, E Peter

    2007-01-01

    Background Quorum-sensing regulation of gene expression in Pseudomonas aeruginosa is complex. Two interconnected acyl-homoserine lactone (acyl-HSL) signal-receptor pairs, 3-oxo-dodecanoyl-HSL-LasR and butanoyl-HSL-RhlR, regulate more than 300 genes. The induction of most of the genes is delayed during growth of P. aeruginosa in complex medium, cannot be advanced by addition of exogenous signal, and requires additional regulatory components. Many of these late genes can be induced by addition of signals early by using specific media conditions. While several factors super-regulate the quorum receptors, others may co-regulate target promoters or may affect expression posttranscriptionally. Results To better understand the contributions of super-regulation and co-regulation to quorum-sensing gene expression, and to better understand the general structure of the quorum sensing network, we ectopically expressed the two receptors (in the presence of their cognate signals) and another component that affects quorum sensing, the stationary phase sigma factor RpoS, early in growth. We determined the effect on target gene expression by microarray and real-time PCR analysis. Our results show that many target genes (e.g. lasB and hcnABC) are directly responsive to receptor protein levels. Most genes (e.g. lasA, lecA, and phnAB), however, are not significantly affected, although at least some of these genes are directly regulated by quorum sensing. The majority of promoters advanced by RhlR appeared to be regulated directly, which allowed us to build a RhlR consensus sequence. Conclusion The direct responsiveness of many quorum sensing target genes to receptor protein levels early in growth confirms the role of super-regulation in quorum sensing gene expression. The observation that the induction of most target genes is not affected by signal or receptor protein levels indicates that either target promoters are co-regulated by other transcription factors, or that expression is

  15. A Comprehensive Image-based Phenomic Analysis Reveals the Complex Genetic Architecture of Shoot Growth Dynamics in Rice (Oryza sativa).

    PubMed

    Campbell, Malachy T; Du, Qian; Liu, Kan; Brien, Chris J; Berger, Bettina; Zhang, Chi; Walia, Harkamal

    2017-07-01

    Early vigor is an important trait for many rice ( L.)-growing environments. However, genetic characterization and improvement for early vigor is hindered by the temporal nature of the trait and strong genotype × environment effects. We explored the genetic architecture of shoot growth dynamics during the early and active tillering stages by applying a functional modeling and genomewide association (GWAS) mapping approach on a diversity panel of ∼360 rice accessions. Multiple loci with small effects on shoot growth trajectory were identified, indicating a complex polygenic architecture. Natural variation for shoot growth dynamics was assessed in a subset of 31 accessions using RNA sequencing and hormone quantification. These analyses yielded a gibberellic acid (GA) catabolic gene, , which could influence GA levels to regulate vigor in the early tillering stage. Given the complex genetic architecture of shoot growth dynamics, the potential of genomic selection (GS) for improving early vigor was explored using all 36,901 single-nucleotide polymorphisms (SNPs) as well as several subsets of the most significant SNPs from GWAS. Shoot growth trajectories could be predicted with reasonable accuracy using the 50 most significant SNPs from GWAS (0.37-0.53); however, the accuracy of prediction was improved by including more markers, which indicates that GS may be an effective strategy for improving shoot growth dynamics during the vegetative growth stage. This study provides insights into the complex genetic architecture and molecular mechanisms underlying early shoot growth dynamics and provides a foundation for improving this complex trait in rice. Copyright © 2017 Crop Science Society of America.

  16. The value and cost of complexity in predictive modelling: role of tissue anisotropic conductivity and fibre tracts in neuromodulation

    NASA Astrophysics Data System (ADS)

    Salman Shahid, Syed; Bikson, Marom; Salman, Humaira; Wen, Peng; Ahfock, Tony

    2014-06-01

    Objectives. Computational methods are increasingly used to optimize transcranial direct current stimulation (tDCS) dose strategies and yet complexities of existing approaches limit their clinical access. Since predictive modelling indicates the relevance of subject/pathology based data and hence the need for subject specific modelling, the incremental clinical value of increasingly complex modelling methods must be balanced against the computational and clinical time and costs. For example, the incorporation of multiple tissue layers and measured diffusion tensor (DTI) based conductivity estimates increase model precision but at the cost of clinical and computational resources. Costs related to such complexities aggregate when considering individual optimization and the myriad of potential montages. Here, rather than considering if additional details change current-flow prediction, we consider when added complexities influence clinical decisions. Approach. Towards developing quantitative and qualitative metrics of value/cost associated with computational model complexity, we considered field distributions generated by two 4 × 1 high-definition montages (m1 = 4 × 1 HD montage with anode at C3 and m2 = 4 × 1 HD montage with anode at C1) and a single conventional (m3 = C3-Fp2) tDCS electrode montage. We evaluated statistical methods, including residual error (RE) and relative difference measure (RDM), to consider the clinical impact and utility of increased complexities, namely the influence of skull, muscle and brain anisotropic conductivities in a volume conductor model. Main results. Anisotropy modulated current-flow in a montage and region dependent manner. However, significant statistical changes, produced within montage by anisotropy, did not change qualitative peak and topographic comparisons across montages. Thus for the examples analysed, clinical decision on which dose to select would not be altered by the omission of anisotropic brain conductivity

  17. Dietary fibre and colonic neoplasia.

    PubMed Central

    Freeman, H J

    1979-01-01

    Dietary plant fibre, or plantix, is thought to play a significant role in the pathogenesis of colon cancer in humans. It is a complex polymeric substance that has several distinct components resistant to hydrolysis by the digestive enzymes of humans. These components include cellulose, hemicelluloses, pectins, lignin, gums, mucilages and, in certain instances, algal polysaccharides. These polymers have different physicochemical properties, and recent evidence from experimental studies in animals treated with carcinogens suggests that some may exert protective effects in the intestine and others may enhance colon carcinogenesis. This review synthesizes information on the chemical composition, methods of analysis and physicochemical properties of dietary plant fibre and reviews available studies examining the role of fibre in colonic neoplasia in animals and humans. PMID:466603

  18. Insights into the complex 3-D architecture of thylakoid membranes in unicellular cyanobacterium Cyanothece sp. ATCC 51142.

    PubMed

    Liberton, Michelle; Austin, Jotham R; Berg, R Howard; Pakrasi, Himadri B

    2011-04-01

    In cyanobacteria and chloroplasts, thylakoids are the complex internal membrane system where the light reactions of oxygenic photosynthesis occur. In plant chloroplasts, thylakoids are differentiated into a highly interconnected system of stacked grana and unstacked stroma membranes. In contrast, in cyanobacteria, the evolutionary progenitors of chloroplasts, thylakoids do not routinely form stacked and unstacked regions, and the architecture of the thylakoid membrane systems is only now being described in detail in these organisms. We used electron tomography to examine the thylakoid membrane systems in one cyanobacterium, Cyanothece sp. ATCC 51142. Our data showed that thylakoids form a complicated branched network with a rudimentary quasi-helical architecture in this organism. A well accepted helical model of grana-stroma architecture of plant thylakoids describes an organization in which stroma thylakoids wind around stacked granum in right-handed spirals. Here we present data showing that the simplified helical architecture in Cyanothece 51142 is left-handed in nature. We propose a model comparing the thylakoid membranes in plants and this cyanobacterium in which the system in Cyanothece 51142 is composed of non-stacked membranes linked by fret-like connections to other membrane components of the system in a limited left-handed arrangement.

  19. Strategies for concurrent processing of complex algorithms in data driven architectures

    NASA Technical Reports Server (NTRS)

    Stoughton, John W.; Mielke, Roland R.; Som, Sukhamony

    1990-01-01

    The performance modeling and enhancement for periodic execution of large-grain, decision-free algorithms in data flow architectures is examined. Applications include real-time implementation of control and signal processing algorithms where performance is required to be highly predictable. The mapping of algorithms onto the specified class of data flow architectures is realized by a marked graph model called ATAMM (Algorithm To Architecture Mapping Model). Performance measures and bounds are established. Algorithm transformation techniques are identified for performance enhancement and reduction of resource (computing element) requirements. A systematic design procedure is described for generating operating conditions for predictable performance both with and without resource constraints. An ATAMM simulator is used to test and validate the performance prediction by the design procedure. Experiments on a three resource testbed provide verification of the ATAMM model and the design procedure.

  20. Strategies for concurrent processing of complex algorithms in data driven architectures

    NASA Technical Reports Server (NTRS)

    Som, Sukhamoy; Stoughton, John W.; Mielke, Roland R.

    1990-01-01

    Performance modeling and performance enhancement for periodic execution of large-grain, decision-free algorithms in data flow architectures are discussed. Applications include real-time implementation of control and signal processing algorithms where performance is required to be highly predictable. The mapping of algorithms onto the specified class of data flow architectures is realized by a marked graph model called algorithm to architecture mapping model (ATAMM). Performance measures and bounds are established. Algorithm transformation techniques are identified for performance enhancement and reduction of resource (computing element) requirements. A systematic design procedure is described for generating operating conditions for predictable performance both with and without resource constraints. An ATAMM simulator is used to test and validate the performance prediction by the design procedure. Experiments on a three resource testbed provide verification of the ATAMM model and the design procedure.

  1. Fun with optical fibres

    NASA Astrophysics Data System (ADS)

    Alti, Kamlesh

    2017-07-01

    Optical fibres play a very crucial role in today’s technologies. Academic courses in optical fibres start at the undergraduate level. Nevertheless, student’s curiosity towards optical fibres starts from the school level. In this paper, some fun experiments have been designed for both school and college students, which have some concrete implications at the research level also.

  2. Fun with Optical Fibres

    ERIC Educational Resources Information Center

    Alti, Kamlesh

    2017-01-01

    Optical fibres play a very crucial role in today's technologies. Academic courses in optical fibres start at the undergraduate level. Nevertheless, student's curiosity towards optical fibres starts from the school level. In this paper, some fun experiments have been designed for both school and college students, which have some concrete…

  3. CW bismuth fibre laser

    SciTech Connect

    Dianov, Evgenii M; Dvoyrin, V V; Mashinsky, V M; Umnikov, A A; Yashkov, M V; Gur'yanov, A N

    2005-12-31

    A new fibre laser based on a bismuth-doped aluminosilicate glass fibre is proposed and fabricated. CW lasing is obtained in the spectral region between 1150 and 1300 nm. The fibres are fabricated by the method of modified chemical vapour deposition. (letters)

  4. Architectural design of the science complex at Elizabeth City State University

    NASA Technical Reports Server (NTRS)

    Jahromi, Soheila

    1993-01-01

    This paper gives an overall view of the architectural design process and elements in taking an idea from conception to execution. The project presented is an example for this process. Once the need for a new structure is established, an architect studies the requirements, opinions and limits in creating a structure that people will exist in, move through, and use. Elements in designing a building include factors such as volume and surface, light and form changes of scale and view, movement and stasis. Some of the other factors are functions and physical conditions of construction. Based on experience, intuition, and boundaries, an architect will utilize all elements in creating a new building. In general, the design process begins with studying the spatial needs which develop into an architectural program. A comprehensive and accurate architectural program is essential for having a successful building. The most attractive building which does not meet the functional needs of its users has failed at the primary reason for its existence. To have a good program an architect must have a full understanding of the daily functions that will take place in the building. The architectural program along with site characteristics are among a few of the important guidelines in studying the form, adjacencies, and circulation for the structure itself and also in relation to the adjacent structures. Conceptual studies are part of the schematic design, which is the first milestone in the design process. The other reference points are design development and construction documents. At each milestone, review and coordination with all the consultants is established, and the user is essential in refining the project. In design development phase, conceptual diagrams take shape, and architectural, structural, mechanical, and electrical systems are developed. The final phase construction documents convey all the information required to construct the building. The design process and elements

  5. Fibre mapping analysis in composite forming: Experimental and numerical comparison

    NASA Astrophysics Data System (ADS)

    Colmars, J.; Rusanov, A.; Ta, A. T.; Naouar, N.; Boisse, P.

    2016-10-01

    The work presented here is part of European project "FibreMap", which aims at the development of an automatic quality control and feedback mechanism to improve draping of carbon fibres on complex parts. The technology that is being developed in the project include a sensor system for robust detection of fibre orientation combined with a robotic system to scan complex parts. This paper focus on a comparison procedure made to compare experimental fibre orientation with finite element simulations results. First comparison results will be shown on a complex part chosen for the project.

  6. Architectures based on the use of gold nanoparticles and ruthenium complexes as a new route to improve genosensor sensitivity.

    PubMed

    García, T; Casero, E; Revenga-Parra, M; Martín-Benito, J; Pariente, F; Vázquez, L; Lorenzo, E

    2008-10-15

    The preparation of DNA-sensing architectures based on gold nanoparticles (Au-NPs) in conjunction with an "in situ" prepared ruthenium complex as a new route to improve the analytical properties of genosensors is described. In the development of these architectures several strategies to obtain Au-NPs modified gold electrodes (Au-NP/Au) have been essayed, in particular covalent binding and electrochemical deposition from a solution containing Au-NPs previously synthesized. UV-vis absorption measurements in conjunction with transmission electron microscope (TEM) images reveal that the synthesized Au-NPs are stable for at least 4 weeks and have a narrow size distribution. Atomic force microscopy (AFM) was employed to characterize the morphology and to estimate the Au-NPs surface coverage of the modified gold electrodes obtained following the different modification strategies. In order to assess the utility of these architectures as DNA-sensing devices, a thiolated capture probe sequence from Helicobacter pylori was immobilized onto the as-prepared surface. This sequence was chosen as a case of study within the framework of developing approaches of wide applicability. The hybridization event is detected using a water-soluble pentaamin ruthenium [3-(2-phenanthren-9-yl-vinyl)-pyridine] complex (Ru(NH(3))(5)L) prepared "in situ". This complex, due to its intercalative character, is able to bind to double stranded DNA more efficiently than to single stranded DNA. In addition, the metal provides with a redox center that can be used as an electrochemical indicator. On the basis of this strategy, complementary target sequences of H. pylori have been detected over the range of 40-800 pmol with a detection limit of 25+/-2 pmol.

  7. Self-assembly of supramolecular architectures and polymers by orthogonal metal complexation and hydrogen-bonding motifs.

    PubMed

    Grimm, Felix; Ulm, Nadine; Gröhn, Franziska; Düring, Jasmin; Hirsch, Andreas

    2011-08-16

    A modular construction kit with two orthogonal noncovalent binding sites for self-assembly of supramolecular architectures is presented. The heteroditopic building blocks contain a terpyridine (tpy) unit for coordination of metal ions and a Hamilton receptor for multiple H-bonding of cyanuric acid derivatives. The association constants of ligand binding of M(II) complexes (M=Ru, Zn, Fe, and Pt) with a dendritic end cap were determined to be in the range of 10(2) and 10(4) L mol(-1) in chloroform. The capabilities for binding of metal ions were investigated by (1)H NMR and UV/Vis spectroscopy. The Fe complexes are most appropriate for the generation of discrete and high-ordered architectures due to their strong tendency to form FeL(2) complexes. Superstructures are readily formed in a one-pot procedure at room temperature. No mutual interactions between the orthogonal binding motifs were observed, and this demonstrates the highly specific nature of each binding process. Decomplexation experiments were carried out to examine the reversibility of Fe-tpy coordination. Substitution of the terminal end cap with a homoditopic bis-cyanurate linkage leads to formation of an iron-containing supramolecular strand. Formation of coordination polymers was confirmed by viscosity measurements. The supramolecular polymer strands can be reversibly cleaved by addition of a terminating cyanuric acid building block, and this proves the dynamic nature of this noncovalent polymerization process.

  8. Network, degeneracy and bow tie. Integrating paradigms and architectures to grasp the complexity of the immune system

    PubMed Central

    2010-01-01

    Recently, the network paradigm, an application of graph theory to biology, has proven to be a powerful approach to gaining insights into biological complexity, and has catalyzed the advancement of systems biology. In this perspective and focusing on the immune system, we propose here a more comprehensive view to go beyond the concept of network. We start from the concept of degeneracy, one of the most prominent characteristic of biological complexity, defined as the ability of structurally different elements to perform the same function, and we show that degeneracy is highly intertwined with another recently-proposed organizational principle, i.e. 'bow tie architecture'. The simultaneous consideration of concepts such as degeneracy, bow tie architecture and network results in a powerful new interpretative tool that takes into account the constructive role of noise (stochastic fluctuations) and is able to grasp the major characteristics of biological complexity, i.e. the capacity to turn an apparently chaotic and highly dynamic set of signals into functional information. PMID:20701759

  9. Genetic architecture of the F7 gene in a Spanish population: implication for mapping complex diseases and for functional assays.

    PubMed

    Sabater-Lleal, M; Almasy, L; Martínez-Marchán, E; Martínez-Sánchez, E; Souto, R; Blangero, J; Souto, Jc; Fontcuberta, J; Soria, J M

    2006-05-01

    Delineating the genetic variability of loci coding for complex diseases helps to understand the individual variation in disease susceptibility and drug response. We present the allelic architecture of the F7 gene. This gene is the major determinant of FVII plasma levels, and these plasma levels constitute an important intermediate risk factor for cardiovascular disease. As part of the Genetic Analysis of Idiopathic Thrombophila Project, we completely re-sequenced the F7 locus (promoter, exons, introns, and 3'-untranslated region) in 40 unrelated individuals. We found 49 polymorphisms with only two amino acid changes suggesting that regulatory non-coding and intronic variants are responsible for the FVII variability. These results are important for mapping susceptibility alleles of complex diseases, because differences in pair-wise linkage disequilibrium patterns between DNA variants and haplotype frequency distributions may help to detect disease-associated alleles. In addition, we present the results of an in silico search that established genomic comparisons among different species. In conclusion, our study of the F7 DNA sequence variations is an example of a strategy for analyzing the genetic architecture of a quantitative trait locus. Furthermore, it provides a model for future analyses of genetic factors that contribute to the susceptibility of complex diseases in humans.

  10. Wavelet-Based Adaptive Solvers on Multi-core Architectures for the Simulation of Complex Systems

    NASA Astrophysics Data System (ADS)

    Rossinelli, Diego; Bergdorf, Michael; Hejazialhosseini, Babak; Koumoutsakos, Petros

    We build wavelet-based adaptive numerical methods for the simulation of advection dominated flows that develop multiple spatial scales, with an emphasis on fluid mechanics problems. Wavelet based adaptivity is inherently sequential and in this work we demonstrate that these numerical methods can be implemented in software that is capable of harnessing the capabilities of multi-core architectures while maintaining their computational efficiency. Recent designs in frameworks for multi-core software development allow us to rethink parallelism as task-based, where parallel tasks are specified and automatically mapped into physical threads. This way of exposing parallelism enables the parallelization of algorithms that were considered inherently sequential, such as wavelet-based adaptive simulations. In this paper we present a framework that combines wavelet-based adaptivity with the task-based parallelism. We demonstrate good scaling performance obtained by simulating diverse physical systems on different multi-core and SMP architectures using up to 16 cores.

  11. Crystal structure of raptor adenovirus 1 fibre head and role of the beta-hairpin in siadenovirus fibre head domains.

    PubMed

    Nguyen, Thanh H; Ballmann, Mónika Z; Do, Huyen T; Truong, Hai N; Benkő, Mária; Harrach, Balázs; van Raaij, Mark J

    2016-06-22

    Most adenoviruses recognize their host cells via an interaction of their fibre head domains with a primary receptor. The structural framework of adenovirus fibre heads is conserved between the different adenovirus genera for which crystal structures have been determined (Mastadenovirus, Aviadenovirus, Atadenovirus and Siadenovirus), but genus-specific differences have also been observed. The only known siadenovirus fibre head structure, that of turkey adenovirus 3 (TAdV-3), revealed a twisted beta-sandwich resembling the reovirus fibre head architecture more than that of other adenovirus fibre heads, plus a unique beta-hairpin embracing a neighbouring monomer. The TAdV-3 fibre head was shown to bind sialyllactose. Raptor adenovirus 1 (RAdV-1) fibre head was expressed, crystallized and its structure was solved and refined at 1.5 Å resolution. The structure could be solved by molecular replacement using the TAdV-3 fibre head structure as a search model, despite them sharing a sequence identity of only 19 %. Versions of both the RAdV-1 and TAdV-3 fibre heads with their beta-hairpin arm deleted were prepared and their stabilities were compared with the non-mutated proteins by a thermal unfolding assay. The structure of the RAdV-1 fibre head contains the same twisted ABCJ-GHID beta-sandwich and beta-hairpin arm as the TAdV-3 fibre head. However, while the predicted electro-potential surface charge of the TAdV-3 fibre head is mainly positive, the RAdV-1 fibre head shows positively and negatively charged patches and does not appear to bind sialyllactose. Deletion of the beta-hairpin arm does not affect the structure of the raptor adenovirus 1 fibre head and only affects the stability of the RAdV-1 and TAdV-3 fibre heads slightly. The high-resolution structure of RAdV-1 fibre head is the second known structure of a siadenovirus fibre head domain. The structure shows that the siadenovirus fibre head structure is conserved, but differences in the predicted surface charge

  12. Complex Small-Molecule Architectures Regulate Phenotypic Plasticity in a Nematode**

    PubMed Central

    Bose, Neelanjan; Ogawa, Akira; von Reuss, Stephan H.; Yim, Joshua J.; Ragsdale, Erik J.; Sommer, Ralf J.; Schroeder, Frank C.

    2013-01-01

    Microorganisms and plants produce a large diversity of secondary metabolites, whereas analyses of metazoan metabolomes have yielded comparatively few types of small molecules. We show that the nematode Pristionchus pacificus constructs elaborate molecular architectures from modified building blocks of primary metabolism, including an unusual xylopyranose-based nucleoside. These compounds act as signaling molecules controlling adult phenotypic plasticity and development and provide striking examples for modular generation of structural diversity in metazoans. PMID:23161728

  13. Architectural Features and Preservation of Ancient Residential Complexes of the Changs in Xiangan, Xiamen

    NASA Astrophysics Data System (ADS)

    Xia, J.; Chiou, S.

    2015-08-01

    Ancient architecture is an important cultural symbol of a nation, which has high historical, artistic and technology of cultural value. A building not only carries the creator of effort, but also the past with the future of the historical traditions and humanistic significance. It is not purely construction of artistic expression, even more the witness of the production and development of social groups. Therefore, it is not only the common cultural heritage of mankind, as more equally important to protect these ancient buildings for the promotion of spiritual civilization and local economic development. In recent years, China and other developing countries, which in the pursuit of rapid economic development, are also facing the problems of development and preservation, Especially influenced by the inherent "reform and innovation" traditional concepts, many ancient villages and buildings with rich cultural connotation are in a great danger. Xiang'an is one of the six administrative regions of Xiamen, The Tungyuan village and numerous surrounding villages which in Xiang'an retain a large number of ancient buildings of Ming and Qing Dynasties, but it has not been given due attention, many ancient buildings are facing the crisis of disappearing. Changs ancient residential is one of typical Minnan architectural which located in Tungyuan village. its main feature is as follows: Cheng is before the rear is Cuo, Facing south, Three bays with double Hucuo , Red brick and White stone wall, Architectural form of Hard mountain type roof and Double cocked dovetail ridge. In this paper, on the basis of the fieldwork, In addition to the overall building community environment and monomer building surveying and mapping, photograph, record, and through the collection, interviews and analysis of relevant historical materials, etc. Grasping the historical background of Changs ancient residential building community, exploring the formation and characteristics of the overall layout of

  14. Uncertainty in diffusion tensor based fibre tracking.

    PubMed

    Hahn, H K; Klein, J; Nimsky, C; Rexilius, J; Peitgen, H O

    2006-01-01

    Diffusion tensor imaging and related fibre tracking techniques have the potential to identify major white matter tracts afflicted by an individual pathology or tracts at risk for a given surgical approach. However, the reliability of these techniques is known to be limited by image distortions, image noise, low spatial resolution, and the problem of identifying crossing fibres. This paper intends to bridge the gap between the requirements of neurosurgical applications and basic research on fibre tracking uncertainty. We acquired echo planar diffusion tensor data from both 1.5 T and 3.0 T scanners. For fibre tracking, an extended deflection-based algorithm is employed with enhanced robustness to impaired fibre integrity such as caused by diffuse or infiltrating pathological processes. Moreover, we present a method to assess and visualize the uncertainty of fibre reconstructions based on variational complex Gaussian noise, which provides an alternative to the bootstrap method. We compare fibre tracking results with and without variational noise as well as with artificially decreased image resolution and signal-to-noise. Using our fibre tracking technique, we found a high robustness to decreased image resolution and signal-to-noise. Still, the effects of image quality on the tracking result will depend on the employed fibre tracking algorithm and must be handled with care, especially when being used for neurosurgical planning or resection guidance. An advantage of the variational noise approach over the bootstrap technique is that it is applicable to any given set of diffusion tensor images. We conclude that the presented approach allows for investigating the uncertainty of diffusion tensor imaging based fibre tracking and might offer a perspective to overcome the problem of size underestimation observed by existing techniques.

  15. Simplifying the design of microstructured optical fibre pressure sensors.

    PubMed

    Osório, Jonas H; Chesini, Giancarlo; Serrão, Valdir A; Franco, Marcos A R; Cordeiro, Cristiano M B

    2017-06-07

    In this paper, we propose a way to simplify the design of microstructured optical fibres with high sensitivity to applied pressure. The use of a capillary fibre with an embedded core allows the exploration of the pressure-induced material birefringence due to the capillary wall displacements and the photoelastic effect. An analytical description of pressure-induced material birefringence is provided, and fibre modal characteristics are explored through numerical simulations. Moreover, a capillary fibre with an embedded core is fabricated and used to probe pressure variations. Even though the embedded-core fibre has a non-optimized structure, measurements showed a pressure sensitivity of (1.04 ± 0.01) nm/bar, which compares well with more complex, specially designed fibre geometries reported in the literature. These results demonstrate that this geometry enables a novel route towards the simplification of microstructured fibre-based pressure sensors.

  16. Complex matrix multiplication operations with data pre-conditioning in a high performance computing architecture

    DOEpatents

    Eichenberger, Alexandre E; Gschwind, Michael K; Gunnels, John A

    2014-02-11

    Mechanisms for performing a complex matrix multiplication operation are provided. A vector load operation is performed to load a first vector operand of the complex matrix multiplication operation to a first target vector register. The first vector operand comprises a real and imaginary part of a first complex vector value. A complex load and splat operation is performed to load a second complex vector value of a second vector operand and replicate the second complex vector value within a second target vector register. The second complex vector value has a real and imaginary part. A cross multiply add operation is performed on elements of the first target vector register and elements of the second target vector register to generate a partial product of the complex matrix multiplication operation. The partial product is accumulated with other partial products and a resulting accumulated partial product is stored in a result vector register.

  17. Simulating Fibre Suspensions: Lagrangian versus Statistical Approach

    NASA Astrophysics Data System (ADS)

    Zhao, L. H.; Andersson, H. I.; Gillissen, J. J. J.; Boersma, B. J.

    Fibre suspensions exhibit complex dynamical flow phenomena and are at the same time of immense practical importance, notably in the pulp and paper industries. NTNU and TU Delft have in a collaborative research project adopted two alternative strategies in the simulation of dilute fibre suspensions, namely a statistical approach [2] and a Lagrangian particle treatment [4]. The two approaches have their own advantages and disadvantages. In this paper we aim for the first time to compare the performance of the two.

  18. Leaf shape evolution has a similar genetic architecture in three edaphic specialists within the Mimulus guttatus species complex.

    PubMed

    Ferris, Kathleen G; Rushton, Tullia; Greenlee, Anna B; Toll, Katherine; Blackman, Benjamin K; Willis, John H

    2015-08-01

    The genetic basis of leaf shape has long interested botanists because leaf shape varies extensively across the plant kingdom and this variation is probably adaptive. However, knowledge of the genetic architecture of leaf shape variation in natural populations remains limited. This study examined the genetic architecture of leaf shape diversification among three edaphic specialists in the Mimulus guttatus species complex. Lobed and narrow leaves have evolved from the entire, round leaves of M. guttatus in M. laciniatus, M. nudatus and a polymorphic serpentine M. guttatus population (M2L). Bulk segregant analysis and next-generation sequencing were used to map quantitative trait loci (QTLs) that underlie leaf shape in an M. laciniatus × M. guttatus F2 population. To determine whether the same QTLs contribute to leaf shape variation in M. nudatus and M2L, F2s from M. guttatus × M. nudatus and lobed M2L × unlobed M. guttatus crosses were genotyped at QTLs from the bulk segregant analysis. Narrow and lobed leaf shapes in M. laciniatus, M. nudatus and M. guttatus are controlled by overlapping genetic regions. Several promising leaf shape candidate genes were found under each QTL. The evolution of divergent leaf shape has taken place multiple times in the M. guttatus species complex and is associated with the occupation of dry, rocky environments. The genetic architecture of elongated and lobed leaves is similar across three species in this group. This may indicate that parallel genetic evolution from standing variation or new mutations is responsible for the putatively adaptive leaf shape variation in Mimulus. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  19. Leaf shape evolution has a similar genetic architecture in three edaphic specialists within the Mimulus guttatus species complex

    PubMed Central

    Ferris, Kathleen G.; Rushton, Tullia; Greenlee, Anna B.; Toll, Katherine; Blackman, Benjamin K.; Willis, John H.

    2015-01-01

    Background and Aims The genetic basis of leaf shape has long interested botanists because leaf shape varies extensively across the plant kingdom and this variation is probably adaptive. However, knowledge of the genetic architecture of leaf shape variation in natural populations remains limited. This study examined the genetic architecture of leaf shape diversification among three edaphic specialists in the Mimulus guttatus species complex. Lobed and narrow leaves have evolved from the entire, round leaves of M. guttatus in M. laciniatus, M. nudatus and a polymorphic serpentine M. guttatus population (M2L). Methods Bulk segregant analysis and next-generation sequencing were used to map quantitative trait loci (QTLs) that underlie leaf shape in an M. laciniatus × M. guttatus F2 population. To determine whether the same QTLs contribute to leaf shape variation in M. nudatus and M2L, F2s from M. guttatus × M. nudatus and lobed M2L × unlobed M. guttatus crosses were genotyped at QTLs from the bulk segregant analysis. Key Results Narrow and lobed leaf shapes in M. laciniatus, M. nudatus and M. guttatus are controlled by overlapping genetic regions. Several promising leaf shape candidate genes were found under each QTL. Conclusions The evolution of divergent leaf shape has taken place multiple times in the M. guttatus species complex and is associated with the occupation of dry, rocky environments. The genetic architecture of elongated and lobed leaves is similar across three species in this group. This may indicate that parallel genetic evolution from standing variation or new mutations is responsible for the putatively adaptive leaf shape variation in Mimulus. PMID:26070644

  20. A Parallel Trade Study Architecture for Design Optimization of Complex Systems

    NASA Technical Reports Server (NTRS)

    Kim, Hongman; Mullins, James; Ragon, Scott; Soremekun, Grant; Sobieszczanski-Sobieski, Jaroslaw

    2005-01-01

    Design of a successful product requires evaluating many design alternatives in a limited design cycle time. This can be achieved through leveraging design space exploration tools and available computing resources on the network. This paper presents a parallel trade study architecture to integrate trade study clients and computing resources on a network using Web services. The parallel trade study solution is demonstrated to accelerate design of experiments, genetic algorithm optimization, and a cost as an independent variable (CAIV) study for a space system application.

  1. Complex modular architecture around a simple toolkit of wing pattern genes.

    PubMed

    Van Belleghem, Steven M; Rastas, Pasi; Papanicolaou, Alexie; Martin, Simon H; Arias, Carlos F; Supple, Megan A; Hanly, Joseph J; Mallet, James; Lewis, James J; Hines, Heather M; Ruiz, Mayte; Salazar, Camilo; Linares, Mauricio; Moreira, Gilson R P; Jiggins, Chris D; Counterman, Brian A; McMillan, W Owen; Papa, Riccardo

    2017-01-01

    Identifying the genomic changes that control morphological variation and understanding how they generate diversity is a major goal of evolutionary biology. In Heliconius butterflies, a small number of genes control the development of diverse wing color patterns. Here, we used full genome sequencing of individuals across the Heliconius erato radiation and closely related species to characterize genomic variation associated with wing pattern diversity. We show that variation around color pattern genes is highly modular, with narrow genomic intervals associated with specific differences in color and pattern. This modular architecture explains the diversity of color patterns and provides a flexible mechanism for rapid morphological diversification.

  2. Complex modular architecture around a simple toolkit of wing pattern genes.

    PubMed

    Van Belleghem, Steven M; Rastas, Pasi; Papanicolaou, Alexie; Martin, Simon H; Arias, Carlos F; Supple, Megan A; Hanly, Joseph J; Mallet, James; Lewis, James J; Hines, Heather M; Ruiz, Mayte; Salazar, Camilo; Linares, Mauricio; Moreira, Gilson R P; Jiggins, Chris D; Counterman, Brian A; McMillan, W Owen; Papa, Riccardo

    2017-01-30

    Identifying the genomic changes that control morphological variation and understanding how they generate diversity is a major goal of evolutionary biology. In Heliconius butterflies, a small number of genes control the development of diverse wing colour patterns. Here, we used full-genome sequencing of individuals across the Heliconius erato radiation and closely related species to characterize genomic variation associated with wing pattern diversity. We show that variation around colour pattern genes is highly modular, with narrow genomic intervals associated with specific differences in colour and pattern. This modular architecture explains the diversity of colour patterns and provides a flexible mechanism for rapid morphological diversification.

  3. Complex modular architecture around a simple toolkit of wing pattern genes

    PubMed Central

    Van Belleghem, Steven M.; Rastas, Pasi; Papanicolaou, Alexie; Martin, Simon H.; Arias, Carlos F.; Supple, Megan A.; Hanly, Joseph J.; Mallet, James; Lewis, James J.; Hines, Heather M.; Ruiz, Mayte; Salazar, Camilo; Linares, Mauricio; Moreira, Gilson R. P.; Jiggins, Chris D.; Counterman, Brian A.; McMillan, W. Owen; Papa, Riccardo

    2017-01-01

    Identifying the genomic changes that control morphological variation and understanding how they generate diversity is a major goal of evolutionary biology. In Heliconius butterflies, a small number of genes control the development of diverse wing color patterns. Here, we used full genome sequencing of individuals across the Heliconius erato radiation and closely related species to characterize genomic variation associated with wing pattern diversity. We show that variation around color pattern genes is highly modular, with narrow genomic intervals associated with specific differences in color and pattern. This modular architecture explains the diversity of color patterns and provides a flexible mechanism for rapid morphological diversification. PMID:28523290

  4. Genome-wide study of an elite rice pedigree reveals a complex history of genetic architecture for breeding improvement

    PubMed Central

    Chen, Shaoxia; Lin, Zechuan; Zhou, Degui; Wang, Chongrong; Li, Hong; Yu, Renbo; Deng, Hanchao; Tang, Xiaoyan; Zhou, Shaochuan; Wang Deng, Xing; He, Hang

    2017-01-01

    Improving breeding has been widely utilized in crop breeding and contributed to yield and quality improvement, yet few researches have been done to analyze genetic architecture underlying breeding improvement comprehensively. Here, we collected genotype and phenotype data of 99 cultivars from the complete pedigree including Huanghuazhan, an elite, high-quality, conventional indica rice that has been grown over 4.5 million hectares in southern China and from which more than 20 excellent cultivars have been derived. We identified 1,313 selective sweeps (SSWs) revealing four stage-specific selection patterns corresponding to improvement preference during 65 years, and 1113 conserved Huanghuazhan traceable blocks (cHTBs) introduced from different donors and conserved in >3 breeding generations were the core genomic regions for superior performance of Huanghuazhan. Based on 151 quantitative trait loci (QTLs) identified for 13 improved traits in the pedigree, we reproduced their improvement process in silico, highlighting improving breeding works well for traits controlled by major/major + minor effect QTLs, but was inefficient for traits controlled by QTLs with complex interactions or explaining low levels of phenotypic variation. These results indicate long-term breeding improvement is efficient to construct superior genetic architecture for elite performance, yet molecular breeding with designed genotype of QTLs can facilitate complex traits improvement. PMID:28374863

  5. The influence of complex white matter architecture on the mean diffusivity in diffusion tensor MRI of the human brain.

    PubMed

    Vos, Sjoerd B; Jones, Derek K; Jeurissen, Ben; Viergever, Max A; Leemans, Alexander

    2012-02-01

    In diffusion tensor magnetic resonance imaging (DT-MRI), limitations concerning complex fiber architecture (when an image voxel contains fiber populations with more than one dominant orientation) are well-known. Fractional anisotropy (FA) values are lower in such areas because of a lower directionality of diffusion on the voxel-scale, which makes the interpretation of FA less straightforward. Moreover, the interpretation of the axial and radial diffusivities is far from trivial when there is more than one dominant fiber orientation within a voxel. In this work, using (i) theoretical considerations, (ii) simulations, and (iii) experimental data, it is demonstrated that the mean diffusivity (or the trace of the diffusion tensor) is lower in complex white matter configurations, compared with tissue where there is a single dominant fiber orientation within the voxel. We show that the magnitude of this reduction depends on various factors, including configurational and microstructural properties (e.g., the relative contributions of different fiber populations) and acquisition settings (e.g., the b-value). These results increase our understanding of the quantitative metrics obtained from DT-MRI and, in particular, the effect of the microstructural architecture on the mean diffusivity. More importantly, they reinforce the growing awareness that differences in DT-MRI metrics need to be interpreted cautiously. Copyright © 2011. Published by Elsevier Inc.

  6. The Next PAGE in Understanding Complex Traits: Design for the Analysis of Population Architecture Using Genetics and Epidemiology (PAGE) Study

    PubMed Central

    Matise, Tara C.; Ambite, Jose Luis; Buyske, Steven; Carlson, Christopher S.; Cole, Shelley A.; Crawford, Dana C.; Haiman, Christopher A.; Heiss, Gerardo; Kooperberg, Charles; Marchand, Loic Le; Manolio, Teri A.; North, Kari E.; Peters, Ulrike; Ritchie, Marylyn D.; Hindorff, Lucia A.; Haines, Jonathan L.

    2011-01-01

    Genetic studies have identified thousands of variants associated with complex traits. However, most association studies are limited to populations of European descent and a single phenotype. The Population Architecture using Genomics and Epidemiology (PAGE) Study was initiated in 2008 by the National Human Genome Research Institute to investigate the epidemiologic architecture of well-replicated genetic variants associated with complex diseases in several large, ethnically diverse population-based studies. Combining DNA samples and hundreds of phenotypes from multiple cohorts, PAGE is well-suited to address generalization of associations and variability of effects in diverse populations; identify genetic and environmental modifiers; evaluate disease subtypes, intermediate phenotypes, and biomarkers; and investigate associations with novel phenotypes. PAGE investigators harmonize phenotypes across studies where possible and perform coordinated cohort-specific analyses and meta-analyses. PAGE researchers are genotyping thousands of genetic variants in up to 121,000 DNA samples from African-American, white, Hispanic/Latino, Asian/Pacific Islander, and American Indian participants. Initial analyses will focus on single nucleotide polymorphisms (SNPs) associated with obesity, lipids, cardiovascular disease, type 2 diabetes, inflammation, various cancers, and related biomarkers. PAGE SNPs are also assessed for pleiotropy using the “phenome-wide association study” approach, testing each SNP for associations with hundreds of phenotypes. PAGE data will be deposited into the National Center for Biotechnology Information's Database of Genotypes and Phenotypes and made available via a custom browser. PMID:21836165

  7. The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif.

    PubMed

    Huth, J R; Bewley, C A; Nissen, M S; Evans, J N; Reeves, R; Gronenborn, A M; Clore, G M

    1997-08-01

    The solution structure of a complex between a truncated form of HMG-I(Y), consisting of the second and third DNA binding domains (residues 51-90), and a DNA dodecamer containing the PRDII site of the interferon-beta promoter has been solved by multidimensional nuclear magnetic resonance spectroscopy. The stoichiometry of the complex is one molecule of HMG-I(Y) to two molecules of DNA. The structure reveals a new architectural minor groove binding motif which stabilizes B-DNA, thereby facilitating the binding of other transcription factors in the opposing major groove. The interactions involve a central Arg-Gly-Arg motif together with two other modules that participate in extensive hydrophobic and polar contracts. The absence of one of these modules in the third DNA binding domain accounts for its-100 fold reduced affinity relative to the second one.

  8. Embedded 3D Photopatterning of Hydrogels with Diverse and Complex Architectures for Tissue Engineering and Disease Models

    PubMed Central

    Davey, Shruti Krishna; Aung, Aereas; Agrawal, Gaurav; Lim, Han Liang; Kar, Mrityunjoy

    2015-01-01

    Techniques that can create three-dimensional (3D) structures to provide architectural support for cells have a significant impact in generating complex and hierarchically organized tissues/organs. In recent times, a number of technologies, including photopatterning, have been developed to create such intricate 3D structures. In this study, we describe an easy-to-implement photopatterning approach, involving a conventional fluorescent microscope and a simple photomask, to encapsulate cells within spatially defined 3D structures. We have demonstrated the ease and the versatility of this approach by creating simple to complex as well as multilayered structures. We have extended this photopatterning approach to incorporate and spatially organize multiple cell types, thereby establishing coculture systems. Such cost-effective and easy-to-use approaches can greatly advance tissue engineering strategies. PMID:26154197

  9. Embedded 3D Photopatterning of Hydrogels with Diverse and Complex Architectures for Tissue Engineering and Disease Models.

    PubMed

    Davey, Shruti Krishna; Aung, Aereas; Agrawal, Gaurav; Lim, Han Liang; Kar, Mrityunjoy; Varghese, Shyni

    2015-11-01

    Techniques that can create three-dimensional (3D) structures to provide architectural support for cells have a significant impact in generating complex and hierarchically organized tissues/organs. In recent times, a number of technologies, including photopatterning, have been developed to create such intricate 3D structures. In this study, we describe an easy-to-implement photopatterning approach, involving a conventional fluorescent microscope and a simple photomask, to encapsulate cells within spatially defined 3D structures. We have demonstrated the ease and the versatility of this approach by creating simple to complex as well as multilayered structures. We have extended this photopatterning approach to incorporate and spatially organize multiple cell types, thereby establishing coculture systems. Such cost-effective and easy-to-use approaches can greatly advance tissue engineering strategies.

  10. Soft glass photonic crystal fibres and their applications

    NASA Astrophysics Data System (ADS)

    Buczyński, Ryszard; Klimczak, Mariusz; Pysz, Dariusz; Stepniewski, Grzegorz; Siwicki, Bartłomiej; Cimek, Jarosław; Kujawa, Ireneusz; Piechal, Bernard; Stepień, Ryszard

    2015-05-01

    Most of the research work related to photonic crystal fibres has to date been focused on silica based fibres. Only in the recent years has there been a fraction of research devoted to fibres based on soft glasses, since some of them offer interesting properties as significantly higher nonlinearity than silica glass and wide transparency in the infrared range. On the other hand, attenuation in those glasses is usually one or more orders of magnitude higher that in silica glass, which limits their application area due to limited length of the fibres, which can be practically used. We report on the development of single-mode photonic crystal fibres made of highly nonlinear lead-bismuth-gallate glass with a zero dispersion wavelength at 1460 nm and flat anomalous dispersion. A two-octave spanning supercontinuum in the range 700-3000 nm was generated in 2 cm of the fibre. In contrast to the silica glass, various oxide based soft glasses with large refractive index difference can jointly undergo multiple thermal processing steps without degradation. The use of two soft glasses gives additional degrees of freedom in the design of photonic crystal fibres. As a result, highly nonlinear fibres with unique dispersion characteristics can be obtained. Soft glass allow also development of fibres with complex subwavelength refractive index distribution inside core of the fibre. A highly birefringent fibre with anisotropic core composed of subwavelength glass layers ordered in a rectangular structure was developed and is demonstrated

  11. Polarisation maintaining fibre with pure silica core and two depressed claddings for fibre optic gyroscope

    NASA Astrophysics Data System (ADS)

    Kurbatov, A. M.; Kurbatov, R. A.; Voloshin, V. V.; Vorob'ev, I. L.; Kolosovsky, A. O.

    2016-12-01

    Polarisation maintaining (PM) fibre is described with pure silica core and two depressed claddings for fibre optic gyro (FOG) sensing coil. Detailed mathematical simulation is presented by supermodes method, which is extremely necessary for such fibre. Simulation is fulfilled by frequency domain finite difference method (FDFDM), taking into account all details of realistic index profile with stress applying parts, while the leakage/bend loss occur in the region with complex index, surrounding the fibre. Cutoff and small bend loss are theoretically predicted and experimentally measured with excellent agreement between theory and experiment. Polarisation maintaining ability is measured in the form of conventional h-parameter (7.1·10-6 1/m) for 90-μm diameter fibre with birefringence value only 3.9·10-4.

  12. Therapeutic role of dietary fibre.

    PubMed Central

    Hunt, R.; Fedorak, R.; Frohlich, J.; McLennan, C.; Pavilanis, A.

    1993-01-01

    The current status of dietary fibre and fibre supplements in health and disease is reported, and the components of dietary fibre and its respective mechanical and metabolic effects with emphasis on its therapeutic potential are reviewed. Practical management guidelines are provided to help physicians encourage patients identified as having fibre deficiency to increase dietary fibre intake to the recommended level. PMID:8388284

  13. The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling

    PubMed Central

    Zelter, Alex; Bonomi, Massimiliano; Kim, Jae ook; Umbreit, Neil T.; Hoopmann, Michael R.; Johnson, Richard; Riffle, Michael; Jaschob, Daniel; MacCoss, Michael J.; Moritz, Robert L.; Davis, Trisha N.

    2015-01-01

    Accurate segregation of chromosomes during cell division is essential. The Dam1 complex binds kinetochores to microtubules and its oligomerization is required to form strong attachments. It is a key target of Aurora B kinase, which destabilizes erroneous attachments allowing subsequent correction. Understanding the roles and regulation of the Dam1 complex requires structural information. Here we apply cross-linking/mass spectrometry and structural modelling to determine the molecular architecture of the Dam1 complex. We find microtubule attachment is accompanied by substantial conformational changes, with direct binding mediated by the carboxy termini of Dam1p and Duo1p. Aurora B phosphorylation of Dam1p C terminus weakens direct interaction with the microtubule. Furthermore, the Dam1p amino terminus forms an interaction interface between Dam1 complexes, which is also disrupted by phosphorylation. Our results demonstrate that Aurora B inhibits both direct interaction with the microtubule and oligomerization of the Dam1 complex to drive error correction during mitosis. PMID:26560693

  14. Architecture, sedentism, and social complexity at Pre-Pottery Neolithic A WF16, Southern Jordan.

    PubMed

    Finlayson, Bill; Mithen, Steven J; Najjar, Mohammad; Smith, Sam; Maričević, Darko; Pankhurst, Nick; Yeomans, Lisa

    2011-05-17

    Recent excavations at Pre-Pottery Neolithic A (PPNA) WF16 in southern Jordan have revealed remarkable evidence of architectural developments in the early Neolithic. This sheds light on both special purpose structures and "domestic" settlement, allowing fresh insights into the development of increasingly sedentary communities and the social systems they supported. The development of sedentary communities is a central part of the Neolithic process in Southwest Asia. Architecture and ideas of homes and households have been important to the debate, although there has also been considerable discussion on the role of communal buildings and the organization of early sedentarizing communities since the discovery of the tower at Jericho. Recently, the focus has been on either northern Levantine PPNA sites, such as Jerf el Ahmar, or the emergence of ritual buildings in the Pre-Pottery Neolithic B of the southern Levant. Much of the debate revolves around a division between what is interpreted as domestic space, contrasted with "special purpose" buildings. Our recent evidence allows a fresh examination of the nature of early Neolithic communities.

  15. Architecture, sedentism, and social complexity at Pre-Pottery Neolithic A WF16, Southern Jordan

    PubMed Central

    Finlayson, Bill; Mithen, Steven J.; Najjar, Mohammad; Smith, Sam; Maričević, Darko; Pankhurst, Nick; Yeomans, Lisa

    2011-01-01

    Recent excavations at Pre-Pottery Neolithic A (PPNA) WF16 in southern Jordan have revealed remarkable evidence of architectural developments in the early Neolithic. This sheds light on both special purpose structures and “domestic” settlement, allowing fresh insights into the development of increasingly sedentary communities and the social systems they supported. The development of sedentary communities is a central part of the Neolithic process in Southwest Asia. Architecture and ideas of homes and households have been important to the debate, although there has also been considerable discussion on the role of communal buildings and the organization of early sedentarizing communities since the discovery of the tower at Jericho. Recently, the focus has been on either northern Levantine PPNA sites, such as Jerf el Ahmar, or the emergence of ritual buildings in the Pre-Pottery Neolithic B of the southern Levant. Much of the debate revolves around a division between what is interpreted as domestic space, contrasted with “special purpose” buildings. Our recent evidence allows a fresh examination of the nature of early Neolithic communities. PMID:21536900

  16. Non-precious metal complexes with an anionic PCP pincer architecture.

    PubMed

    Murugesan, Sathiyamoorthy; Kirchner, Karl

    2016-01-14

    This perspective article provides an overview of the advancements in the field of non-precious metal complexes featuring anionic PCP pincer ligands with the inclusion of aliphatic systems. It covers research from the beginning in 1976 until late 2015 and provides a summary of key developments in this area, which is, to date, limited to the metals nickel, cobalt, iron, and molybdenum. While the research in nickel PCP complexes is already quite extensive, the chemistry of cobalt, iron, and molybdenum PCP complexes is comparatively sparse. With other non-precious metals such as copper, manganese, chromium or vanadium no PCP complexes are known as yet. In the case of nickel PCP complexes already many catalytic applications such as Suzuki-Miyaura coupling, C-S cross coupling, Kharasch and Michael additions, hydrosilylation of aldehydes and ketones, cyanomethylation of aldehydes, and hydroamination of nitriles were reported. While iron PCP complexes were found to be active catalysts for the hydrosilylation of aldehydes and ketones as well as the dehydrogenation of ammonia-borane, cobalt PCP complexes were not applied to any catalytic reactions. Surprisingly, only one molybdenum PCP complex is reported, which was capable of cleaving dinitrogen to give a nitride complex. This perspective underlines that the combination of cheap and abundant metals such as nickel, cobalt, and iron with PCP pincer ligands may result in the development of novel, versatile, and efficient catalysts for atom-efficient catalytic reactions.

  17. Complexity of architectural silhouettes: from vague impressions to definite design features.

    PubMed

    Stamps, A E

    1998-12-01

    Nine 2-dimensional shapes were created that varied in four geometric factors: number of vertexes, symmetry, variation of lengths of line segments, and variation of angles. The shapes were evaluated in a paired-comparison experiment on the criterion of perceived complexity. Analysis of variance suggested that the most important predictor of shape complexity was the number of vertexes. P2/A (perimeter squared divided by the area) was also strongly correlated with judged complexity. Symmetry was a significant but weak predictor of complexity.

  18. Fibres For Sensors

    NASA Astrophysics Data System (ADS)

    Payne, D. N.

    1984-11-01

    Sensors which rely on the external modulation of the properties of an optical fibre (intrinsic sensors) are receiving much attention since they can be made extremely sensitive, and can be used for distributed measurements. Distributed sensing provides some particularly exciting prospects for acoustic, magnetic and electric field monitoring. To date, however, the great majority of experimental and commercial fibre sensors employ telecommunications-grade fibres, largely as a result of their ready availability. Not only does this policy frequently lead to a design compromise, but in some cases makes the performance marginal or untenable as a result of excessive environmental sensitivity. Despite this, little attention has been given to the design of special sensor fibres with enhanced (or depressed) sensitivity to specific measurands. The position is somewhat better with respect to fibres designed to eliminate sensor polarisation problems (e.g. polar isation-maintaining fibres), but even here further work is required to provide the performance demanded.

  19. Does Supporting Multiple Student Strategies Lead to Greater Learning and Motivation? Investigating a Source of Complexity in the Architecture of Intelligent Tutoring Systems

    ERIC Educational Resources Information Center

    Waalkens, Maaike; Aleven, Vincent; Taatgen, Niels

    2013-01-01

    Intelligent tutoring systems (ITS) support students in learning a complex problem-solving skill. One feature that makes an ITS architecturally complex, and hard to build, is support for strategy freedom, that is, the ability to let students pursue multiple solution strategies within a given problem. But does greater freedom mean that students…

  20. Reconstitution of the augmin complex provides insights into its architecture and function

    PubMed Central

    Hsia, Kuo-Chiang; Wilson-Kubalek, Elizabeth M.; Dottore, Alejandro; Hao, Qi; Tsai, Kuang-Lei; Forth, Scott; Shimamoto, Yuta; Milligan, Ronald A.; Kapoor, Tarun M.

    2014-01-01

    Proper microtubule nucleation during cell division requires augmin, a microtubule-associated hetero-octameric protein complex. In current models, augmin recruits γ-tubulin, via its hDgt6 subunit’s C-terminus, to nucleate microtubules within spindles. However, augmin’s biochemical complexity has restricted analysis of its structural organization and function. Here, we reconstitute human augmin and show it is a Y-shaped complex that can adopt multiple conformations. Further, we find that a dimeric sub-complex retains in vitro microtubule-binding properties of octameric complexes, but not proper metaphase spindle localization. Addition of octameric augmin complexes to Xenopus egg extracts promotes microtubule aster formation, an activity enhanced by Ran-GTP. This activity requires microtubule binding, but not the characterized hDgt6 γ-tubulin-recruitment domain. Tetrameric sub-complexes induce asters, but activity and microtubule bundling within asters are reduced compared to octameric complexes. Together, our findings shed light on augmin’s structural organization, microtubule binding properties and define subunits required for its function in organizing microtubule-based structures. PMID:25173975

  1. Functional characterization and architecture of recombinant yeast SWR1 histone exchange complex

    PubMed Central

    Lin, Chia-Liang; Chaban, Yuriy; Rees, David M.; McCormack, Elizabeth A.; Ocloo, Lorraine

    2017-01-01

    Abstract We have prepared recombinant fourteen subunit yeast SWR1 complex from insect cells using a modified MultiBac system. The 1.07 MDa recombinant protein complex has histone-exchange activity. Full exchange activity is realized with a single SWR1 complex bound to a nucleosome. We also prepared mutant complexes that lack a variety of subunits or combinations of subunits and these start to reveal roles for some of these subunits as well as indicating interactions between them in the full complex. Complexes containing a series of N-terminally and C-terminally truncated Swr1 subunits reveal further details about interactions between subunits as well as their binding sites on the Swr1 subunit. Finally, we present electron microscopy studies revealing the dynamic nature of the complex and a 21 Å resolution reconstruction of the intact complex provides details not apparent in previously reported structures, including a large central cavity of sufficient size to accommodate a nucleosome. PMID:28499038

  2. HIPPI and Fibre Channel

    SciTech Connect

    Tolmie, D.E.

    1992-01-01

    The High-Performance Parallel Interface (HIPPI) and Fibre Channel are near-gigabit per second data communications interfaces being developed in ANSI standards Task Group X3T9.3. HIPPI is the current interface of choice in the high-end and supercomputer arena, and Fibre Channel is a follow-on effort. HIPPI came from a local area network background, and Fibre Channel came from a mainframe to peripheral interface background.

  3. Gravity spun polycaprolactone fibres for soft tissue engineering: interaction with fibroblasts and myoblasts in cell culture.

    PubMed

    Williamson, Matthew Richard; Adams, Eric F; Coombes, Allan G A

    2006-03-01

    Poly(epsilon-caprolactone) (PCL) fibres were produced by wet spinning from solutions in acetone under low shear (gravity flow) conditions. As-spun PCL fibres exhibited a mean strength and stiffness of 7.9 MPa and 0.1 GPa, respectively and a rough, porous surface morphology. Cold drawing to an extension of 500% resulted in increases in fibre strength (43 MPa) and stiffness (0.3 GPa) and development of an oriented, fibrillar surface texture. The proliferation rate of Swiss 3T3 mouse fibroblasts and C2C12 mouse myoblasts on as-spun, 500% cold-drawn and gelatin-modified PCL fibres was determined in cell culture to provide a basic measure of the biocompatibility of the fibres. Proliferation of both cell types was consistently higher on gelatin-coated fibres relative to as-spun fibres at time points below 7 days. Fibroblast growth rates on cold-drawn PCL fibres exceeded those on as-spun fibres but myoblast proliferation was similar on both substrates. After 1 day in culture, both cell types had spread and coalesced on the fibres to form a cell layer, which conformed closely to the underlying topography. The high fibre compliance combined with a potential for modifying the fibre surface chemistry with cell adhesion molecules and the surface architecture by cold drawing to enhance proliferation of fibroblasts and myoblasts, recommends further investigation of gravity-spun PCL fibres for 3-D scaffold production in soft tissue engineering.

  4. Voronoi cells, fractal dimensions and fibre composites.

    PubMed

    Summerscales, J.; Guild, F. J.; Pearce, N. R. L.; Russell, P. M.

    2001-02-01

    The use of fibre-reinforced polymer matrix composite materials is growing at a faster rate than the gross domestic product (GDP) in many countries. An improved understanding of their processing and mechanical behaviour would extend the potential applications of these materials. For unidirectional composites, it is predicted that localized absence of fibres is related to longitudinal compression failure. The use of woven reinforcements permits more effective manufacture than for unidirectional fibres. It has been demonstrated experimentally that compression strengths of woven composites are reduced when fibres are clustered. Summerscales predicted that clustering of fibres would increase the permeability of the reinforcement and hence expedite the processing of these materials. Commercial fabrics are available which employ this concept using flow-enhancing bound tows. The net effect of clustering fibres is to enhance processability whilst reducing the mechanical properties. The effects reported above were qualitative correlations. To improve the design tools for reinforcement fabrics we have sought to quantify the changes in the micro/meso-structure of woven reinforcement fabrics. Gross differences in the appearance of laminate sections are apparent for different weave styles. The use of automated image analysis is essential for the quantification of subtle changes in fabric architecture. This paper considers Voronoi tessellation and fractal dimensions for the quantification of the microstructures of woven fibre-reinforced composites. It reviews our studies in the last decade of the process-property-structure relationships for commercial and experimental fabric reinforcements in an attempt to resolve the processing vs. properties dilemma. A new flow-enhancement concept has been developed which has a reduced impact on laminate mechanical properties.

  5. Progress and development in fibre laser technology

    NASA Astrophysics Data System (ADS)

    Horley, Ray; Norman, Stephen; Zervas, Mikhail N.

    2007-10-01

    High performance fibre lasers are now well established as an extremely robust and reliable technology enabling a growing and diverse number of demanding industrial and medical and applications. Compared to rival technologies, such as carbon-dioxide (CO II), Lamp/Diode-Pumped Solid-State (L/DPSS) and disk lasers, fibre lasers offer a number of unique characteristics that have resulted in their wide adoption in an increasing number of industrial sectors. In addition to replacing conventional lasers in existing applications, fibre lasers have been very successful in enabling new applications, both factors which explain their increasing market share. In this paper we describe the basic features of fibre lasers, and discuss their generic advantages compared with other laser technologies and consider how these may translate to defence applications. We explain our proprietary cladding-pumping technology (GTWave TM) and the laser architectures we use to implement our commercial products. We present parametric performance data that show the vast range of pulse waveforms that can be produced and discuss some new industrial applications that they have recently enabled. Finally, we reference some of the leading research results for multi-kW continuous-wave (CW) fibre lasers and summarise SPIE's published work in this field.

  6. Self-consistent theory of transcriptional control in complex regulatory architectures

    PubMed Central

    Brewster, Robert C.; Weinert, Franz M.; Phillips, Rob; Kegel, Willem K.

    2017-01-01

    Individual regulatory proteins are typically charged with the simultaneous regulation of a battery of different genes. As a result, when one of these proteins is limiting, competitive effects have a significant impact on the transcriptional response of the regulated genes. Here we present a general framework for the analysis of any generic regulatory architecture that accounts for the competitive effects of the regulatory environment by isolating these effects into an effective concentration parameter. These predictions are formulated using the grand-canonical ensemble of statistical mechanics and the fold-change in gene expression is predicted as a function of the number of transcription factors, the strength of interactions between the transcription factors and their DNA binding sites, and the effective concentration of the transcription factor. The effective concentration is set by the transcription factor interactions with competing binding sites within the cell and is determined self-consistently. Using this approach, we analyze regulatory architectures in the grand-canonical ensemble ranging from simple repression and simple activation to scenarios that include repression mediated by DNA looping of distal regulatory sites. It is demonstrated that all the canonical expressions previously derived in the case of an isolated, non-competing gene, can be generalised by a simple substitution to their grand canonical counterpart, which allows for simple intuitive incorporation of the influence of multiple competing transcription factor binding sites. As an example of the strength of this approach, we build on these results to present an analytical description of transcriptional regulation of the lac operon. PMID:28686609

  7. Arp2/3 complex inhibition radically alters lamellipodial actin architecture, suspended cell shape, and the cell spreading process

    PubMed Central

    Henson, John H.; Yeterian, Mesrob; Weeks, Richard M.; Medrano, Angela E.; Brown, Briana L.; Geist, Heather L.; Pais, Mollyann D.; Oldenbourg, Rudolf; Shuster, Charles B.

    2015-01-01

    Recent studies have investigated the dendritic actin cytoskeleton of the cell edge's lamellipodial (LP) region by experimentally decreasing the activity of the actin filament nucleator and branch former, the Arp2/3 complex. Here we extend these studies via pharmacological inhibition of the Arp2/3 complex in sea urchin coelomocytes, cells that possess an unusually broad LP region and display correspondingly exaggerated centripetal flow. Using light and electron microscopy, we demonstrate that Arp2/3 complex inhibition via the drug CK666 dramatically altered LP actin architecture, slowed centripetal flow, drove a lamellipodial-to-filopodial shape change in suspended cells, and induced a novel actin structural organization during cell spreading. A general feature of the CK666 phenotype in coelomocytes was transverse actin arcs, and arc generation was arrested by a formin inhibitor. We also demonstrate that CK666 treatment produces actin arcs in other cells with broad LP regions, namely fish keratocytes and Drosophila S2 cells. We hypothesize that the actin arcs made visible by Arp2/3 complex inhibition in coelomocytes may represent an exaggerated manifestation of the elongate mother filaments that could possibly serve as the scaffold for the production of the dendritic actin network. PMID:25568343

  8. Molecular Architecture of the 40S⋅eIF1⋅eIF3 Translation Initiation Complex

    PubMed Central

    Erzberger, Jan P.; Stengel, Florian; Pellarin, Riccardo; Zhang, Suyang; Schaefer, Tanja; Aylett, Christopher H.S.; Cimermančič, Peter; Boehringer, Daniel; Sali, Andrej; Aebersold, Ruedi; Ban, Nenad

    2014-01-01

    Summary Eukaryotic translation initiation requires the recruitment of the large, multiprotein eIF3 complex to the 40S ribosomal subunit. We present X-ray structures of all major components of the minimal, six-subunit Saccharomyces cerevisiae eIF3 core. These structures, together with electron microscopy reconstructions, cross-linking coupled to mass spectrometry, and integrative structure modeling, allowed us to position and orient all eIF3 components on the 40S⋅eIF1 complex, revealing an extended, modular arrangement of eIF3 subunits. Yeast eIF3 engages 40S in a clamp-like manner, fully encircling 40S to position key initiation factors on opposite ends of the mRNA channel, providing a platform for the recruitment, assembly, and regulation of the translation initiation machinery. The structures of eIF3 components reported here also have implications for understanding the architecture of the mammalian 43S preinitiation complex and the complex of eIF3, 40S, and the hepatitis C internal ribosomal entry site RNA. PMID:25171412

  9. Metal coordination architectures of N-propionyl-1-hydroxy-2-naphthoylhydrazide: From metalladiazamacrocycles to trinuclear complexes

    NASA Astrophysics Data System (ADS)

    Shi, Xuefeng; Li, Dacheng; Wang, Suna; Zeng, Suyuan; Wang, Daqi; Dou, Jianmin

    2010-09-01

    Two metalladiazamacrocycles, 24-membered octanuclear [Mn 8(pnhz) 8(DMF) 5(MeOH) 3]2DMF 3.5MeOH ( 1) and 18 -membered hexanuclear [Fe 6(pnhz) 6(DMF) 6] ( 2), and two linear trinuclear complexes, [Cu 3(pnhz) 2(Py) 6] 2Py ( 3) and [Ni 3(pnhz) 2(Py) 4] ( 4), have been synthesized based on a trianionic pentadentate bridging ligand N-propionyl-1-hydroxy-2-naphthoylhydrazide (H 3pnhz). The complexes are characterized by elemental analysis, IR, UV-vis spectroscopy and single-crystal X-ray diffraction. The nature of metal ions and steric effect of N-propionyl-1-hydroxy-2-naphthoylhydrazide ligand play key roles in the formation of complexes with different nuclearity. Complexes 1, 2 and 3 exhibit antiferromagnetic coupling interactions between the metal centers.

  10. Architecture of the ribosome-channel complex derived from native membranes.

    PubMed

    Ménétret, Jean-François; Hegde, Ramanujan S; Heinrich, Sven U; Chandramouli, Preethi; Ludtke, Steven J; Rapoport, Tom A; Akey, Christopher W

    2005-04-29

    The mammalian Sec61 complex forms a protein translocation channel whose function depends upon its interaction with the ribosome and with membrane proteins of the endoplasmic reticulum (ER). To study these interactions, we determined structures of "native" ribosome-channel complexes derived from ER membranes. We find that the ribosome is linked to the channel by seven connections, but the junction may still provide a path for domains of nascent membrane proteins to move into the cytoplasm. In addition, the native channel is significantly larger than a channel formed by the Sec61 complex, due to the presence of a second membrane protein. We identified this component as TRAP, the translocon-associated protein complex. TRAP interacts with Sec61 through its transmembrane domain and has a prominent lumenal domain. The presence of TRAP in the native channel indicates that it may play a general role in translocation. Crystal structures of two Sec61 homologues were used to model the channel. This analysis indicates that there are four Sec61 complexes and two TRAP molecules in each native channel. Thus, we suggest that a single Sec61 complex may form a conduit for translocating polypeptides, while three copies of Sec61 play a structural role or recruit accessory factors such as TRAP.

  11. Architecture of CRM1/Exportin1 suggests how cooperativity is achieved during formation of a nuclear export complex.

    PubMed

    Petosa, Carlo; Schoehn, Guy; Askjaer, Peter; Bauer, Ulrike; Moulin, Martine; Steuerwald, Ulrich; Soler-López, Montserrat; Baudin, Florence; Mattaj, Iain W; Müller, Christoph W

    2004-12-03

    CRM1/Exportin1 mediates the nuclear export of proteins bearing a leucine-rich nuclear export signal (NES) by forming a cooperative ternary complex with the NES-bearing substrate and the small GTPase Ran. We present a structural model of human CRM1 based on a combination of X-ray crystallography, homology modeling, and electron microscopy. The architecture of CRM1 resembles that of the import receptor transportin1, with 19 HEAT repeats and a large loop implicated in Ran binding. Residues critical for NES recognition are identified adjacent to the cysteine residue targeted by leptomycin B (LMB), a specific CRM1 inhibitor. We present evidence that a conformational change of the Ran binding loop accounts for the cooperativity of Ran- and substrate binding and for the selective enhancement of CRM1-mediated export by the cofactor RanBP3. Our findings indicate that a single architectural and mechanistic framework can explain the divergent effects of RanGTP on substrate binding by many import and export receptors.

  12. Optical probing of long-range spatial correlation and symmetry in complex biophotonic architectures on transparent insect wings

    NASA Astrophysics Data System (ADS)

    Kumar, Pramod; Shamoon, Danish; Singh, Dhirendra P.; Mandal, Sudip; Singh, Kamal P.

    2015-02-01

    We experimentally probe the structural organization of complex bio-photonic architecture on transparent insect wings by a simple, non-invasive, real-time optical technique. A stable and reproducible far-field diffraction pattern in transmission was observed using collimated cw and broadband fs laser pulses. A quantitative analysis of the observed diffraction pattern unveiled long-range quasi-periodic order in the arrangement of the microstructures over mm scale. These observations agree well with the Fourier analysis of SEM images of the wing taken at various length scales. We propose a simple quantitative model based on optical diffraction by an array of non overlapping microstructures with minimal disorder which supports our experimental observations. We observed a rotation of the original diffraction profile by scanning the laser beam across the wing sample which gives direct signature of organizational symmetry in microstructure arrangements at various length scales. In addition, we report the first optical detection of reorganization in the photonic architecture on the Drosophila wings by various genetic mutations. These results have potential for the design and development of diffractive optical components for applied photonics and may open up new opportunities in biomimetic device research.

  13. Multiple across-strain and within-strain QTLs suggest highly complex genetic architecture for hypoxia tolerance in channel catfish.

    PubMed

    Wang, Xiaozhu; Liu, Shikai; Jiang, Chen; Geng, Xin; Zhou, Tao; Li, Ning; Bao, Lisui; Li, Yun; Yao, Jun; Yang, Yujia; Zhong, Xiaoxiao; Jin, Yulin; Dunham, Rex; Liu, Zhanjiang

    2017-02-01

    The ability to survive hypoxic conditions is important for various organisms, especially for aquatic animals. Teleost fish, representing more than 50 % of vertebrate species, are extremely efficient in utilizing low levels of dissolved oxygen in water. However, huge variations exist among various taxa of fish in their ability to tolerate hypoxia. In aquaculture, hypoxia tolerance is among the most important traits because hypoxia can cause major economic losses. Genetic enhancement for hypoxia tolerance in catfish is of great interest, but little was done with analysis of the genetic architecture of hypoxia tolerance. The objective of this study was to conduct a genome-wide association study to identify QTLs for hypoxia tolerance using the catfish 250K SNP array with channel catfish families from six strains. Multiple significant and suggestive QTLs were identified across and within strains. One significant QTL and four suggestive QTLs were identified across strains. Six significant QTLs and many suggestive QTLs were identified within strains. There were rare overlaps among the QTLs identified within the six strains, suggesting a complex genetic architecture of hypoxia tolerance. Overall, within-strain QTLs explained larger proportion of phenotypic variation than across-strain QTLs. Many of genes within these identified QTLs have known functions for regulation of oxygen metabolism and involvement in hypoxia responses. Pathway analysis indicated that most of these genes were involved in MAPK or PI3K/AKT/mTOR signaling pathways that were known to be important for hypoxia-mediated angiogenesis, cell proliferation, apoptosis and survival.

  14. Molecular architecture of the αβ T cell receptor-CD3 complex.

    PubMed

    Birnbaum, Michael E; Berry, Richard; Hsiao, Yu-Shan; Chen, Zhenjun; Shingu-Vazquez, Miguel A; Yu, Xiaoling; Waghray, Deepa; Fischer, Suzanne; McCluskey, James; Rossjohn, Jamie; Walz, Thomas; Garcia, K Christopher

    2014-12-09

    αβ T-cell receptor (TCR) activation plays a crucial role for T-cell function. However, the TCR itself does not possess signaling domains. Instead, the TCR is noncovalently coupled to a conserved multisubunit signaling apparatus, the CD3 complex, that comprises the CD3εγ, CD3εδ, and CD3ζζ dimers. How antigen ligation by the TCR triggers CD3 activation and what structural role the CD3 extracellular domains (ECDs) play in the assembled TCR-CD3 complex remain unclear. Here, we use two complementary structural approaches to gain insight into the overall organization of the TCR-CD3 complex. Small-angle X-ray scattering of the soluble TCR-CD3εδ complex reveals the CD3εδ ECDs to sit underneath the TCR α-chain. The observed arrangement is consistent with EM images of the entire TCR-CD3 integral membrane complex, in which the CD3εδ and CD3εγ subunits were situated underneath the TCR α-chain and TCR β-chain, respectively. Interestingly, the TCR-CD3 transmembrane complex bound to peptide-MHC is a dimer in which two TCRs project outward from a central core composed of the CD3 ECDs and the TCR and CD3 transmembrane domains. This arrangement suggests a potential ligand-dependent dimerization mechanism for TCR signaling. Collectively, our data advance our understanding of the molecular organization of the TCR-CD3 complex, and provides a conceptual framework for the TCR activation mechanism.

  15. Molecular architecture of the αβ T cell receptor–CD3 complex

    PubMed Central

    Birnbaum, Michael E.; Berry, Richard; Hsiao, Yu-Shan; Chen, Zhenjun; Shingu-Vazquez, Miguel A.; Yu, Xiaoling; Waghray, Deepa; Fischer, Suzanne; McCluskey, James; Rossjohn, Jamie; Walz, Thomas; Garcia, K. Christopher

    2014-01-01

    αβ T-cell receptor (TCR) activation plays a crucial role for T-cell function. However, the TCR itself does not possess signaling domains. Instead, the TCR is noncovalently coupled to a conserved multisubunit signaling apparatus, the CD3 complex, that comprises the CD3εγ, CD3εδ, and CD3ζζ dimers. How antigen ligation by the TCR triggers CD3 activation and what structural role the CD3 extracellular domains (ECDs) play in the assembled TCR–CD3 complex remain unclear. Here, we use two complementary structural approaches to gain insight into the overall organization of the TCR–CD3 complex. Small-angle X-ray scattering of the soluble TCR–CD3εδ complex reveals the CD3εδ ECDs to sit underneath the TCR α-chain. The observed arrangement is consistent with EM images of the entire TCR–CD3 integral membrane complex, in which the CD3εδ and CD3εγ subunits were situated underneath the TCR α-chain and TCR β-chain, respectively. Interestingly, the TCR–CD3 transmembrane complex bound to peptide–MHC is a dimer in which two TCRs project outward from a central core composed of the CD3 ECDs and the TCR and CD3 transmembrane domains. This arrangement suggests a potential ligand-dependent dimerization mechanism for TCR signaling. Collectively, our data advance our understanding of the molecular organization of the TCR–CD3 complex, and provides a conceptual framework for the TCR activation mechanism. PMID:25422432

  16. Collection mode surface plasmon fibre sensors: a new biosensing platform.

    PubMed

    François, A; Boehm, J; Oh, S Y; Kok, T; Monro, T M

    2011-03-15

    Sensors based on surface plasmon resonance (SPR) allow rapid, label-free, highly sensitive detection, and indeed this phenomenon underpins the only label-free optical biosensing technology that is available commercially. In these sensors, the existence of surface plasmons is inferred indirectly from absorption features that correspond to the coupling of light into a thin metallic film. Although SPR is not intrinsically a radiative process, when the metallic coating which support the plasmonic wave exhibits a significant surface roughness, the surface plasmon can itself couple to the local photon states, and emit light. Here we show that using silver coated optical fibres, this novel SPR transducing mechanism offers significant advantages compare to traditional reflectance based measurements such as lower dependency on the metallic thickness and higher signal to noise ratio. Furthermore, we show that more complex sensor architectures with multiple sensing regions scattered along a single optical fibre enable multiplexed detection and dynamic self referencing of the sensing signal. Moreover, this alternative approach allows to combine two different sensing technologies, SPR and fluorescence sensing within the same device, which has never been demonstrated previously. As a preliminary proof of concept of potential application, this approach has been used to demonstrate the detection of the seasonal influenza A virus.

  17. Architecture of complex I and its implications for electron transfer and proton pumping.

    PubMed

    Zickermann, Volker; Kerscher, Stefan; Zwicker, Klaus; Tocilescu, Maja A; Radermacher, Michael; Brandt, Ulrich

    2009-06-01

    Proton pumping NADH:ubiquinone oxidoreductase (complex I) is the largest and remains by far the least understood enzyme complex of the respiratory chain. It consists of a peripheral arm harbouring all known redox active prosthetic groups and a membrane arm with a yet unknown number of proton translocation sites. The ubiquinone reduction site close to iron-sulfur cluster N2 at the interface of the 49-kDa and PSST subunits has been mapped by extensive site directed mutagenesis. Independent lines of evidence identified electron transfer events during reduction of ubiquinone to be associated with the potential drop that generates the full driving force for proton translocation with a 4H(+)/2e(-) stoichiometry. Electron microscopic analysis of immuno-labelled native enzyme and of a subcomplex lacking the electron input module indicated a distance of 35-60 A of cluster N2 to the membrane surface. Resolution of the membrane arm into subcomplexes showed that even the distal part harbours subunits that are prime candidates to participate in proton translocation because they are homologous to sodium/proton antiporters and contain conserved charged residues in predicted transmembrane helices. The mechanism of redox linked proton translocation by complex I is largely unknown but has to include steps where energy is transmitted over extremely long distances. In this review we compile the available structural information on complex I and discuss implications for complex I function.

  18. Architecture of complex I and its implications for electron transfer and proton pumping

    PubMed Central

    Zickermann, Volker; Kerscher, Stefan; Zwicker, Klaus; Tocilescu, Maja A.; Radermacher, Michael; Brandt, Ulrich

    2009-01-01

    Proton pumping NADH:ubiquinone oxidoreductase (complex I) is the largest and remains by far the least understood enzyme complex of the respiratory chain. It consists of a peripheral arm harbouring all known redox active prosthetic groups and a membrane arm with a yet unknown number of proton translocation sites. The ubiquinone reduction site close to iron-sulfur cluster N2 at the interface of the 49-kDa and PSST subunits has been mapped by extensive site directed mutagenesis. Independent lines of evidence identified electron transfer events during reduction of ubiquinone to be associated with the potential drop that generates the full driving force for proton translocation with a 4 H+/2e− stoichiometry. Electron microscopic analysis of immuno-labelled native enzyme and of a subcomplex lacking the electron input module indicated a distance of 35–60 Å of cluster N2 to the membrane surface. Resolution of the membrane arm into subcomplexes showed that even the distal part harbours subunits that are prime candidates to participate in proton translocation because they are homologous to sodium/proton antiporters and contain conserved charged residues in predicted transmembrane helices. The mechanism of redox linked proton translocation by complex I is largely unknown but has to include steps where energy is transmitted over extremely long distances. In this review we compile the available structural information on complex I and discuss implications for complex I function. PMID:19366614

  19. Acquisition Program Teamwork and Performance Seen Anew: Exposing the Interplay of Architecture and Behaviors in Complex Defense Programs

    DTIC Science & Technology

    2016-04-30

    for assuming past performance is a good predictor of the future” (Khamooshi & Golafshani, 2014). EV Variants and Control Points Colin and Vanhoucke...qÜáêíÉÉåíÜ=^ååì~ä= ^Åèìáëáíáçå=oÉëÉ~êÅÜ= póãéçëáìã= qÜìêëÇ~ó=pÉëëáçåë= sçäìãÉ=ff= = Acquisition Program Teamwork and Performance Seen Anew: Exposing the...and Performance Seen Anew: Exposing the Interplay of Architecture and Behaviors in Complex Defense Programs Eric Rebentisch, Research Associate, MIT

  20. Multiplexed fibre optic sensing in the distal lung (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Choudhary, Tushar R.; Tanner, Michael G.; Megia-Fernandez, Alicia; Harrington, Kerrianne; Wood, Harry A.; Chankeshwara, Sunay; Zhu, Patricia; Choudhury, Debaditya; Yu, Fei; Thomson, Robert R.; Duncan, Rory R.; Dhaliwal, Kevin; Bradley, Mark

    2017-02-01

    We present a toolkit for a multiplexed pH and oxygen sensing probe in the distal lung using multicore fibres. Measuring physiological relevant parameters like pH and oxygen is of significant importance in understanding changes associated with disease pathology. We present here, a single multicore fibre based pH and oxygen sensing probe which can be used with a standard bronchoscope to perform in vivo measurements in the distal lung. The multiplexed probe consists of fluorescent pH sensors (fluorescein based) and oxygen sensors (Palladium porphyrin complex based) covalently bonded to silica microspheres (10 µm) loaded on the distal facet of a 19 core (10 µm core diameter) multicore fibre (total diameter of 150 µm excluding coating). Pits are formed by selectively etching the cores using hydrofluoric acid, multiplexing is achieved through the self-location of individual probes on differing cores. This architecture can be expanded to include probes for further parameters. Robust measurements are demonstrated of self-referencing fluorophores, not limited by photobleaching, with short (100ms) measurement times at low ( 10µW) illumination powers. We have performed on bench calibration and tests of in vitro tissue models and in an ovine whole lung model to validate our sensors. The pH sensor is demonstrated in the physiologically relevant range of pH 5 to pH 8.5 and with an accuracy of ± 0.05 pH units. The oxygen sensor is demonstrated in gas mixtures downwards from 20% oxygen and in liquid saturated with 20% oxygen mixtures ( 8mg/L) down to full depletion (0mg/L) with 0.5mg/L accuracy.

  1. MRN1 Implicates Chromatin Remodeling Complexes and Architectural Factors in mRNA Maturation

    PubMed Central

    Düring, Louis; Thorsen, Michael; Petersen, Darima Sophia Njama; Køster, Brian; Jensen, Torben Heick; Holmberg, Steen

    2012-01-01

    A functional relationship between chromatin structure and mRNA processing events has been suggested, however, so far only a few involved factors have been characterized. Here we show that rsc nhp6ΔΔ mutants, deficient for the function of the chromatin remodeling factor RSC and the chromatin architectural proteins Nhp6A/Nhp6B, accumulate intron-containing pre-mRNA at the restrictive temperature. In addition, we demonstrate that rsc8-ts16 nhp6ΔΔ cells contain low levels of U6 snRNA and U4/U6 di-snRNA that is further exacerbated after two hours growth at the restrictive temperature. This change in U6 snRNA and U4/U6 di-snRNA levels in rsc8-ts16 nhp6ΔΔ cells is indicative of splicing deficient conditions. We identify MRN1 (multi-copy suppressor of rsc nhp6ΔΔ) as a growth suppressor of rsc nhp6ΔΔ synthetic sickness. Mrn1 is an RNA binding protein that localizes both to the nucleus and cytoplasm. Genetic interactions are observed between 2 µm-MRN1 and the splicing deficient mutants snt309Δ, prp3, prp4, and prp22, and additional genetic analyses link MRN1, SNT309, NHP6A/B, SWI/SNF, and RSC supporting the notion of a role of chromatin structure in mRNA processing. PMID:23028530

  2. Use of Dynamic Models and Operational Architecture to Solve Complex Navy Challenges

    NASA Technical Reports Server (NTRS)

    Grande, Darby; Black, J. Todd; Freeman, Jared; Sorber, TIm; Serfaty, Daniel

    2010-01-01

    The United States Navy established 8 Maritime Operations Centers (MOC) to enhance the command and control of forces at the operational level of warfare. Each MOC is a headquarters manned by qualified joint operational-level staffs, and enabled by globally interoperable C41 systems. To assess and refine MOC staffing, equipment, and schedules, a dynamic software model was developed. The model leverages pre-existing operational process architecture, joint military task lists that define activities and their precedence relations, as well as Navy documents that specify manning and roles per activity. The software model serves as a "computational wind-tunnel" in which to test a MOC on a mission, and to refine its structure, staffing, processes, and schedules. More generally, the model supports resource allocation decisions concerning Doctrine, Organization, Training, Material, Leadership, Personnel and Facilities (DOTMLPF) at MOCs around the world. A rapid prototype effort efficiently produced this software in less than five months, using an integrated process team consisting of MOC military and civilian staff, modeling experts, and software developers. The work reported here was conducted for Commander, United States Fleet Forces Command in Norfolk, Virginia, code N5-0LW (Operational Level of War) that facilitates the identification, consolidation, and prioritization of MOC capabilities requirements, and implementation and delivery of MOC solutions.

  3. Complex composite engineering architectures for nuclear and high-radiation environments

    SciTech Connect

    Kornreich, Drew E; Vaidya, Rajendra U; Ammerman, Curtt N

    2010-01-01

    Integrated Computational Materials Engineering (ICME) is a novel overarching approach to bridge length and time scales in computational materials science and engineering. This approach integrates all elements of multi-scale modeling (including various empirical and science-based models) with materials informatics to provide users the opportunity to tailor material selections based on stringent application needs. Typically, materials engineering has focused on structural requirements (stress, strain, modulus, fracture toughness etc.) while multi-scale modeling has been science focused (mechanical threshold strength model, grain-size models, solid-solution strengthening models etc.). Materials informatics (mechanical property inventories) on the other hand, is extensively data focused. All of these elements are combined within the framework of ICME to create architecture for the development, selection and design new composite materials for challenging environments. We propose development of the foundations for applying ICME to composite materials development for nuclear and high-radiation environments (including nuclear-fusion energy reactors, nuclear-fission reactors, and accelerators). We expect to combine all elements of current material models (including thermo-mechanical and finite-element models) into the ICME framework. This will be accomplished through the use of a various mathematical modeling constructs. These constructs will allow the integration of constituent models, which in tum would allow us to use the adaptive strengths of using a combinatorial scheme (fabrication and computational) for creating new composite materials. A sample problem where these concepts are used is provided in this summary.

  4. Supramolecular architecture of betulin diacetate complexes with arabinogalactan from Larix sibirica.

    PubMed

    Mikhailenko, Mikhail A; Shakhtshneider, Tatyana P; Eltsov, Ilia V; Kozlov, Alexander S; Kuznetsova, Svetlana A; Karacharov, Аnton А; Boldyrev, Vladimir V

    2016-03-15

    Supramolecular ensembles of arabinogalactan (AG) and its complexes with betulin diacetate (BDA) were studied in water and dimethyl sulfoxide (DMSO) using ablation, induced by submillimeter radiation from the free electron laser. Solutions of 1wt% AG resulted in formation of aerosol particles with a maximum size of 60-70nm. In contrast, with DMSO as the solvent, the majority of particles were significantly smaller. Nevertheless, the addition of water shifted the particle size distribution to a larger size, suggesting the cross-linking of AG chains due to hydrogen bonding through water molecules. The ensembles of molecules were larger in solutions of the AG-BDA complex as compared to pure AG aqueous solution, and the distribution was narrow. The role of side chain interactions in the formation of AG-BDA complexes in aqueous solutions was confirmed by NMR.

  5. The Architecture of Complex Systems: Emergence of Scaling in Real Networks

    NASA Astrophysics Data System (ADS)

    Barabási, Albert-László

    2002-03-01

    Networks with complex topology describe systems as diverse as the cell or the World Wide Web. The analysis of the metabolic and protein network of various organisms show that cells and complex man-made networks, such as the Internet or the world wide web, share the same large-scale topology. In the past few years we have learned that the emergence of these networks is driven by self-organizing processes that are governed by simple but generic laws, that can be captured using the tools of statistical mechanics. The goal of the talk is to briefly review these advances, aiming to uncover the organizing principles that govern the topology of complex networks. For more information see http://www.nd.edu/ networks.

  6. Fractal dimension of trabecular bone: comparison of three histomorphometric computed techniques for measuring the architectural two-dimensional complexity.

    PubMed

    Chappard, D; Legrand, E; Haettich, B; Chalès, G; Auvinet, B; Eschard, J P; Hamelin, J P; Baslé, M F; Audran, M

    2001-11-01

    Trabecular bone has been reported as having two-dimensional (2-D) fractal characteristics at the histological level, a finding correlated with biomechanical properties. However, several fractal dimensions (D) are known and computational ways to obtain them vary considerably. This study compared three algorithms on the same series of bone biopsies, to obtain the Kolmogorov, Minkowski-Bouligand, and mass-radius fractal dimensions. The relationships with histomorphometric descriptors of the 2-D trabecular architecture were investigated. Bone biopsies were obtained from 148 osteoporotic male patients. Bone volume (BV/TV), trabecular characteristics (Tb.N, Tb.Sp, Tb.Th), strut analysis, star volumes (marrow spaces and trabeculae), inter-connectivity index, and Euler-Poincaré number were computed. The box-counting method was used to obtain the Kolmogorov dimension (D(k)), the dilatation method for the Minkowski-Bouligand dimension (D(MB)), and the sandbox for the mass-radius dimension (D(MR)) and lacunarity (L). Logarithmic relationships were observed between BV/TV and the fractal dimensions. The best correlation was obtained with D(MR) and the lowest with D(MB). Lacunarity was correlated with descriptors of the marrow cavities (ICI, star volume, Tb.Sp). Linear relationships were observed among the three fractal techniques which appeared highly correlated. A cluster analysis of all histomorphometric parameters provided a tree with three groups of descriptors: for trabeculae (Tb.Th, strut); for marrow cavities (Euler, ICI, Tb.Sp, star volume, L); and for the complexity of the network (Tb.N and the three D's). A sole fractal dimension cannot be used instead of the classic 2-D descriptors of architecture; D rather reflects the complexity of branching trabeculae. Computation time is also an important determinant when choosing one of these methods.

  7. Identification of ORC1/CDC6-Interacting Factors in Trypanosoma brucei Reveals Critical Features of Origin Recognition Complex Architecture

    PubMed Central

    Tiengwe, Calvin; Marcello, Lucio; Farr, Helen; Gadelha, Catarina; Burchmore, Richard; Barry, J. David; Bell, Stephen D.; McCulloch, Richard

    2012-01-01

    DNA Replication initiates by formation of a pre-replication complex on sequences termed origins. In eukaryotes, the pre-replication complex is composed of the Origin Recognition Complex (ORC), Cdc6 and the MCM replicative helicase in conjunction with Cdt1. Eukaryotic ORC is considered to be composed of six subunits, named Orc1–6, and monomeric Cdc6 is closely related in sequence to Orc1. However, ORC has been little explored in protists, and only a single ORC protein, related to both Orc1 and Cdc6, has been shown to act in DNA replication in Trypanosoma brucei. Here we identify three highly diverged putative T. brucei ORC components that interact with ORC1/CDC6 and contribute to cell division. Two of these factors are so diverged that we cannot determine if they are eukaryotic ORC subunit orthologues, or are parasite-specific replication factors. The other we show to be a highly diverged Orc4 orthologue, demonstrating that this is one of the most widely conserved ORC subunits in protists and revealing it to be a key element of eukaryotic ORC architecture. Additionally, we have examined interactions amongst the T. brucei MCM subunits and show that this has the conventional eukaryotic heterohexameric structure, suggesting that divergence in the T. brucei replication machinery is limited to the earliest steps in origin licensing. PMID:22412905

  8. Insight into the architecture of the NuRD complex: structure of the RbAp48-MTA1 subcomplex.

    PubMed

    Alqarni, Saad S M; Murthy, Andal; Zhang, Wei; Przewloka, Marcin R; Silva, Ana P G; Watson, Aleksandra A; Lejon, Sara; Pei, Xue Y; Smits, Arne H; Kloet, Susan L; Wang, Hongxin; Shepherd, Nicholas E; Stokes, Philippa H; Blobel, Gerd A; Vermeulen, Michiel; Glover, David M; Mackay, Joel P; Laue, Ernest D

    2014-08-08

    The nucleosome remodeling and deacetylase (NuRD) complex is a widely conserved transcriptional co-regulator that harbors both nucleosome remodeling and histone deacetylase activities. It plays a critical role in the early stages of ES cell differentiation and the reprogramming of somatic to induced pluripotent stem cells. Abnormalities in several NuRD proteins are associated with cancer and aging. We have investigated the architecture of NuRD by determining the structure of a subcomplex comprising RbAp48 and MTA1. Surprisingly, RbAp48 recognizes MTA1 using the same site that it uses to bind histone H4, showing that assembly into NuRD modulates RbAp46/48 interactions with histones. Taken together with other results, our data show that the MTA proteins act as scaffolds for NuRD complex assembly. We further show that the RbAp48-MTA1 interaction is essential for the in vivo integration of RbAp46/48 into the NuRD complex.

  9. Biological durability and oxidative potential of man-made vitreous fibres as compared to crocidolite asbestos fibres.

    PubMed

    Hippeli, S; Dornisch, K; Wiethege, T; Gillissen, A; Müller, K M; Elstner, E F

    2001-01-01

    In this study we investigated relationships between redox properties and biodurability of crocidolite asbestos fibres and three different man-made vitreous fibres (MMVF): traditional stone wool fibres (MMVF 21), glass fibres (MMVF 11) and refractory ceramic fibres (RCF). Each fibre type was incubated up to 22 weeks in four different incubation media: gamble solution (GS) pH 5.0 and pH 7.4, representing blood plasma without proteins, and surfactant-like solution (SLS) pH 5.0 and pH 7.4. During incubation time aliquots of incubation mixtures were removed and analysed in a biochemical model reaction, mimicking activated phagocytes. In addition, changes of fibre morphology and chemical composition were examined using SEM- and EDX-technology. In the presence of crocidolite asbestos fibres and MMVF 21 the formation of OH*-radicals according to the Haber-Weiss sequence could be demonstrated, whereas MMVF 11 and RCF showed no reactivity. Crocidolite asbestos fibres exhibited a significant higher activity compared with the stone wool fibres at the onset of incubation. The oxidative capacities of these fibre types were shown to depend on both specific surface area and iron content. The oxidative potentials of crocidolite asbestos fibres as well as MMVF 21 were not constant during incubation over several weeks in each incubation medium. The reactivities showed sinoidal curves including reactivities much higher than those at the onset of incubation time. These irregular changes of oxidative capacity may be explained by changes of the redox state of fibre surface-complexed iron. Furthermore our results showed clear differences between incubation of fibres in GS and SLS, respectively, indicating that phospholipids play an important part in fibre dissolution behaviour and oxidative reactivity. In conclusion we suggest, that biodurability testing procedures should not exclusively concentrate on dissolution rates of fibres. They should include fibre characteristics concerning known

  10. Genome-wide binding analysis of the transcription activator ideal plant architecture1 reveals a complex network regulating rice plant architecture.

    PubMed

    Lu, Zefu; Yu, Hong; Xiong, Guosheng; Wang, Jing; Jiao, Yongqing; Liu, Guifu; Jing, Yanhui; Meng, Xiangbing; Hu, Xingming; Qian, Qian; Fu, Xiangdong; Wang, Yonghong; Li, Jiayang

    2013-10-01

    Ideal plant architecture1 (IPA1) is critical in regulating rice (Oryza sativa) plant architecture and substantially enhances grain yield. To elucidate its molecular basis, we first confirmed IPA1 as a functional transcription activator and then identified 1067 and 2185 genes associated with IPA1 binding sites in shoot apices and young panicles, respectively, through chromatin immunoprecipitation sequencing assays. The Squamosa promoter binding protein-box direct binding core motif GTAC was highly enriched in IPA1 binding peaks; interestingly, a previously uncharacterized indirect binding motif TGGGCC/T was found to be significantly enriched through the interaction of IPA1 with proliferating cell nuclear antigen promoter binding factor1 or promoter binding factor2. Genome-wide expression profiling by RNA sequencing revealed IPA1 roles in diverse pathways. Moreover, our results demonstrated that IPA1 could directly bind to the promoter of rice teosinte branched1, a negative regulator of tiller bud outgrowth, to suppress rice tillering, and directly and positively regulate dense and erect panicle1, an important gene regulating panicle architecture, to influence plant height and panicle length. The elucidation of target genes of IPA1 genome-wide will contribute to understanding the molecular mechanisms underlying plant architecture and to facilitating the breeding of elite varieties with ideal plant architecture.

  11. Genome-Wide Binding Analysis of the Transcription Activator IDEAL PLANT ARCHITECTURE1 Reveals a Complex Network Regulating Rice Plant Architecture[W

    PubMed Central

    Lu, Zefu; Yu, Hong; Xiong, Guosheng; Wang, Jing; Jiao, Yongqing; Liu, Guifu; Jing, Yanhui; Meng, Xiangbing; Hu, Xingming; Qian, Qian; Fu, Xiangdong; Wang, Yonghong; Li, Jiayang

    2013-01-01

    IDEAL PLANT ARCHITECTURE1 (IPA1) is critical in regulating rice (Oryza sativa) plant architecture and substantially enhances grain yield. To elucidate its molecular basis, we first confirmed IPA1 as a functional transcription activator and then identified 1067 and 2185 genes associated with IPA1 binding sites in shoot apices and young panicles, respectively, through chromatin immunoprecipitation sequencing assays. The SQUAMOSA PROMOTER BINDING PROTEIN-box direct binding core motif GTAC was highly enriched in IPA1 binding peaks; interestingly, a previously uncharacterized indirect binding motif TGGGCC/T was found to be significantly enriched through the interaction of IPA1 with proliferating cell nuclear antigen PROMOTER BINDING FACTOR1 or PROMOTER BINDING FACTOR2. Genome-wide expression profiling by RNA sequencing revealed IPA1 roles in diverse pathways. Moreover, our results demonstrated that IPA1 could directly bind to the promoter of rice TEOSINTE BRANCHED1, a negative regulator of tiller bud outgrowth, to suppress rice tillering, and directly and positively regulate DENSE AND ERECT PANICLE1, an important gene regulating panicle architecture, to influence plant height and panicle length. The elucidation of target genes of IPA1 genome-wide will contribute to understanding the molecular mechanisms underlying plant architecture and to facilitating the breeding of elite varieties with ideal plant architecture. PMID:24170127

  12. Regional heritability advanced complex trait analysis for GPU and traditional parallel architectures.

    PubMed

    Cebamanos, L; Gray, A; Stewart, I; Tenesa, A

    2014-04-15

    Quantification of the contribution of genetic variation to phenotypic variation for complex traits becomes increasingly computationally demanding with increasing numbers of single-nucleotide polymorphisms and individuals. To meet the challenges in making feasible large-scale studies, we present the REgional heritability advanced complex trait analysis software. Adapted from advanced complex trait analysis (and, in turn, genome-wide complex trait analysis), it is tailored to exploit the parallelism present in modern traditional and graphics processing unit (GPU)-accelerated machines, from workstations to supercomputers. We adapt the genetic relationship matrix estimation algorithm to remove limitations on memory, allowing the analysis of large datasets. We build on this to develop a version of the code able to efficiently exploit GPU-accelerated systems for both the genetic relationship matrix and REstricted maximum likelihood (REML) parts of the analysis, offering substantial speedup over the traditional central processing unit version. We develop the ability to analyze multiple small regions of the genome across multiple compute nodes in parallel, following the 'regional heritability' approach. We demonstrate the new software using 1024 GPUs in parallel on one of the world's fastest supercomputers. The code is freely available at http://www.epcc.ed.ac.uk/software-products CONTACT: a.gray@ed.ac.uk. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  13. MICOS coordinates with respiratory complexes and lipids to establish mitochondrial inner membrane architecture

    PubMed Central

    Friedman, Jonathan R; Mourier, Arnaud; Yamada, Justin; McCaffery, J Michael; Nunnari, Jodi

    2015-01-01

    The conserved MICOS complex functions as a primary determinant of mitochondrial inner membrane structure. We address the organization and functional roles of MICOS and identify two independent MICOS subcomplexes: Mic27/Mic10/Mic12, whose assembly is dependent on respiratory complexes and the mitochondrial lipid cardiolipin, and Mic60/Mic19, which assembles independent of these factors. Our data suggest that MICOS subcomplexes independently localize to cristae junctions and are connected via Mic19, which functions to regulate subcomplex distribution, and thus, potentially also cristae junction copy number. MICOS subunits have non-redundant functions as the absence of both MICOS subcomplexes results in more severe morphological and respiratory growth defects than deletion of single MICOS subunits or subcomplexes. Mitochondrial defects resulting from MICOS loss are caused by misdistribution of respiratory complexes in the inner membrane. Together, our data are consistent with a model where MICOS, mitochondrial lipids and respiratory complexes coordinately build a functional and correctly shaped mitochondrial inner membrane. DOI: http://dx.doi.org/10.7554/eLife.07739.001 PMID:25918844

  14. Fibre and enteral nutrition.

    PubMed Central

    Silk, D B

    1989-01-01

    The recent launch of a number of fibre enriched polymeric diet in the United States and Europe has stimulated considerable interest in the topic of fibre and enteral nutrition, and several commercial concerns appear to be under considerable pressures from their consumers to produce similar products. As a means of identifying areas of potential application of fibre to enteral nutrition some of the recent knowledge gained about the physical properties of dietary fibre and the processes involved in the intestinal assimilation of fibre has been reviewed. Two areas of interest are identifiable. The first relates to the bulking properties of fibre and the application of this to the regulation of bowel function in enterally fed patients. It is clear from the clinical studies that have been reviewed that there remains a paucity of controlled data, and a great deal more research is needed before widespread use of fibre supplemented diets can be supported. Perhaps of greater interest academically is the potentially beneficial effects that appear to be exerted by the VFA's, liberated as a consequence of colonic bacterial fermentation of fibre, on morphology and function of ileal and colonic mucosa. Although there are a number of potential applications of fibre supplemented enteral diets in this area, more research is required before any firm recommendations can be made about recommending their use. The one exception concerns patients with the nutritionally inadequate short bowel syndrome. There does seem to be sufficient experimental evidence to suggest that clinical studies should be commenced using a pectin supplemented predigested 'elemental' diet in these patients. Overall therefore, one is forced to conclude that the increasing interest and use of fibre supplemented enteral diets is being driven more by market than scientific forces. Nevertheless, the promotion of these diets has already provided a powerful stimulus to the scientific community, and it remains entirely

  15. Building multistate redox-active architectures using metal-complex functionalized perylene bis-imides.

    PubMed

    Goretzki, Gudrun; Davies, E Stephen; Argent, Stephen P; Warren, John E; Blake, Alexander J; Champness, Neil R

    2009-11-02

    A series of multistate redox-active architectures has been synthesized, structurally characterized, and their optical and redox properties investigated. Specifically, two redox-active ferrocene or cobalt-dithiolene moieties have been introduced to the "bay" region of perylene-bisimides. Three of these disubstituted perylene-bisimide species have been structurally characterized by single crystal X-ray diffraction, confirming the twisted nature of the central perylene core. The first isomeric pair of disubstituted perylene-bisimide isomers, N,N'-di-(n-butyl)-1,7-diferrocenyl-perylene-3,4:9,10-tetracarboxylic acid bisimide (2) and N,N'-di-(n-butyl)-1,6-diferrocenyl-perylene-3,4:9,10-tetracarboxylic acid bisimide (3), structurally characterized by single crystal X-ray diffraction are reported and compared. Structural characterization of the cobalt-dithiolene substituted perylene-bisimide, N,N'-di-(n-butyl)-1,7-dicyclopentadienyl-cobalt(II)-dithiolenyl-perylene-3,4:9,10-tetracarboxylic acid bisimide (4), reveals the expected twisting of the perylene core and confirms the ene-dithiolate geometry of the cobalt dithiolene moiety. Cyclic voltammetry measurements, coupled with spectroelectrochemcial and electron paramagnetic resonance studies, of 1-4, where 1 is N,N'-di-(n-butyl)-1,7-diethynylferrocenyl-perylene-3,4:9,10-tetracarboxylic acid bisimide, reveal the two anticipated perylene-bisimide based reductions. In addition, for the ferrocene substituted compounds, 1-3, a single reversible two-electron oxidation is seen with only a small degree of communication between the ferrocene groups observed in the 1,6-isomer where the two ferrocene groups are attached to the same naphthyl moiety. In the case of 4, two reversible reductions associated with the cobalt-dithiolene moieties are observed, confirming communication across the reduced perylene core.

  16. Genetic architecture of complex agronomic traits examined in two testcross populations of rye (Secale cereale L.)

    PubMed Central

    2012-01-01

    Background Rye is an important European crop used for food, feed, and bioenergy. Several quality and yield-related traits are of agronomic relevance for rye breeding programs. Profound knowledge of the genetic architecture of these traits is needed to successfully implement marker-assisted selection programs. Nevertheless, little is known on quantitative loci underlying important agronomic traits in rye. Results We used 440 F3:4 inbred lines from two biparental populations (Pop-A, Pop-B) fingerprinted with about 800 to 900 SNP, SSR and/or DArT markers and outcrossed them to a tester for phenotyping. The resulting hybrids and their parents were evaluated for grain yield, single-ear weight, test weight, plant height, thousand-kernel weight, falling number, protein, starch, soluble and total pentosan contents in up to ten environments in Central Europe. The quality of the phenotypic data was high reflected by moderate to high heritability estimates. QTL analyses revealed a total of 31 QTL for Pop-A and 52 for Pop-B. QTL x environment interactions were significant (P < 0.01) in most cases but variance of QTL main effect was more prominent. Conclusions QTL mapping was successfully applied based on two segregating rye populations. QTL underlying grain yield and several quality traits had small effects. In contrast, thousand-kernel weight, test weight, falling number and starch content were affected by several major QTL with a high frequency of occurrence in cross validation. These QTL explaining a large proportion of the genotypic variance can be exploited in marker-assisted selection programs and are candidates for further genetic dissection. PMID:23244545

  17. Modelling the extrusion of preforms for microstructured optical fibres

    NASA Astrophysics Data System (ADS)

    Tronnolone, Hayden; Stokes, Yvonne; Crowdy, Darren

    2013-11-01

    Owing to a novel design, microstructured optical fibres (MOFs) promise the realisation of fibres with effectively any desired optical properties. MOFs are typically constructed from glass and employ a series of air channels aligned along the fibre axis to form a waveguide. The construction of MOFs by first extruding a preform and then drawing this into the final fibre has the potential to produce fibres on an industrial scale; however, this is hindered by a limited understanding of the fluid flow that arises during this process. We focus on the extrusion stage of fabrication and discuss a model of the fibre evolution based upon complex-variable techniques. The relative influence of the various physical processes involved is discussed, along with limitations of the model.

  18. A fibre optic oxygen sensor for monitoring of human breathing

    NASA Astrophysics Data System (ADS)

    Chen, Rongsheng; Farmery, Andrew D.; Chen, Rui; Hahn, Clive E. W.

    2011-11-01

    A reliable and cost effective fibre optic oxygen sensor for monitoring of human breathing has been developed using a normal 200μm silica core/silica cladding optical fibre and a polymer sensing matrix. The fibre optic oxygen sensor is based on the fluorescence quenching of a fluorophore by oxygen. The sensing matrix, containing immobilized Pt(II) complexes, was coated at the end of the silica core/silica cladding optical fibre. The sensitivity and time response of the sensor were evaluated using the method of luminescence lifetime measurement. The polymer substrate influence on the time response of the sensor was improved by using a fibre taper design, and the response time of the optimized sensor was less than 200ms. This silica fibre based optic oxygen sensor is suitable for monitoring of patient breathing in intensive care unit in terms of safety and low cost.

  19. Corolla Is a Novel Protein That Contributes to the Architecture of the Synaptonemal Complex of Drosophila

    PubMed Central

    Collins, Kimberly A.; Unruh, Jay R.; Slaughter, Brian D.; Yu, Zulin; Lake, Cathleen M.; Nielsen, Rachel J.; Box, Kimberly S.; Miller, Danny E.; Blumenstiel, Justin P.; Perera, Anoja G.; Malanowski, Kathryn E.; Hawley, R. Scott

    2014-01-01

    In most organisms the synaptonemal complex (SC) connects paired homologs along their entire length during much of meiotic prophase. To better understand the structure of the SC, we aim to identify its components and to determine how each of these components contributes to SC function. Here, we report the identification of a novel SC component in Drosophila melanogaster female oocytes, which we have named Corolla. Using structured illumination microscopy, we demonstrate that Corolla is a component of the central region of the SC. Consistent with its localization, we show by yeast two-hybrid analysis that Corolla strongly interacts with Cona, a central element protein, demonstrating the first direct interaction between two inner-synaptonemal complex proteins in Drosophila. These observations help provide a more complete model of SC structure and function in Drosophila females. PMID:24913682

  20. Epistasis and natural selection shape the mutational architecture of complex traits.

    PubMed

    Jones, Adam G; Bürger, Reinhard; Arnold, Stevan J

    2014-05-14

    The evolutionary trajectories of complex traits are constrained by levels of genetic variation as well as genetic correlations among traits. As the ultimate source of all genetic variation is mutation, the distribution of mutations entering populations profoundly affects standing variation and genetic correlations. Here we use an individual-based simulation model to investigate how natural selection and gene interactions (that is, epistasis) shape the evolution of mutational processes affecting complex traits. We find that the presence of epistasis allows natural selection to mould the distribution of mutations, such that mutational effects align with the selection surface. Consequently, novel mutations tend to be more compatible with the current forces of selection acting on the population. These results suggest that in many cases mutational effects should be seen as an outcome of natural selection rather than as an unbiased source of genetic variation that is independent of other evolutionary processes.

  1. Heptacoordinate Co(II) complex: a new architecture for photochemical hydrogen production.

    PubMed

    Lucarini, Fiorella; Pastore, Mariachiara; Vasylevskyi, Serhii; Varisco, Massimo; Solari, Euro; Crochet, Aurelien; Fromm, Katharina M; Zobi, Fabio; Ruggi, Albert

    2017-04-11

    Hydrogen is a promising potential clean source of energy which can be produced using abundant and renewable resources (e.g. water and sunlight). Recently, hexacoordinate polypyridine cobalt complexes have gained great attention because of their stability and activity in water reduction catalysis. To further investigate the effect of coordination geometry on the catalytic activity, we synthesized and characterized the first heptacoordinate cobalt catalyst for light-driven hydrogen production in water. Photochemical experiments using [Ru(bpy)3]2+ as photosensitizer gave a turnover number (TON) of 16300 mol H2 (mol cat.)-1 achieved in two hours of irradiation with visible (475 nm) light. The results suggest that heptacoordinate cobalt complexes, never used so far in the field of light-driven hydrogen evolution, represent a promising alternative platform for the development of highly active photocatalysts.

  2. Critical Infrastructures as Complex Systems: A Multi-level Protection Architecture

    NASA Astrophysics Data System (ADS)

    Assogna, Pierluigi; Bertocchi, Glauco; Dicarlo, Antonio; Milicchio, Franco; Paoluzzi, Alberto; Scorzelli, Giorgio; Vicentino, Michele; Zollo, Roberto

    This paper describes a security platform as a complex system of holonic communities, that are hierarchically organized, but self-reconfigurable when some of them are detached or cannot otherwise operate. Furthermore, every possible subset of holons may work autonomously, while maintaining self-conscience of its own mission, action lines and goals. Each holonic unit, either elementary or composite, retains some capabilities for sensing (perception), transmissive apparatus (communication), computational processes (elaboration), authentication/authorization (information security), support for data exchange (visualization & interaction), actuators (mission), ambient representation (geometric reasoning), knowledge representation (logic reasoning), situation representation and forecasting (simulation), intelligent feedback (command & control). The higher the organizational level of the holonic unit, the more complex and sophisticated each of its characteristic features.

  3. Architecture of the botulinum neurotoxin complex: a molecular machine for protection and delivery

    PubMed Central

    Lam, Kwok-Ho; Jin, Rongsheng

    2015-01-01

    Botulinum neurotoxins (BoNTs) are extremely poisonous protein toxins that cause the fatal paralytic disease botulism. They are naturally produced in bacteria with several nontoxic neurotoxin-associated proteins (NAPs) and together they form a progenitor toxin complex (PTC), the largest bacterial toxin complex known. In foodborne botulism, the PTC functions as a molecular machine that helps BoNT breach the host defense in the gut. Here, we discuss the substantial recent advance in elucidating the atomic structures and assembly of the 14-subunit PTC, including structures of BoNT and four NAPs. These structural studies shed light on the molecular mechanisms by which BoNT is protected against the acidic environment and proteolytic destruction in the gastrointestinal tract, and how it is delivered across the intestinal epithelial barrier. PMID:25889616

  4. Mechanism of replication machinery assembly as revealed by the DNA ligase-PCNA-DNA complex architecture.

    PubMed

    Mayanagi, Kouta; Kiyonari, Shinichi; Saito, Mihoko; Shirai, Tsuyoshi; Ishino, Yoshizumi; Morikawa, Kosuke

    2009-03-24

    The 3D structure of the ternary complex, consisting of DNA ligase, the proliferating cell nuclear antigen (PCNA) clamp, and DNA, was investigated by single-particle analysis. This report presents the structural view, where the crescent-shaped DNA ligase with 3 distinct domains surrounds the central DNA duplex, encircled by the closed PCNA ring, thus forming a double-layer structure with dual contacts between the 2 proteins. The relative orientations of the DNA ligase domains, which remarkably differ from those of the known crystal structures, suggest that a large domain rearrangement occurs upon ternary complex formation. A second contact was found between the PCNA ring and the middle adenylation domain of the DNA ligase. Notably, the map revealed a substantial DNA tilt from the PCNA ring axis. This structure allows us to propose a switching mechanism for the replication factors operating on the PCNA ring.

  5. Posttranslational marks control architectural and functional plasticity of the nuclear pore complex basket

    PubMed Central

    Niño, Carlos A.; Guet, David; Gay, Alexandre; Brutus, Sergine; Jourquin, Frédéric; Mendiratta, Shweta; Salamero, Jean; Géli, Vincent

    2016-01-01

    The nuclear pore complex (NPC) serves as both the unique gate between the nucleus and the cytoplasm and a major platform that coordinates nucleocytoplasmic exchanges, gene expression, and genome integrity. To understand how the NPC integrates these functional constraints, we dissected here the posttranslational modifications of the nuclear basket protein Nup60 and analyzed how they intervene to control the plasticity of the NPC. Combined approaches highlight the role of monoubiquitylation in regulating the association dynamics of Nup60 and its partner, Nup2, with the NPC through an interaction with Nup84, a component of the Y complex. Although major nuclear transport routes are not regulated by Nup60 modifications, monoubiquitylation of Nup60 is stimulated upon genotoxic stress and regulates the DNA-damage response and telomere repair. Together, these data reveal an original mechanism contributing to the plasticity of the NPC at a molecular-organization and functional level. PMID:26783300

  6. Gene Expression Changes and Early Events in Cotton Fibre Development

    PubMed Central

    Lee, Jinsuk J.; Woodward, Andrew W.; Chen, Z. Jeffrey

    2007-01-01

    Background Cotton is the dominant source of natural textile fibre and a significant oil crop. Cotton fibres, produced by certain species in the genus Gossypium, are seed trichomes derived from individual cells of the epidermal layer of the seed coat. Cotton fibre development is delineated into four distinct and overlapping developmental stages: fibre initiation, elongation, secondary wall biosynthesis and maturation. Scope Recent advances in gene expression studies are beginning to provide new insights into a better understanding of early events in cotton fibre development. Fibre cell development is a complex process involving many pathways, including various signal transduction and transcriptional regulation components. Several analyses using expressed sequence tags and microarray have identified transcripts that preferentially accumulate during fibre development. These studies, as well as complementation and overexpression experiments using cotton genes in arabidopsis and tobacco, indicate some similar molecular events between trichome development from the leaf epidermis and fibre development from the ovule epidermis. Specifically, MYB transcription factors regulate leaf trichome development in arabidopsis and may regulate seed trichome development in cotton. In addition, transcript profiling and ovule culture experiments both indicate that several phytohormones and other signalling pathways mediate cotton fibre development. Auxin and gibberellins promote early stages of fibre initiation; ethylene- and brassinosteroid-related genes are up-regulated during the fibre elongation phase; and genes associated with calmodulin and calmodulin-binding proteins are up-regulated in fibre initials. Additional genomic data, mutant and functional analyses, and genome mapping studies promise to reveal the critical factors mediating cotton fibre cell development. PMID:17905721

  7. Effect of PEG-PDMAEMA Block Copolymer Architecture on Polyelectrolyte Complex Formation with Heparin.

    PubMed

    Välimäki, Salla; Khakalo, Alexey; Ora, Ari; Johansson, Leena-Sisko; Rojas, Orlando J; Kostiainen, Mauri A

    2016-09-12

    Heparin is a naturally occurring polyelectrolyte consisting of a sulfated polysaccharide backbone. It is widely used as an anticoagulant during major surgical operations. However, the associated bleeding risks require rapid neutralization after the operation. The only clinically approved antidote for heparin is protamine sulfate, which is, however, ineffective against low molecular weight heparin and can cause severe adverse reactions in patients. In this study, the facile synthesis of cationic-neutral diblock copolymers and their effective heparin binding is presented. Poly(ethylene glycol)-poly(2-(dimethylamino)ethyl methacrylate) (PEG-PDMAEMA) block copolymers were synthesized in two steps via atom-transfer radical polymerization (ATRP) using PEG as a macroinitiator. Solution state binding between heparin and a range of PEG-PDMAEMA block copolymers and one homopolymer was studied with dynamic light scattering and methylene blue displacement assay. Also in vitro binding in plasma was studied by utilizing a chromogenic heparin anti-Xa assay. Additionally, quartz crystal microbalance and multiparametric surface plasmon resonance were used to study the surface adsorption kinetics of the polymers on a heparin layer. It was shown that the block copolymers and heparin form electrostatically bound complexes with varying colloidal properties, where the block lengths play a key role in controlling the heparin binding affinity, polyelectrolyte complex size and surface charge. With the optimized polymers (PEG114PDMAEMA52 and PEG114PDMAEMA100), heparin could be neutralized in a dose-dependent manner, and bound efficiently into small neutral complexes, with a hydrodynamic radius less than 100 nm. These complexes had only a limited effect on cell viability. Based on these studies, our approach paves the way for the development of new polymeric heparin binding agents.

  8. Some aspects of radical chemistry in the assembly of complex molecular architectures

    PubMed Central

    Quiclet-Sire, Béatrice

    2013-01-01

    Summary This review article describes briefly some of the radical processes developed in the authors’ laboratory as they pertain to the concise assembly of complex molecular scaffolds. The emphasis is placed on the use of nitrogen-centred radicals, on the degenerate addition–transfer of xanthates, especially on its potential for intermolecular carbon–carbon bond formation, and on the generation and capture of radicals through electron transfer processes. PMID:23616797

  9. Molecular architecture of the HerA-NurA DNA double-strand break resection complex.

    PubMed

    Byrne, Robert Thomas; Schuller, Jan Michael; Unverdorben, Pia; Förster, Friedrich; Hopfner, Karl-Peter

    2014-12-20

    DNA double-strand breaks can be repaired by homologous recombination, during which the DNA ends are long-range resected by helicase-nuclease systems to generate 3' single strand tails. In archaea, this requires the Mre11-Rad50 complex and the ATP-dependent helicase-nuclease complex HerA-NurA. We report the cryo-EM structure of Sulfolobus solfataricus HerA-NurA at 7.4Å resolution and present the pseudo-atomic model of the complex. HerA forms an ASCE hexamer that tightly interacts with a NurA dimer, with each NurA protomer binding three adjacent HerA HAS domains. Entry to NurA's nuclease active sites requires dsDNA to pass through a 23Å wide channel in the HerA hexamer. The structure suggests that HerA is a dsDNA translocase that feeds DNA into the NurA nuclease sites.

  10. A 2,300-year-old architectural and astronomical complex in the Chincha Valley, Peru

    PubMed Central

    Stanish, Charles; Tantaleán, Henry; Nigra, Benjamin T.; Griffin, Laura

    2014-01-01

    Recent archaeological research on the south coast of Peru discovered a Late Paracas (ca. 400–100 BCE) mound and geoglyph complex in the middle Chincha Valley. This complex consists of linear geoglyphs, circular rock features, ceremonial mounds, and settlements spread over a 40-km2 area. A striking feature of this culturally modified landscape is that the geoglyph lines converge on mounds and habitation sites to form discrete clusters. Likewise, these clusters contain a number of paired line segments and at least two U-shaped structures that marked the setting sun of the June solstice in antiquity. Excavations in three mounds confirm that they were built in Late Paracas times. The Chincha complex therefore predates the better-known Nasca lines to the south by several centuries and provides insight into the development and use of geoglyphs and platform mounds in Paracas society. The data presented here indicate that Paracas peoples engineered a carefully structured, ritualized landscape to demarcate areas and times for key ritual and social activities. PMID:24799703

  11. Architecture of the RNA polymerase II-Mediator core initiation complex.

    PubMed

    Plaschka, C; Larivière, L; Wenzeck, L; Seizl, M; Hemann, M; Tegunov, D; Petrotchenko, E V; Borchers, C H; Baumeister, W; Herzog, F; Villa, E; Cramer, P

    2015-02-19

    The conserved co-activator complex Mediator enables regulated transcription initiation by RNA polymerase (Pol) II. Here we reconstitute an active 15-subunit core Mediator (cMed) comprising all essential Mediator subunits from Saccharomyces cerevisiae. The cryo-electron microscopic structure of cMed bound to a core initiation complex was determined at 9.7 Å resolution. cMed binds Pol II around the Rpb4-Rpb7 stalk near the carboxy-terminal domain (CTD). The Mediator head module binds the Pol II dock and the TFIIB ribbon and stabilizes the initiation complex. The Mediator middle module extends to the Pol II foot with a 'plank' that may influence polymerase conformation. The Mediator subunit Med14 forms a 'beam' between the head and middle modules and connects to the tail module that is predicted to bind transcription activators located on upstream DNA. The Mediator 'arm' and 'hook' domains contribute to a 'cradle' that may position the CTD and TFIIH kinase to stimulate Pol II phosphorylation.

  12. Molecular architecture of the ATP-dependent chromatin-remodeling complex SWR1.

    PubMed

    Nguyen, Vu Q; Ranjan, Anand; Stengel, Florian; Wei, Debbie; Aebersold, Ruedi; Wu, Carl; Leschziner, Andres E

    2013-09-12

    The ATP-dependent chromatin-remodeling complex SWR1 exchanges a variant histone H2A.Z/H2B dimer for a canonical H2A/H2B dimer at nucleosomes flanking histone-depleted regions, such as promoters. This localization of H2A.Z is conserved throughout eukaryotes. SWR1 is a 1 megadalton complex containing 14 different polypeptides, including the AAA+ ATPases Rvb1 and Rvb2. Using electron microscopy, we obtained the three-dimensional structure of SWR1 and mapped its major functional components. Our data show that SWR1 contains a single heterohexameric Rvb1/Rvb2 ring that, together with the catalytic subunit Swr1, brackets two independently assembled multisubunit modules. We also show that SWR1 undergoes a large conformational change upon engaging a limited region of the nucleosome core particle. Our work suggests an important structural role for the Rvbs and a distinct substrate-handling mode by SWR1, thereby providing a structural framework for understanding the complex dimer-exchange reaction.

  13. Supramolecular architecture of metal-organic frameworks involving dinuclear copper paddle-wheel complexes.

    PubMed

    Gomathi, Sundaramoorthy; Muthiah, Packianathan Thomas

    2013-12-15

    The two centrosymmetric dinuclear copper paddle-wheel complexes tetrakis(μ-4-hydroxybenzoato-κ(2)O:O')bis[aquacopper(II)] dimethylformamide disolvate dihydrate, [Cu2(C7H5O3)4(H2O)2]·2C3H7NO·2H2O, (I), and tetrakis(μ-4-methoxybenzoato-κ(2)O:O')bis[(dimethylformamide-κO)copper(II)], [Cu2(C8H7O3)4(C3H7NO)2], (II), crystallize with half of the dinuclear paddle-wheel cage unit in the asymmetric unit and, in addition, complex (I) has one dimethylformamide (DMF) and one water solvent molecule in the asymmetric unit. In both (I) and (II), two Cu(II) ions are bridged by four syn,syn-η(1):η(1):μ carboxylate groups, showing a paddle-wheel cage-type structure with a square-pyramidal coordination geometry. The equatorial positions of (I) and (II) are occupied by the carboxylate groups of 4-hydroxy- and 4-methoxybenzoate ligands, and the axial positions are occupied by aqua and DMF ligands, respectively. The three-dimensional supramolecular metal-organic framework of (I) consists of three different R2(2)(20) and an R4(4)(36) ring motif formed via O-H···O and OW-HW···O hydrogen bonds. Complex (II) simply packs as molecular species.

  14. A 2,300-year-old architectural and astronomical complex in the Chincha Valley, Peru.

    PubMed

    Stanish, Charles; Tantaleán, Henry; Nigra, Benjamin T; Griffin, Laura

    2014-05-20

    Recent archaeological research on the south coast of Peru discovered a Late Paracas (ca. 400-100 BCE) mound and geoglyph complex in the middle Chincha Valley. This complex consists of linear geoglyphs, circular rock features, ceremonial mounds, and settlements spread over a 40-km(2) area. A striking feature of this culturally modified landscape is that the geoglyph lines converge on mounds and habitation sites to form discrete clusters. Likewise, these clusters contain a number of paired line segments and at least two U-shaped structures that marked the setting sun of the June solstice in antiquity. Excavations in three mounds confirm that they were built in Late Paracas times. The Chincha complex therefore predates the better-known Nasca lines to the south by several centuries and provides insight into the development and use of geoglyphs and platform mounds in Paracas society. The data presented here indicate that Paracas peoples engineered a carefully structured, ritualized landscape to demarcate areas and times for key ritual and social activities.

  15. The architecture of the 12RSS in V(D)J recombination signal and synaptic complexes

    PubMed Central

    Ciubotaru, Mihai; Surleac, Marius D.; Metskas, Lauren Ann; Koo, Peter; Rhoades, Elizabeth; Petrescu, Andrei J.; Schatz, David G.

    2015-01-01

    V(D)J recombination is initiated by RAG1 and RAG2, which together with HMGB1 bind to a recombination signal sequence (12RSS or 23RSS) to form the signal complex (SC) and then capture a complementary partner RSS, yielding the paired complex (PC). Little is known regarding the structural changes that accompany the SC to PC transition or the structural features that allow RAG to distinguish its two asymmetric substrates. To address these issues, we analyzed the structure of the 12RSS in the SC and PC using fluorescence resonance energy transfer (FRET) and molecular dynamics modeling. The resulting models indicate that the 12RSS adopts a strongly bent V-shaped structure upon RAG/HMGB1 binding and reveal structural differences, particularly near the heptamer, between the 12RSS in the SC and PC. Comparison of models of the 12RSS and 23RSS in the PC reveals broadly similar shapes but a distinct number and location of DNA bends as well as a smaller central cavity for the 12RSS. These findings provide the most detailed view yet of the 12RSS in RAG–DNA complexes and highlight structural features of the RSS that might underlie activation of RAG-mediated cleavage and substrate asymmetry important for the 12/23 rule of V(D)J recombination. PMID:25550426

  16. Arp2/3 complex inhibition radically alters lamellipodial actin architecture, suspended cell shape, and the cell spreading process.

    PubMed

    Henson, John H; Yeterian, Mesrob; Weeks, Richard M; Medrano, Angela E; Brown, Briana L; Geist, Heather L; Pais, Mollyann D; Oldenbourg, Rudolf; Shuster, Charles B

    2015-03-01

    Recent studies have investigated the dendritic actin cytoskeleton of the cell edge's lamellipodial (LP) region by experimentally decreasing the activity of the actin filament nucleator and branch former, the Arp2/3 complex. Here we extend these studies via pharmacological inhibition of the Arp2/3 complex in sea urchin coelomocytes, cells that possess an unusually broad LP region and display correspondingly exaggerated centripetal flow. Using light and electron microscopy, we demonstrate that Arp2/3 complex inhibition via the drug CK666 dramatically altered LP actin architecture, slowed centripetal flow, drove a lamellipodial-to-filopodial shape change in suspended cells, and induced a novel actin structural organization during cell spreading. A general feature of the CK666 phenotype in coelomocytes was transverse actin arcs, and arc generation was arrested by a formin inhibitor. We also demonstrate that CK666 treatment produces actin arcs in other cells with broad LP regions, namely fish keratocytes and Drosophila S2 cells. We hypothesize that the actin arcs made visible by Arp2/3 complex inhibition in coelomocytes may represent an exaggerated manifestation of the elongate mother filaments that could possibly serve as the scaffold for the production of the dendritic actin network. © 2015 Henson et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  17. The Impact of Population Demography and Selection on the Genetic Architecture of Complex Traits

    PubMed Central

    Lohmueller, Kirk E.

    2014-01-01

    Population genetic studies have found evidence for dramatic population growth in recent human history. It is unclear how this recent population growth, combined with the effects of negative natural selection, has affected patterns of deleterious variation, as well as the number, frequency, and effect sizes of mutations that contribute risk to complex traits. Because researchers are performing exome sequencing studies aimed at uncovering the role of low-frequency variants in the risk of complex traits, this topic is of critical importance. Here I use simulations under population genetic models where a proportion of the heritability of the trait is accounted for by mutations in a subset of the exome. I show that recent population growth increases the proportion of nonsynonymous variants segregating in the population, but does not affect the genetic load relative to a population that did not expand. Under a model where a mutation's effect on a trait is correlated with its effect on fitness, rare variants explain a greater portion of the additive genetic variance of the trait in a population that has recently expanded than in a population that did not recently expand. Further, when using a single-marker test, for a given false-positive rate and sample size, recent population growth decreases the expected number of significant associations with the trait relative to the number detected in a population that did not expand. However, in a model where there is no correlation between a mutation's effect on fitness and the effect on the trait, common variants account for much of the additive genetic variance, regardless of demography. Moreover, here demography does not affect the number of significant associations detected. These findings suggest recent population history may be an important factor influencing the power of association tests and in accounting for the missing heritability of certain complex traits. PMID:24875776

  18. Self-assembly of four new extended architectures based on reduced polyoxometalate clusters and cadmium complexes

    NASA Astrophysics Data System (ADS)

    Ma, Ying; Li, Yangguang; Wang, Enbo; Lu, Ying; Wang, Xinlong; Xu, Xinxin

    2006-08-01

    Four new [P 4Mo 6] cluster-based extended structures containing cadmium complexes, [Cd 3(4,4'-Hbpy) 2(4,4'-bpy) 2(H 2O) 8][Cd(H 2PO 4) 2(HPO 4) 4(PO 4) 2(MoO 2) 12(OH) 6]·7H 2O 1, (4,4'-Hbpy) 2[Cd(4,4'-bpy) 3(H 2O) 3][Cd(4,4'-bpy)(H 2O)] 2[Cd(H 2PO 4) 2(HPO 4) 4 (PO 4) 2(MoO 2) 12(OH) 6]·H 2O 2, [Cd 4(phen) 2(H 2O) 4][Cd(phen)(H 2O)] 2[Cd(HPO 4) 4 (HPO 4) 4(MoO 2) 12(OH) 6]·5H 2O 3 and [Cd 4(2,2'-bpy) 2(H 2O) 4][Cd(2,2'-bpy)(H 2O)] 2 [Cd(HPO 4) 4(HPO 4) 4(MoO 2) 12(OH) 6]·3H 2O 4 (4,4'-bpy=4,4'-bpyridine, phen=1,10-phenanthroline, 2,2'-bpy=2,2'-bpyridine), have been synthesized and characterized by elemental analysis, IR, TG and single crystal X-ray diffraction. The structure of compound 1 is constructed from the Cd[P 4Mo 6] 2 dimers linked by [Cd 3(4,4'-Hbpy) 2(4,4'-bpy) 2(H 2O) 8] subunits to generate a plane layer. Compound 2 consists of the positive 2D sheets that constructed from Cd[P 4Mo 6] 2 dimers linked by [Cd(4,4'-bpy)(H 2O)] complexes, then the 2D sheets are further linked up together to form a 3D supramolecular framework via extensive hydrogen-bonding interactions among the [P 4Mo 6] clusters, free 4,4'-bpy molecules, dissociated [Cd(4,4'-bpy) 3(H 2O) 3] 2+ complexes and water molecules. Compounds 3 and 4 show new 2D layered structure, with Cd[P 4Mo 6] 2 building blocks connected by tetra-nuclear [Cd 4{(phen) 2/(2,2'-bpy) 2}(H 2O) 4] clusters and [Cd(phen/2,2'-bpy)(H 2O)] complexes. The fluorescent activities of compounds 3 and 4 are reported.

  19. Complex Genotype by Environment interactions and changing genetic architectures across thermal environments in the Australian field cricket, Teleogryllus oceanicus

    PubMed Central

    2011-01-01

    Background Biologists studying adaptation under sexual selection have spent considerable effort assessing the relative importance of two groups of models, which hinge on the idea that females gain indirect benefits via mate discrimination. These are the good genes and genetic compatibility models. Quantitative genetic studies have advanced our understanding of these models by enabling assessment of whether the genetic architectures underlying focal phenotypes are congruent with either model. In this context, good genes models require underlying additive genetic variance, while compatibility models require non-additive variance. Currently, we know very little about how the expression of genotypes comprised of distinct parental haplotypes, or how levels and types of genetic variance underlying key phenotypes, change across environments. Such knowledge is important, however, because genotype-environment interactions can have major implications on the potential for evolutionary responses to selection. Results We used a full diallel breeding design to screen for complex genotype-environment interactions, and genetic architectures underlying key morphological traits, across two thermal environments (the lab standard 27°C, and the cooler 23°C) in the Australian field cricket, Teleogryllus oceanicus. In males, complex three-way interactions between sire and dam parental haplotypes and the rearing environment accounted for up to 23 per cent of the scaled phenotypic variance in the traits we measured (body mass, pronotum width and testes mass), and each trait harboured significant additive genetic variance in the standard temperature (27°C) only. In females, these three-way interactions were less important, with interactions between the paternal haplotype and rearing environment accounting for about ten per cent of the phenotypic variance (in body mass, pronotum width and ovary mass). Of the female traits measured, only ovary mass for crickets reared at the cooler

  20. Multicomponent Nanomaterials with Complex Networked Architectures from Orthogonal Degradation and Binary Metal Backfilling in ABC Triblock Terpolymers

    PubMed Central

    2015-01-01

    Selective degradation of block copolymer templates and backfilling the open mesopores is an effective strategy for the synthesis of nanostructured hybrid and inorganic materials. Incorporation of more than one type of inorganic material in orthogonal ways enables the synthesis of multicomponent nanomaterials with complex yet well-controlled architectures; however, developments in this field have been limited by the availability of appropriate orthogonally degradable block copolymers for use as templates. We report the synthesis and self-assembly into cocontinuous network structures of polyisoprene-block-polystyrene-block-poly(propylene carbonate) where the polyisoprene and poly(propylene carbonate) blocks can be orthogonally removed from the polymer film. Through sequential block etching and backfilling the resulting mesopores with different metals, we demonstrate first steps toward the preparation of three-component polymer–inorganic hybrid materials with two distinct metal networks. Multiblock copolymers in which two blocks can be degraded and backfilled independently of each other, without interference from the other, may be used in a wide range of applications requiring periodically ordered complex multicomponent nanoarchitectures. PMID:25836760

  1. Multicomponent nanomaterials with complex networked architectures from orthogonal degradation and binary metal backfilling in ABC triblock terpolymers

    SciTech Connect

    Cowman, Christina D.; Padgett, Elliot; Tan, Kwan Wee; Hovden, Robert; Gu, Yibei; Andrejevic, Nina; Muller, David; Coates, Geoffrey W.; Wiesner, Ulrich

    2015-04-02

    Selective degradation of block copolymer templates and backfilling the open mesopores is an effective strategy for the synthesis of nanostructured hybrid and inorganic materials. Incorporation of more than one type of inorganic material in orthogonal ways enables the synthesis of multicomponent nanomaterials with complex yet well-controlled architectures; however, developments in this field have been limited by the availability of appropriate orthogonally degradable block copolymers for use as templates. We report the synthesis and self-assembly into cocontinuous network structures of polyisoprene-block-polystyrene-block-poly(propylene carbonate) where the polyisoprene and poly(propylene carbonate) blocks can be orthogonally removed from the polymer film. Through sequential block etching and backfilling the resulting mesopores with different metals, we demonstrate first steps toward the preparation of three-component polymer–inorganic hybrid materials with two distinct metal networks. Lastly, multiblock copolymers in which two blocks can be degraded and backfilled independently of each other, without interference from the other, may be used in a wide range of applications requiring periodically ordered complex multicomponent nanoarchitectures.

  2. Multicomponent nanomaterials with complex networked architectures from orthogonal degradation and binary metal backfilling in ABC triblock terpolymers

    DOE PAGES

    Cowman, Christina D.; Padgett, Elliot; Tan, Kwan Wee; ...

    2015-04-02

    Selective degradation of block copolymer templates and backfilling the open mesopores is an effective strategy for the synthesis of nanostructured hybrid and inorganic materials. Incorporation of more than one type of inorganic material in orthogonal ways enables the synthesis of multicomponent nanomaterials with complex yet well-controlled architectures; however, developments in this field have been limited by the availability of appropriate orthogonally degradable block copolymers for use as templates. We report the synthesis and self-assembly into cocontinuous network structures of polyisoprene-block-polystyrene-block-poly(propylene carbonate) where the polyisoprene and poly(propylene carbonate) blocks can be orthogonally removed from the polymer film. Through sequential block etchingmore » and backfilling the resulting mesopores with different metals, we demonstrate first steps toward the preparation of three-component polymer–inorganic hybrid materials with two distinct metal networks. Lastly, multiblock copolymers in which two blocks can be degraded and backfilled independently of each other, without interference from the other, may be used in a wide range of applications requiring periodically ordered complex multicomponent nanoarchitectures.« less

  3. Multicomponent Nanomaterials with Complex Networked Architectures from Orthogonal Degradation and Binary Metal Backfilling in ABC Triblock Terpolymers.

    PubMed

    Cowman, Christina D; Padgett, Elliot; Tan, Kwan Wee; Hovden, Robert; Gu, Yibei; Andrejevic, Nina; Muller, David; Coates, Geoffrey W; Wiesner, Ulrich

    2015-05-13

    Selective degradation of block copolymer templates and backfilling the open mesopores is an effective strategy for the synthesis of nanostructured hybrid and inorganic materials. Incorporation of more than one type of inorganic material in orthogonal ways enables the synthesis of multicomponent nanomaterials with complex yet well-controlled architectures; however, developments in this field have been limited by the availability of appropriate orthogonally degradable block copolymers for use as templates. We report the synthesis and self-assembly into cocontinuous network structures of polyisoprene-block-polystyrene-block-poly(propylene carbonate) where the polyisoprene and poly(propylene carbonate) blocks can be orthogonally removed from the polymer film. Through sequential block etching and backfilling the resulting mesopores with different metals, we demonstrate first steps toward the preparation of three-component polymer-inorganic hybrid materials with two distinct metal networks. Multiblock copolymers in which two blocks can be degraded and backfilled independently of each other, without interference from the other, may be used in a wide range of applications requiring periodically ordered complex multicomponent nanoarchitectures.

  4. Photosynthate Regulation of the Root System Architecture Mediated by the Heterotrimeric G Protein Complex in Arabidopsis

    PubMed Central

    Mudgil, Yashwanti; Karve, Abhijit; Teixeira, Paulo J. P. L.; Jiang, Kun; Tunc-Ozdemir, Meral; Jones, Alan M.

    2016-01-01

    Assimilate partitioning to the root system is a desirable developmental trait to control but little is known of the signaling pathway underlying partitioning. A null mutation in the gene encoding the Gβ subunit of the heterotrimeric G protein complex, a nexus for a variety of signaling pathways, confers altered sugar partitioning in roots. While fixed carbon rapidly reached the roots of wild type and agb1-2 mutant seedlings, agb1 roots had more of this fixed carbon in the form of glucose, fructose, and sucrose which manifested as a higher lateral root density. Upon glucose treatment, the agb1-2 mutant had abnormal gene expression in the root tip validated by transcriptome analysis. In addition, PIN2 membrane localization was altered in the agb1-2 mutant. The heterotrimeric G protein complex integrates photosynthesis-derived sugar signaling incorporating both membrane-and transcriptional-based mechanisms. The time constants for these signaling mechanisms are in the same range as photosynthate delivery to the root, raising the possibility that root cells are able to use changes in carbon fixation in real time to adjust growth behavior. PMID:27610112

  5. Architecture of the Atg17 Complex as a Scaffold for Autophagosome Biogenesis

    PubMed Central

    Hurley, James H.

    2013-01-01

    SUMMARY Macroautophagy is a bulk clearance mechanism in which the double-membraned phagophore grows and engulfs cytosolic material. In yeast, the phagophore nucleates from a cluster of 20-30 nm diameter Atg9-containing vesicles located at a multiprotein assembly known as the preautophagosomal structure (PAS). The crystal structure of a 2:2:2 complex of the earliest-acting PAS proteins, Atg17, Atg29, and Atg31, was solved at 3.05 Å resolution. Atg17 is crescent-shaped with a 10 nm radius of curvature. Dimerization of the Atg17-Atg31-Atg29 complex is critical for both PAS formation and autophagy and each dimer contains two separate and complete crescents. Upon induction of autophagy, Atg17-Atg31-Atg29 assembles with Atg1 and Atg13, which in turn initiates the formation of the phagophore. The C-terminal EAT domain of Atg1 was shown to sense membrane curvature, dimerize, and tether lipid vesicles. These data suggest a structural mechanism for the organization of Atg9 vesicles into the early phagophore. PMID:23219485

  6. Complex neural architecture in the diploblastic larva of Clava multicornis (Hydrozoa, Cnidaria).

    PubMed

    Piraino, Stefano; Zega, Giuliana; Di Benedetto, Cristiano; Leone, Antonella; Dell'Anna, Alessandro; Pennati, Roberta; Carnevali, Daniela Candia; Schmid, Volker; Reichert, Heinrich

    2011-07-01

    The organization of the cnidarian nervous system has been widely documented in polyps and medusae, but little is known about the nervous system of planula larvae, which give rise to adult forms after settling and metamorphosis. We describe histological and cytological features of the nervous system in planulae of the hydrozoan Clava multicornis. These planulae do not swim freely in the water column but rather crawl on the substrate by means of directional, coordinated ciliary movement coupled to lateral muscular bending movements associated with positive phototaxis. Histological analysis shows pronounced anteroposterior regionalization of the planula's nervous system, with different neural cell types highly concentrated at the anterior pole. Transmission electron microscopy of planulae shows the nervous system to be unusually complex, with a large, orderly array of sensory cells at the anterior pole. In the anterior half of the planula, the basiectodermal plexus of neurites forms an extensive orthogonal network, whereas more posteriorly neurites extend longitudinally along the body axis. Additional levels of nervous system complexity are uncovered by neuropeptide-specific immunocytochemistry, which reveals distinct neural subsets having specific molecular phenotypes. Together these observations imply that the nervous system of the planula of Clava multicornis manifests a remarkable level of histological, cytological, and functional organization, the features of which may be reminiscent of those present in early bilaterian animals. Copyright © 2011 Wiley-Liss, Inc.

  7. Architecture of the Xenopus nuclear pore complex revealed by three- dimensional cryo-electron microscopy

    PubMed Central

    1993-01-01

    The nuclear pore complex spans the nuclear envelope and functions as a macromolecular transporter in the ATP-dependent process of nucleocytoplasmic transport. In this report, we present three dimensional (3D) structures for both membrane-associated and detergent- extracted Xenopus NPCs, imaged in frozen buffers by cryo-electron microscopy. A comparison of the differing configurations present in the 3D maps suggests that the spokes may possess an intrinsic conformational flexibility. When combined with recent data from a 3D map of negatively stained NPCs (Hinshaw, J. E., B. O. Carragher, and R. A. Milligan. 1992. Cell. 69:1133-1141), these observations suggest a minimal domain model for the spoke-ring complex which may account for the observed plasticity of this assembly. Moreover, lumenal domains in adjacent spokes are interconnected by radial arm dimers, forming a lumenal ring that may be responsible for anchoring the NPC within the nuclear envelope pore. Importantly, the NPC transporter is visualized as a centrally tapered cylinder that spans the entire width of the NPC, in a direction normal to the nuclear envelope. The central positioning, tripartite structure, and hollow nature of the transporter suggests that it may form a macromolecular transport channel, with a globular gating domain at each end. Finally, the packing of the transporter within the spokes creates a set of eight internal channels that may be responsible, in part, for the diffusion of ions and small molecules across the nuclear envelope. PMID:8314837

  8. New generation of optical fibres

    SciTech Connect

    Dianov, E M; Semjonov, S L; Bufetov, I A

    2016-01-31

    The growing need for information in contemporary society is the motivating force behind the development of fibre optics in general and optical fibre communications in particular. Intensive research effort has been concentrated on designing new types of optical fibres and extending their application field. This paper reviews results of research on new types of optical fibres: bismuthdoped active fibres, multicore fibres and hollow-core fibres, which can be used as key components of systems that ensure further increase in optical information transfer rate. (invited paper)

  9. Initiator-integrated 3D printing enables the formation of complex metallic architectures.

    PubMed

    Wang, Xiaolong; Guo, Qiuquan; Cai, Xiaobing; Zhou, Shaolin; Kobe, Brad; Yang, Jun

    2014-02-26

    Three-dimensional printing was used to fabricate various metallic structures by directly integrating a Br-containing vinyl-terminated initiator into the 3D resin followed by surface-initiated atomic-transfer radical polymerization (ATRP) and subsequent electroless plating. Cu- and Ni-coated complex structures, such as microlattices, hollow balls, and even Eiffel towers, were prepared. Moreover, the method is also capable of fabricating ultralight cellular metals with desired structures by simply etching the polymer template away. By combining the merits of 3D printing in structure design with those of ATRP in surface modification and polymer-assisted ELP of metals, this universal, robust, and cost-effective approach has largely extended the capability of 3D printing and will make 3D printing technology more practical in areas of electronics, acoustic absorption, thermal insulation, catalyst supports, and others.

  10. Architecture of the tectonically influenced Sobrarbe deltaic complex in the Ainsa Basin, northern Spain

    NASA Astrophysics Data System (ADS)

    Dreyer, Tom; Corregidor, Jordi; Arbues, Pau; Puigdefabregas, Cai

    1999-09-01

    The syn-tectonic Sobrarbe deltaic complex (Eocene of the Ainsa Basin, Spanish Pyrenees) is confined by lateral thrust ramps and influenced by intra-basinal growth anticlines. Six facies associations have been distinguished within the deltaic complex: (i) slope marls and turbidite sandstones; (ii) distal delta front silty and bioturbated sandstones; (iii) proximal delta front and delta plain deposits (tidal inlet, tidal flat, mouth-bar, bay, distributary channel, and floodplain environments); (iv) biogenic deposits at flooding surfaces; (v) collapse zone sediments; and (vi) Nummulite-dominated shallow-marine carbonates. The deltaic complex comprises four composite sequences, which each contain a number of minor sequences of the genetic (maximum flooding surface bounded) type. Regressive unconformities and their correlative surfaces separate the composite sequences (CS), and each CS can be divided into lowstand, transgressive and highstand components. At the base, the Comaron CS is a WNW-prograding deltaic complex containing six minor sequences characterized by basinward-stepping sandstone wedges separated by transgressive mudstones. Double regressive unconformities are often associated with these sandstone wedges proximally in the basin. Growth of the intra-basinal Arcusa anticline caused gentle folding of the Comaron CS, and syn-growth strata at the base of the overlying Las Gorgas CS contain a prominent forced regressive sandstone wedge (the Las Gorgas sandbody) and display thinning of bedsets onto the crest of the anticline. Moreover, it can be demonstrated that relative sea-level rise took place in the growth synclines at the same time as a fall in relative sea level occurred on the growth anticlines. The tectonic deformation caused a shift in the direction of deltaic progradation towards the north-northwest, as demonstrated by the well-developed clinoforms in the highstand sequence set of the Las Gorgas CS. A second phase of tectonic activity, this time

  11. Polyhomologation based on in situ generated boron-thexyl-silaboracyclic initiating sites: a novel strategy towards the synthesis of polyethylene-based complex architectures.

    PubMed

    Zhang, Zhen; Zhang, Hefeng; Gnanou, Yves; Hadjichristidis, Nikos

    2015-06-21

    A novel strategy, based on the in situ generated boron-thexyl-silaboracyclic initiating sites for the polyhomologation of dimethylsulfoxonium methylide, has been developed for the synthesis of complex polyethylene-based architectures. As examples, the synthesis of a 4-arm polyethylene star, three (polystyrene)(polyethylene)2 3-miktoarm stars and a PE-branched double graft copolymer is given.

  12. Evaluating genome architecture of a complex region via generalized bipartite matching.

    PubMed

    Lo, Christine; Kim, Sangwoo; Zakov, Shay; Bafna, Vineet

    2013-01-01

    With the remarkable development in inexpensive sequencing technologies and supporting computational tools, we have the promise of medicine being personalized by knowledge of the individual genome. Current technologies provide high throughput, but short reads. Reconstruction of the donor genome is based either on de novo assembly of the (short) reads, or on mapping donor reads to a standard reference. While such techniques demonstrate high success rates for inferring 'simple' genomic segments, they are confounded by segments with complex duplication patterns, including regions of direct medical relevance, like the HLA and the KIR regions.In this work, we address this problem with a method for assessing the quality of a predicted genome sequence for complex regions of the genome. This method combines two natural types of evidence: sequence similarity of the mapped reads to the predicted donor genome, and distribution of reads across the predicted genome. We define a new scoring function for read-to-genome matchings, which penalizes for sequence dissimilarities and deviations from expected read location distribution, and present an efficient algorithm for finding matchings that minimize the penalty. The algorithm is based on a formal problem, first defined in this paper, called Coverage Sensitive many-to-many min-cost bipartite Matching (CSM). This new problem variant generalizes the standard (one-to-one) weighted bipartite matching problem, and can be solved using network flows. The resulting Java-based tool, called SAGE (Scoring function for Assembled GEnomes), is freely available upon request. We demonstrate over simulated data that SAGE can be used to infer correct haplotypes of the highly repetitive KIR region on the Human chromosome 19.

  13. Evaluating genome architecture of a complex region via generalized bipartite matching

    PubMed Central

    2013-01-01

    With the remarkable development in inexpensive sequencing technologies and supporting computational tools, we have the promise of medicine being personalized by knowledge of the individual genome. Current technologies provide high throughput, but short reads. Reconstruction of the donor genome is based either on de novo assembly of the (short) reads, or on mapping donor reads to a standard reference. While such techniques demonstrate high success rates for inferring 'simple' genomic segments, they are confounded by segments with complex duplication patterns, including regions of direct medical relevance, like the HLA and the KIR regions. In this work, we address this problem with a method for assessing the quality of a predicted genome sequence for complex regions of the genome. This method combines two natural types of evidence: sequence similarity of the mapped reads to the predicted donor genome, and distribution of reads across the predicted genome. We define a new scoring function for read-to-genome matchings, which penalizes for sequence dissimilarities and deviations from expected read location distribution, and present an efficient algorithm for finding matchings that minimize the penalty. The algorithm is based on a formal problem, first defined in this paper, called Coverage Sensitive many-to-many min-cost bipartite Matching (CSM). This new problem variant generalizes the standard (one-to-one) weighted bipartite matching problem, and can be solved using network flows. The resulting Java-based tool, called SAGE (Scoring function for Assembled GEnomes), is freely available upon request. We demonstrate over simulated data that SAGE can be used to infer correct haplotypes of the highly repetitive KIR region on the Human chromosome 19. PMID:23734567

  14. Presynaptic Calcium Signalling in Cerebellar Mossy Fibres

    PubMed Central

    Thomsen, Louiza B.; Jörntell, Henrik; Midtgaard, Jens

    2009-01-01

    Whole-cell recordings were obtained from mossy fibre terminals in adult turtles in order to characterize the basic membrane properties. Calcium imaging of presynaptic calcium signals was carried out in order to analyse calcium dynamics and presynaptic GABA B inhibition. A tetrodotoxin (TTX)-sensitive fast Na+ spike faithfully followed repetitive depolarizing pulses with little change in spike duration or amplitude, while a strong outward rectification dominated responses to long-lasting depolarizations. High-threshold calcium spikes were uncovered following addition of potassium channel blockers. Calcium imaging using Calcium-Green dextran revealed a stimulus-evoked all-or-none TTX-sensitive calcium signal in simple and complex rosettes. All compartments of a complex rosette were activated during electrical activation of the mossy fibre, while individual simple and complex rosettes along an axon appeared to be isolated from one another in terms of calcium signalling. CGP55845 application showed that GABA B receptors mediated presynaptic inhibition of the calcium signal over the entire firing frequency range of mossy fibres. A paired-pulse depression of the calcium signal lasting more than 1 s affected burst firing in mossy fibres; this paired-pulse depression was reduced by GABA B antagonists. While our results indicated that a presynaptic rosette electrophysiologically functioned as a unit, topical GABA application showed that calcium signals in the branches of complex rosettes could be modulated locally, suggesting that cerebellar glomeruli may be dynamically sub-compartmentalized due to ongoing inhibition mediated by Golgi cells. This could provide a fine-grained control of mossy fibre-granule cell information transfer and synaptic plasticity within a mossy fibre rosette. PMID:20162034

  15. Energy transfer in optical fibres

    SciTech Connect

    Biryukov, A S; Dianov, Evgenii M

    2007-04-30

    The possibility of energy transfer over long distances in the form of laser radiation propagating in dielectric optical fibres is discussed. Because nonlinear-optical phenomena in glasses prevent the transfer of high radiation powers in standard two-layer fibres, the outlook for this transfer is associated with the development of the technology of microstructure fibres with a hollow core and with further progress in the development of high-power fibre lasers. (optical fibres)

  16. Influence of Ligand Architecture in Tuning Reaction Bifurcation Pathways for Chlorite Oxidation by Non-Heme Iron Complexes.

    PubMed

    Barman, Prasenjit; Faponle, Abayomi S; Vardhaman, Anil Kumar; Angelone, Davide; Löhr, Anna-Maria; Browne, Wesley R; Comba, Peter; Sastri, Chivukula V; de Visser, Sam P

    2016-10-05

    Reaction bifurcation processes are often encountered in the oxidation of substrates by enzymes and generally lead to a mixture of products. One particular bifurcation process that is common in biology relates to electron transfer versus oxygen atom transfer by high-valent iron(IV)-oxo complexes, which nature uses for the oxidation of metabolites and drugs. In biomimicry and bioremediation, an important reaction relates to the detoxification of ClOx(-) in water, which can lead to a mixture of products through bifurcated reactions. Herein we report the first three water-soluble non-heme iron(II) complexes that can generate chlorine dioxide from chlorite at ambient temperature and physiological pH. These complexes are highly active oxygenation oxidants and convert ClO2(-) into either ClO2 or ClO3¯ via high-valent iron(IV)-oxo intermediates. We characterize the short-lived iron(IV)-oxo species and establish rate constants for the bifurcation mechanism leading to ClO2 and ClO3(-) products. We show that the ligand architecture of the metal center plays a dominant role by lowering the reduction potential of the metal center. Our experiments are supported by computational modeling, and a predictive valence bond model highlights the various factors relating to the substrate and oxidant that determine the bifurcation pathway and explains the origins of the product distributions. Our combined kinetic, spectroscopic, and computational studies reveal the key components necessary for the future development of efficient chlorite oxidation catalysts.

  17. Molecular Architecture of the Major Histocompatibility Complex Class I-Binding Site of Ly49 Natural Killer Cell Receptors

    SciTech Connect

    Deng,L.; Cho, S.; Malchiodi, E.; Kerzic, M.; Dam, J.; Mariuzza, R.

    2008-01-01

    Natural killer (NK) cells play a vital role in the detection and destruction of virally infected and tumor cells during innate immune responses. The highly polymorphic Ly49 family of NK receptors regulates NK cell function by sensing major histocompatibility complex class I (MHC-I) molecules on target cells. Despite the determination of two Ly49-MHC-I complex structures, the molecular features of Ly49 receptors that confer specificity for particular MHC-I alleles have not been identified. To understand the functional architecture of Ly49-binding sites, we determined the crystal structures of Ly49C and Ly49G and completed refinement of the Ly49C-H-2Kb complex. This information, combined with mutational analysis of Ly49A, permitted a structure-based classification of Ly49s that we used to dissect the binding site into three distinct regions, each having different roles in MHC recognition. One region, located at the center of the binding site, has a similar structure across the Ly49 family and mediates conserved interactions with MHC-I that contribute most to binding. However, the preference of individual Ly49s for particular MHC-I molecules is governed by two regions that flank the central region and are structurally more variable. One of the flanking regions divides Ly49s into those that recognize both H-2D and H-2K versus only H-2D ligands, whereas the other discriminates among H-2D or H-2K alleles. The modular design of Ly49-binding sites provides a framework for predicting the MHC-binding specificity of Ly49s that have not been characterized experimentally.

  18. Structural architecture of the sheeted dike complex and extensional tectonics of the Jurassic Mirdita ophiolite, Albania

    NASA Astrophysics Data System (ADS)

    Phillips-Lander, Charity M.; Dilek, Yildirim

    2009-03-01

    The Jurassic Mirdita ophiolite in northern Albania occurs in a ˜ 40 km-wide zone bounded by the passive margins of Apulia (W) and Pelagonia (E). The ˜ 3 km-thick Western Mirdita ophiolite (WMO) contains lherzolitic peridotites and gabbros overlain by basaltic pillow lavas, whereas the ˜ 12 km-thick Eastern Mirdita ophiolite (EMO) represents a Penrose-type oceanic crust with suprasubduction zone affinities. The 1 km-thick sheeted dike complex (SDC) in the EMO shows mutually intrusive relations with the underlying gabbros, is overlain by a 1.1-km-thick extrusive sequence, and records a history of complex seafloor spreading and rift tectonics in a suprasubduction zone environment. Crosscutting relations within the SDC indicate four generations of dike intrusions becoming progressively younger to the east. Early D1 and D2 dikes have basalt and basaltic andesite compositions and NNE and NNW attitudes, respectively, with moderate to gentle dips to the east. They are cut by mineralized, dike-parallel normal faults defining local grabens. Younger D3 dikes display andesitic and boninitic compositions and have WNW strikes with steep dips. These dikes are cut by both dike-parallel and dike-orthogonal faults that form locally well-developed graben structures with extensive epidosite and chalcopyrite mineralization. The youngest D4 dikes with 240°-290°orientations occur as isolated swarms intruding earlier dike generations in the eastern part of the SDC, range in composition from quartz-microdiorite to rhyodacite and rhyolite, and are cut by ˜ NW-oriented faults and shear zones. Changes in dike compositions from basalt and basaltic andesite to andesite, boninite, rhyodacite and rhyolite through time in the SDC are consistent with changes in the lava chemistry stratigraphically upward and eastward in the extrusive sequence, indicating significant chemical variations in melt compositions as the EMO evolved. Development of the SDC and its extensive normal faulting were a

  19. Molecular architecture of a dynamin adaptor: implications for assembly of mitochondrial fission complexes

    PubMed Central

    Koirala, Sajjan; Bui, Huyen T.; Schubert, Heidi L.; Eckert, Debra M.; Hill, Christopher P.

    2010-01-01

    Recruitment and assembly of some dynamin-related guanosine triphosphatases depends on adaptor proteins restricted to distinct cellular membranes. The yeast Mdv1 adaptor localizes to mitochondria by binding to the membrane protein Fis1. Subsequent Mdv1 binding to the mitochondrial dynamin Dnm1 stimulates Dnm1 assembly into spirals, which encircle and divide the mitochondrial compartment. In this study, we report that dimeric Mdv1 is joined at its center by a 92-Å antiparallel coiled coil (CC). Modeling of the Fis1–Mdv1 complex using available crystal structures suggests that the Mdv1 CC lies parallel to the bilayer with N termini at opposite ends bound to Fis1 and C-terminal β-propeller domains (Dnm1-binding sites) extending into the cytoplasm. A CC length of appropriate length and sequence is necessary for optimal Mdv1 interaction with Fis1 and Dnm1 and is important for proper Dnm1 assembly before membrane scission. Our results provide a framework for understanding how adaptors act as scaffolds to orient and stabilize the assembly of dynamins on membranes. PMID:21149566

  20. Binary architecture of the Nav1.2-β2 signaling complex

    PubMed Central

    Das, Samir; Gilchrist, John; Bosmans, Frank; Van Petegem, Filip

    2016-01-01

    To investigate the mechanisms by which β-subunits influence Nav channel function, we solved the crystal structure of the β2 extracellular domain at 1.35Å. We combined these data with known bacterial Nav channel structural insights and novel functional studies to determine the interactions of specific residues in β2 with Nav1.2. We identified a flexible loop formed by 72Cys and 75Cys, a unique feature among the four β-subunit isoforms. Moreover, we found that 55Cys helps to determine the influence of β2 on Nav1.2 toxin susceptibility. Further mutagenesis combined with the use of spider toxins reveals that 55Cys forms a disulfide bond with 910Cys in the Nav1.2 domain II pore loop, thereby suggesting a 1:1 stoichiometry. Our results also provide clues as to which disulfide bonds are formed between adjacent Nav1.2 912/918Cys residues. The concepts emerging from this work will help to form a model reflecting the β-subunit location in a Nav channel complex. DOI: http://dx.doi.org/10.7554/eLife.10960.001 PMID:26894959

  1. The Complex Point Cloud for the Knowledge of the Architectural Heritage. Some Experiences

    NASA Astrophysics Data System (ADS)

    Aveta, C.; Salvatori, M.; Vitelli, G. P.

    2017-05-01

    The present paper aims to present a series of experiences and experimentations that a group of PhD from the University of Naples Federico II conducted over the past decade. This work has concerned the survey and the graphic restitution of monuments and works of art, finalized to their conservation. The targeted query of complex point cloud acquired by 3D scanners, integrated with photo sensors and thermal imaging, has allowed to explore new possibilities of investigation. In particular, we will present the scientific results of the experiments carried out on some important historical artifacts with distinct morphological and typological characteristics. According to aims and needs that emerged during the connotative process, with the support of archival and iconographic historical research, the laser scanner technology has been used in many different ways. New forms of representation, obtained directly from the point cloud, have been tested for the elaboration of thematic studies for documenting the pathologies and the decay of materials, for correlating visible aspects with invisible aspects of the artifact.

  2. Functional architecture of the Reb1-Ter complex of Schizosaccharomyces pombe

    PubMed Central

    Jaiswal, Rahul; Choudhury, Malay; Zaman, Shamsu; Singh, Samarendra; Santosh, Vishaka; Bastia, Deepak; Escalante, Carlos R.

    2016-01-01

    Reb1 of Schizosaccharomyces pombe represents a family of multifunctional proteins that bind to specific terminator sites (Ter) and cause polar termination of transcription catalyzed by RNA polymerase I (pol I) and arrest of replication forks approaching the Ter sites from the opposite direction. However, it remains to be investigated whether the same mechanism causes arrest of both DNA transactions. Here, we present the structure of Reb1 as a complex with a Ter site at a resolution of 2.7 Å. Structure-guided molecular genetic analyses revealed that it has distinct and well-defined DNA binding and transcription termination (TTD) domains. The region of the protein involved in replication termination is distinct from the TTD. Mechanistically, the data support the conclusion that transcription termination is not caused by just high affinity Reb1-Ter protein–DNA interactions. Rather, protein–protein interactions between the TTD with the Rpa12 subunit of RNA pol I seem to be an integral part of the mechanism. This conclusion is further supported by the observation that double mutations in TTD that abolished its interaction with Rpa12 also greatly reduced transcription termination thereby revealing a conduit for functional communications between RNA pol I and the terminator protein. PMID:27035982

  3. Fibres get functional

    NASA Astrophysics Data System (ADS)

    Graham-Rowe, Duncan

    2011-02-01

    New forms of advanced optical fibres featuring exotic glasses, carefully designed microstructures and cores that are either hollow, fluidic, semiconductor or piezoelectric are giving light guides a new lease of life, reports Duncan Graham-Rowe.

  4. Ultrafast fibre lasers

    NASA Astrophysics Data System (ADS)

    Fermann, Martin E.; Hartl, Ingmar

    2013-11-01

    Ultrafast fibre lasers are fundamental building blocks of many photonic systems used in industrial and medical applications as well as for scientific research. Here, we review the essential components and operation regimes of ultrafast fibre lasers and discuss how they are instrumental in a variety of applications. In regards to laser technology, we discuss the present state of the art of large-mode-area fibres and their utilization in high-power, chirped-pulse amplification systems. In terms of commercial applications, we introduce industrial micromachining and medical imaging, and describe emerging applications in the mid-infrared and extreme-ultraviolet spectral regions, as facilitated by frequency shifting induced by fibre frequency combs.

  5. Microstructured fibres: a positive impact on defence technology?

    NASA Astrophysics Data System (ADS)

    O'Driscoll, E. J.; Watson, M. A.; Delmonte, T.; Petrovich, M. N.; Feng, X.; Flanagan, J. C.; Hayes, J. R.; Richardson, D. J.

    2006-09-01

    In this paper we seek to assess the potential impact of microstructured fibres for security and defence applications. Recent literature has presented results on using microstructured fibre for delivery of high power, high quality radiation and also on the use of microstructured fibre for broadband source generation. Whilst these two applications may appear contradictory to one another the inherent design flexibility of microstructured fibres allows fibres to be fabricated for the specific application requirements, either minimising (for delivery) or maximising (for broadband source generation) the nonlinear effects. In platform based laser applications such as infrared counter measures, remote sensing and laser directed-energy weapons, a suitable delivery fibre providing high power, high quality light delivery would allow a laser to be sited remotely from the sensor/device head. This opens up the possibility of several sensor/device types sharing the same multi-functional laser, thus reducing the complexity and hence the cost of such systems. For applications requiring broadband source characteristics, microstructured fibres can also offer advantages over conventional sources. By exploiting the nonlinear effects it is possible to realise a multifunctional source for applications such as active hyperspectral imaging, countermeasures, and biochemical sensing. These recent results suggest enormous potential for these novel fibre types to influence the next generation of photonic systems for security and defence applications. However, it is important to establish where the fibres can offer the greatest advantages and what research still needs to be done to drive the technology towards real platform solutions.

  6. The hygroscopic behavior of plant fibres: a review

    NASA Astrophysics Data System (ADS)

    Célino, Amandine; Freour, Sylvain; Jacquemin, Frederic; Casari, Pascal

    2013-12-01

    Environmental concern has resulted in a renewed interest in bio-based materials. Among them, plant fibres are perceived as an environmentally friendly substitute to glass fibres for the reinforcement of composites, particularly in automotive engineering. Due to their wide availability, low cost, low density, high-specific mechanical properties and eco-friendly image, they are increasingly being employed as reinforcements in polymer matrix composites. Indeed, their complex microstructure as a composite material makes plant fibre a really interesting and challenging subject to study. Research subjects about such fibres are abundant because there are always some issues to prevent their use at large scale (poor adhesion, variability, low thermal resistance, hydrophilic behavior). The choice of natural fibres rather than glass fibres as filler yields a change of the final properties of the composite. One of the most relevant differences between the two kinds of fibre is their response to humidity. Actually, glass fibres are considered as hydrophobic whereas plant fibres have a pronounced hydrophilic behavior. Composite materials are often submitted to variable climatic conditions during their lifetime, including unsteady hygroscopic conditions. However, in humid conditions, strong hydrophilic behaviour of such reinforcing fibres leads to high level of moisture absorption in wet environments. This results in the structural modification of the fibres and an evolution of their mechanical properties together with the composites in which they are fitted in. Thereby, the understanding of these moisture absorption mechanisms as well as the influence of water on the final properties of these fibres and their composites is of great interest to get a better control of such new biomaterials. This is the topic of this review paper.

  7. Fibre glass induced synovitis.

    PubMed Central

    Cleland, L G; Vernon-Roberts, B; Smith, K

    1984-01-01

    Chronic synovitis developed in the dorsal extensor sheath of the hand of a 25-year-old manufacturer of fibre glass reinforced boats and surfboards . Particles found in synovial fluid aspirates were similar in morphology and elemental content to unused fibre glass and particles found in dust from the workshop floor. It was concluded that hard disc grinding required during manufacture resulted in percutaneous implantation of small glass particles, leading to chronic synovitis and effusion. Images PMID:6742919

  8. Structural architecture and glacitectonic evolution of the Mud Buttes cupola hill complex, southern Alberta, Canada

    NASA Astrophysics Data System (ADS)

    Phillips, Emrys; Evans, David J. A.; Atkinson, Nigel; Kendall, Allison

    2017-05-01

    This paper presents the results of a detailed multidisciplinary study of the deformed bedrock and overlying Quaternary sediments exposed at the Mud Buttes in southern Alberta, Canada. This large, arcuate cupola hill is composed of intensely folded and thrust sandstones, siltstones and mudstones of the Cretaceous Belly River Group. Glacitectonism responsible for the development of this internally complex landform occurred at the margin of the newly defined Prospect Valley lobe of the Laurentide Ice Sheet. Analysis of the deformation structures reveals that construction of this landform occurred in response to at least two phases of south-directed ice sheet advance separated by a period of retreat. The first phase led to the formation of a forward propagating imbricate thrust stack leading to polyphase deformation of the Belly River Group. D1 thrusting led to the detachment of thrust-bound slices of bedrock which were accreted to the base of the developing imbricate stack. This process resulted in the structurally higher and older thrust-slices being progressively ;back-rotated; (tilted), accompanied by D2 thrusting and folding. Further thrusting during D3 was restricted to the core of the Mud Buttes as the deforming sequence accommodated further compression imposed by the advancing ice. Minor oscillations of the ice margin led to localised brittle-ductile shearing (D4) of the bedrock immediately adjacent to the ice contact part of the thrust stack. The second phase of ice advance led to the accretion of a relatively simple thrust and folded sequence seen the northern side of Mud Buttes. The resulting composite thrust moraine was subsequently overridden by ice advancing from the NNW to form a dome-like cupola-hill. This readvance of the Prospect Valley lobe led to the formation of a thin carapace of Quaternary sediments mantling the Mud Buttes which include glacitectonite, till and an organic-rich clay-silt (?palaeosol).

  9. A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea

    PubMed Central

    Bajaj, Deepak; Das, Shouvik; Upadhyaya, Hari D.; Ranjan, Rajeev; Badoni, Saurabh; Kumar, Vinod; Tripathi, Shailesh; Gowda, C. L. Laxmipathi; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K.; Parida, Swarup K.

    2015-01-01

    The study identified 9045 high-quality SNPs employing both genome-wide GBS- and candidate gene-based SNP genotyping assays in 172, including 93 cultivated (desi and kabuli) and 79 wild chickpea accessions. The GWAS in a structured population of 93 sequenced accessions detected 15 major genomic loci exhibiting significant association with seed coat color. Five seed color-associated major genomic loci underlying robust QTLs mapped on a high-density intra-specific genetic linkage map were validated by QTL mapping. The integration of association and QTL mapping with gene haplotype-specific LD mapping and transcript profiling identified novel allelic variants (non-synonymous SNPs) and haplotypes in a MATE secondary transporter gene regulating light/yellow brown and beige seed coat color differentiation in chickpea. The down-regulation and decreased transcript expression of beige seed coat color-associated MATE gene haplotype was correlated with reduced proanthocyanidins accumulation in the mature seed coats of beige than light/yellow brown seed colored desi and kabuli accessions for their coloration/pigmentation. This seed color-regulating MATE gene revealed strong purifying selection pressure primarily in LB/YB seed colored desi and wild Cicer reticulatum accessions compared with the BE seed colored kabuli accessions. The functionally relevant molecular tags identified have potential to decipher the complex transcriptional regulatory gene function of seed coat coloration and for understanding the selective sweep-based seed color trait evolutionary pattern in cultivated and wild accessions during chickpea domestication. The genome-wide integrated approach employed will expedite marker-assisted genetic enhancement for developing cultivars with desirable seed coat color types in chickpea. PMID:26635822

  10. Genetic Architecture of MicroRNA Expression: Implications for the Transcriptome and Complex Traits

    PubMed Central

    Gamazon, Eric R.; Ziliak, Dana; Im, Hae Kyung; LaCroix, Bonnie; Park, Danny S.; Cox, Nancy J.; Huang, R. Stephanie

    2012-01-01

    We sought to comprehensively and systematically characterize the relationship between genetic variation, miRNA expression, and mRNA expression. Genome-wide expression profiling of samples of European and African ancestry identified in each population hundreds of miRNAs whose increased expression is correlated with correspondingly reduced expression of target mRNAs. We scanned 3′ UTR SNPs with a potential functional effect on miRNA binding for cis-acting expression quantitative trait loci (eQTLs) for the corresponding proximal target genes. To extend sequence-based, localized analyses of SNP effect on miRNA binding, we proceeded to dissect the genetic basis of miRNA expression variation; we mapped miRNA expression levels—as quantitative traits—to loci in the genome as miRNA eQTLs, demonstrating that miRNA expression is under significant genetic control. We found that SNPs associated with miRNA expression are significantly enriched with those SNPs already shown to be associated with mRNA. Moreover, we discovered that many of the miRNA-associated genetic variations identified in our study are associated with a broad spectrum of human complex traits from the National Human Genome Research Institute catalog of published genome-wide association studies. Experimentally, we replicated miRNA-induced mRNA expression inhibition and the cis-eQTL relationship to the target gene for several identified relationships among SNPs, miRNAs, and mRNAs in an independent set of samples; furthermore, we conducted miRNA overexpression and inhibition experiments to functionally validate the miRNA-mRNA relationships. This study extends our understanding of the genetic regulation of the transcriptome and suggests that genetic variation might underlie observed relationships between miRNAs and mRNAs more commonly than has previously been appreciated. PMID:22658545

  11. Carbohydrate Recognition by an Architecturally Complex α-N-Acetylglucosaminidase from Clostridium perfringens

    PubMed Central

    Ficko-Blean, Elizabeth; Stuart, Christopher P.; Suits, Michael D.; Cid, Melissa; Tessier, Matthew; Woods, Robert J.; Boraston, Alisdair B.

    2012-01-01

    CpGH89 is a large multimodular enzyme produced by the human and animal pathogen Clostridium perfringens. The catalytic activity of this exo-α-d-N-acetylglucosaminidase is directed towards a rare carbohydrate motif, N-acetyl-β-d-glucosamine-α-1,4-d-galactose, which is displayed on the class III mucins deep within the gastric mucosa. In addition to the family 89 glycoside hydrolase catalytic module this enzyme has six modules that share sequence similarity to the family 32 carbohydrate-binding modules (CBM32s), suggesting the enzyme has considerable capacity to adhere to carbohydrates. Here we suggest that two of the modules, CBM32-1 and CBM32-6, are not functional as carbohydrate-binding modules (CBMs) and demonstrate that three of the CBMs, CBM32-3, CBM32-4, and CBM32-5, are indeed capable of binding carbohydrates. CBM32-3 and CBM32-4 have a novel binding specificity for N-acetyl-β-d-glucosamine-α-1,4-d-galactose, which thus complements the specificity of the catalytic module. The X-ray crystal structure of CBM32-4 in complex with this disaccharide reveals a mode of recognition that is based primarily on accommodation of the unique bent shape of this sugar. In contrast, as revealed by a series of X-ray crystal structures and quantitative binding studies, CBM32-5 displays the structural and functional features of galactose binding that is commonly associated with CBM family 32. The functional CBM32s that CpGH89 contains suggest the possibility for multivalent binding events and the partitioning of this enzyme to highly specific regions within the gastrointestinal tract. PMID:22479408

  12. Thermal recycling and re-manufacturing of glass fibre thermosetting composites

    NASA Astrophysics Data System (ADS)

    Fraisse, A.; Beauson, J.; Brøndsted, P.; Madsen, B.

    2016-07-01

    The impact of using thermally recycled glass fibre in re-manufactured composites was investigated. A unidirectional glass fibre thermosetting composite laminate was manufactured. The matrix in one part of the laminate was burnt off to recover the glass fibres. These recycled glass fibres were used to manufacture a new composite laminate with the same fibre architecture as the pristine one. The fibres, the matrix and the composite laminates were thoroughly characterised and analysed. The results show that good materials quality was obtained for both laminates. A difference in fibre packing behaviour was observed in the composites with the pristine and the recycled fibres, which lead to a lower fibre volume fraction in the latter one. The Young's modulus of the composites was not changed by the recycling process, if the lower fibre volume fraction is taken into account. However, a marked drop in the maximum stress of the composites was reported, which was found to be related to the loss in maximum stress of the fibres.

  13. Quantitative description of collagen fibre network on trabecular bone surfaces based on AFM imaging.

    PubMed

    Hua, W-D; Chen, P-P; Xu, M-Q; Ao, Z; Liu, Y; Han, D; He, F

    2016-04-01

    The collagen fibre network is an important part of extracellular matrix (ECM) on trabecular bone surface. The geometry features of the network can provide us insights into its physical and physiological properties. However, previous researches have not focused on the geometry and the quantitative description of the collagen fibre network on trabecular bone surface. In this study,we developed a procedure to quantitatively describe the network and verified the validity of the procedure. The experiment proceeds as follow. Atomic force microscopy (AFM) was used to acquire submicron resolution images of the trabecular surface. Then, an image analysing procedure was built to extract important parameters, including, fibre orientation, fibre density, fibre width, fibre crossing numbers, the number of holes formed by fibre s, and the area of holes from AFM images. In order to verify the validity of the parameters extracted by image analysing methods, we adopted two other methods, which are statistical geometry model and computer simulation, to calculate those same parameters and check the consistency of the three methods' results. Statistical tests indicate that there is no significant difference between three groups. We conclude that, (a) the ECM on trabecular surface mainly consists of random collagen fibre network with oriented fibres; (b) our method based on image analysing can be used to characterize quantitative geometry features of the collagen fibre network effectively. This method may provide a basis for quantitative investigating the architecture and function of collagen fibre network.

  14. Ground-penetrating radar survey on the island of Pantelleria (Italy) reveals an ancient architectural complex with likely Punic and Roman components

    NASA Astrophysics Data System (ADS)

    Urban, Thomas M.; Murray, Carrie Ann; Vella, Clive; Lahikainen, Amanda

    2015-12-01

    A ground-penetrating radar (GPR) survey conducted on the small volcanic island of Pantelleria, in the Strait of Sicily, south-central Mediterranean, revealed an apparent complex of Punic/Roman architecture. The survey focused on the Lago di Venere area, where a previously investigated ritual Punic site was built alongside a brackish volcanic lake. The site also exhibits evidence of earlier Eneolithic components and later Roman components. The full extent of the site has remained undetermined, however, with only the small area of the Punic ritual complex having been excavated from 1996 to 2002. The GPR survey was intended to explore whether additional architecture remained unseen in surrounding areas, thus taking a first step toward determining the site's full spatial extent and archaeological potential. This survey revealed a complex of architectural ruins beneath an active agricultural field immediately west of the previously excavated features, and extending to a depth of approximately 2 m. These newly discovered features expand the known architectural footprint of the immediate site by three-fold. This GPR study is the first published archaeo-geophysical investigation on the island.

  15. The endosomal sorting complex ESCRT-II mediates the assembly and architecture of ESCRT-III helices.

    PubMed

    Henne, William Mike; Buchkovich, Nicholas J; Zhao, Yingying; Emr, Scott D

    2012-10-12

    The endosomal sorting complexes required for transport (ESCRTs) constitute hetero-oligomeric machines that mediate topologically similar membrane-sculpting processes, including cytokinesis, retroviral egress, and multivesicular body (MVB) biogenesis. Although ESCRT-III drives membrane remodeling that creates MVBs, its structure and the mechanism of vesicle formation are unclear. Using electron microscopy, we visualize an ESCRT-II:ESCRT-III supercomplex and propose how it mediates vesicle formation. We define conformational changes that activate ESCRT-III subunit Snf7 and show that it assembles into spiraling ~9 nm protofilaments on lipid monolayers. A high-content flow cytometry assay further demonstrates that mutations halting ESCRT-III assembly block ESCRT function. Strikingly, the addition of Vps24 and Vps2 transforms flat Snf7 spirals into membrane-sculpting helices. Finally, we show that ESCRT-II and ESCRT-III coassemble into ~65 nm diameter rings indicative of a cargo-sequestering supercomplex. We propose that ESCRT-III has distinct architectural stages that are modulated by ESCRT-II to mediate cargo capture and vesicle formation by ordered assembly.

  16. Comparison between traditional strength training and complex contrast training on repeated sprint ability and muscle architecture in elite soccer players.

    PubMed

    Spineti, Juliano; Figueiredo, Tiago; Bastos DE Oliveira, Viviane; Assis, Marcio; Fernandes DE Oliveira, Liliam; Miranda, Humberto; Machado DE Ribeiro Reis, Victor M; Simão, Roberto

    2016-11-01

    The purpose of this study was to compare traditional strength training (TST) and complex contrast training (CCT) on the repeated-shuttle-sprint ability (RSSA), the countermovement squat jump (CMJ) height, the one repetition maximum (1RM) at squat on the Smith machine, and on muscle architecture in young, male elite soccer players. Twenty-two soccer players (mean age 18.4±0.4 years; mean weight 70.2±9.1 kg; mean height 179.9±7.5 cm) who belonged to the under-20 age group were randomly assigned into two groups: CCT (N.=10) or TST (N.=12). During the study period, the soccer players trained with CCT through power exercises performed before high-velocity exercises and TST based on a set-repetition format through daily, undulatory periodization. After statistical analysis (P<0.05), the results demonstrated that the specific CCT regimen provided a significant improvement in the RSSA percent decrement (moderate effect size), CMJ (large effect size) and 1RM ability (large effect size). However, the TST promoted significant changes in 1RM (large effect size) and a significant increase in the muscle thickness of the vastus intermedius (moderate effect size). The CCT protocol could be used to improve the RSSA parameters, CMJ and 1RM, and the TST developed dynamic strength and muscle growth. Coaches can choose either CCT or TST protocols according to the needs of their soccer players.

  17. Novel in situ multiharmonic EQCM-D approach to characterize complex carbon pore architectures for capacitive deionization of brackish water.

    PubMed

    Shpigel, Netanel; Levi, Mikhael D; Sigalov, Sergey; Aurbach, Doron; Daikhin, Leonid; Presser, Volker

    2016-03-23

    Multiharmonic analysis by electrochemical quartz-crystal microbalance with dissipation monitoring (EQCM-D) is introduced as an excellent tool for quantitative studying electrosorption of ions from aqueous solution in mesoporous (BP-880) or mixed micro-mesoporous (BP-2000) carbon electrodes. Finding the optimal conditions for gravimetric analysis of the ionic content in the charged carbon electrodes, we propose a novel approach to modeling the charge-dependent gravimetric characteristics by incorporation of Gouy-Chapman-Stern electric double layer model for ions electrosorption into meso- and micro-mesoporous carbon electrodes. All three parameters of the gravimetric equation evaluated by fitting it to the experimental mass changes curves were validated using supplementary nitrogen gas sorption analysis and complementing atomic force microscopy. Important overlap between gravimetric EQCM-D analysis of the ionic content of porous carbon electrodes and the classical capacitive deionization models has been established. The necessity and usefulness of non-gravimetric EQCM-D characterizations of complex carbon architectures, providing insight into their unique viscoelastic behavior and porous structure changes, have been discussed in detail.

  18. RWD domain: a recurring module in kinetochore architecture shown by a Ctf19-Mcm21 complex structure

    SciTech Connect

    Schmitzberger, Florian; Harrison, Stephen C

    2012-04-30

    The proteins Ctf19, Okp1, Mcm21 and Ame1 are the components of COMA, a subassembly of budding-yeast kinetochores. We have determined the crystal structure of a conserved COMA subcomplex - the Ctf19 - Mcm21 heterodimer - from Kluyveromyces lactis. Both proteins contain 'double-RWD' domains, which together form a Y-shaped framework with flexible N-terminal extensions. The kinetochore proteins Csm1, Spc24 and Spc25 have related single RWD domains, and Ctf19 and Mcm21 associate with pseudo-twofold symmetry analogous to that in the Csm1 homodimer and the Spc24-Spc25 heterodimer. The double-RWD domain core of the Ctf19-Mcm21 heterodimer is sufficient for association with Okp1-Ame1; the less conserved N-terminal regions may interact with components of a more extensive 'CTF19 complex'. Our structure shows the RWD domain to be a recurring module of kinetochore architecture that may be present in other kinetochore substructures. Like many eukaryotic molecular machines, kinetochores may have evolved from simpler assemblies by multiplication of a few ancestral modules.

  19. The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes.

    PubMed

    Silva-Rocha, Rafael; Martínez-García, Esteban; Calles, Belén; Chavarría, Max; Arce-Rodríguez, Alejandro; de Las Heras, Aitor; Páez-Espino, A David; Durante-Rodríguez, Gonzalo; Kim, Juhyun; Nikel, Pablo I; Platero, Raúl; de Lorenzo, Víctor

    2013-01-01

    The 'Standard European Vector Architecture' database (SEVA-DB, http://seva.cnb.csic.es) was conceived as a user-friendly, web-based resource and a material clone repository to assist in the choice of optimal plasmid vectors for de-constructing and re-constructing complex prokaryotic phenotypes. The SEVA-DB adopts simple design concepts that facilitate the swapping of functional modules and the extension of genome engineering options to microorganisms beyond typical laboratory strains. Under the SEVA standard, every DNA portion of the plasmid vectors is minimized, edited for flaws in their sequence and/or functionality, and endowed with physical connectivity through three inter-segment insulators that are flanked by fixed, rare restriction sites. Such a scaffold enables the exchangeability of multiple origins of replication and diverse antibiotic selection markers to shape a frame for their further combination with a large variety of cargo modules that can be used for varied end-applications. The core collection of constructs that are available at the SEVA-DB has been produced as a starting point for the further expansion of the formatted vector platform. We argue that adoption of the SEVA format can become a shortcut to fill the phenomenal gap between the existing power of DNA synthesis and the actual engineering of predictable and efficacious bacteria.

  20. The Integrated Survey for Excavated Architectures: the Complex of Casalnuovo District Within the World Heritage Site "sassi" (matera, Italy)

    NASA Astrophysics Data System (ADS)

    Cardinale, T.; Valva, R.; Lucarelli, M.

    2015-02-01

    Never as within the complex of Sassi (Matera, South of Italy), the parties have a volumetric material identity and a special construction condition for which, first of all, you need to know the whole to which they give life, and then the individual components and their connections. In the course of time, in the Lucan city, there were stable and favorable conditions that allowed the development of an architectural language, of juxtaposition of the materials, interpenetration of space and conformation of the volumes, which generated an exceptional urban phenomenon. The distribution of these building artifacts in symbiotic connection with the connective calcareous texture that hosts them , resulted in a spontaneously harmonious figurative balance that characterizes the constructive expedients employed and the distributive and morphological solutions. This is the reason why the Sassi, and the overlooking Park of Rupestrian Churches of Matera Murgia, have been entered in 1993 in the UNESCO World Heritage List. The complexity of a built space, such as this one, determines the need for a non-traditional approach, so you have to combine last generation tools and canonical ones for survey, drawing and representation, within a dialectic between memory and design, tradition and innovation. For this reason, an appropriate cognitive apparatus has been set up for the entire technical process, making use of different non-destructive and non-contact techniques: digital photogrammetry, total station, laser scanner and thermography, in order to obtain a three-dimensional computer model, useful for the diagnosis and the preservation of the integrity of cultural heritage.

  1. Understanding how the complex molecular architecture of mannan-degrading hydrolases contributes to plant cell wall degradation.

    PubMed

    Zhang, Xiaoyang; Rogowski, Artur; Zhao, Lei; Hahn, Michael G; Avci, Utku; Knox, J Paul; Gilbert, Harry J

    2014-01-24

    Microbial degradation of plant cell walls is a central component of the carbon cycle and is of increasing importance in environmentally significant industries. Plant cell wall-degrading enzymes have a complex molecular architecture consisting of catalytic modules and, frequently, multiple non-catalytic carbohydrate binding modules (CBMs). It is currently unclear whether the specificities of the CBMs or the topology of the catalytic modules are the primary drivers for the specificity of these enzymes against plant cell walls. Here, we have evaluated the relationship between CBM specificity and their capacity to enhance the activity of GH5 and GH26 mannanases and CE2 esterases against intact plant cell walls. The data show that cellulose and mannan binding CBMs have the greatest impact on the removal of mannan from tobacco and Physcomitrella cell walls, respectively. Although the action of the GH5 mannanase was independent of the context of mannan in tobacco cell walls, a significant proportion of the polysaccharide was inaccessible to the GH26 enzyme. The recalcitrant mannan, however, was fully accessible to the GH26 mannanase appended to a cellulose binding CBM. Although CE2 esterases display similar specificities against acetylated substrates in vitro, only CjCE2C was active against acetylated mannan in Physcomitrella. Appending a mannan binding CBM27 to CjCE2C potentiated its activity against Physcomitrella walls, whereas a xylan binding CBM reduced the capacity of esterases to deacetylate xylan in tobacco walls. This work provides insight into the biological significance for the complex array of hydrolytic enzymes expressed by plant cell wall-degrading microorganisms.

  2. Involvement of the Rho–mDia1 pathway in the regulation of Golgi complex architecture and dynamics

    PubMed Central

    Zilberman, Yuliya; Alieva, Naila O.; Miserey-Lenkei, Stéphanie; Lichtenstein, Alexandra; Kam, Zvi; Sabanay, Helena; Bershadsky, Alexander

    2011-01-01

    In mammalian cells, the Golgi apparatus is a ribbon-like, compact structure composed of multiple membrane stacks connected by tubular bridges. Microtubules are known to be important to Golgi integrity, but the role of the actin cytoskeleton in the maintenance of Golgi architecture remains unclear. Here we show that an increase in Rho activity, either by treatment of cells with lysophosphatidic acid or by expression of constitutively active mutants, resulted in pronounced fragmentation of the Golgi complex into ministacks. Golgi dispersion required the involvement of mDia1 formin, a downstream target of Rho and a potent activator of actin polymerization; moreover, constitutively active mDia1, in and of itself, was sufficient for Golgi dispersion. The dispersion process was accompanied by formation of dynamic F-actin patches in the Golgi area. Experiments with cytoskeletal inhibitors (e.g., latrunculin B, blebbistatin, and Taxol) revealed that actin polymerization, myosin-II–driven contractility, and microtubule-based intracellular movement were all involved in the process of Golgi dispersion induced by Rho–mDia1 activation. Live imaging of Golgi recovery revealed that fusion of the small Golgi stacks into larger compartments was repressed in cells with active mDia1. Furthermore, the formation of Rab6-positive transport vesicles derived from the Golgi complex was enhanced upon activation of the Rho–mDia1 pathway. Transient localization of mDia1 to Rab6-positive vesicles was detected in cells expressing active RhoA. Thus, the Rho–mDia1 pathway is involved in regulation of the Golgi structure, affecting remodeling of Golgi membranes. PMID:21680709

  3. Cell-mediated fibre recruitment drives extracellular matrix mechanosensing in engineered fibrillar microenvironments

    NASA Astrophysics Data System (ADS)

    Baker, Brendon M.; Trappmann, Britta; Wang, William Y.; Sakar, Mahmut S.; Kim, Iris L.; Shenoy, Vivek B.; Burdick, Jason A.; Chen, Christopher S.

    2015-12-01

    To investigate how cells sense stiffness in settings structurally similar to native extracellular matrices, we designed a synthetic fibrous material with tunable mechanics and user-defined architecture. In contrast to flat hydrogel surfaces, these fibrous materials recapitulated cell-matrix interactions observed with collagen matrices including stellate cell morphologies, cell-mediated realignment of fibres, and bulk contraction of the material. Increasing the stiffness of flat hydrogel surfaces induced mesenchymal stem cell spreading and proliferation; however, increasing fibre stiffness instead suppressed spreading and proliferation for certain network architectures. Lower fibre stiffness permitted active cellular forces to recruit nearby fibres, dynamically increasing ligand density at the cell surface and promoting the formation of focal adhesions and related signalling. These studies demonstrate a departure from the well-described relationship between material stiffness and spreading established with hydrogel surfaces, and introduce fibre recruitment as a previously undescribed mechanism by which cells probe and respond to mechanics in fibrillar matrices.

  4. Turbulence hierarchy in a random fibre laser

    NASA Astrophysics Data System (ADS)

    González, Iván R. Roa; Lima, Bismarck C.; Pincheira, Pablo I. R.; Brum, Arthur A.; Macêdo, Antônio M. S.; Vasconcelos, Giovani L.; de S. Menezes, Leonardo; Raposo, Ernesto P.; Gomes, Anderson S. L.; Kashyap, Raman

    2017-05-01

    Turbulence is a challenging feature common to a wide range of complex phenomena. Random fibre lasers are a special class of lasers in which the feedback arises from multiple scattering in a one-dimensional disordered cavity-less medium. Here we report on statistical signatures of turbulence in the distribution of intensity fluctuations in a continuous-wave-pumped erbium-based random fibre laser, with random Bragg grating scatterers. The distribution of intensity fluctuations in an extensive data set exhibits three qualitatively distinct behaviours: a Gaussian regime below threshold, a mixture of two distributions with exponentially decaying tails near the threshold and a mixture of distributions with stretched-exponential tails above threshold. All distributions are well described by a hierarchical stochastic model that incorporates Kolmogorov's theory of turbulence, which includes energy cascade and the intermittence phenomenon. Our findings have implications for explaining the remarkably challenging turbulent behaviour in photonics, using a random fibre laser as the experimental platform.

  5. The structural architecture of the Los Humeros volcanic complex and geothermal field, Trans-Mexican Volcanic Belt, Central Mexico

    NASA Astrophysics Data System (ADS)

    Norini, Gianluca; Groppelli, Gianluca; Sulpizio, Roberto; Carrasco Núñez, Gerardo; Davila Harris, Pablo

    2014-05-01

    The development of geothermal energy in Mexico is a very important goal, given the presence of a large heat anomaly, associated with the Trans-Mexican Volcanic Belt, the renewability of the resource and the low environmental impact. The Quaternary Los Humeros volcanic complex is an important geothermal target, whose evolution involved at least two caldera events, that alternated with other explosive and effusive activity. The first caldera forming event was the 460 ka eruption that produced the Xaltipan ignimbrite and formed a 15-20 km wide caldera. The second collapse event occurred 100 ka with the formation of the Zaragoza ignimbrite and a nested 8-10 km wide caldera. The whole volcano structure, the style of the collapses and the exact location of the calderas scarps and ring faults are still a matter of debate. The Los Humeros volcano hosts the productive Los Humeros Geothermal Field, with an installed capacity of 40 MW and additional 75 MW power plants under construction. Recent models of the geothermal reservoir predict the existence of at least two reservoirs in the geothermal system, separated by impermeable rock units. Hydraulic connectivity and hydrothermal fluids circulation occurs through faults and fractures, allowing deep steam to ascend while condensate flows descend. As a consequence, the plans for the exploration and exploitation of the geothermal reservoir have been based on the identification of the main channels for the circulation of hydrothermal fluids, constituted by faults, so that the full comprehension of the structural architecture of the caldera is crucial to improve the efficiency and minimize the costs of the geothermal field operation. In this study, we present an analysis of the Los Humeros volcanic complex focused on the Quaternary tectonic and volcanotectonics features, like fault scarps and aligned/elongated monogenetic volcanic centres. Morphostructural analysis and field mapping reveal the geometry, kinematics and dynamics of

  6. Improved tractography using asymmetric fibre orientation distributions.

    PubMed

    Bastiani, Matteo; Cottaar, Michiel; Dikranian, Krikor; Ghosh, Aurobrata; Zhang, Hui; Alexander, Daniel C; Behrens, Timothy E; Jbabdi, Saad; Sotiropoulos, Stamatios N

    2017-09-01

    Diffusion MRI allows us to make inferences on the structural organisation of the brain by mapping water diffusion to white matter microstructure. However, such a mapping is generally ill-defined; for instance, diffusion measurements are antipodally symmetric (diffusion along x and -x are equal), whereas the distribution of fibre orientations within a voxel is generally not symmetric. Therefore, different sub-voxel patterns such as crossing, fanning, or sharp bending, cannot be distinguished by fitting a voxel-wise model to the signal. However, asymmetric fibre patterns can potentially be distinguished once spatial information from neighbouring voxels is taken into account. We propose a neighbourhood-constrained spherical deconvolution approach that is capable of inferring asymmetric fibre orientation distributions (A-fods). Importantly, we further design and implement a tractography algorithm that utilises the estimated A-fods, since the commonly used streamline tractography paradigm cannot directly take advantage of the new information. We assess performance using ultra-high resolution histology data where we can compare true orientation distributions against sub-voxel fibre patterns estimated from down-sampled data. Finally, we explore the benefits of A-fods-based tractography using in vivo data by evaluating agreement of tractography predictions with connectivity estimates made using different in-vivo modalities. The proposed approach can reliably estimate complex fibre patterns such as sharp bending and fanning, which voxel-wise approaches cannot estimate. Moreover, histology-based and in-vivo results show that the new framework allows more accurate tractography and reconstruction of maps quantifying (symmetric and asymmetric) fibre complexity. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  7. Fibre based cellular transfection.

    PubMed

    Tsampoula, X; Taguchi, K; Cizmár, T; Garces-Chavez, V; Ma, N; Mohanty, S; Mohanty, K; Gunn-Moore, F; Dholakia, K

    2008-10-13

    Optically assisted transfection is emerging as a powerful and versatile method for the delivery of foreign therapeutic agents to cells at will. In particular the use of ultrashort pulse lasers has proved an important route to transiently permeating the cell membrane through a multiphoton process. Though optical transfection has been gaining wider usage to date, all incarnations of this technique have employed free space light beams. In this paper we demonstrate the first system to use fibre delivery for the optical transfection of cells. We engineer a standard optical fibre to generate an axicon tip with an enhanced intensity of the remote output field that delivers ultrashort (~ 800 fs) pulses without requiring the fibre to be placed in very close proximity to the cell sample. A theoretical model is also developed in order to predict the light propagation from axicon tipped and bare fibres, in both air and water environments. The model proves to be in good agreement with the experimental findings and can be used to establish the optimum fibre parameters for successful cellular transfection. We readily obtain efficiencies of up to 57 % which are comparable with free space transfection. This advance paves the way for optical transfection of tissue samples and endoscopic embodiments of this technique.

  8. Specimen specific parameter identification of ovine lumbar intervertebral discs: On the influence of fibre-matrix and fibre-fibre shear interactions.

    PubMed

    Reutlinger, Christoph; Bürki, Alexander; Brandejsky, Vaclav; Ebert, Lars; Büchler, Philippe

    2014-02-01

    Numerical models of the intervertebral disc, which address mechanical questions commonly make use of the difference in water content between annulus and nucleus, and thus fluid and solid parts are separated. Despite this simplification, models remain complex due to the anisotropy and nonlinearity of the annulus and regional variations of the collagen fibre density. Additionally, it has been shown that cross-links make a large contribution to the stiffness of the annulus. Because of this complex composite structure, it is difficult to reproduce several sets of experimental data with one single set of material parameters. This study addresses the question to which extent the ultrastructure of the intervertebral disc should be modelled so that its moment-angle behaviour can be adequately described. Therefore, a hyperelastic constitutive law, based on continuum mechanical principles was derived, which does not only consider the anisotropy from the collagen fibres, but also interactions among the fibres and between the fibres and the ground substance. Eight ovine lumbar intervertebral discs were tested on a custom made spinal loading simulator in flexion/extension, lateral bending and axial rotation. Specimen-specific geometrical models were generated using CT images and T2 maps to distinguish between annulus fibrosus and nucleus pulposus. For the identification of the material parameters the annulus fibrosus was described with two scenarios: with and without fibre-matrix and fibre-fibre interactions. Both scenarios showed a similar behaviour on a load displacement level. Comparing model predictions to the experimental data, the mean RMS of all specimens and all load cases was 0.54±0.15° without the interaction and 0.54±0.19° when the fibre-matrix and fibre-fibre interactions were included. However, due to the increased stiffness when cross-links effects were included, this scenario showed more physiological stress-strain relations in uniaxial and biaxial stress

  9. Radioluminescence of some optical fibres.

    PubMed

    Nowotny, R

    2007-02-21

    Measurement of radiation fields with small scintillators as detectors for radiation dose is an attractive method provided that the scintillator luminescence can be discriminated against other unwanted signals. In diagnostic radiology radioluminescence of the optical fibres required for a transmission of the luminescence to an optical detector is the only source for such an impairment of the signal. To find fibres with low radioluminosity a survey of ten commercial fibres including polystyrene (PS), polystyrene wavelength shifting fibres, poly-methylmetacrylate (PMMA) and silica as fibre core material was made. Measurements were made with two photomultipliers of different spectral response and a clinical x-ray unit. Lowest radioluminosity was obtained with PMMA fibres. Depending on spectral sensitivity of the multiplier clear PS fibres give five to ten times the luminescence of PMMA. From the silica fibres only one high-OH fibre gave comparable results for wavelength up to 520 nm. Wavelength shifting fibres and silica fibres with low OH-content show strong fluorescence and are not suitable fibre materials.

  10. Fibre gratings and their applications

    SciTech Connect

    Vasil'ev, Sergei A; Medvedkov, O I; Korolev, I G; Bozhkov, A S; Kurkov, Andrei S; Dianov, Evgenii M

    2005-12-31

    A brief review is given of the state of the art in the research on the photosensitivity of fibres and photoinduced fibre gratings. The most important properties of fibre gratings are considered and the main methods of their production and their applications are discussed. The photosensitive compositions of silica glasses are presented and methods for increasing their photosensitivity are indicated. (review)

  11. Architecture of the Igneous Lower Crust at Oceanic Core Complexes: constraints from IODP Hole U1309D

    NASA Astrophysics Data System (ADS)

    Christofferson, C. A.; Cheadle, M. J.; John, B. E.; Schoolmeesters, N.; Swapp, S. M.; Grimes, C. B.

    2011-12-01

    Slow spreading mid-ocean ridges are a ubiquitous part of the global ridge system, yet remain poorly understood. The crust produced at these ridges is fundamentally different than that produced at fast spreading ridges where the crustal architecture largely conforms to the standard Penrose type crust. At slow spread ridges, a reduced magma supply to the crust allows extensional faulting to play a much more important role in accommodating plate separation than at fast spread ridges. Oceanic core complexes (OCCs), a product of such faulting, denude lower crust to the surface via detachment faulting, and thus provide a means to study the architecture of slow spread lower crust. We report a detailed lithologic analysis of IODP Hole U1309D drilled into the Atlantis Massif OCC (30°N MAR). The abundance of sharp contacts between thin inter-layered gabbroic and ultramafic rocks throughout the core supports crustal construction via small (10-40m thick) injections of magma. Paleomagnetic remanance data allows re-orientation of the observed contacts and igneous fabrics to their original orientation at intrusion, and suggest that most contacts and fabrics were sub-vertical. These data therefore imply that construction of slow spread gabbroic lower crust at OCCs is dominated by dike-like intrusions rather than by sills. Combined U-Pb and (U-Th)/He zircon thermochronometry are used to predict a 3-4km thick zone of accretion that lies 6-7 km below seafloor, at the root of the detachment fault. Existing seismic data estimate the depth of the Moho to be 5km at Atlantis Massif constraining the width of the accretion zone in the footwall of the detachment fault to be 4km. Igneous fabrics from unfaulted gabbroic rocks provide an additional major constraint on the processes occurring within this zone of magmatic accretion. Electron backscatter diffraction (EBSD) was used to characterize the fabrics of slow-spread gabbros from the Atlantis Massif OCC, and other OCCs on the MAR (the 15

  12. Can supplementary dietary fibre suppress breast cancer growth?

    PubMed Central

    Stoll, B. A.

    1996-01-01

    Case-control studies in diverse populations around the world have reported a lower risk of breast cancer in association with higher intake of dietary fibre and complex carbohydrates. Although this has not been confirmed in prospective studies in the USA, the observations have prompted the hypothesis that prolonged use of dietary fibre supplements might reduce breast cancer risk in high-incidence populations. Several possible mechanisms of action have been suggested, all involving a reduction of bioactive oestrogen levels in the blood. The various mechanisms are not necessarily mutually exclusive. First, a high-fibre diet might reduce circulating oestrogen levels by reducing the enterohepatic recirculation of oestrogen. Second, many plants and vegetables contain isoflavones and lignans capable of conversion in the bowel into weak oestrogens that may compete with oestradiol for target binding-sites. Third, a high-fibre diet is less often associated with obesity, which tends to increase availability of the biologically active 16-alpha metabolites of oestrone. Fourth, a high-fibre diet usually has a lower content of fat and a higher content of antioxidant vitamins, which may protect against breast cancer risk. Finally, diets rich in fibre and complex carbohydrates have been shown to improve insulin sensitivity, with an associated reduction in circulating oestrogen levels. Synergism between these effects offers a possible mechanism by which a high fibre intake might suppress breast cancer growth in women. PMID:8605086

  13. Small fibre neuropathy.

    PubMed

    Cazzato, Daniele; Lauria, Giuseppe

    2017-10-01

    To provide a review on the state-of-art of clinical features, diagnostics, genetics and treatments of small fibre neuropathy (SFN). The spectrum of clinical features has been widened from the classical presentation of burning feet as length-dependent SFN to that of small fibre dysfunction and/or degeneration associated with focal, diffuse and episodic neuropathic pain syndromes. The involvement of small nerve fibres in neurodegenerative diseases has been further defined, challenging the relationship between neuropathic pain symptoms and small fibre loss. The clinical reliability of skin biopsy has been strengthened by the availability of normative values for both the immunohistochemistry techniques used and their comparison, and by side and short-term follow-up analyses. Corneal confocal microscopy has implemented its diagnostic potentiality because of the availability of age-adjusted and sex-adjusted normative values. Genetic studies expanded the panel on genes involved in SFN because of the discovery of new mutations in SCN10A and SCN11A, besides the first found in SCN9A, and identification of mutations in COL6A5 in patients with itching. In the last 5 years, the chapter of SFN has been widened by new clinical and genetics descriptions leading to a more comprehensive approach to patients in clinical practice and research.

  14. Bismuth-ring-doped fibres

    SciTech Connect

    Zlenko, Aleksandr S; Dvoirin, Vladislav V; Bogatyrev, Vladimir A; Firstov, Sergei V; Akhmetshin, Ural G

    2009-11-30

    A new process for bismuth doping of optical fibres is proposed in which the dopant is introduced into a thin layer surrounding the fibre core. This enables bismuth stabilisation in the silica glass, with no limitations on the core composition. In particular, the GeO{sub 2} content of the fibre core in this study is 16 mol %. Spectroscopic characterisation of such fibres and optical gain measurements suggest that the proposed approach has considerable potential for laser applications. (optical fibres and fibreoptic sensors)

  15. Overall Architecture of the Intraflagellar Transport (IFT)-B Complex Containing Cluap1/IFT38 as an Essential Component of the IFT-B Peripheral Subcomplex.

    PubMed

    Katoh, Yohei; Terada, Masaya; Nishijima, Yuya; Takei, Ryota; Nozaki, Shohei; Hamada, Hiroshi; Nakayama, Kazuhisa

    2016-05-20

    Intraflagellar transport (IFT) is essential for assembly and maintenance of cilia and flagella as well as ciliary motility and signaling. IFT is mediated by multisubunit complexes, including IFT-A, IFT-B, and the BBSome, in concert with kinesin and dynein motors. Under high salt conditions, purified IFT-B complex dissociates into a core subcomplex composed of at least nine subunits and at least five peripherally associated proteins. Using the visible immunoprecipitation assay, which we recently developed as a convenient protein-protein interaction assay, we determined the overall architecture of the IFT-B complex, which can be divided into core and peripheral subcomplexes composed of 10 and 6 subunits, respectively. In particular, we identified TTC26/IFT56 and Cluap1/IFT38, neither of which was included with certainty in previous models of the IFT-B complex, as integral components of the core and peripheral subcomplexes, respectively. Consistent with this, a ciliogenesis defect of Cluap1-deficient mouse embryonic fibroblasts was rescued by exogenous expression of wild-type Cluap1 but not by mutant Cluap1 lacking the binding ability to other IFT-B components. The detailed interaction map as well as comparison of subcellular localization of IFT-B components between wild-type and Cluap1-deficient cells provides insights into the functional relevance of the architecture of the IFT-B complex. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  16. Segmental fibre type composition of the rat iliopsoas muscle.

    PubMed

    Vlahovic, Hrvoje; Bazdaric, Ksenija; Marijancic, Verner; Soic-Vranic, Tamara; Malnar, Daniela; Arbanas, Juraj

    2017-01-18

    The iliopsoas of the rat is composed of two muscles - the psoas major muscle and the iliacus muscle. The psoas major muscle arises from all the lumbar vertebrae and the iliacus muscle from the fifth and sixth lumbar vertebrae and ilium. Their common insertion point is the lesser trochanter of the femur, and their common action is the lateral rotation of the femur and flexion of the hip joint. Unlike humans, the rat is a quadruped and only occasionally rises up on its hind legs. Therefore, it is expected that the fibre type composition of the rat iliopsoas muscle will be different than that of humans. The iliopsoas muscle of the rat is generally considered to be a fast muscle. However, previous studies of the fibre type composition of the rat psoas muscle showed different results. Moreover, very little is known about the composition of the rat iliacus muscle. The aim of our study was to examine the fibre type composition of the rat iliopsoas muscle in order to better understand the complex function of the listed muscle. The psoas major muscle was examined segmentally at four different levels of its origin. Type I, IIA, IIB and IIX muscle fibres were typed using monoclonal antibodies for myosin heavy chain identification. The percentage of muscle fibre types and muscle fibre cross-sectional areas were calculated. In our study we showed that in the rat iliopsoas muscle both the iliacus and the psoas major muscles had a predominance of fast muscle fibre types, with the highest percentage of the fastest IIB muscle fibres. Also, the IIB muscle fibres showed the largest cross-sectional area (CSA) in both muscles. As well, the psoas major muscle showed segmental differences of fibre type composition. Our results showed changes in percentages, as well as the CSAs of muscle fibre types in cranio-caudal direction. The most significant changes were visible in type IIB muscle fibres, where there was a decrease of percentages and the CSAs from the cranial towards the caudal part

  17. Quantitative trait loci in hop (Humulus lupulus L.) reveal complex genetic architecture underlying variation in sex, yield and cone chemistry

    PubMed Central

    2013-01-01

    advance our understanding of the genetic control of traits of current economic and breeding significance in hop and demonstrate the complex genetic architecture underlying variation in these traits. The linkage information obtained in this study, based on transferable markers, can be used to facilitate the validation of QTL, crucial to the success of MAS. PMID:23718194

  18. Force measurements in skinned muscle fibres

    PubMed Central

    Hellam, D. C.; Podolsky, R. J.

    1969-01-01

    1. Isometric force was measured in skinned segments of frog semitendinosus muscle fibres exposed to solutions in which the calcium ion concentration was controlled with EGTA. 2. The threshold for force development, calculated from an apparent stability constant for the CaEGTA complex of 106.69 M-1 at pH 7·0, was generally close to pCa 7·5. Maximum force was reached at about pCa 6·0. 3. Maximum force is proportional to the cross-sectional area of the fibres. 4. The rate of force development was slower than that expected from simple diffusion of a substance from the bathing solution into the fibre. The delay appears to be due to slow equilibration of the EGTA buffer system during calcium uptake by the sarcoplasmic reticulum. 5. Addition of deoxycholate (DOC) to the bathing solution produced a reversible increase in the rate of force development. The steady force was also increased for values of pCa that gave less than maximum force, which shifted the force—pCa relation toward lower calcium concentrations by about 0·5 pCa unit. 6. The length—force relation in partially activated preparations is similar to that reported for electrically activated intact fibres. This result suggests that in the region of myofilament overlap the affinity of the binding sites for calcium is uniform along the length of the calciumbinding myofilament. PMID:5765859

  19. Limits to the Use of the Zachman Framework in Developing and Evolving Architectures for Complex Systems of Systems

    DTIC Science & Technology

    2016-06-13

    PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Carnegie Mellon University, Software Engineering Institute,Pittsburgh,PA,15213 8. PERFORMING...12. DISTRIBUTION/AVAILABILITY STATEMENT Approved for public release; distribution unlimited 13. SUPPLEMENTARY NOTES presented at Software ...Exploring Enterprise, System of Systems, System, and Software Architectures, John Bergey, Stephen Blanchette, Jr., Paul Clements, Mike Gagliardi, John

  20. All-Optical Fibre Networks For Coal Mines

    NASA Astrophysics Data System (ADS)

    Zientkiewicz, Jacek K.

    1987-09-01

    A topic of the paper is fiber-optic integrated network (FOIN) suited to the most hostile environments existing in coal mines. The use of optical fibres for transmission of mine instrumentation data offers the prospects of improved safety and immunity to electromagnetic interference (EMI). The feasibility of optically powered sensors has opened up new opportunities for research into optical signal processing architectures. This article discusses a new fibre-optic sensor network involving a time domain multiplexing(TDM)scheme and optical signal processing techniques. The pros and cons of different FOIN topologies with respect to coal mine applications are considered. The emphasis has been placed on a recently developed all-optical fibre network using spread spectrum code division multiple access (COMA) techniques. The all-optical networks have applications in explosive environments where electrical isolation is required.

  1. The modelling of fibre reorientation in soft tissue.

    PubMed

    Karsaj, Igor; Sansour, Carlo; Sorić, Jurica

    2009-10-01

    In this paper, a hyperelastic and thermodynamically consistent model for soft tissue is developed that is able to describe the change of the initial orientation of the collagen fibres. Full numerical implementation is considered as well. The collagen architecture is assumed to reorient driven by a specific thermodynamical force. The anisotropy is described by a strain energy function, which is decomposed into a part related to the matrix and a part related to the fibres. The initial fibre orientation is defined by a structural tensor, while the current orientation is described by a time-dependent structural tensor, which results from the initial one by a rotational transformation. The rotation tensor is obtained via an integration process of a rate tensor, which depends on an adequately defined thermodynamical force. The integration is achieved via an exponential map algorithm, where it is shown that the rotation is necessarily a two-parametric one. Efficiency of the proposed formulation is demonstrated using some numerical examples.

  2. The muscular organization of the stomach of capybara (Hydrochoerus hydrochaeris): an architectural view.

    PubMed

    Moraes, Priscilla Teixeira de Barros; de Souza, Wilson Machado; da Silva Neto, Paulo Bezerra; Barretto, Carla Siqueira de Figueiredo; Ribeiro, Antonio Augusto Coppi Maciel

    2005-03-01

    Twenty-two stomachs from adult capybaras were used in this study, and an acid digestion mesoscopic technique was pursued using different concentrations of nitric acid to observe the muscular organization of the stomach. The capybara's stomach possessed a muscular coat composed of four layers or strata: external longitudinal, external oblique, circular and internal oblique. Also, the cardiac and pyloric sphincter muscles were comprised of three or two different layers, respectively. Furthermore, the internal oblique fibres were observed extending from the cardiac portion of the stomach to the smaller curvature, where they participated in the formation of the Ansa cardiaca together with the external longitudinal fibres. This muscular architectural arrangement was compared to that in small rodents (rat, hamster, guinea pig), as well as in rabbits and pigs. In conclusion, the stomach of the capybara has a very particular, complex and defined muscular organization that differs from that in other rodents, or domestic animals, in particular, pigs.

  3. FIBER OPTICS: Fibre optics: Forty years later

    NASA Astrophysics Data System (ADS)

    Dianov, Evgenii M.

    2010-01-01

    This paper presents a brief overview of the state of the art in fibre optics and its main applications: optical fibre communications, fibre lasers and fibre sensors for various physical property measurements. The future of fibre optics and the status of this important area of the modern technology in Russia are discussed.

  4. Small fibre neuropathy.

    PubMed

    Lauria, Giuseppe; Merkies, Ingemar S J; Faber, Catharina G

    2012-10-01

    This review summarizes the most recent advances in classification, diagnostic assessment, and treatment of small fibre neuropathy (SFN). Clinically based diagnostic criteria for SFN have been proposed and reliably supported by the recent availability of age-adjusted and sex-adjusted normative values for intraepidermal nerve fibre density. Apart from skin biopsy, corneal confocal microscopy and nociceptive evoked potentials have been implemented to investigate SFN of different causes, and correlated with skin biopsy findings, especially in diabetic patients. The association between SFN and several metabolic and immune-mediated systemic diseases, and drugs toxic to this subset of peripheral nerve fibres has been reported. An exciting advance has been the identification of gain-of-function mutations in the SCN9A gene encoding for Nav1.7 sodium channel in patients with SFN, leading to the definition of a new genetic channelopathy. SFN represents a distinct condition encountered in patients with different acquired and genetic disorders. The recent improved definition of clinical and skin biopsy criteria allows clinicians to reliably meet the diagnosis, identify the underlying cause, and prescribe appropriate treatments. This meaningful approach permits the correct management of patients in clinical practice and the design of symptomatic and disease-modifying clinical trials.

  5. Distributed ultrafast fibre laser

    PubMed Central

    Liu, Xueming; Cui, Yudong; Han, Dongdong; Yao, Xiankun; Sun, Zhipei

    2015-01-01

    A traditional ultrafast fibre laser has a constant cavity length that is independent of the pulse wavelength. The investigation of distributed ultrafast (DUF) lasers is conceptually and technically challenging and of great interest because the laser cavity length and fundamental cavity frequency are changeable based on the wavelength. Here, we propose and demonstrate a DUF fibre laser based on a linearly chirped fibre Bragg grating, where the total cavity length is linearly changeable as a function of the pulse wavelength. The spectral sidebands in DUF lasers are enhanced greatly, including the continuous-wave (CW) and pulse components. We observe that all sidebands of the pulse experience the same round-trip time although they have different round-trip distances and refractive indices. The pulse-shaping of the DUF laser is dominated by the dissipative processes in addition to the phase modulations, which makes our ultrafast laser simple and stable. This laser provides a simple, stable, low-cost, ultrafast-pulsed source with controllable and changeable cavity frequency. PMID:25765454

  6. Fibre-optical microendoscopy.

    PubMed

    Gu, M; Bao, H; Kang, H

    2014-04-01

    Microendoscopy has been an essential tool in exploring micro/nano mechanisms in vivo due to high-quality imaging performance, compact size and flexible movement. The investigations into optical fibres, micro-scanners and miniature lens have boosted efficiencies of remote light delivery to sample site and signal collection. Given the light interaction with materials in the fluorescence imaging regime, this paper reviews two classes of compact microendoscopy based on a single fibre: linear optical microendoscopy and nonlinear optical microendoscopy. Due to the fact that fluorescence occurs only in the focal volume, nonlinear optical microendoscopy can provide stronger optical sectioning ability than linear optical microendoscopy, and is a good candidate for deep tissue imaging. Moreover, one-photon excited fluorescence microendoscopy as the linear optical microendoscopy suffers from severe photobleaching owing to the linear dependence of photobleaching rate on excitation laser power. On the contrary, nonlinear optical microendoscopy, including two-photon excited fluorescence microendoscopy and second harmonic generation microendoscopy, has the capability to minimize or avoid the photobleaching effect at a high excitation power and generate high image contrast. The combination of various nonlinear signals gained by the nonlinear optical microendoscopy provides a comprehensive insight into biophenomena in internal organs. Fibre-optical microendoscopy overcomes physical limitations of traditional microscopy and opens up a new path to achieve early cancer diagnosis and microsurgery in a minimally invasive and localized manner.

  7. Properties of nanocomposite PP fibres

    NASA Astrophysics Data System (ADS)

    Smole, Majda S.; Stakne, Kristina; Svetec, Diana G.; Kleinschek, Karin S.; Ribitsch, Volker

    2005-06-01

    PP-based nanocomposite fibres were prepared by direct polymer melt intercalation. With the intention to determine the size and dispersion of nanoparticles in the polymer matrix, fibres were plasma etched and SEM observations were performed. The influence of nanofiller content and coupling agent on electrokinetic properties was studied. PP monofilament fibres exhibit hydrophobe character with negative zeta potential value. The zeta potential value of co-polymer PP fibre decreases with increasing PPAA content and the isoelectric point IEP of co-polymer samples shifts towards acid region. Addition of modified montmorillonite due to the particles electropositive character, affects the reduction of zeta potential value and a slight shift of IEP towards neutral region is observed. Nano-particles content influences electrokinetic fibres properties, i.e. ZP value is changed, however IE point is not significantly changed by different concentrations of nanofiller. In addition to, mechanical properties of nanocomposite fibres were determined.

  8. Characterization of mature maize (Zea mays L.) root system architecture and complexity in a diverse set of Ex-PVP inbreds and hybrids.

    PubMed

    Hauck, Andrew L; Novais, Joana; Grift, Tony E; Bohn, Martin O

    2015-01-01

    The mature root system is a vital plant organ, which is critical to plant performance. Commercial maize (Zea mays L.) breeding has resulted in a steady increase in plant performance over time, along with noticeable changes in above ground vegetative traits, but the corresponding changes in the root system are not presently known. In this study, roughly 2500 core root systems from field trials of a set of 10 diverse elite inbreds formerly protected by Plant Variety Protection plus B73 and Mo17 and the 66 diallel intercrosses among them were evaluated for root traits using high throughput image-based phenotyping. Overall root architecture was modeled by root angle (RA) and stem diameter (SD), while root complexity, the amount of root branching, was quantified using fractal analysis to obtain values for fractal dimension (FD) and fractal abundance (FA). For each trait, per se line effects were highly significant and the most important contributor to trait performance. Mid-parent heterosis and specific combining ability was also highly significant for FD, FA, and RA, while none of the traits showed significant general combining ability. The interaction between the environment and the additive line effect was also significant for all traits. Within the inbred and hybrid generations, FD and FA were highly correlated (rp ≥ 0.74), SD was moderately correlated to FD and FA (0.69 ≥ rp ≥ 0.48), while the correlation between RA and other traits was low (0.13 ≥ rp ≥ -0.40). Inbreds with contrasting effects on complexity and architecture traits were observed, suggesting that root complexity and architecture traits are inherited independently. A more comprehensive understanding of the maize root system and the way it interacts with the environment will be useful for defining adaptation to nutrient acquisition and tolerance to stress from drought and high plant densities, critical factors in the yield gains of modern hybrids.

  9. Compressive failure of fibre composites

    NASA Astrophysics Data System (ADS)

    Budiansky, B.; Fleck, N. A.

    1993-01-01

    A REVIEW OF experimental data and elementary theoretical formulas for compressive failure of polymer matrix fibre composites indicates that the dominant failure mode is by plastic kinking. Initial local fibre misalignment plays a central role in the plastic kinking process. Theoretical analyses and numerical results for compressive kinking are presented, encompassing effects of strain-hardening, kink inclination, and applied shear stress. The assumption of rigid fibres is assessed critically, and the legitimacy of its use for polymer matrix composites is established.

  10. Grid Architecture 2

    SciTech Connect

    Taft, Jeffrey D.

    2016-01-01

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

  11. Fibre constituents of some foods.

    PubMed

    Rani, B; Kawatra, A

    1994-06-01

    Some plant foods viz. bottlegourd, carrot, cauliflower, cabbage, green bengalgram, pea, apple, plum, guava, karonda, blackgram husk and lentil husk were analysed for their dietary fibre components. The total dietary fibre contents of these foods varied from 14.68 to 78.21 percent on dry matter basis. As compared to fruits and vegetables, the husks had higher amount of total dietary fibre. Cellulose represented as the major fibre constituent in most of the foods whereas, husks were observed to be good sources of hemicellulose. All foods were low in pectin and lignin contents except guava.

  12. Sulphur-doped silica fibres

    SciTech Connect

    Gerasimova, V I; Rybaltovskii, A O; Chernov, P V; Mashinsky, V M; Sazhin, O D; Medvedkov, O I; Rybaltovsky, A A; Khrapko, R R

    2003-01-31

    An optical fibre with low optical losses is manufactured from a sulphur-doped quartz glass. Optical absorption spectra are measured for various parts of the fibre core. Most of the bands of these spectra are assigned to oxygen-deficient centres and colour centres containing sulphur atoms. The photosensitivity of glasses exposed to laser radiation at wavelengths of 193 and 244 nm is investigated to estimate the possibility of their application for producing photorefracting devices. A Bragg grating of the refractive index with {Delta}n = 7.8 x 10{sup -4} is written in a sulphur-doped silica fibre. (fibre optics)

  13. Meniscus on a shaped fibre: singularities and hodograph formulation

    PubMed Central

    Alimov, Mars M.; Kornev, Konstantin G.

    2014-01-01

    Using the method of matched asymptotic expansions, the problem of the capillary rise of a meniscus on the complex-shaped fibres was reduced to a nonlinear problem of determination of a minimal surface. This surface has to satisfy a special boundary condition at infinity. The proposed formulation allows one to interpret the meniscus problem as a problem of flow of a fictitious non-Newtonian fluid through a porous medium. As an example, the shape of a meniscus on a fibre of an oval cross section was analysed employing Chaplygin's hodograph transformation. It was discovered that the contact line may form singularities even if the fibre has a smooth profile: this statement was illustrated with an oval fibre profile having infinite curvature at two endpoints. PMID:25104910

  14. Meniscus on a shaped fibre: singularities and hodograph formulation.

    PubMed

    Alimov, Mars M; Kornev, Konstantin G

    2014-08-08

    Using the method of matched asymptotic expansions, the problem of the capillary rise of a meniscus on the complex-shaped fibres was reduced to a nonlinear problem of determination of a minimal surface. This surface has to satisfy a special boundary condition at infinity. The proposed formulation allows one to interpret the meniscus problem as a problem of flow of a fictitious non-Newtonian fluid through a porous medium. As an example, the shape of a meniscus on a fibre of an oval cross section was analysed employing Chaplygin's hodograph transformation. It was discovered that the contact line may form singularities even if the fibre has a smooth profile: this statement was illustrated with an oval fibre profile having infinite curvature at two endpoints.

  15. The Formation and Binding of Gold Nanoparticles onto Wool Fibres

    SciTech Connect

    Johnston, James H.; Burridge, Kerstin A.; Kelly, Fern M.

    2009-07-23

    This paper presents the novel use of nanosize gold with different plasmon resonance colours, as stable colourfast colourants on wool fibres for use in high quality fabrics and textiles. The gold nanoparticles are synthesised by the controlled reduction of Au{sup 3+} in the AuCl{sub 4}{sup -} complex to Au{sup 0} onto the surface of the wool where they attach to the S in the cystine amino acids in wool keratin proteins. Scanning electronmicroscopy shows the nanoparticles are present on the cuticles of the fibre surface and are concentrated at the edges of these cuticles. EDS analysis shows a strong correlation of Au with S and X-ray photoelectron spectroscopy suggests Au-S bond formation. Hence the nanogold colourants are chemically bound to the wool fibre surface and do not fade as traditional organic dyes do. A range of coloured fibres have been produced.

  16. Architectural Adventures in Your Community

    ERIC Educational Resources Information Center

    Henn, Cynthia A.

    2007-01-01

    Due to architecture's complexity, it can be challenging to develop lessons for the students, and consequently, the teaching of architecture is frequently overlooked. Every community has an architectural history. For example, the community in which the author's students live has a variety of historic houses from when the community originated (the…

  17. Retention of Cationic Starch onto Cellulose Fibres

    NASA Astrophysics Data System (ADS)

    Missaoui, Mohamed; Mauret, Evelyne; Belgacem, Mohamed Naceur

    2008-08-01

    Three methods of cationic starch titration were used to quantify its retention on cellulose fibres, namely: (i) the complexation of CS with iodine and measurement of the absorbency of the ensuing blue solution by UV-vis spectroscopy; (ii) hydrolysis of the starch macromolecules followed by the conversion of the resulting sugars to furan-based molecules and quantifying the ensuing mixture by measuring their absorbance at a Ι of 490 nm, using the same technique as previous one and; finally (iii) hydrolysis of starch macromolecules by trifluoro-acetic acid and quantification of the sugars in the resulting hydrolysates by high performance liquid chromatography. The three methods were found to give similar results within the range of CS addition from 0 to 50 mg per g of cellulose fibres.

  18. The genetic architecture of local adaptation and reproductive isolation in sympatry within the Mimulus guttatus species complex.

    PubMed

    Ferris, Kathleen G; Barnett, Laryssa L; Blackman, Benjamin K; Willis, John H

    2017-01-01

    The genetic architecture of local adaptation has been of central interest to evolutionary biologists since the modern synthesis. In addition to classic theory on the effect size of adaptive mutations by Fisher, Kimura and Orr, recent theory addresses the genetic architecture of local adaptation in the face of ongoing gene flow. This theory predicts that with substantial gene flow between populations local adaptation should proceed primarily through mutations of large effect or tightly linked clusters of smaller effect loci. In this study, we investigate the genetic architecture of divergence in flowering time, mating system-related traits, and leaf shape between Mimulus laciniatus and a sympatric population of its close relative M. guttatus. These three traits are probably involved in M. laciniatus' adaptation to a dry, exposed granite outcrop environment. Flowering time and mating system differences are also reproductive isolating barriers making them 'magic traits'. Phenotypic hybrids in this population provide evidence of recent gene flow. Using next-generation sequencing, we generate dense SNP markers across the genome and map quantitative trait loci (QTLs) involved in flowering time, flower size and leaf shape. We find that interspecific divergence in all three traits is due to few QTL of large effect including a highly pleiotropic QTL on chromosome 8. This QTL region contains the pleiotropic candidate gene TCP4 and is involved in ecologically important phenotypes in other Mimulus species. Our results are consistent with theory, indicating that local adaptation and reproductive isolation with gene flow should be due to few loci with large and pleiotropic effects. © 2016 John Wiley & Sons Ltd.

  19. Applications for carbon fibre recovered from composites

    NASA Astrophysics Data System (ADS)

    Pickering; Liu, Z.; Turner, TA; Wong, KH

    2016-07-01

    Commercial operations to recover carbon fibre from waste composites are now developing and as more recovered fibre becomes available new applications for recovered fibre are required. Opportunities to use recovered carbon fibre as a structural reinforcement are considered involving the use of wet lay processes to produce nonwoven mats. Mats with random in-plane fibre orientation can readily be produced using existing commercial processes. However, the fibre volume fraction, and hence the mechanical properties that can be achieved, result in composites with limited mechanical properties. Fibre volume fractions of 40% can be achieved with high moulding pressures of over 100 bar, however, moulding at these pressures results in substantial fibre breakage which reduces the mean fibre length and the properties of the composite manufactured. Nonwoven mats made from aligned, short carbon fibres can achieve higher fibre volume fractions with lower fibre breakage even at high moulding pressure. A process for aligning short fibres is described and a composite of over 60% fibre volume fraction has been manufactured at a pressures up to 100 bar with low fibre breakage. Further developments of the alignment process have been undertaken and a composite of 46% fibre volume fraction has been produced moulded at a pressure of 7 bar in an autoclave, exhibiting good mechanical properties that compete with higher grade materials. This demonstrates the potential for high value applications for recovered carbon fibre by fibre alignment.

  20. Fair performance comparison of different carbon blacks in lithium-sulfur batteries with practical mass loadings - Simple design competes with complex cathode architecture

    NASA Astrophysics Data System (ADS)

    Jozwiuk, Anna; Sommer, Heino; Janek, Jürgen; Brezesinski, Torsten

    2015-11-01

    The lithium-sulfur system is one of the most promising next generation battery systems, as elemental sulfur is cheap, abundant and has a high theoretical specific capacity. Although much research is conducted on complex sulfur/carbon composites and architectures, it is difficult to compare the performance of the cathodes to one another. Factors, such as different electrolyte composition and cell components strongly affect the cyclability of the battery. Here, we show the importance of optimizing "standard" conditions to allow for fair performance comparison of different carbon blacks. Our optimal electrolyte-to-sulfur ratio is 11 μL mgsulfur-1 and high concentrations of LiNO3 (>0.6 M) are needed because nitrate is consumed continuously during cycling. Utilizing these standard conditions, we tested the cycling behavior of four types of cathodes with individual carbon blacks having different specific surface areas, namely Printex-A, Super C65, Printex XE-2 and Ketjenblack EC-600JD. Both the specific capacity and polysulfide adsorption capability clearly correlate with the surface area of the carbon being used. High specific capacities (>1000 mAh gsulfur-1 at C/5) are achieved with high surface area carbons. We also demonstrate that a simple cathode using Ketjenblack EC-600JD as the conductive matrix material can well compete with those having complex architectures or additives.

  1. A Luminescent Cocaine Detection Platform Using a Split G-Quadruplex-Selective Iridium(III) Complex and a Three-Way DNA Junction Architecture.

    PubMed

    Ma, Dik-Lung; Wang, Modi; He, Bingyong; Yang, Chao; Wang, Wanhe; Leung, Chung-Hang

    2015-09-02

    In this study, a series of 10 in-house cyclometalated iridium(III) complexes bearing different auxiliary ligands were tested for their selectivity toward split G-quadruplex in order to construct a label-free switch-on cocaine detection platform employing a three-way junction architecture and a G-quadruplex motif as a signal output unit. Through two rounds of screening, we discovered that the iridium(III) complex 7 exhibited excellent selectivity toward the intermolecular G-quadruplex motif. A detection limit as low as 30 nM for cocaine can be achieved by this sensing approach with a linear relationship between luminescence intensity and cocaine concentration established from 30 to 300 nM. Furthermore, this sensing approach could detect cocaine in diluted oral fluid. We hope that our simple, signal-on, label-free oligonucleotide-based sensing method for cocaine using a three-way DNA junction architecture could act as a useful platform in bioanalytical research.

  2. Use of biological priors enhances understanding of genetic architecture and genomic prediction of complex traits within and between dairy cattle breeds.

    PubMed

    Fang, Lingzhao; Sahana, Goutam; Ma, Peipei; Su, Guosheng; Yu, Ying; Zhang, Shengli; Lund, Mogens Sandø; Sørensen, Peter

    2017-08-10

    A better understanding of the genetic architecture underlying complex traits (e.g., the distribution of causal variants and their effects) may aid in the genomic prediction. Here, we hypothesized that the genomic variants of complex traits might be enriched in a subset of genomic regions defined by genes grouped on the basis of "Gene Ontology" (GO), and that incorporating this independent biological information into genomic prediction models might improve their predictive ability. Four complex traits (i.e., milk, fat and protein yields, and mastitis) together with imputed sequence variants in Holstein (HOL) and Jersey (JER) cattle were analysed. We first carried out a post-GWAS analysis in a HOL training population to assess the degree of enrichment of the association signals in the gene regions defined by each GO term. We then extended the genomic best linear unbiased prediction model (GBLUP) to a genomic feature BLUP (GFBLUP) model, including an additional genomic effect quantifying the joint effect of a group of variants located in a genomic feature. The GBLUP model using a single random effect assumes that all genomic variants contribute to the genomic relationship equally, whereas GFBLUP attributes different weights to the individual genomic relationships in the prediction equation based on the estimated genomic parameters. Our results demonstrate that the immune-relevant GO terms were more associated with mastitis than milk production, and several biologically meaningful GO terms improved the prediction accuracy with GFBLUP for the four traits, as compared with GBLUP. The improvement of the genomic prediction between breeds (the average increase across the four traits was 0.161) was more apparent than that it was within the HOL (the average increase across the four traits was 0.020). Our genomic feature modelling approaches provide a framework to simultaneously explore the genetic architecture and genomic prediction of complex traits by taking advantage of

  3. Polylactic acid fibre-reinforced polycaprolactone scaffolds for bone tissue engineering.

    PubMed

    Guarino, Vincenzo; Causa, Filippo; Taddei, Paola; di Foggia, Michele; Ciapetti, Gabriela; Martini, Desirèe; Fagnano, Concezio; Baldini, Nicola; Ambrosio, Luigi

    2008-09-01

    The employment of composite scaffolds with a well-organized architecture and multi-scale porosity certainly represents a valuable approach for achieving a tissue engineered construct to reproduce the middle and long-term behaviour of hierarchically complex tissues such as spongy bone. In this paper, fibre-reinforced composites scaffold for bone tissue engineering applications is described. These are composed of poly-L-lactide acid (PLLA) fibres embedded in a porous poly(epsilon-caprolactone) matrix, and were obtained by synergistic use of phase inversion/particulate leaching technique and filament winding technology. Porosity degree as high as 79.7% was achieved, the bimodal pore size distribution showing peaks at ca 10 and 200 microm diameter, respectively, accounting for 53.7% and 46.3% of the total porosity. In vitro degradation was carried out in PBS and SBF without significant degradation of the scaffold after 35 days, while in NaOH solution, a linear increase of weight lost was observed with preferential degradation of PLLA component. Subsequently, marrow stromal cells (MSC) and human osteoblasts (HOB) reached a plateau at 3 weeks, while at 5 weeks the number of cells was almost the same. Human marrow stromal cell and trabecular osteoblasts rapidly proliferate on the scaffold up to 3 weeks, promoting an oriented migration of bone cells along the fibre arrangement. Moreover, the role of seeded HOB and MSC on composite degradation mechanism was assessed by demonstrating a more relevant contribution to PLLA degradation of MSC when compared to HOB. The novel PCL/PLLA composite scaffolds thus showed promise whenever tuneable porosity, controlled degradability and guided cell-material interaction are simultaneously requested.

  4. Determining the Architecture of a Protein-DNA Complex by Combining FeBABE Cleavage Analyses, 3-D Printed Structures, and the ICM Molsoft Program.

    PubMed

    James, Tamara; Hsieh, Meng-Lun; Knipling, Leslie; Hinton, Deborah

    2015-01-01

    Determining the structure of a protein-DNA complex can be difficult, particularly if the protein does not bind tightly to the DNA, if there are no homologous proteins from which the DNA binding can be inferred, and/or if only portions of the protein can be crystallized. If the protein comprises just a part of a large multi-subunit complex, other complications can arise such as the complex being too large for NMR studies, or it is not possible to obtain the amounts of protein and nucleic acids needed for crystallographic analyses. Here, we describe a technique we used to map the position of an activator protein relative to the DNA within a large transcription complex. We determined the position of the activator on the DNA from data generated using activator proteins that had been conjugated at specific residues with the chemical cleaving reagent, iron bromoacetamidobenzyl-EDTA (FeBABE). These analyses were combined with 3-D models of the available structures of portions of the activator protein and B-form DNA to obtain a 3-D picture of the protein relative to the DNA. Finally, the Molsoft program was used to refine the position, revealing the architecture of the protein-DNA within the transcription complex.

  5. The Human Embryoid Body Cystic Core Exhibits Architectural Complexity Revealed by use of High Throughput Polymer Microarrays.

    PubMed

    Tomov, Martin L; Olmsted, Zachary T; Paluh, Janet L

    2015-07-01

    In pluripotent stem cell differentiation, embryoid bodies (EBs) provide a three-dimensional [3D] multicellular precursor in lineage specification. The internal structure of EBs is not well characterized yet is predicted to be an important parameter to differentiation. Here, we use custom SU-8 molds to generate transparent lithography-templated arrays of polydimethylsiloxane (LTA-PDMS) for high throughput analysis of human embryonic stem cell (hESC) EB formation and internal architecture. EBs formed in 200 and 500 μm diameter microarray wells by use of single cells, 2D clusters, or 3D early aggregates were compared. We observe that 200 μm EBs are monocystic versus 500 μm multicystic EBs that contain macro, meso and microsized cysts. In adherent differentiation of 500 μm EBs, the multicystic character impairs the 3D to 2D transition creating non-uniform monolayers. Our findings reveal that EB core structure has a size-dependent character that influences its architecture and cell population uniformity during early differentiation. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. The influence of fibre shape in lung deposition-mathematical estimates.

    PubMed

    Harris, R L; Timbrell, V

    1975-09-01

    Inhaled fibres deposit by sedimentation, diffusion, impaction, and interception in airways of the respiratory system. Long straight fibres may exhibit periodic motiion with ordered orientation in those airways having laminar flow. We assume that irregular fibres are randomly oriented in airways. Mathematical models based on respiratory system architecture, respiratory airflow, and mathematical expressions for deposition mechanisms have been developed to predict deposition in respiratory compartments of fibres in ordered orientation and of various fibre confirgurations in random orientations. The size and shape characteristics of chamber aerosols generated with U.I.C.C. asbestos specimens have been determined. Combinations of the chamber aerosol data with mathematical estimates of deposition suggest that fibre shape as well as size influences the magnitude of deposition in pulmonary spaces. For size distributions such as those of the U.I.C.C. asbestos chamber aerosols, the mathematical models predict pulmonary spaces deposition for straight fibres in ordered orientation about twice as great as for irregular fibres in random orientation.

  7. Fluoride Glass Fibres For Telecommunications

    NASA Astrophysics Data System (ADS)

    Maze, Gwenael; Cardin, Vincent; Poulain, Marcel

    1983-09-01

    Zirconium fluoride glasses are the best known and the most stable beryllium-free glasses. They offer numerous potential uses for I.R.-transmitting fibres and ultra-long repeaterless optical wave-guides. Various problems arise in the manufacturing of fluoride glass fibres, essentially because of the steep viscosity profile and the devitrification phenomena. This paper discusses the processes for manufacturing step-index preforms and for drawing fibres. Optical quality preforms have been obtained and fibres have been drawn over more than 1 km. A spectral loss measurement system has been constructed using fluoride glass optical components. Several curves showing the optical attenuation versus wavelength are presented and discussed. These fibres are now available for optical transmission in infra-red systems.

  8. Reticulation des fibres lignocellulosiques

    NASA Astrophysics Data System (ADS)

    Landrevy, Christel

    Pour faire face à la crise économique la conception de papier à valeur ajoutée est développée par les industries papetières. Le but de se projet est l'amélioration des techniques actuelles de réticulation des fibres lignocellulosiques de la pâte à papier visant à produire un papier plus résistant. En effet, lors des réactions de réticulation traditionnelles, de nombreuses liaisons intra-fibres se forment ce qui affecte négativement l'amélioration anticipée des propriétés physiques du papier ou du matériau produit. Pour éviter la formation de ces liaisons intra-fibres, un greffage sur les fibres de groupements ne pouvant pas réagir entre eux est nécessaire. La réticulation des fibres par une réaction de « click chemistry » appelée cycloaddition de Huisgen entre un azide et un alcyne vrai, catalysée par du cuivre (CuAAC) a été l'une des solutions trouvée pour remédier à ce problème. De plus, une adaptation de cette réaction en milieux aqueux pourrait favoriser son utilisation en milieu industriel. L'étude que nous désirons entreprendre lors de ce projet vise à optimiser la réaction de CuAAC et les réactions intermédiaires (propargylation, tosylation et azidation) sur la pâte kraft, en milieu aqueux. Pour cela, les réactions ont été adaptées en milieu aqueux sur la cellulose microcristalline afin de vérifier sa faisabilité, puis transférée à la pâte kraft et l'influence de différents paramètres comme le temps de réaction ou la quantité de réactifs utilisée a été étudiée. Dans un second temps, une étude des différentes propriétés conférées au papier par les réactions a été réalisée à partir d'une série de tests papetiers optiques et physiques. Mots Clés Click chemistry, Huisgen, CuAAC, propargylation, tosylation, azidation, cellulose, pâte kraft, milieu aqueux, papier.

  9. Omnis fibra ex fibra: fibre economies in Bonnet's and Diderot's models of organic order.

    PubMed

    Cheung, Tobias

    2010-01-01

    In a long-term transformation, that begins in Antiquity but takes a crucial turn in the Renaissance anatomies, the "fibre" becomes from around 1750 the operative building block and at the same time the first unifying principle of function-structure-complexes of organic bodies. It occupies the role that the cell takes up in the cell economies of the second third of the nineteenth century. In this paper, I will first discuss some key notions, technical analogies, and images that are related to "fibre"-concepts from Andreas Vesalius to Albrecht von Haller and then focus on Charles Bonnet's and Denis Diderot's fibre ceconomies. In Bonnet's and Diderot's fibre economies, the self-active, regulating properties of fibre-agents and their material structures, that reach from fibre bundles, tissues and membranes to apparati of organs, are united within the concrete whole of individual organized "systems" or "networks."

  10. Advances in fibre-optic sensing in medicine and biology

    NASA Astrophysics Data System (ADS)

    Rolfe, Peter; Scopesi, Fabio; Serra, Giovanni

    2007-06-01

    This paper presents a review of medical and biological applications of optical fibres, which span a wide range from light-pipes and pressure or displacement sensors through to complex chemical sensors. Coherent fibre bundles are needed for endoscopic imaging whilst single fibres may be used in both near infrared tomography and optical coherence tomography. Delivery of light to tissues, for example to activate targeted chemo-therapeutic agents (PDT), is also achieved conveniently with fibres. Chemical sensing can simply be achieved by transporting light to and from a measurement site with a plain fibre light guide for spectrophotometric or fluorimetry analysis. A further family of fibre-optic chemical sensors has either surface attached molecular recognition sites or a reaction chamber for achieving specific molecular detection. These chemical sensors may be based on the principles of surface plasmon resonance, interferometry, spectrophotometry or fluorimetry. Biological recognition with enzymes or antigen-antibody binding are used to achieve high specificity. The range of potential target molecules has increased rapidly over recent years from simple gases and ions through to large molecules such as DNA.

  11. Automatic Segmentation of Human Cortical Layer-Complexes and Architectural Areas Using Ex vivo Diffusion MRI and Its Validation

    PubMed Central

    Bastiani, Matteo; Oros-Peusquens, Ana-Maria; Seehaus, Arne; Brenner, Daniel; Möllenhoff, Klaus; Celik, Avdo; Felder, Jörg; Bratzke, Hansjürgen; Shah, Nadim J.; Galuske, Ralf; Goebel, Rainer; Roebroeck, Alard

    2016-01-01

    Recently, several magnetic resonance imaging contrast mechanisms have been shown to distinguish cortical substructure corresponding to selected cortical layers. Here, we investigate cortical layer and area differentiation by automatized unsupervised clustering of high-resolution diffusion MRI data. Several groups of adjacent layers could be distinguished in human primary motor and premotor cortex. We then used the signature of diffusion MRI signals along cortical depth as a criterion to detect area boundaries and find borders at which the signature changes abruptly. We validate our clustering results by histological analysis of the same tissue. These results confirm earlier studies which show that diffusion MRI can probe layer-specific intracortical fiber organization and, moreover, suggests that it contains enough information to automatically classify architecturally distinct cortical areas. We discuss the strengths and weaknesses of the automatic clustering approach and its appeal for MR-based cortical histology. PMID:27891069

  12. Two-dimensional layer architecture assembled by Keggin polyoxotungstate, Cu(II)-EDTA complex and sodium linker: Synthesis, crystal structures, and magnetic properties

    SciTech Connect

    Liu Hong; Xu Lin Gao Guanggang; Li Fengyan; Yang Yanyan; Li Zhikui; Sun Yu

    2007-05-15

    Reaction of Keggin polyoxotungstate with copper(II)-EDTA (EDTA=ethylenediamine tetraacetate) complex under mild conditions led to the formation of hybrid inorganic-organic compounds Na{sub 4}(OH)[(Cu{sub 2}EDTA)PW{sub 12}O{sub 40}].17H{sub 2}O (1) and Na{sub 4}[(Cu{sub 2}EDTA)SiW{sub 12}O{sub 40}].19H{sub 2}O (2). The single-crystal X-ray diffraction analyses reveal their two structural features: (1) one-dimensional chain structure consisting of Keggin polyoxotungstate and copper(II)-EDTA complex; (2) Two-dimensional layer architecture assembled by the one-dimensional chain structure and sodium linker. The results of magnetic measurements in the temperature range 300-2 K indicated the existence of ferromagnetic exchange interactions between the Cu{sup II} ions for both compounds. In addition, TGA analysis, IR spectra, and electrochemical properties were also investigated to well characterize these two compounds. - Graphical abstract: Two new polyoxometalate-based hybrids, Na{sub 4}(OH)[Cu{sub 2}(EDTA)PW{sub 12}O{sub 40}].17H{sub 2}O (1) and Na{sub 4}[Cu{sub 2}(EDTA)SiW{sub 12}O{sub 40}].19H{sub 2}O (2), have been synthesized and structurally characterized, which consist of one-dimensional chain structure assembled by Keggin polyoxotungstate and copper(II)-EDTA complex. The chains are further connected to form two-dimensional layer architecture assembled by the one-dimensional chain structure and sodium linker.

  13. Dichroism measurements in forensic fibre examination: part 5-pigmented fibres.

    PubMed

    De Wael, K; Lepot, L

    2012-09-01

    A number of pigmented fibre samples were examined with plane polarized light on their dichroic behaviour by optical light microscopy (OLM) and microspectrophotometry with plane polarized light (MSP-PPL). It was found that about half of the samples show a strong dichroic effect and another 20% have a weak dichroism. Both regular (80%) and inversed dichroic effects (20%) occur. The dichroic characteristics of pigmented fibres can be compared to these of sheet polarizers. It is suggested that the dichroic behaviour of pigmented fibres depends strongly on the crystal structure (shape of the pigment grains) and the draw ratio (orientation of the polymer chains).

  14. Fibre laser based on tellurium-doped active fibre

    SciTech Connect

    Alyshev, S V; Ryumkin, K E; Shubin, A V; Medvedkov, O I; Dianov, E M; Khopin, V F; Gur'yanov, A N

    2014-02-28

    We have studied the lasing properties of tellurium-doped germanosilicate fibre, identified its gain and excited-state absorption bands, and assessed the effect of cooling to low temperature (77 K) on the bands. The excitation spectrum of the near-IR luminescence in the fibre has been measured. Lasing at 1.55 mm has been demonstrated for the first time in this gain medium at liquidnitrogen temperature and pump wavelengths of 1.064 and 1.085 mm. The measured Raman spectrum of the fibre provides some insight into the structure of the near-IR luminescence centre. (letters)

  15. Architecture and mechanism of the late endosomal Rab7-like Ypt7 guanine nucleotide exchange factor complex Mon1–Ccz1

    PubMed Central

    Kiontke, Stephan; Langemeyer, Lars; Kuhlee, Anne; Schuback, Saskia; Raunser, Stefan; Ungermann, Christian; Kümmel, Daniel

    2017-01-01

    The Mon1–Ccz1 complex (MC1) is the guanine nucleotide exchange factor (GEF) for the Rab GTPase Ypt7/Rab7 and is required for endosomal maturation and fusion at the vacuole/lysosome. Here we present the overall architecture of MC1 from Chaetomium thermophilum, and in combining biochemical studies and mutational analysis in yeast, we identify the domains required for catalytic activity, complex assembly and localization of MC1. The crystal structure of a catalytic MC1 core complex bound to Ypt7 provides mechanistic insight into its function. We pinpoint the determinants that allow for a discrimination of the Rab7-like Ypt7 over the Rab5-like Vps21, which are both located on the same membrane. MC1 shares structural similarities with the TRAPP complex, but employs a novel mechanism to promote nucleotide exchange that utilizes a conserved lysine residue of Ypt7, which is inserted upon MC1 binding into the nucleotide-binding pocket of Ypt7 and contributes to specificity. PMID:28051187

  16. Finite element modelling of the flexural performance of resorbable phosphate glass fibre reinforced PLA composite bone plates.

    PubMed

    Harper, L T; Ahmed, I; Felfel, R M; Qian, C

    2012-11-01

    A finite element method is presented to predict the flexural properties of resorbable phosphate glass fibre reinforced PLA composite bone plates. A novel method for meshing discontinuous fibre architectures is presented, which removes many of the limitations imposed by conventional finite element approaches. The model is used to understand the effects of increasing the span-to-thickness ratio for different fibre architectures used for PBG/PLA composites. A span-to-thickness ratio of 16:1 is found to be appropriate for materials with randomly orientated fibres, which agrees well with the test standard. However, for highly aligned materials the model indicates that a span-to-thickness ratio of 80:1 is required, in order to minimise the effects of shear deflection. The model is validated against flexural stiffness data from the literature for a range of polymers, fibres and fibre volume fractions. Generally there is less than 10% error between the FE predictions and experimental values. The model is subsequently used to perform a parametric study to understand what material developments are required to match the properties of PGF/PLA composites to cortical bone. It is concluded that alignment of the fibre is necessary to exceed the 20 GPa target, since the current manufacturing methods limit the fibre length to ∼10 mm, which consequently restricts the flexural modulus to ∼19 GPa (at 50% volume fraction). Copyright © 2012 Elsevier Ltd. All rights reserved.

  17. Tapered optical fibres for sensing

    NASA Astrophysics Data System (ADS)

    Martan, Tomas; Kanka, Jiri; Kasik, Ivan; Matejec, Vlastimil

    2008-11-01

    Recently, optical fibre tapers have intensively been investigated for many applications e.g. in telecommunications, medicine and (bio-) chemical sensing. The paper deals with enhancement of evanescent-field sensitivity of the solid-core microstructured fibre with steering-wheel air-cladding. Enhancement of a performance of the microstructured fibre is based on reduction of fibre core diameter down to narrow filament by tapering thereby defined part of light power is guided by an evanescent wave traveling in axial cladding air holes. The original fibre structure with outer diameter of 125 µm was reduced 2×, 2.5×, 3.33×, and 4× for increasing relatively small intensity overlap of guided core mode at wavelength of 1.55 μm with axial air holes. The inner structures of tapered microstructured fibre with steering-wheel aircladding were numerically analyzed and mode intensity distributions were calculated using the FDTD technique. Analyzed fiber tapers were prepared by constructed fibre puller employing 'flame brush technique'.

  18. Helically twisted photonic crystal fibres.

    PubMed

    Russell, P St J; Beravat, R; Wong, G K L

    2017-02-28

    Recent theoretical and experimental work on helically twisted photonic crystal fibres (PCFs) is reviewed. Helical Bloch theory is introduced, including a new formalism based on the tight-binding approximation. It is used to explore and explain a variety of unusual effects that appear in a range of different twisted PCFs, including fibres with a single core and fibres with N cores arranged in a ring around the fibre axis. We discuss a new kind of birefringence that causes the propagation constants of left- and right-spinning optical vortices to be non-degenerate for the same order of orbital angular momentum (OAM). Topological effects, arising from the twisted periodic 'space', cause light to spiral around the fibre axis, with fascinating consequences, including the appearance of dips in the transmission spectrum and low loss guidance in coreless PCF. Discussing twisted fibres with a single off-axis core, we report that optical activity in a PCF is opposite in sign to that seen in a step-index fibre. Fabrication techniques are briefly described and emerging applications reviewed. The analytical results of helical Bloch theory are verified by an extensive series of 'numerical experiments' based on finite-element solutions of Maxwell's equations in a helicoidal frame.This article is part of the themed issue 'Optical orbital angular momentum'. © 2017 The Authors.

  19. Helically twisted photonic crystal fibres

    PubMed Central

    Beravat, R.; Wong, G. K. L.

    2017-01-01

    Recent theoretical and experimental work on helically twisted photonic crystal fibres (PCFs) is reviewed. Helical Bloch theory is introduced, including a new formalism based on the tight-binding approximation. It is used to explore and explain a variety of unusual effects that appear in a range of different twisted PCFs, including fibres with a single core and fibres with N cores arranged in a ring around the fibre axis. We discuss a new kind of birefringence that causes the propagation constants of left- and right-spinning optical vortices to be non-degenerate for the same order of orbital angular momentum (OAM). Topological effects, arising from the twisted periodic ‘space’, cause light to spiral around the fibre axis, with fascinating consequences, including the appearance of dips in the transmission spectrum and low loss guidance in coreless PCF. Discussing twisted fibres with a single off-axis core, we report that optical activity in a PCF is opposite in sign to that seen in a step-index fibre. Fabrication techniques are briefly described and emerging applications reviewed. The analytical results of helical Bloch theory are verified by an extensive series of ‘numerical experiments’ based on finite-element solutions of Maxwell's equations in a helicoidal frame. This article is part of the themed issue ‘Optical orbital angular momentum’. PMID:28069771

  20. Helically twisted photonic crystal fibres

    NASA Astrophysics Data System (ADS)

    Russell, P. St. J.; Beravat, R.; Wong, G. K. L.

    2017-02-01

    Recent theoretical and experimental work on helically twisted photonic crystal fibres (PCFs) is reviewed. Helical Bloch theory is introduced, including a new formalism based on the tight-binding approximation. It is used to explore and explain a variety of unusual effects that appear in a range of different twisted PCFs, including fibres with a single core and fibres with N cores arranged in a ring around the fibre axis. We discuss a new kind of birefringence that causes the propagation constants of left- and right-spinning optical vortices to be non-degenerate for the same order of orbital angular momentum (OAM). Topological effects, arising from the twisted periodic `space', cause light to spiral around the fibre axis, with fascinating consequences, including the appearance of dips in the transmission spectrum and low loss guidance in coreless PCF. Discussing twisted fibres with a single off-axis core, we report that optical activity in a PCF is opposite in sign to that seen in a step-index fibre. Fabrication techniques are briefly described and emerging applications reviewed. The analytical results of helical Bloch theory are verified by an extensive series of `numerical experiments' based on finite-element solutions of Maxwell's equations in a helicoidal frame. This article is part of the themed issue 'Optical orbital angular momentum'.

  1. Molecular architecture and dynamics of ASH1 mRNA recognition by its mRNA-transport complex.

    PubMed

    Edelmann, Franziska Theresia; Schlundt, Andreas; Heym, Roland Gerhard; Jenner, Andreas; Niedner-Boblenz, Annika; Syed, Muhammad Ibrahim; Paillart, Jean-Christophe; Stehle, Ralf; Janowski, Robert; Sattler, Michael; Jansen, Ralf-Peter; Niessing, Dierk

    2017-02-01

    mRNA localization is an essential mechanism of gene regulation and is required for processes such as stem-cell division, embryogenesis and neuronal plasticity. It is not known which features in the cis-acting mRNA localization elements (LEs) are specifically recognized by motor-containing transport complexes. To the best of our knowledge, no high-resolution structure is available for any LE in complex with its cognate protein complex. Using X-ray crystallography and complementary techniques, we carried out a detailed assessment of an LE of the ASH1 mRNA from yeast, its complex with its shuttling RNA-binding protein She2p, and its highly specific, cytoplasmic complex with She3p. Although the RNA alone formed a flexible stem loop, She2p binding induced marked conformational changes. However, only joining by the unstructured She3p resulted in specific RNA recognition. The notable RNA rearrangements and joint action of a globular and an unfolded RNA-binding protein offer unprecedented insights into the step-wise maturation of an mRNA-transport complex.

  2. The Inhibitor DBMIB Provides Insight into the Functional Architecture of the Qo Site in the Cytochrome b(6)f Complex

    SciTech Connect

    Roberts, Arthur G.; Bowman, Michael K.; Kramer, David M.

    2004-06-22

    Previously, we showed that two equivalents of the quinone analog, 2,5-dibromo-3-methyl-6-isopropylbenzoquinone (DBMIB), could occupy the Qo site of the cytochrome (cyt) b6f complex simultaneously. In this work, study of electron paramagnetic resonance (EPR) spectra from oriented cyt b6f complex shows that the Rieske iron-sulfur protein (ISP) is in distinct orientations, depending on the stoichiometry of the inhibitor at the Qo site. With a single DBMIB at the Qo site, the ISP is oriented with the 2Fe2S cluster toward cyt f, which is similar to the orientation of the ISP in the x-ray crystal structure of the cyt b6f complex from thermophilic cyanobacteria, Mastigocladus laminosus, in the presence of DBMIB, as well as that of the chicken mitochondrial cyt bc1 complex in the presence of the class II inhibitor myxothiazol, which binds in the so-called ''proximal niche,'' near the cyt bL heme. These data suggest that the high affinity DBMIB site is at the proximal niche Qo pocket. With 2 equivalents or more of DBMIB bound, the Rieske ISP is in a position that resembles the ISPB position of chicken mitochondrial cyt bc1 complex in the presence of stigmatellin and Chlamydamonas reinhardtii cyt b6f complex in the presence of tridecyl-stigmatellin (TDS), which suggests that the low affinity DBMIB site is at the distal niche. The close interaction of DBMIB bound at the distal niche with the ISP induced the well-known effects on the 2Fe2S EPR spectrum and redox potential. To further test the effects of DBMIB on the ISP, the extents of cyt f oxidation after flash excitation in the presence of photosystem II inhibitor DCMU were measured as a function of DBMIB concentration in thylakoids. Addition of DBMIB concentrations where single binding was expected, did not markedly affect the extent of cyt f oxidation, whereas higher concentrations, where double occupancy was expected, increased the extent of cyt f oxidation to levels similar to cyt f oxidation in the presence of

  3. Whispering-gallery waves in optical fibres

    SciTech Connect

    Sychugov, V A; Torchigin, V P; Tsvetkov, M Yu

    2002-08-31

    The process of excitation of whispering-gallery waves (WGWs) in optical fibres (microcavities) with the help of a bitapered fibre is analysed. It is shown that useful information on the WGW modes can be obtained from the spectrograms recorded by scanning the exciting-radiation frequency. Based on the geometrical-optic approximation, the longitudinal sizes of the WGW modes are estimated and it is shown that the ultimate diameter of the fibre exists for optical fibres (microcavities) where a mode can be still excited with the help of a bitapered fibre. (fibre optics. optical fibres)

  4. Optical fibre sensing during critical care

    NASA Astrophysics Data System (ADS)

    Hernandez, F. U.; Wang, T.; Korposh, S.; Correia, R.; Hayes-Gill, B. R.; Hromadka, J.; Mohd Hazlan, N. N.; Norris, A.; Evans, D.; Lee, S.-W.; Morgan, S. P.

    2017-04-01

    Optical fibre sensing is a platform technology for applications in biomedical and environmental monitoring. Fibre Bragg Gratings can be used to monitor parameters such as pressure and temperature. Alternatively, coating the fibres with functional layers, either at the tip of the fibre, on a U-shaped fibre, or a long period grating enables sensing of analytes in liquids and gases. This paper describes the application of optical fibre sensing techniques during mechanical ventilation via an endotracheal tube in critical care. Functional coatings on the fibres are used to monitor humidity of inspired air and can be used to monitor other analytes.

  5. Supramolecular architectures in luminescent Zn(II) and Cd(II) complexes containing imidazole derivatives: Crystal structures, vibrational and thermal properties, Hirshfeld surface analysis and electrostatic potentials

    NASA Astrophysics Data System (ADS)

    Di Santo, Alejandro; Echeverría, Gustavo A.; Piro, Oscar E.; Pérez, Hiram; Ben Altabef, Aida; Gil, Diego M.

    2017-04-01

    Three novel zinc and cadmium complexes with 1-methylimidazole and 2-methylimidazole as ligands, mono-nuclear dichloro-bis(1-methylimidazole) zinc(II) and dibromo-bis(2-methylimidazole)cadmium(II) monohydrate complexes, and poly-nuclear bis(1-methylimidazole)-di-(μ2-bromo)cadmium(II) complex, namely, compounds 1-3, respectively, have been synthesized. The complexes were characterized by IR and Raman spectroscopies, thermal analysis and fluorescence. All the compounds exhibit interesting luminescent properties in solid state originated from intra-ligand (π→π*) transitions. Crystal structures of 1-3 were determined by single-crystal X-ray diffraction. Compound 1 crystallizes in P21/n space group, the Zn(II) ion lies at a crystal general position in a tetrahedral environment, and the mono-nuclear units are weakly bonded to one another by Csbnd H⋯Cl hydrogen bonds. Compound 2 crystallizes in Pnma space group, and mirror-related tetrahedral units around Cd(II) ion are H-bonded through a water molecule. Compound 3 crystallizes in P21/c space group, and the Cd(II) ion presents a centrosymmetric octahedral coordination. Neighboring and equatorial edge-sharing octahedra conform a polymeric arrangement that extends along the crystal a-axis. Weak hydrogen bonds are the major driving forces in the crystal packing of the three complexes. Hirshfeld surface analysis reveals a detailed scrutiny of intermolecular interactions experienced by each complex. The surfaces mapped over dnorm property highlight the X···H (X = Cl, Br) as the main intermolecular contacts for the three complexes, being also relevant the presence of O⋯H contacts for complex 2. The surfaces mapped over Shape index and curvedness properties for the two Cd complexes allow identify π … π stacking interactions which are absent in the Zn complex. 2D fingerprint plots have been used to quantify the relative contribution of the intermolecular contacts to crystal stability of compounds, showing

  6. Neurochemical Architecture of the Central Complex Related to Its Function in the Control of Grasshopper Acoustic Communication

    PubMed Central

    Kunst, Michael; Pförtner, Ramona; Aschenbrenner, Katja; Heinrich, Ralf

    2011-01-01

    The central complex selects and coordinates the species- and situation-specific song production in acoustically communicating grasshoppers. Control of sound production is mediated by several neurotransmitters and modulators, their receptors and intracellular signaling pathways. It has previously been shown that muscarinic cholinergic excitation in the central complex promotes sound production whereas both GABA and nitric oxide/cyclic GMP signaling suppress its performance. The present immunocytochemical and pharmacological study investigates the question whether GABA and nitric oxide mediate inhibition of sound production independently. Muscarinic ACh receptors are expressed by columnar output neurons of the central complex that innervate the lower division of the central body and terminate in the lateral accessory lobes. GABAergic tangential neurons that innervate the lower division of the central body arborize in close proximity of columnar neurons and thus may directly inhibit these central complex output neurons. A subset of these GABAergic tangential neurons accumulates cyclic GMP following the release of nitric oxide from neurites in the upper division of the central body. While sound production stimulated by muscarine injection into the central complex is suppressed by co-application of sodium nitroprusside, picrotoxin-stimulated singing was not affected by co-application of this nitric oxide donor, indicating that nitric oxide mediated inhibition requires functional GABA signaling. Hence, grasshopper sound production is controlled by processing of information in the lower division of the central body which is subject to modulation by nitric oxide released from neurons in the upper division. PMID:21980504

  7. Architecture & Environment

    ERIC Educational Resources Information Center

    Erickson, Mary; Delahunt, Michael

    2010-01-01

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

  8. Architecture & Environment

    ERIC Educational Resources Information Center

    Erickson, Mary; Delahunt, Michael

    2010-01-01

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

  9. The Genetic Architecture of a Complex Ecological Trait: Host Plant Use in the Specialist Moth, Heliothis subflexa

    PubMed Central

    Oppenheim, Sara J.; Gould, Fred; Hopper, Keith R.

    2012-01-01

    We used genetic mapping to examine the genetic architecture of differences in host plant use between two species of noctuid moths, Heliothis subflexa, a specialist on Physalis spp., and its close relative, the broad generalist H. virescens. We introgressed H. subflexa chromosomes into the H. virescens background and analyzed 1,462 backcross insects. The effects of H. subflexa-origin chromosomes were small when measured as the percent variation explained in backcross populations (0.2 to 5%), but were larger when considered in relation to the interspecific difference explained (1.5 to 165%). Most significant chromosomes had effects on more than one trait, and their effects varied between years, sexes, and genetic backgrounds. Different chromosomes could produce similar phenotypes, suggesting that the same trait might be controlled by different chromosomes in different backcross populations. It appears that many loci of small effect contribute to the use of Physalis by H. subflexa. We hypothesize that behavioral changes may have paved the way for physiological adaptation to Physalis by the generalist ancestor of H. subflexa and H. virescens. PMID:23106701

  10. Complex organizational defects of fibroblast architecture in the mouse spleen with Nkx2.3 homeodomain deficiency.

    PubMed

    Bovári, Judit; Czömpöly, Tamás; Olasz, Katinka; Arnold, Hans-Henning; Balogh, Péter

    2007-01-01

    The capacity of secondary lymphoid organs to provide suitable tissue environment for mounting immune responses is dependent on their compartmentalized stromal constituents, including distinct fibroblasts. In addition to various members of the tumor necrosis factor/lymphotoxin beta family as important morphogenic regulators of peripheral lymphoid tissue development, the formation of stromal elements of spleen is also influenced by the Nkx2.3 homeodomain transcription factor in a tissue-specific fashion. Here we extend our previous work on the role of Nkx2.3-mediated regulation in the development of spleen architecture by analyzing the structure of reticular fibroblastic meshwork of spleen in inbred Nkx2.3-deficient mice. Using immunohistochemistry and dual-label immunofluorescence we found both distributional abnormalities, manifested as poor reticular compartmentalization of T-zone and circumferential reticulum, and developmental blockade, resulting in the absence of a complementary fibroblast subpopulation of white pulp. The disregulated distribution of fibroblasts was accompanied with an increased binding of immunohistochemically detectable complement factor C4 by T-cell zone-associated reticular fibroblasts, distinct from follicular dendritic cells with inherently high-level expression of bound C4. These data indicate that the impact of Nkx2.3 gene deficiency on fibroblast ontogeny within the spleen extends beyond its distributional effects, and that the formation of various white pulp fibroblast subsets is differentially affected by the presence of Nkx2.3 activity, possibly also influencing their role in various immune functions linked with complement activation and deposition.

  11. COST Action FP1005 ``Fibre suspension flow modelling''

    NASA Astrophysics Data System (ADS)

    Marchioli, Cristian

    2013-11-01

    Fibre suspensions are extremely complex solid-liquid systems since their components (fibres, flocs, air bubbles and additives) interact mutually in a complex way. The dynamics of fibre suspensions are crucial in many real-life applications, such as pulp and paper production. Current understanding of suspension flow dynamics remains poor and incomplete, resulting in conservative design of industrial equipments, low energy efficiency and equipment oversizing. In this paper, the most recent advancements in modelling and experimentation of fibre suspensions dynamics are presented. These advancements have been obtained in the framework of Action FP1005, funded by the COST Programme (European Cooperation in Science and Technology) to coordinate nationally-funded research on a European level. The Action aims at developing and validating numerical models for prediction of fibre suspensions as well as measurement techniques. The Action offers a forum to solve test cases and to compare simulated results to experiments, resulting in more reliable simulation tools to industry. Successfull introduction of such tool into industrial practice is crucial to innovate and increase competitivity of papermaking industry.

  12. Cellulose Fibre-Reinforced Biofoam for Structural Applications

    PubMed Central

    Obradovic, Jasmina; Voutilainen, Mikko; Virtanen, Pasi; Lassila, Lippo; Fardim, Pedro

    2017-01-01

    Traditionally, polymers and macromolecular components used in the foam industry are mostly derived from petroleum. The current transition to a bio-economy creates demand for the use of more renewable feedstocks. Soybean oil is a vegetable oil, composed mainly of triglycerides, that is suitable material for foam production. In this study, acrylated epoxidized soybean oil and variable amounts of cellulose fibres were used in the production of bio-based foam. The developed macroporous bio-based architectures were characterised by several techniques, including porosity measurements, nanoindentation testing, scanning electron microscopy, and thermogravimetric analysis. It was found that the introduction of cellulose fibres during the foaming process was necessary to create the three-dimensional polymer foams. Using cellulose fibres has potential as a foam stabiliser because it obstructs the drainage of liquid from the film region in these gas-oil interfaces while simultaneously acting as a reinforcing agent in the polymer foam. The resulting foams possessed a porosity of approximately 56%, and the incorporation of cellulose fibres did not affect thermal behaviour. Scanning electron micrographs showed randomly oriented pores with irregular shapes and non-uniform pore size throughout the samples. PMID:28772981

  13. The Genetic Architecture of Complex Traits in Teosinte (Zea mays ssp. parviglumis): New Evidence from Association Mapping

    USDA-ARS?s Scientific Manuscript database

    Our previous association analyses showed that variation at major regulatory genes contributes to standing variation for complex traits in Balsas teosinte, the progenitor of maize. This study expands our previous association mapping effort in teosinte by testing 123 markers in 52 candidate genes for ...

  14. The genetic architecture of a complex ecological trait: host plant use in the specialist moth, HELIOTHIS SUBFLEXA

    USDA-ARS?s Scientific Manuscript database

    The study of the genetic basis of ecological adaptation remains in its infancy, and most studies have focused on phenotypically simple traits. Host plant use by herbivorous insects is phenotypically complex. While research has illuminated the evolutionary determinants of host use, knowledge of its...

  15. Controlling the phase structures of polymer/surfactant complexes by changing macromolecular architecture and adding n-alcohols.

    PubMed

    Percebom, Ana Maria; Loh, Watson

    2016-03-15

    Phase behavior of complex salts formed by a cationic surfactant and different ethoxylated polyions was investigated in water and with addition of two n-alcohols of different chain lengths: n-butanol and n-decanol. The polyion possesses a main chain of methacrylic acid randomly grafted with oligo(ethylene oxide) chains. Strong electrostatic interaction between the anionic main chain and the cationic surfactant hexadecyltrimethylammonium (C16TA) leads to the formation of C16TAP(MA-MAEO(n)) x:y complex salts. Modifications in polyion structure, such as changes in the proportion of grafted comonomers and in the side chain length caused differences in the overall balance of interactions with water and n-alcohols, altering the complex salt solubility and, consequently, the formed liquid-crystalline structures. The role of n-decanol as a cosurfactant was verified, but the hydrophilic side chains expanded the capacity of the formed liquid crystalline phases to incorporate water. Additionally, a novel structure, probably cubic bicontinuous (Pn3m), was observed coexisting with lamellar phases at low water concentration. Because n-butanol is known for being a good solvent for poly(ethylene oxide), these side chains intensified the role of this short chain n-alcohol as cosolvent for C16TAP(MA-MAEO(n)) x:y complex salts, favoring the formation of disordered solutions, including a bicontinuous microemulsion.

  16. Crystal structure of [alpha]-COP in complex with [epsilon]-COP provides insight into the architecture of the COPI vesicular coat

    SciTech Connect

    Hsia, Kuo-Chiang; Hoelz, André

    2010-07-23

    The heptameric coatomer complex forms the protein shell of membrane-bound vesicles that are involved in transport from the Golgi to the endoplasmatic reticulum and in intraGolgi trafficking. The heptamer can be dissected into a heterotetrameric F-subcomplex, which displays similarities to the adapter complex of the 'inner' coat in clathrin-coated vesicles, and a heterotrimeric B-subcomplex, which is believed to form an 'outer' coat with a morphology distinct from that of clathrin-coated vesicles. We have determined the crystal structure of the complex between the C-terminal domain (CTD) of {alpha}-COP and full-length {epsilon}-COP, two components of the B-subcomplex, at a 2.9 {angstrom} resolution. The {alpha}-COP{sup CTD} {center_dot} {epsilon}-COP heterodimer forms a rod-shaped structure, in which {epsilon}-COP adopts a tetratricopeptide repeat (TPR) fold that deviates substantially from the canonical superhelical conformation. The {alpha}-COP CTD adopts a U-shaped architecture that complements the TPR fold of {epsilon}-COP. The {epsilon}-COP TPRs form a circular bracelet that wraps around a protruding {beta}-hairpin of the {alpha}-COP CTD, thus interlocking the two proteins. The {alpha}-COPCTD {center_dot} {epsilon}-COP complex forms heterodimers in solution, and we demonstrate biochemically that the heterodimer directly interacts with the Dsl1 tethering complex. These data suggest that the heterodimer is exposed on COPI vesicles, while the remaining part of the B-subcomplex oligomerizes underneath into a cage.

  17. EDITORIAL: The 20th International Conference on Optical Fibre Sensors, OFS-20 The 20th International Conference on Optical Fibre Sensors, OFS-20

    NASA Astrophysics Data System (ADS)

    Culshaw, Brian; Ecke, Wolfgang; Jones, Julian; Tatam, Ralph; Willsch, Reinhardt

    2010-09-01

    Welcome to our special issue on fibre optic sensors. Fibre optic sensors were first suggested in the patent literature in the mid 1960s as an innovative means for making measurements. This proposed a surface finish measurement tool with high precision and resulted in an instrument that remains available today. Much has happened since, with significant innovation in the techniques through which light propagating whilst guided in a fibre can be unambiguously, repeatedly and predictably modulated in response to an external phenomenon. The technique offers not only the precision mentioned earlier but also inherent electromagnetic immunity, the capability to sense at long distances, light weight, small size and a multiplicity of network architectures, all of which can be interrogated from a single point. Even so, fibre sensors is a niche technology, attractive only when its very special features offer substantial user benefit. There are, however, many such niches exemplified in the electrical power supply industry, in gyroscopes for navigational instruments, in hydrophones and geophones. Then there are the distributed sensing architectures that enable useful measurements of pressure, strain and temperature fields affecting the optical properties of the fibre itself to map these parameter fields as a function of position along lengths of fibre to many tens of kilometres. The fibre sensing concept spawned its own research community, and the international conference on Optical Fibre Sensors first appeared in 1983 in London then emerged into a series travelling from Europe to the Americas and into the Asia-Pacific region. The 20th in the series took place in Edinburgh at the end of 2009 and this special issue of Measurement Science and Technology presents extended versions of some of the papers that first appeared at the conference. The science and technology of fibre sensing have evolved significantly over the history of the conference, drawing on developments in optical

  18. Project Integration Architecture: Application Architecture

    NASA Technical Reports Server (NTRS)

    Jones, William Henry

    2005-01-01

    The Project Integration Architecture (PIA) implements a flexible, object-oriented, wrapping architecture which encapsulates all of the information associated with engineering applications. The architecture allows the progress of a project to be tracked and documented in its entirety. Additionally, by bringing all of the information sources and sinks of a project into a single architectural space, the ability to transport information between those applications is enabled.

  19. High power operation of cladding pumped holmium-doped silica fibre lasers.

    PubMed

    Hemming, Alexander; Bennetts, Shayne; Simakov, Nikita; Davidson, Alan; Haub, John; Carter, Adrian

    2013-02-25

    We report the highest power operation of a resonantly cladding-pumped, holmium-doped silica fibre laser. The cladding pumped all-glass fibre utilises a fluorine doped glass layer to provide low loss cladding guidance of the 1.95 µm pump radiation. The operation of both single mode and large-mode area fibre lasers was demonstrated, with up to 140 W of output power achieved. A slope efficiency of 59% versus launched pump power was demonstrated. The free running emission was measured to be 2.12-2.15 µm demonstrating the potential of this architecture to address the long wavelength operation of silica based fibre lasers with high efficiency.

  20. Electron microscopy and in vitro deneddylation reveal similar architectures and biochemistry of isolated human and Flag-mouse COP9 signalosome complexes

    SciTech Connect

    Rockel, Beate; Schmaler, Tilo; Huang, Xiaohua; Dubiel, Wolfgang

    2014-07-25

    Highlights: • Deneddylation rates of human erythrocyte and mouse fibroblast CSN are very similar. • 3D models of native human and mouse CSN reveal common architectures. • The cryo-structure of native mammalian CSN shows a horseshoe subunit arrangement. - Abstract: The COP9 signalosome (CSN) is a regulator of the ubiquitin (Ub) proteasome system (UPS). In the UPS, proteins are Ub-labeled for degradation by Ub ligases conferring substrate specificity. The CSN controls a large family of Ub ligases called cullin-RING ligases (CRLs), which ubiquitinate cell cycle regulators, transcription factors and DNA damage response proteins. The CSN possesses structural similarities with the 26S proteasome Lid complex and the translation initiation complex 3 (eIF3) indicating similar ancestry and function. Initial structures were obtained 14 years ago by 2D electron microscopy (EM). Recently, first 3D molecular models of the CSN were created on the basis of negative-stain EM and single-particle analysis, mostly with recombinant complexes. Here, we compare deneddylating activity and structural features of CSN complexes purified in an elaborate procedure from human erythrocytes and efficiently pulled down from mouse Flag-CSN2 B8 fibroblasts. In an in vitro deneddylation assay both the human and the mouse CSN complexes deneddylated Nedd8-Cul1 with comparable rates. 3D structural models of the erythrocyte CSN as well as of the mouse Flag-CSN were generated by negative stain EM and by cryo-EM. Both complexes show a central U-shaped segment from which several arms emanate. This structure, called the horseshoe, is formed by the PCI domain subunits. CSN5 and CSN6 point away from the horseshoe. Compared to 3D models of negatively stained CSN complexes, densities assigned to CSN2 and CSN4 are better defined in the cryo-map. Because biochemical and structural results obtained with CSN complexes isolated from human erythrocytes and purified by Flag-CSN pulldown from mouse B8 fibroblasts

  1. Architecture and evolution of an Early Permian carbonate complex on a tectonically active island in east-central California

    USGS Publications Warehouse

    Stevens, Calvin H.; Magginetti, Robert T.; Stone, Paul

    2015-01-01

    The newly named Upland Valley Limestone represents a carbonate complex that developed on and adjacent to a tectonically active island in east-central California during a brief interval of Early Permian (late Artinskian) time. This lithologically unique, relatively thin limestone unit lies within a thick sequence of predominantly siliciclastic rocks and is characterized by its high concentration of crinoidal debris, pronounced lateral changes in thickness and lithofacies, and a largely endemic fusulinid fauna. Most outcrops represent a carbonate platform and debris derived from it and shed downslope, but another group of outcrops represents one or possibly more isolated carbonate buildups that developed offshore from the platform. Tectonic activity in the area occurred before, probably during, and after deposition of this short-lived carbonate complex.

  2. In-line microfluidic integration of photonic crystal fibres as a highly sensitive refractometer.

    PubMed

    Wu, Chuang; Tse, Ming-Leung Vincent; Liu, Zhengyong; Guan, Bai-Ou; Zhang, A Ping; Lu, Chao; Tam, Hwa-Yaw

    2014-11-07

    Photonic crystal fibres appear to be an ideal platform for the realisation of novel optofluidic devices and sensors due to their waveguide nature and microstructured architecture. In this paper, we present the fabrication and characterisation of an in-line photonic crystal fibre microfluidic refractometer enabled by a C-shaped fibre. The C-shaped fibre spliced in-between the photonic crystal fibre and the single-mode fibre allows simultaneous in-line optical signal delivery and analyte fluid feeding. Through an arc discharge pre-treatment technique, we successfully achieve selective exploitation of only the central two channels of the photonic crystal fibre for microfluidic sensing. After constructing a Sagnac interferometer, a highly sensitive refractometer with a sensitivity of 8699 nm per RIU was achieved experimentally; this agrees very well with the theoretical value of 8675 nm per RIU. As a demonstration for label-free optical sensing application, the refractometer was used to measure the concentration of NaCl solution with a sensitivity of 15.08 nm/(1 wt%) and a detection limit of 2.3 × 10(-3) wt% (23 ppm).

  3. Osteogenic differentiation and mineralization in fibre-reinforced tubular scaffolds: theoretical study and experimental evidences

    PubMed Central

    Guarino, Vincenzo; Urciuolo, Francesco; Alvarez-Perez, Marco A.; Mele, Benedetto; Netti, Paolo A.; Ambrosio, Luigi

    2012-01-01

    The development of composite scaffolds with well-organized architecture and multi-scale properties (i.e. porosity, degradation) represents a valid approach for achieving a tissue-engineered construct capable of reproducing the medium- and long-term in vitro behaviour of hierarchically complex tissues such as spongy bone. To date, the implementation of scaffold design strategies able to summarize optimal scaffold architecture as well as intrinsic mechanical, chemical and fluid transport properties still remains a challenging issue. In this study, poly ɛ-caprolactone/polylactid acid (PCL/PLA) tubular devices (fibres of PLA in a PCL matrix) obtained by phase inversion/salt leaching and filament winding techniques were proposed as cell instructive scaffold for bone osteogenesis. Continuous fibres embedded in the polymeric matrix drastically improved the mechanical response as confirmed by compression elastic moduli, which vary from 0.214 ± 0.065 to 1.174 ± 0.143 MPa depending on the relative fibre/matrix and polymer/solvent ratios. Moreover, computational fluid dynamic simulations demonstrated the ability of composite structure to transfer hydrodynamic forces during in vitro culture, thus indicating the optimal flow rate conditions that, case by case, enables specific cellular events—i.e. osteoblast differentiation from human mesenchymal stem cells (hMSCs), mineralization, etc. Hence, we demonstrate that the hMSC differentiation preferentially occurs in the case of higher perfusion rates—over 0.05 ml min–1—as confirmed by the expression of alkaline phosphate and osteocalcin markers. In particular, the highest osteopontin values and a massive mineral phase precipitation of bone-like phases detected in the case of intermediate flow rates (i.e. 0.05 ml min–1) allows us to identify the best condition to stimulate the bone extracellular matrix in-growth, in agreement with the hydrodynamic model prediction. All these results concur to prove the succesful use of

  4. Get in the Loop: Fibre Channel, SSA, and Ultra SCSI Connect the Digital Studio.

    ERIC Educational Resources Information Center

    Sauer, Jeff

    1997-01-01

    Removable hard drives and Ethernet are common ways to move data around the media studio, but new protocols allow multiple computers to share an array on one bus. Examines shared storage configurations using fibre channel arbitrated loop (FC-AL) and serial storage architecture (SSA), both serial storage solutions, as well as on small computer…

  5. Get in the Loop: Fibre Channel, SSA, and Ultra SCSI Connect the Digital Studio.

    ERIC Educational Resources Information Center

    Sauer, Jeff

    1997-01-01

    Removable hard drives and Ethernet are common ways to move data around the media studio, but new protocols allow multiple computers to share an array on one bus. Examines shared storage configurations using fibre channel arbitrated loop (FC-AL) and serial storage architecture (SSA), both serial storage solutions, as well as on small computer…

  6. Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates

    PubMed Central

    Yuan, Bo; Liu, Pengfei; Gupta, Aditya; Beck, Christine R.; Tejomurtula, Anusha; Campbell, Ian M.; Gambin, Tomasz; Simmons, Alexandra D.; Withers, Marjorie A.; Harris, R. Alan; Rogers, Jeffrey; Schwartz, David C.; Lupski, James R.

    2015-01-01

    Many loci in the human genome harbor complex genomic structures that can result in susceptibility to genomic rearrangements leading to various genomic disorders. Nephronophthisis 1 (NPHP1, MIM# 256100) is an autosomal recessive disorder that can be caused by defects of NPHP1; the gene maps within the human 2q13 region where low copy repeats (LCRs) are abundant. Loss of function of NPHP1 is responsible for approximately 85% of the NPHP1 cases—about 80% of such individuals carry a large recurrent homozygous NPHP1 deletion that occurs via nonallelic homologous recombination (NAHR) between two flanking directly oriented ~45 kb LCRs. Published data revealed a non-pathogenic inversion polymorphism involving the NPHP1 gene flanked by two inverted ~358 kb LCRs. Using optical mapping and array-comparative genomic hybridization, we identified three potential novel structural variant (SV) haplotypes at the NPHP1 locus that may protect a haploid genome from the NPHP1 deletion. Inter-species comparative genomic analyses among primate genomes revealed massive genomic changes during evolution. The aggregated data suggest that dynamic genomic rearrangements occurred historically within the NPHP1 locus and generated SV haplotypes observed in the human population today, which may confer differential susceptibility to genomic instability and the NPHP1 deletion within a personal genome. Our study documents diverse SV haplotypes at a complex LCR-laden human genomic region. Comparative analyses provide a model for how this complex region arose during primate evolution, and studies among humans suggest that intra-species polymorphism may potentially modulate an individual’s susceptibility to acquiring disease-associated alleles. PMID:26641089

  7. Parallel, Multigrid Finite Element Simulator for Fractured/Faulted and Other Complex Reservoirs based on Common Component Architecture (CCA)

    SciTech Connect

    Milind Deo; Chung-Kan Huang; Huabing Wang

    2008-08-31

    Black-oil, compositional and thermal simulators have been developed to address different physical processes in reservoir simulation. A number of different types of discretization methods have also been proposed to address issues related to representing the complex reservoir geometry. These methods are more significant for fractured reservoirs where the geometry can be particularly challenging. In this project, a general modular framework for reservoir simulation was developed, wherein the physical models were efficiently decoupled from the discretization methods. This made it possible to couple any discretization method with different physical models. Oil characterization methods are becoming increasingly sophisticated, and it is possible to construct geologically constrained models of faulted/fractured reservoirs. Discrete Fracture Network (DFN) simulation provides the option of performing multiphase calculations on spatially explicit, geologically feasible fracture sets. Multiphase DFN simulations of and sensitivity studies on a wide variety of fracture networks created using fracture creation/simulation programs was undertaken in the first part of this project. This involved creating interfaces to seamlessly convert the fracture characterization information into simulator input, grid the complex geometry, perform the simulations, and analyze and visualize results. Benchmarking and comparison with conventional simulators was also a component of this work. After demonstration of the fact that multiphase simulations can be carried out on complex fracture networks, quantitative effects of the heterogeneity of fracture properties were evaluated. Reservoirs are populated with fractures of several different scales and properties. A multiscale fracture modeling study was undertaken and the effects of heterogeneity and storage on water displacement dynamics in fractured basements were investigated. In gravity-dominated systems, more oil could be recovered at a given pore

  8. Physical limits to biomechanical sensing in disordered fibre networks

    NASA Astrophysics Data System (ADS)

    Beroz, Farzan; Jawerth, Louise M.; Münster, Stefan; Weitz, David A.; Broedersz, Chase P.; Wingreen, Ned S.

    2017-07-01

    Cells actively probe and respond to the stiffness of their surroundings. Since mechanosensory cells in connective tissue are surrounded by a disordered network of biopolymers, their in vivo mechanical environment can be extremely heterogeneous. Here we investigate how this heterogeneity impacts mechanosensing by modelling the cell as an idealized local stiffness sensor inside a disordered fibre network. For all types of networks we study, including experimentally-imaged collagen and fibrin architectures, we find that measurements applied at different points yield a strikingly broad range of local stiffnesses, spanning roughly two decades. We verify via simulations and scaling arguments that this broad range of local stiffnesses is a generic property of disordered fibre networks. Finally, we show that to obtain optimal, reliable estimates of global tissue stiffness, a cell must adjust its size, shape, and position to integrate multiple stiffness measurements over extended regions of space.

  9. Seismic stratigraphy, facies architecture, and reservoir character of a pleistocene shelf-margin delta complex, Eugene Island Block 330 field, offshore Louisiana

    SciTech Connect

    Hart, B.S.; Sibley, D.M.; Flemings, P.B.

    1997-03-01

    The GA interval of the Eugene Island Block 330 field is the deposit of late Pleistocene ({approximately}0.8 Ma) shelf-margin lowstand delta complex. We integrated three-dimensional (3-D) seismic, wireline log, core, and cuttings data to examine the delta`s internal architecture and to reconstruct its depositional history. This interval displays a complex vertical and lateral interfingering of channel, clinoform, and base-of-slope failure deposits over short distances (a few kilometers), and is the product of delta lobe progradation structural development (growth faults, rollover anticline) and relative sea level change. We then integrated our sequence stratigraphic interpretation with production data. Hydrocarbon accumulations in the interval are primarily associated with updip facies (delta mouth bar, delta front) beneath the flooding surface at the top of the interval, and not the sequence boundary at the base of the interval. Maps of seismic amplitudes associated with the top of the GA interval show patchy (mouth bar deposits) and curvilinear (interdistributary delta front) trends that indicate reservoir heterogeneities associated with depositional features. There is a good qualitative relationship between seismic amplitude and production characteristics, with the best production being from high-amplitude areas that sit high on the structure.

  10. The complex facies architecture and emplacement sequence of a Miocene submarine mega-pillow lava flow system, Muriwai, North Island, New Zealand

    NASA Astrophysics Data System (ADS)

    Bear, A. N.; Cas, R. A. F.

    2007-02-01

    The early Miocene Waiatarua Formation at Maori Bay, Muriwai, North Island, New Zealand consists of a complex association of basaltic andesite volcanic facies including entablature-jointed thick massive facies, colonnade-jointed thin massive sheet facies, mega-pillow facies, normal pillow facies and minor associated fragmental facies, including vitric sandstone and breccia interpreted as hyaloclastite and peperite. Field observations suggest that the facies, which form the Waiatarua Formation lava, were emplaced as multiple flow lobes in a single lava flow from one sustained eruption. Magma discharge rate at the vent was high; however magma supply rate to the more distal and lateral portions of the flow, as its surface area increased, varied considerably. Higher magma supply rates produced thick, massive and thin sheet facies, whereas mega-pillow facies and normal pillow facies were produced contemporaneously with the thick and thin massive sheet facies but were restricted to portions of the distal flow subjected to lower magma supply rates. The evolution of the Waiatarua formation lava flow at Maori Bay has been reconstructed from the complex facies architecture. This suggests that the propagation of the lava involved 7 discrete lobes that were emplaced successively.

  11. Comparing GWAS Results of Complex Traits Using Full Genetic Model and Additive Models for Revealing Genetic Architecture

    PubMed Central

    Monir, Md. Mamun; Zhu, Jun

    2017-01-01

    Most of the genome-wide association studies (GWASs) for human complex diseases have ignored dominance, epistasis and ethnic interactions. We conducted comparative GWASs for total cholesterol using full model and additive models, which illustrate the impacts of the ignoring genetic variants on analysis results and demonstrate how genetic effects of multiple loci could differ across different ethnic groups. There were 15 quantitative trait loci with 13 individual loci and 3 pairs of epistasis loci identified by full model, whereas only 14 loci (9 common loci and 5 different loci) identified by multi-loci additive model. Again, 4 full model detected loci were not detected using multi-loci additive model. PLINK-analysis identified two loci and GCTA-analysis detected only one locus with genome-wide significance. Full model identified three previously reported genes as well as several new genes. Bioinformatics analysis showed some new genes are related with cholesterol related chemicals and/or diseases. Analyses of cholesterol data and simulation studies revealed that the full model performs were better than the additive-model performs in terms of detecting power and unbiased estimations of genetic variants of complex traits. PMID:28079101

  12. LUPA: a European initiative taking advantage of the canine genome architecture for unravelling complex disorders in both human and dogs.

    PubMed

    Lequarré, Anne-Sophie; Andersson, Leif; André, Catherine; Fredholm, Merete; Hitte, Christophe; Leeb, Tosso; Lohi, Hannes; Lindblad-Toh, Kerstin; Georges, Michel

    2011-08-01

    The domestic dog offers a unique opportunity to explore the genetic basis of disease, morphology and behaviour. Humans share many diseases with our canine companions, making dogs an ideal model organism for comparative disease genetics. Using newly developed resources, genome-wide association studies in dog breeds are proving to be exceptionally powerful. Towards this aim, veterinarians and geneticists from 12 European countries are collaborating to collect and analyse the DNA from large cohorts of dogs suffering from a range of carefully defined diseases of relevance to human health. This project, named LUPA, has already delivered considerable results. The consortium has collaborated to develop a new high density single nucleotide polymorphism (SNP) array. Mutations for four monogenic diseases have been identified and the information has been utilised to find mutations in human patients. Several complex diseases have been mapped and fine mapping is underway. These findings should ultimately lead to a better understanding of the molecular mechanisms underlying complex diseases in both humans and their best friend.

  13. The Genetic Architecture of Complex Traits in Teosinte (Zea mays ssp. parviglumis): New Evidence From Association Mapping

    PubMed Central

    Weber, Allison L.; Briggs, William H.; Rucker, Jesse; Baltazar, Baltazar M.; de Jesús Sánchez-Gonzalez, José; Feng, Ping; Buckler, Edward S.; Doebley, John

    2008-01-01

    Previous association analyses showed that vari