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Sample records for reveals structural aspects

  1. Structure and mechanism of calmodulin binding to a signaling sphingolipid reveal new aspects of lipid-protein interactions

    Science.gov (United States)

    Kovacs, Erika; Harmat, Veronika; Tóth, Judit; Vértessy, Beáta G.; Módos, Károly; Kardos, József; Liliom, Károly

    2010-01-01

    Lipid-protein interactions are rarely characterized at a structural molecular level due to technical difficulties; however, the biological significance of understanding the mechanism of these interactions is outstanding. In this report, we provide mechanistic insight into the inhibitory complex formation of the lipid mediator sphingosylphosphorylcholine with calmodulin, the most central and ubiquitous regulator protein in calcium signaling. We applied crystallographic, thermodynamic, kinetic, and spectroscopic approaches using purified bovine calmodulin and bovine cerebral microsomal fraction to arrive at our conclusions. Here we present 1) a 1.6-Å resolution crystal structure of their complex, in which the sphingolipid occupies the conventional hydrophobic binding site on calmodulin; 2) a peculiar stoichiometry-dependent binding process: at low or high protein-to-lipid ratio calmodulin binds lipid micelles or a few lipid molecules in a compact globular conformation, respectively, and 3) evidence that the sphingolipid displaces calmodulin from its targets on cerebral microsomes. We have ascertained the specificity of the interaction using structurally related lipids as controls. Our observations reveal the structural basis of selective calmodulin inhibition by the sphingolipid. On the basis of the crystallographic and biophysical characterization of the calmodulin–sphingosylphosphorylcholine interaction, we propose a novel lipid-protein binding model, which might be applicable to other interactions as well.—Kovacs, E., Harmat, V., Tóth, J., Vértessy, B. G., Módos, K., Kardos, J., Liliom, K. Structure and mechanism of calmodulin binding to a signaling sphingolipid reveal new aspects of lipid-protein interactions. PMID:20522785

  2. New aspects of the structure of the proton revealed by the collider Hera; Nouveaux aspects de la structure du proton avec le collisionneur HERA

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Z

    2000-12-01

    Since its commissioning in 1991, the ep collider HERA has been running successfully for almost a decade without stopping improving its performance. In this report, the inclusive cross section and structure function measurements for the deep inelastic scattering of neutral and charged current processes in the full HERA kinematic domain are reviewed. The results are compared with the Standard Model expectations for the deep inelastic scattering processes. The new insights into the proton structure and on the underlying strong and electroweak interactions are discussed. (author)

  3. Aspects of hadronic structure

    International Nuclear Information System (INIS)

    Ferreira, P.L.

    1984-01-01

    An overview of the current phenomenological models of hadron structure, whose theoretical basis is the Quantum Chromodynamics (QCD), is presented. A short introduction to the QCD permits to focalize the relevant properties which are attached to those models. Following, bag-like models (in particular, MIT bag and chiral extensions) and potential-like models among them the Karl and Isgur non-relativistic model and a semi-relativistic model, free of the Klein paradox, with equal scalar-vetorial mixture of confinement potential are shortly studied. Enphasis is given to the baryons, treated, basically, as three-quarks systems. (L.C.) [pt

  4. 'Shelter' object safety. Structural aspects

    International Nuclear Information System (INIS)

    Krivosheev, P.I.; Nemchinov, Yu.I.; Bambura, A.N.; Sokolov, A.P.; Shenderovich, V.Ya.; Vasyagin, R.V.; Klyuchnikov, A.A.; Shcherbin, V.N.; Rud'ko, V.M.; Tokarevskij, V.V.; Belousov, E.L.; Khejger, D.; Gorodetskij, L.

    2001-01-01

    In 1997 the group of the international experts including Ukrainian organizations and 'Shelter' Object ChNPP are developed the plan of SO transformation into ecological safe status (plan SIP). The realization of the plan was carried out on basis of international tender. The results of structural aspects of SO safety and it transformation into ecological safe state (ESS) are resented in this report

  5. Licensing aspects of structural integrity

    International Nuclear Information System (INIS)

    Turner, M.J.; Hemsworth, B.; Boydon, F.M.D.; Harrop, L.P.; Waters, R.

    1992-01-01

    Examples are given of the wide variety of structural integrity assessments of nuclear plant carried out by the United Kingdom Nuclear Installations Inspectorate (NII) and the consequent need for a flexible approach within the framework provided by the Safety Assessment Principles. The paper describes the use of the Special Case Procedure and draws the distinction between the assessment of incredibility of failure of components and components whose failures are considered within the design basis. Assessment examples provided are the Sizewell B reactor pressure vessel, Magnox reactor pressure vessels, the Prototype Fast Reactor core support structure, Advanced Gas-cooled Reactor steam plant, Thermal Oxide Reprocessing Plant (THORP) vessels, and Steam Generating Heavy Water Reactor pressure tubes. (author)

  6. Structuring factoring business: accounting aspects

    Directory of Open Access Journals (Sweden)

    I.M. Vygivska

    2017-08-01

    Full Text Available The article theoretically substantiates the fact that factoring belongs to the main operational activity of a factoring company, and this allowed structuring the factoring business by types of activity. The lack of a unified approach to the classification of factoring (factoring services made it possible to systematize and refine their classification as a basis for developing accounting and analytical support for risk management of factoring business. The authors single out such classification signs as: the right of the reverse claim (reverse, irretrievable, a territorial feature (international, internal, the subject of the factoring contract (real, consensual, the availability of notification of the debtor (conventional, confidential. The structuring of factoring business contributes to the identification of the risks of the economic activities of a factoring company depending on the type of factoring, the development of methodological support for the bookkeeping of factoring transactions in a risk environment, the search for risk management practices and the determination of management effectiveness in general.

  7. Statistical aspects of nuclear structure

    International Nuclear Information System (INIS)

    Parikh, J.C.

    1977-01-01

    The statistical properties of energy levels and a statistical approach to transition strengths are discussed in relation to nuclear structure studies at high excitation energies. It is shown that the calculations can be extended to the ground state domain also. The discussion is based on the study of random matrix theory of level density and level spacings, using the Gaussian Orthogonal Ensemble (GOE) concept. The short range and long range correlations are also studied statistically. The polynomial expansion method is used to obtain excitation strengths. (A.K.)

  8. Some aspects of fluid-structure coupling

    International Nuclear Information System (INIS)

    Kulak, R.F.

    1982-01-01

    The numerical simulation of nonlinear, transient fluid-structure interactions (FSI) is a current area of concern by researchers in various fields, including the field of nuclear reactor safety. This paper primarily discusses the formulation used in an algorithm that couples three-dimensional hydrodynamic and structural domains. The fluid domain is governed by the Navier-Stokes equations, and the structural domain is governed by the equations of nonlinear structural dynamics. Here, both the fluid and structure are discretized using finite elements. The fluid is discretized with eight-noded quasi-Eulerian hexahedrons and the structural components are represented by Lagrangian triangular plate elements. The semi-discretized equations of motion are solved using an explicit temporal integrator. The coupling is accomplished by satisfying interface mechanics. The structure imposes kinematic constraints to the moving fluid boundary, and the fluid in turn provides an external loading on the structure. At each interface node, normals are computed from the nodal basis functions of only the hydrodynamic nodes. By defining the interface normal in this manner, it becomes independent of the type of structural boundary (i.e. shell, plate, continuum etc.) and thus makes this aspect of the coupling independent of the structure type. Results for several problems are presented and these include a comparison between analytical results for a FSI problem and numerical predictions

  9. Clustering aspects in nuclear structure functions

    International Nuclear Information System (INIS)

    Hirai, M.; Saito, K.; Watanabe, T.; Kumano, S.

    2011-01-01

    For understanding an anomalous nuclear effect experimentally observed for the beryllium-9 nucleus at the Thomas Jefferson National Accelerator Facility, clustering aspects are studied in structure functions of deep inelastic lepton-nucleus scattering by using momentum distributions calculated in antisymmetrized (or fermionic) molecular dynamics (AMD) and also in a simple shell model for comparison. According to AMD, the 9 Be nucleus consists of two α-like clusters with a surrounding neutron. The clustering produces high-momentum components in nuclear wave functions, which affects nuclear modifications of the structure functions. We investigated whether clustering features could appear in the structure function F 2 of 9 Be along with studies for other light nuclei. We found that nuclear modifications of F 2 are similar in both AMD and shell models within our simple convolution description although there are slight differences in 9 Be. It indicates that the anomalous 9 Be result should be explained by a different mechanism from the nuclear binding and Fermi motion. If nuclear-modification slopes d(F 2 A /F 2 D )/dx are shown by the maximum local densities, the 9 Be anomaly can be explained by the AMD picture, namely by the clustering structure, whereas it certainly cannot be described in the simple shell model. This fact suggests that the large nuclear modification in 9 Be should be explained by large densities in the clusters. For example, internal nucleon structure could be modified in the high-density clusters. The clustering aspect of nuclear structure functions is an unexplored topic which is interesting for future investigations.

  10. Structural aspects of some hydrobenzofuran neolignans

    International Nuclear Information System (INIS)

    Yoshida, Massayoshi

    2012-01-01

    The neolignans are defined as dimers of allylphenol and propenylphenol between itself or crossed, whose bond does not occur by the 8-8' carbons like lignans. This review centered on stereochemical aspects of the hydrobenzofuran type, a widespread skeleton among neolignans. The chemical structures established based on spectrometric data are registered in the literature. The absolute configurations reported previously were determined by chiroptical techniques. Some chemical transformations with neolignans, performed in previous studies, afforded products which are accumulated in other vegetal species and contributed to assign the unknown stereochemistry of these natural compounds. Possible biosynthetic pathways are also proposed. (author)

  11. Rheology of transgenic switchgrass reveals practical aspects of biomass processing.

    Science.gov (United States)

    Wan, Guigui; Frazier, Taylor; Jorgensen, Julianne; Zhao, Bingyu; Frazier, Charles E

    2018-01-01

    Mechanical properties of transgenic switchgrass have practical implications for biorefinery technologies. Presented are fundamentals for simple (thermo)mechanical measurements of genetically transformed switchgrass. Experimental basics are provided for the novice, where the intention is to promote collaboration between plant biologists and materials scientists. Stem sections were subjected to two stress modes: (1) torsional oscillation in the linear response region, and (2) unidirectional torsion to failure. Specimens were analyzed while submerged/saturated in ethylene glycol, simulating natural hydration and allowing experimental temperatures above 100 °C for an improved view of the lignin glass transition. Down-regulation of the 4-Coumarate:coenzyme A ligase gene (reduced lignin content and altered monomer composition) generally resulted in less stiff and weaker stems. These observations were associated with a reduction in the temperature and activation energy of the lignin glass transition, but surprisingly with no difference in the breadth and intensity of the tan  δ signal. The results showed promise in further investigations of how rheological methods relate to stem lignin content, composition, and functional properties in the field and in bioprocessing. Measurements such as these are complicated by small specimen size; however, torsional rheometers (relatively common in polymer laboratories) are well suited for this task. As opposed to the expense and complication of relative humidity control, solvent-submersion rheological methods effectively reveal fundamental structure/property relationships in plant tissues. Demonstrated are low-strain linear methods, and also nonlinear yield and failure analysis; the latter is very uncommon for typical rheological equipment.

  12. Exotic nuclei: another aspect of nuclear structure

    International Nuclear Information System (INIS)

    Dobaczewski, J.; Blumenfeld, Y.; Flocard, H.; Garcia Borge, M.J.; Nowacki, F.; Rombouts, S.; Theisen, Ch.; Marques, F.M.; Lacroix, D.; Dessagne, P.; Gaeggeler, H.

    2002-01-01

    This document gathers the lectures made at the Joliot Curie international summer school in 2002 whose theme that year was exotic nuclei. There were 11 contributions whose titles are: 1) interactions, symmetry breaking and effective fields from quarks to nuclei; 2) status and perspectives for the study of exotic nuclei: experimental aspects; 3) the pairing interaction and the N = Z nuclei; 4) borders of stability region and exotic decays; 5) shell structure of nuclei: from stability to decay; 6) variational approach of system with a few nucleons; 7) from heavy to super-heavy nuclei; 8) halos, molecules and multi-neutrons; 9) macroscopic approaches for fusion reactions; 10) beta decay: a tool for spectroscopy; 11) the gas phase chemistry of super-heavy elements

  13. Gauge field vacuum structure in geometrical aspect

    International Nuclear Information System (INIS)

    Konopleva, N.P.

    2003-01-01

    Vacuum conception is one of the main conceptions of quantum field theory. Its meaning in classical field theory is also very profound. In this case the vacuum conception is closely connected with ideas of the space-time geometry. The global and local geometrical space-time conceptions lead to different vacuum definitions and therefore to different ways of physical theory construction. Some aspects of the gauge field vacuum structure are analyzed. It is shown that in the gauge field theory the vacuum Einstein equation solutions describe the relativistic vacuum as common vacuum of all gauge fields and its sources. Instantons (both usual and hyperbolical) are regarded as nongravitating matter, because they have zero energy-momentum tensors and correspond to vacuum Einstein equations

  14. Conjugated Polymers and Oligomers: Structural and Soft Matter Aspects

    DEFF Research Database (Denmark)

    This book identifies modern topics and current trends of structural and soft matter aspects of conjugated polymers and oligomers. Each chapter recognizes an active research line where structural perspective dominates research and therefore the book covers fundamental aspects of persistent...

  15. Some structural aspects of urbanization in Ethiopia.

    Science.gov (United States)

    Rafiq, M; Hailemariam, A

    1987-07-01

    This article studies the emerging patterns of urbanization in Ethiopia. Over the period from 1967-1984, a number of structural changes have occurred which are likely to play a dominant role in the future urban growth in Ethiopia. In spite of its long history of settled population, Ethiopia did not witness sustained growth of urban centers. Ethiopia is 1 of the least urbanized areas in the Third World. A 3rd aspect of urbanization in Ethiopia is the wide range of regional differentials in the level of urbanization. Most of the urban population is concentrated in 2 administrative regions--Shoa and Eritrea. A more balanced urban growth may, inter alia, involve a better spread in terms of higher education, industrialization, provision of health and social services, and the development of communication and commercial infrastructure. Another striking feature of urbanization in Ethiopia is that growth has not been disproportionately concentrated in the largest urban centers. The largest urban centers have not assumed an inordinately higher level of primacy. The basic form of the curve depicting the relationship between the size of a locality and its rank has remained unchanged over the period. The post-revolution land reforms and the new socioeconomic structure emerging from reorganization of the society appear to have a rural-urban migration inhibiting effect. Some of the country's regional differentials may be associated with environmental factors.

  16. Some aspects of arctic offshore floating structures

    Energy Technology Data Exchange (ETDEWEB)

    Lubbad, Raed Khalil

    2011-01-15

    The present work highlights some aspects related to the analyses of Arctic offshore floating structures. This thesis consists of five papers, which can be divided into two main categories. One category deals with the dynamics of slender structures with an emphasis on the prediction and suppression of vortex induced vibrations (VIV), and the other category examines the process of interaction between sloping structures and sea ice with focus on developing a numerical model to simulate this process in real time. Slender structures, such as mooring lines and marine risers, are very important for the offshore petroleum industry, which is currently approaching deeper waters. Increasingly, attention has been focused on predicting the susceptibility of these structures to VIV. In this thesis, two asymptotic techniques namely, the local analysis and the WKB methods, were used to derive closed-form solutions for the natural frequencies and mode shapes of slender line-like structures. Both the top-tensioned nearly-vertical configuration and the catenary configuration were considered. The accuracy of the solutions derived was established through comparison with other analytic solution techniques and with results of numerical finite element solutions. The effects of the bending stiffness and the effects of approximating the tension variation as a linear function were discussed. Experimental data on the multi-modal in-line and cross-flow response behaviour of a towed catenary model were analysed to examine the usefulness of the solutions for predicting the response frequencies and envelopes due to VIV. Helical strakes are often used as a mitigating measure to suppress the VIV of slender structures. This thesis presented an innovative method to fit ropes helically to a riser in the installation phase. Such a procedure will help to overcome the handling problem associated with the use of conventional sharp-edged strakes. Experimental investigations were then performed to verify

  17. The main aspects of the Vivitron mechanical structure

    International Nuclear Information System (INIS)

    Gaudiot, G.; Koenig, R.; Esteve, T.; Peter, R.; Strebel, A.

    1989-05-01

    The main aspects of the Vivitron mechanical structure are discussed through a description of the tank and the internal structure. The results of the calculated constraints on the structure are presented

  18. Structures of Astromaterials Revealed by EBSD

    Science.gov (United States)

    Zolensky, M.

    2018-01-01

    Groups at the Johnson Space Center and the University of Tokyo have been using electron back-scattered diffraction (EBSD) to reveal the crystal structures of extraterrestrial minerals for many years. Even though we also routinely use transmission electron microscopy, synchrotron X-ray diffraction (SXRD), and conventional electron diffraction, we find that EBSD is the most powerful technique for crystal structure elucidation in many instances. In this talk I describe a few of the cases where we have found EBSD to provide crucial, unique information. See attachment.

  19. Structural aspects of high temperature superconductors

    International Nuclear Information System (INIS)

    Sequeira, A.

    1991-01-01

    This paper reports that the general structure of HTSC is known to be perovskite related involving layered stacking of perovskite and rock-salt like slabs with a specific sequence for a given type of structure. The prototype structures of various type of HTSC are now well established. Their detailed structural parameters are well documented. It is clear from that the number of oxygen atoms present in many of these structures is different from, and generally much less than, the number of anionic sites available. If the number of oxygens are in excess, they could of course occupy the interstitial sites. For example, in pure oxygen La 2 CuO 4+δ , the excess oxygen has been shown to go into interstitial sites. Although the prototypic structures of all HTSC are well established, their actual structures can have significant variations from the prototypes. In fact, their real structures are not yet fully known. Being nonstoichiometric, they are essentially metastable, entropy stabilized structures which exhibit wide compositional fluctuations and oxygen disorder effects. Their superconducting properties are known to be sensitive to their oxygen content and according to some theories the mechanism of superconductivity is presumably related to the oxygen defects or defectons. Neutron diffraction happens to be the method of choice for probing detailed structural features involving oxygen defects and associated distortions which are known to play a significant role on the properties of HTSC

  20. Structural integrity aspects of reactor safety

    Indian Academy of Sciences (India)

    A large experimental programme supported the structural integrity demonstration. ... Categories in which the structures, systems and components (SSC) are .... One of the ways in which the decision to live with the defect can be aided is the .... The Advanced Heavy Water Reactor (AHWR) (figure 18) being designed by BARC ...

  1. Structuring group medical practices: tax planning aspects.

    Science.gov (United States)

    Gassman, A S; Conetta, T F

    1992-01-01

    This article is the first in a series addressing the structuring of group medical practice entities, shareholder relationships, and general representation factors. In this article, a general background in federal tax planning is provided, including strategies for minimization of income tax payment and the potential problems that may be encountered when a group practice is not carefully structured.

  2. Concrete structures under impact loading: general aspects

    Directory of Open Access Journals (Sweden)

    Cornelia Baeră

    2016-09-01

    Full Text Available Dynamic loading conditions distress the structural integrity of a structure differently than the static ones. Such actions transfer high rate strains and instant energy waves to the structure, inducing the possibility of imminent collapse and casualties as a direct consequence. In the latest years, considering the dramatic increase of terrorist threats and global warming, the structural safety criteria imply more than ever the need to withstand this kind of loading (e.g., missiles and blast, projectiles, strong winds, tornados and earthquakes in addition to the static ones. The aim of this paper is to provide a general overview with regard to impact loading in terms of defining the phenomenon from physical and mechanical perspective, its complex local or global effect on the targeted structure, relevant material characteristics, main research approaches, namely theoretical studies and experimental procedures developed for improving the predictability of the dynamic loads and their effects. New directions in developing superior cementitious composites, with better characteristics in terms of dynamic loading performance are also emphasized.

  3. Molecular and structural aspects of oocyte maturation

    NARCIS (Netherlands)

    Hölzenspies, J.J.

    2009-01-01

    In the mammalian ovary, oocytes are contained within follicles, specialized structures that facilitate oocyte growth and development. During the reproductive cycle, several follicles are recruited into growth, and through a process of selection, one (human, cow) or several (mouse, pig) of these

  4. Structural aspects of the Chernobyl accident

    International Nuclear Information System (INIS)

    Murray, R.C.; Cummings, G.E.

    1988-01-01

    On April 26, 1986 the world's worst nuclear power plant accident occurred at the Unit 4 of the Chernobyl Nuclear Power Station in the USSR. This paper presents a discussion of the design of the Chernobyl Power Plant, the sequence of events that led to the accident and the damage caused by the resulting explosion. The structural design features that contributed to the accident and resulting damage will be highlighted. Photographs and sketches obtained from various worldwide news agencies will be shown to try and gain a perspective of the extent of the damage. The aftermath, clean-up, and current situation will be discussed and the important lessons learned for the structural engineer will be presented. 15 refs., 10 figs

  5. Towards aspect-oriented functional--structural plant modelling.

    Science.gov (United States)

    Cieslak, Mikolaj; Seleznyova, Alla N; Prusinkiewicz, Przemyslaw; Hanan, Jim

    2011-10-01

    Functional-structural plant models (FSPMs) are used to integrate knowledge and test hypotheses of plant behaviour, and to aid in the development of decision support systems. A significant amount of effort is being put into providing a sound methodology for building them. Standard techniques, such as procedural or object-oriented programming, are not suited for clearly separating aspects of plant function that criss-cross between different components of plant structure, which makes it difficult to reuse and share their implementations. The aim of this paper is to present an aspect-oriented programming approach that helps to overcome this difficulty. The L-system-based plant modelling language L+C was used to develop an aspect-oriented approach to plant modelling based on multi-modules. Each element of the plant structure was represented by a sequence of L-system modules (rather than a single module), with each module representing an aspect of the element's function. Separate sets of productions were used for modelling each aspect, with context-sensitive rules facilitated by local lists of modules to consider/ignore. Aspect weaving or communication between aspects was made possible through the use of pseudo-L-systems, where the strict-predecessor of a production rule was specified as a multi-module. The new approach was used to integrate previously modelled aspects of carbon dynamics, apical dominance and biomechanics with a model of a developing kiwifruit shoot. These aspects were specified independently and their implementation was based on source code provided by the original authors without major changes. This new aspect-oriented approach to plant modelling is well suited for studying complex phenomena in plant science, because it can be used to integrate separate models of individual aspects of plant development and function, both previously constructed and new, into clearly organized, comprehensive FSPMs. In a future work, this approach could be further

  6. ASPECTS REGARDING THE STRUCTURE OF GRADUATION PAPERS IN INDUSTRIAL DESIGN

    Directory of Open Access Journals (Sweden)

    BOLOŞ Codruţa

    2008-07-01

    Full Text Available The paper presents aspects regarding the structure, themes and content of graduation papers in the specialization of Industrial Design within Petru Maior University of Târgu Mures.

  7. Towards aspect-oriented functional–structural plant modelling

    Science.gov (United States)

    Cieslak, Mikolaj; Seleznyova, Alla N.; Prusinkiewicz, Przemyslaw; Hanan, Jim

    2011-01-01

    Background and Aims Functional–structural plant models (FSPMs) are used to integrate knowledge and test hypotheses of plant behaviour, and to aid in the development of decision support systems. A significant amount of effort is being put into providing a sound methodology for building them. Standard techniques, such as procedural or object-oriented programming, are not suited for clearly separating aspects of plant function that criss-cross between different components of plant structure, which makes it difficult to reuse and share their implementations. The aim of this paper is to present an aspect-oriented programming approach that helps to overcome this difficulty. Methods The L-system-based plant modelling language L+C was used to develop an aspect-oriented approach to plant modelling based on multi-modules. Each element of the plant structure was represented by a sequence of L-system modules (rather than a single module), with each module representing an aspect of the element's function. Separate sets of productions were used for modelling each aspect, with context-sensitive rules facilitated by local lists of modules to consider/ignore. Aspect weaving or communication between aspects was made possible through the use of pseudo-L-systems, where the strict-predecessor of a production rule was specified as a multi-module. Key Results The new approach was used to integrate previously modelled aspects of carbon dynamics, apical dominance and biomechanics with a model of a developing kiwifruit shoot. These aspects were specified independently and their implementation was based on source code provided by the original authors without major changes. Conclusions This new aspect-oriented approach to plant modelling is well suited for studying complex phenomena in plant science, because it can be used to integrate separate models of individual aspects of plant development and function, both previously constructed and new, into clearly organized, comprehensive FSPMs. In

  8. Fragile yet Ductile : Structural Aspects of Reinforced Glass Beams

    NARCIS (Netherlands)

    Louter, P.C.

    2011-01-01

    This dissertation investigates the structural aspects of reinforced glass beams. The concept of these beams, which are intended for building applications, is to provide redundancy even if the glass is broken. This redundancy is obtained through a small reinforcement section that is bonded at the

  9. Course 12: Proteins: Structural, Thermodynamic and Kinetic Aspects

    Science.gov (United States)

    Finkelstein, A. V.

    1 Introduction 2 Overview of protein architectures and discussion of physical background of their natural selection 2.1 Protein structures 2.2 Physical selection of protein structures 3 Thermodynamic aspects of protein folding 3.1 Reversible denaturation of protein structures 3.2 What do denatured proteins look like? 3.3 Why denaturation of a globular protein is the first-order phase transition 3.4 "Gap" in energy spectrum: The main characteristic that distinguishes protein chains from random polymers 4 Kinetic aspects of protein folding 4.1 Protein folding in vivo 4.2 Protein folding in vitro (in the test-tube) 4.3 Theory of protein folding rates and solution of the Levinthal paradox

  10. STRUCTURED MOLECULAR GAS REVEALS GALACTIC SPIRAL ARMS

    Energy Technology Data Exchange (ETDEWEB)

    Sawada, Tsuyoshi [Joint ALMA Office, Alonso de Cordova 3107, Vitacura, Santiago 763-0355 (Chile); Hasegawa, Tetsuo [NAOJ Chile Observatory, Joaquin Montero 3000 Oficina 702, Vitacura, Santiago 763-0409 (Chile); Koda, Jin, E-mail: sawada.tsuyoshi@nao.ac.jp [Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800 (United States)

    2012-11-01

    We explore the development of structures in molecular gas in the Milky Way by applying the analysis of the brightness distribution function and the brightness distribution index (BDI) in the archival data from the Boston University-Five College Radio Astronomy Observatory {sup 13}CO J = 1-0 Galactic Ring Survey. The BDI measures the fractional contribution of spatially confined bright molecular emission over faint emission extended over large areas. This relative quantity is largely independent of the amount of molecular gas and of any conventional, pre-conceived structures, such as cores, clumps, or giant molecular clouds. The structured molecular gas traced by higher BDI is located continuously along the spiral arms in the Milky Way in the longitude-velocity diagram. This clearly indicates that molecular gas changes its structure as it flows through the spiral arms. Although the high-BDI gas generally coincides with H II regions, there is also some high-BDI gas with no/little signature of ongoing star formation. These results support a possible evolutionary sequence in which unstructured, diffuse gas transforms itself into a structured state on encountering the spiral arms, followed by star formation and an eventual return to the unstructured state after the spiral arm passage.

  11. Structural analysis of a ship on global aspect using ANSYS

    Science.gov (United States)

    Rahman, M. Muzibur; Kamol, Rajia Sultana; Islam, Reyana

    2017-12-01

    Ship is a complex geometry which undergoes a combination of loadings such as hydrostatic, hydrodynamic, wind, wave etc. at sea and thus adequate strength in a ship has always been one of the most challenging tasks for the ship designers. International Maritime Organization (IMO) and classification societies are providing the standards to ensure the adequacy of strength for the ship against all demands throughout its service life. Thus, structural analysis is needed to assess the overall strength of hull, and the means in this regard are based on finite element method which may be applied either local or global aspect of the ship. This paper is an attempt to carry out the structural analysis of a ship in global aspect using ANSYS software to locate the most stress concentration and deformed area, which will have ultimate effect on fatigue fracture.

  12. Structural and chemical aspects of HPMA copolymers as drug carriers.

    Science.gov (United States)

    Ulbrich, Karel; Subr, Vladimír

    2010-02-17

    Synthetic strategies and chemical and structural aspects of the synthesis of HPMA copolymer conjugates with various drugs and other biologically active molecules are described and discussed in this chapter. The discussion is held from the viewpoint of design and structure of the polymer backbone and biodegradable spacer between a polymer and drug, structure and methods of attachment of the employed drugs to the carrier and structure and methods of conjugation with targeting moieties. Physicochemical properties of the water-soluble polymer-drug conjugates and polymer micelles including mechanisms of drug release are also discussed. Detailed description of biological behavior of the polymer-drug conjugates as well as application of the copolymers for surface modification and targeting of gene delivery vectors are not included, they are presented and discussed in separate chapters of this issue. Copyright 2009 Elsevier B.V. All rights reserved.

  13. Three-Dimensional Structural Aspects of Protein–Polysaccharide Interactions

    Directory of Open Access Journals (Sweden)

    Masamichi Nagae

    2014-03-01

    Full Text Available Linear polysaccharides are typically composed of repeating mono- or disaccharide units and are ubiquitous among living organisms. Polysaccharide diversity arises from chain-length variation, branching, and additional modifications. Structural diversity is associated with various physiological functions, which are often regulated by cognate polysaccharide-binding proteins. Proteins that interact with linear polysaccharides have been identified or developed, such as galectins and polysaccharide-specific antibodies, respectively. Currently, data is accumulating on the three-dimensional structure of polysaccharide-binding proteins. These proteins are classified into two types: exo-type and endo-type. The former group specifically interacts with the terminal units of polysaccharides, whereas the latter with internal units. In this review, we describe the structural aspects of exo-type and endo-type protein-polysaccharide interactions. Further, we discuss the structural basis for affinity and specificity enhancement in the face of inherently weak binding interactions.

  14. High aspect ratio titanium nitride trench structures as plasmonic biosensor

    DEFF Research Database (Denmark)

    Shkondin, Evgeniy; Repän, Taavi; Takayama, Osamu

    2017-01-01

    High aspect ratio titanium nitride (TiN) grating structures are fabricated by the combination of deep reactive ion etching (DRIE) and atomic layer deposition (ALD) techniques. TiN is deposited at 500 ◦C on a silicon trench template. Silicon between vertical TiN layers is selectively etched...... to fabricate the high aspect ratio TiN trenches with the pitch of 400 nm and height of around 2.7 µm. Dielectric functions of TiN films with different thicknesses of 18 - 105 nm and post-annealing temperatures of 700 - 900 ◦C are characterized by an ellipsometer. We found that the highest annealing temperature...... of 900 ◦C gives the most pronounced plasmonic behavior with the highest plasma frequency, ωp = 2.53 eV (λp = 490 nm). Such high aspect ratio trench structures function as a plasmonic grating sensor that supports the Rayleigh-Woods anomalies (RWAs), enabling the measurement of changes in the refractive...

  15. Selected Aspects of Computer Modeling of Reinforced Concrete Structures

    Directory of Open Access Journals (Sweden)

    Szczecina M.

    2016-03-01

    Full Text Available The paper presents some important aspects concerning material constants of concrete and stages of modeling of reinforced concrete structures. The problems taken into account are: a choice of proper material model for concrete, establishing of compressive and tensile behavior of concrete and establishing the values of dilation angle, fracture energy and relaxation time for concrete. Proper values of material constants are fixed in simple compression and tension tests. The effectiveness and correctness of applied model is checked on the example of reinforced concrete frame corners under opening bending moment. Calculations are performed in Abaqus software using Concrete Damaged Plasticity model of concrete.

  16. Power system damping - Structural aspects of controlling active power

    Energy Technology Data Exchange (ETDEWEB)

    Samuelsson, O.

    1997-04-01

    Environmental and economical aspects make it difficult to build new power lines and to reinforce existing ones. The continued growth in demand for electric power must therefore to a great extent be met by increased loading of available lines. A consequence is that power system damping is reduced, leading to a risk of poorly damped power oscillations between the generators. This thesis proposes the use of controlled active loads to increase damping of such electro-mechanical oscillations. The focus is on structural aspects of controller interaction and of sensor and actuator placement. On-off control based on machine frequency in a single machine infinite bus system is analysed using energy function analysis and phase plane plots. An on-off controller with estimated machine frequency as input has been implemented. At a field test it damped oscillations of a 0.9 MW hydro power generator by controlling a 20kW load. The linear analysis uses two power system models with three and twenty-three machines respectively. Each damper has active power as output and local bus frequency or machine frequency as input. The power system simulator EUROSTAG is used both for generation of the linearized models and for time simulations. Measures of active power mode controllability and phase angle mode observability are obtained from the eigenvectors of the differential-algebraic models. The geographical variation in the network of these quantities is illustrated using the resemblance to bending modes of flexible mechanical structures. Eigenvalue sensitivities are used to determine suitable damper locations. A spring-mass equivalent to an inter-area mode provides analytical expressions, that together with the concept of impedance matching explain the structural behaviour of the power systems. For large gains this is investigated using root locus plots. 64 refs, 99 figs, 20 tabs

  17. DNA markers reveal genetic structure and localized diversity of ...

    African Journals Online (AJOL)

    uqhdesma

    2016-10-12

    Oct 12, 2016 ... STRUCTURE analysis revealed 4 clusters of genetically ..... 10000 cycles and 50000 Markov Chain Monte Carlo (MCMC) iterations and 10 replicate runs performed for each K value to ..... WL, Lee M, Porter K (2000). Genetic ...

  18. KEY ASPECTS OF ENSURING ENERGY EFFICIENCY OF BUILDINGS AND STRUCTURES

    Directory of Open Access Journals (Sweden)

    S.G. Abramyan

    2017-06-01

    Full Text Available The paper is based on the review of the foreign and national academic literature and intended to emphasize the issues of ensuring energy efficiency of buildings and structures applicable to all the countries as for reconstruction of existing buildings as for erection of new ones . The author highlights the key aspects of the provision of energy efficiency of buildings and structures in some foreign countries. The conclusion is made that the studies are mainly aimed at discovering new heat insulation materials, whereby polystyrene insulation is found to be the most widespread wall insulation material in a number of countries. At the same time, it is observed that the ongoing research is focused on solutions to optimize the structure of walling systems in terms of both insulant thickness and the number and sequence of insulation layers in the walling structure. A conclusion is made that hyper insulation of external walls leads to considerable expenses arising due to cooling during the summer season. The use of prefabricated vacuum panels as a heat insulation layer and off-the-shelf single-layer structures, subject to their heat insulation characteristics, appears a more constructive way to meet the energy efficiency requirements, as the arrangement of ideal air space in multilayered walls proves a significant challenge today. One of the most promising ways to ensure energy efficiency is the use of multifunctional polyvalent walls and provision of polyvalent heat supply from renewable energy sources. Since energy efficiency depends on the spatial arrangement of buildings, construction must ensure a minimum ratio of the area of enclosing structures to the overall building volume (by adding on new facilities in case of reconstruction. It is noted that a systemic approach to ensuring energy efficiency of buildings is impossible without proper regard to the environmental parameters of heat insulation materials.

  19. Structural Reliability Aspects in Design of Wind Turbines

    DEFF Research Database (Denmark)

    Sørensen, John Dalsgaard

    2007-01-01

    Reliability assessment, optimal design and optimal operation and maintenance of wind turbines are an area of significant interest for the fast growing wind turbine industry for sustainable production of energy. Offshore wind turbines in wind farms give special problems due to wake effects inside...... the farm. Reliability analysis and optimization of wind turbines require that the special conditions for wind turbine operation are taken into account. Control of the blades implies load reductions for large wind speeds and parking for high wind speeds. In this paper basic structural failure modes for wind...... turbines are described. Further, aspects are presented related to reliability-based optimization of wind turbines, assessment of optimal reliability level and operation and maintenance....

  20. Structural aspects of Lorentz-violating quantum field theory

    Science.gov (United States)

    Cambiaso, M.; Lehnert, R.; Potting, R.

    2018-01-01

    In the last couple of decades the Standard Model Extension has emerged as a fruitful framework to analyze the empirical and theoretical extent of the validity of cornerstones of modern particle physics, namely, of Special Relativity and of the discrete symmetries C, P and T (or some combinations of these). The Standard Model Extension allows to contrast high-precision experimental tests with posited alterations representing minute Lorentz and/or CPT violations. To date no violation of these symmetry principles has been observed in experiments, mostly prompted by the Standard-Model Extension. From the latter, bounds on the extent of departures from Lorentz and CPT symmetries can be obtained with ever increasing accuracy. These analyses have been mostly focused on tree-level processes. In this presentation I would like to comment on structural aspects of perturbative Lorentz violating quantum field theory. I will show that some insight coming from radiative corrections demands a careful reassessment of perturbation theory. Specifically I will argue that both the standard renormalization procedure as well as the Lehmann-Symanzik-Zimmermann reduction formalism need to be adapted given that the asymptotic single-particle states can receive quantum corrections from Lorentz-violating operators that are not present in the original Lagrangian.

  1. Structure defects in malachite revealed by positron annihilation

    International Nuclear Information System (INIS)

    Geffroy, B.; Diallo, I.; Paulin, R.

    1984-01-01

    Positron lifetime is measured between 77 and 400 K in two malachite samples with different mineralogical structures. The complex spectrum found in zoned malachite reveals a microporosity which remains stable in this range of temperature. Besides, above 200 K, equilibrium defects appear. Their formation energy is estimated to be Esub(f) = 0.27 +- 0.02 eV [fr

  2. Structure defects in malachite revealed by positron annihilation

    Energy Technology Data Exchange (ETDEWEB)

    Geffroy, B; Diallo, I; Paulin, R [Institut National des Sciences et Techniques Nucleaires, CEN/Saclay, 91 - Gif-sur-Yvette (France)

    1984-01-01

    Positron lifetime is measured between 77 and 400 K in two malachite samples with different mineralogical structures. The complex spectrum found in zoned malachite reveals a microporosity which remains stable in this range of temperature. Besides, above 200 K, equilibrium defects appear. Their formation energy is estimated to be Esub(f) = 0.27 +- 0.02 eV.

  3. COGNITIVE STRUCTURING OF TEXT COMPREHENSION PROCESS IN THE ASPECT OF MICROLINGUISTICS

    Directory of Open Access Journals (Sweden)

    Kolodina Nina Ivanovna

    2014-09-01

    Full Text Available The theory of mnemo-units of knowledge in the aspect of microliguistics is deliberated in the article. Mnemo-unit of knowledge is considered to be a unit of knowledge in the operative memory, which cannot be verbalized but can be explained. The singling out such units, on the one hand, gives the opportunity to construct the structural scheme of comprehension process, and, on the other hand, to justify the theory of comprehension process as the process of operating with tiny recognized and unrecognized units which have schematic or contour fixation in the human's memory. The process of text comprehension is analyzed and compared with the process of making saccades. Given examples about the eyesight fixation on the words picked out on the line allow to speak about the fixation of attention only on these words. The summing up of such theоretic and practical data leads to the opportunity to base the theory of mnemo-units of knowledge in the aspect of microlinguistics. The comprehension process demands supporting the steady connections between the mnemo-units of knowledge. In their turn, the steady connections between the mnemo-units of knowledge, which are necessary for production of thinking forms, are insured by constant activization of the same units at the same sequence. Constant and sequent activization of the same units of knowledge leads to the human thinking process stereotyping. The cognitive model of structural thinking process is built in the article. The analysis of received data on stereotyped comprehension process allows to reveal the fact that the activization of one mnemo-units group demands the activization of another mnemo-units group. Activated mnemo-units groups determine the psychological structure of personality. In this aspect the motivation and the behavior are the necessary steps in the cognitive model of structural comprehension process while the psychological structure is considered.

  4. Mathematical aspects of Rietveld refinement and crystal structure ...

    Indian Academy of Sciences (India)

    Administrator

    The core mathematics, goodness-of-fit parameters of Rietveld refinement technique is introduced for structural ... transducers in medical and solar applications (Obmann ..... Prince 1985 in Structure and statistics in crystallography (ed.).

  5. Structural and computational aspects of simple and influence games

    OpenAIRE

    Riquelme Csori, Fabián

    2014-01-01

    Simple games are a fundamental class of cooperative games. They have a huge relevance in several areas of computer science, social sciences and discrete applied mathematics. The algorithmic and computational complexity aspects of simple games have been gaining notoriety in the recent years. In this thesis we review different computational problems related to properties, parameters, and solution concepts of simple games. We consider different forms of representation of simple games, regular...

  6. Generic structural mechanics aspects of fusion magnet systems

    International Nuclear Information System (INIS)

    Reich, M.; Powell, J.R.

    1980-01-01

    Structural mechanic requirements for future large superconducting fusion magnets are assessed. Current structural analysis methods and standards do not yet appear sufficient for a complete evaluation of such systems, under all potential operating and accident conditions. Recommendations are made for development of needed structural methods and specialized standards for fusion magnets. These include, among others, better composite structural methods with various failure criteria for metallic, as well as non-metallic materials, coupled thermal-electrical-structural codes, incorporating winding and fabrication effects, and use of probabilistic methods for life prediction. In order to help meet program goals for fusion commericialization, it is recommended that such work be initiated relatively soon. (orig.)

  7. Revealing the hidden structural phases of FeRh

    Science.gov (United States)

    Kim, Jinwoong; Ramesh, R.; Kioussis, Nicholas

    2016-11-01

    Ab initio electronic structure calculations reveal that tetragonal distortion has a dramatic effect on the relative stability of the various magnetic structures (C-, A-, G-, A'-AFM, and FM) of FeRh giving rise to a wide range of novel stable/metastable structures and magnetic phase transitions between these states. We predict that the cubic G-AFM structure, which was believed thus far to be the ground state, is metastable and that the tetragonally expanded G-AFM is the stable structure. The low energy barrier separating these states suggests phase coexistence at room temperature. We propose an A'-AFM phase to be the global ground state among all magnetic phases which arises from the strain-induced tuning of the exchange interactions. The results elucidate the underlying mechanism for the recent experimental findings of electric-field control of magnetic phase transition driven via tetragonal strain. The magnetic phase transitions open interesting prospects for exploiting strain engineering for the next-generation memory devices.

  8. Some Fundamental Aspects of Mechanics of Nano composite Materials and Structural Members

    International Nuclear Information System (INIS)

    Guz, A.N.; Rushchitsky, J.J.

    2013-01-01

    This paper is devoted to formulation and analysis of fundamental aspects of mechanics of nano composite materials and structural members. These aspects most likely do not exhaust all of the possible fundamental characteristics of mechanics of nano composite materials and structural members, but, nevertheless, they permit to form the skeleton of direction of mechanics in hand. The proposed nine aspects are described and commented briefly.

  9. The Acceptance of Universalism: The Importance of Selected Aspects of School Structure.

    Science.gov (United States)

    Martin, Robert A.

    This report describes a study that investigated empirically the relationships between selected aspects of the organizational structure of elementary schools and the extent to which students endorsed the norm of universalism. Four aspects of structure were studied: degree of departmentalization, school enrollment, student-teacher ratio, and extent…

  10. Diffusion Tensor Tractography Reveals Disrupted Structural Connectivity during Brain Aging

    Science.gov (United States)

    Lin, Lan; Tian, Miao; Wang, Qi; Wu, Shuicai

    2017-10-01

    Brain aging is one of the most crucial biological processes that entail many physical, biological, chemical, and psychological changes, and also a major risk factor for most common neurodegenerative diseases. To improve the quality of life for the elderly, it is important to understand how the brain is changed during the normal aging process. We compared diffusion tensor imaging (DTI)-based brain networks in a cohort of 75 healthy old subjects by using graph theory metrics to describe the anatomical networks and connectivity patterns, and network-based statistic (NBS) analysis was used to identify pairs of regions with altered structural connectivity. The NBS analysis revealed a significant network comprising nine distinct fiber bundles linking 10 different brain regions showed altered white matter structures in young-old group compare with middle-aged group (p < .05, family-wise error-corrected). Our results might guide future studies and help to gain a better understanding of brain aging.

  11. Some aspects of the interaction between systems- and structural reliability

    International Nuclear Information System (INIS)

    Schueller, G.K.; Schmitt, W.

    1979-01-01

    The purpose of this paper is to study the interaction between systems- and structural reliability analysis with reference to the design of structural components of LWR. Presently the evaluation of systems reliability is carried out apart from structural reliability analysis. Moreover, two basically different methodologies are used for analysis. While in systems analysis the simplified binary approach is still generally accepted, in structural reliability one has to resort to more sophisticated procedures to obtain realistic results. The interactive effect may be illustrated as follows: For example, the integrity of the primary circuit interacts with the integrity of the containment structure. This means that the probability of occurrence of the pipe rupture which may cause a LOCA and consequently leads to a build-up of temperature and pressure within the containment affects directly its structural reliability. The piping system, particularly the primary piping, in turn interacts with the protective system, which is part of the safety system. This piping structure is also subjected to various operational loading conditions. In a numerical example dealing with leakage probabilities of pipes it is shown how methods of structural reliability may be used to gain more insight in the estimation of failure rates of system components. (orig.)

  12. The study of fkbp and ubiquitin reveals interesting aspects of Artemia stress history.

    Science.gov (United States)

    Maniatsi, Stefania; Farmaki, Theodora; Abatzopoulos, Theodore J

    2015-08-01

    Research on stress responses in animals has increased greatly during the last decades. Though most studies focus on the cellular and molecular bases of the stress response mechanisms, the ecological and evolutionary aspects of stress responses gain more and more interest. Here, we use species and parthenogenetic strains of the genus Artemia, an extremophile model organism, to study, for the first time, a protein well known for its chaperone activity and its involvement in stress responses. More specifically, transcription and protein accumulation of an FK506-Binding Protein (FKBP) homologue were investigated under heat and salt stresses. Additionally, the mRNA levels of ubiquitin, a heat-inducible protein related to the proteasomal pathway, were quantitated under these conditions. Biochemical and phylogenetic analyses showed that the studied FKBP orthologue is a typical representative of the family that clusters with other crustacean sequences. The expression was increased in both fkbp and ubiquitin genes after salt and heat stresses. However, our results in combination with the fact that Artemia species and parthenogenetic strains, selected for this study, exhibit different heat or salt tolerance provide useful hints about the evolutionary significance of FKBP and ubiquitin. Regarding FKBP, mRNA expression and protein accumulation seem to depend on the environmental conditions and the evolutionary history of each Artemia population while ubiquitin has a clear and more conserved role under heat shock. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Nicotinamide riboside kinase structures reveal new pathways to NAD+.

    Directory of Open Access Journals (Sweden)

    Wolfram Tempel

    2007-10-01

    Full Text Available The eukaryotic nicotinamide riboside kinase (Nrk pathway, which is induced in response to nerve damage and promotes replicative life span in yeast, converts nicotinamide riboside to nicotinamide adenine dinucleotide (NAD+ by phosphorylation and adenylylation. Crystal structures of human Nrk1 bound to nucleoside and nucleotide substrates and products revealed an enzyme structurally similar to Rossmann fold metabolite kinases and allowed the identification of active site residues, which were shown to be essential for human Nrk1 and Nrk2 activity in vivo. Although the structures account for the 500-fold discrimination between nicotinamide riboside and pyrimidine nucleosides, no enzyme feature was identified to recognize the distinctive carboxamide group of nicotinamide riboside. Indeed, nicotinic acid riboside is a specific substrate of human Nrk enzymes and is utilized in yeast in a novel biosynthetic pathway that depends on Nrk and NAD+ synthetase. Additionally, nicotinic acid riboside is utilized in vivo by Urh1, Pnp1, and Preiss-Handler salvage. Thus, crystal structures of Nrk1 led to the identification of new pathways to NAD+.

  14. Towards revealing the structure of bacterial inclusion bodies.

    Science.gov (United States)

    Wang, Lei

    2009-01-01

    Protein aggregation is a widely observed phenomenon in human diseases, biopharmaceutical production, and biological research. Protein aggregates are generally classified as highly ordered, such as amyloid fibrils, or amorphous, such as bacterial inclusion bodies. Amyloid fibrils are elongated filaments with diameters of 6-12 nm, they are comprised of residue-specific cross-beta structure, and display characteristic properties, such as binding with amyloid-specific dyes. Amyloid fibrils are associated with dozens of human pathological conditions, including Alzheimer disease and prion diseases. Distinguished from amyloid fibrils, bacterial inclusion bodies display apparent amorphous morphology. Inclusion bodies are formed during high-level recombinant protein production, and formation of inclusion bodies is a major concern in biotechnology. Despite of the distinctive morphological difference, bacterial inclusion bodies have been found to have some amyloid-like properties, suggesting that they might contain structures similar to amyloid-like fibrils. Recent structural data further support this hypothesis, and this review summarizes the latest progress towards revealing the structural details of bacterial inclusion bodies.

  15. Quantal and dissipative aspects in nuclear structure and dynamics

    International Nuclear Information System (INIS)

    Lacroix, Denis

    1999-01-01

    This work is devoted to the description of both quantal and statistical aspects in a coherent theoretical framework that goes beyond a mean-field approximation. It is shown that among the possible methods, the Extended mean-field theory (ETDHF) is able to describe relaxation by including correlation effects. This theory is first applied to cold and hot giant resonances. After having developed a extended version of the linear response theory the effect of collisions on the response of 40 Ca is studied. It is shown that collisions contribute to the spreading width of giant resonances and become a dominant decay channel at high temperature. The generalization of these methods through the modelization of the Hamiltonian as a series of couplings in cascade has enabled to go beyond ETDHF. Thus, phenomena as multi-scale Ericson fluctuations and interferences in the nuclear response are predicted. The study of larger amplitudes requires the introduction of transport theories for the nuclear dynamics. Thus the deexcitation of hot and compressed nuclei has been studied with mean-field theories. This analysis has clarified the link between the equation of state and the dynamical expansion in finite Systems. A comparison with semi-classical has further shown the importance of quantum effects and has demonstrated the necessity to take into account nucleon collisions in a quantum framework. The possibility to apply ETDHF to nuclear dynamics in the general case is then discussed. A rapid and reliable method, tested on a schematic model is proposed to solve the extended mean-field. The application of ETDHF to the monopolar expansion of 16 O has finally demonstrated the interesting perspectives of this theory for describing dissipative aspects in quantum dynamics. Finally, the introduction of quantum stochastic approaches is discussed. (author) [fr

  16. Important aspects of Eastern Mediterranean large-scale variability revealed from data of three fixed observatories

    Science.gov (United States)

    Bensi, Manuel; Velaoras, Dimitris; Cardin, Vanessa; Perivoliotis, Leonidas; Pethiakis, George

    2015-04-01

    Long-term variations of temperature and salinity observed in the Adriatic and Aegean Seas seem to be regulated by larger-scale circulation modes of the Eastern Mediterranean (EMed) Sea, such as the recently discovered feedback mechanisms, namely the BiOS (Bimodal Oscillating System) and the internal thermohaline pump theories. These theories are the results of interpretation of many years' observations, highlighting possible interactions between two key regions of the EMed. Although repeated oceanographic cruises carried out in the past or planned for the future are a very useful tool for understanding the interaction between the two basins (e.g. alternating dense water formation, salt ingressions), recent long time-series of high frequency (up to 1h) sampling have added valuable information to the interpretation of internal mechanisms for both areas (i.e. mesoscale eddies, evolution of fast internal processes, etc.). During the last 10 years, three deep observatories were deployed and maintained in the Adriatic, Ionian, and Aegean Seas: they are respectively, the E2-M3A, the Pylos, and the E1-M3A. All are part of the largest European network of Fixed Point Open Ocean Observatories (FixO3, http://www.fixo3.eu/). Herein, from the analysis of temperature and salinity, and potential density time series collected at the three sites from the surface down to the intermediate and deep layers, we will discuss the almost perfect anti-correlated behavior between the Adriatic and the Aegean Seas. Our data, collected almost continuously since 2006, reveal that these observatories well represent the thermohaline variability of their own areas. Interestingly, temperature and salinity in the intermediate layer suddenly increased in the South Adriatic from the end of 2011, exactly when they started decreasing in the Aegean Sea. Moreover, Pylos data used together with additional ones (e.g. Absolute dynamic topography, temperature and salinity data from other platforms) collected

  17. Wetland Microtopographic Structure is Revealed with Terrestrial Laser Scanning

    Science.gov (United States)

    Diamond, J.; Stovall, A. E.; Mclaughlin, D. L.; Slesak, R.

    2017-12-01

    Wetland microtopographic structure and its function has been the subject of research for decades, and several investigations suggest that microtopography is generated by autogenic ecohydrologic processes. But due to the difficulty of capturing the true spatial variability of wetland microtopography, many of the hypotheses for self-organization have remained elusive to test. We employ a novel method of Terrestrial Laser Scanning (TLS) that reveals an unprecedented high-resolution (structure of wetland microtopography in 10 black ash (Fraxinus nigra) stands of northern Minnesota, USA. Here we present the first efforts to synthesize this information and show that TLS provides a good representation of real microtopographic structure, where TLS accurately measured hummock height, but occlusion of low points led to a slight negative bias. We further show that TLS can accurately locate microtopographic high points (hummocks), as well as estimate their height and area. Using these new data, we estimate distributions in both microtopographic elevation and hummock area in each wetland and relate these to monitored hydrologic regime; in doing so, we test hypotheses linking emergent microtopographic patterns to putative hydrologic controls. Finally, we discuss future efforts to enumerate consequent influences of microtopography on wetland systems (soil properties and vegetation composition).

  18. New Aspects of Photocurrent Generation at Graphene pn Junctions Revealed by Ultrafast Optical Measurements

    Science.gov (United States)

    Aivazian, Grant; Sun, Dong; Jones, Aaron; Ross, Jason; Yao, Wang; Cobden, David; Xu, Xiaodong

    2012-02-01

    The remarkable electrical and optical properties of graphene make it a promising material for new optoelectronic applications. However, one important, but so far unexplored, property is the role of hot carriers in charge and energy transport at graphene interfaces. Here we investigate the photocurrent (PC) dynamics at a tunable graphene pn junction using ultrafast scanning PC microscopy. Pump-probe measurements show a temperature dependent relaxation time of photogenerated carriers that increases from 1.5ps at 290K to 4ps at 20K; while the amplitude of the PC is independent of the lattice temperature. These observations imply that it is hot carriers, not phonons, which dominate ultrafast energy transport. Gate dependent measurements show many interesting features such as pump induced saturation, enhancement, and sign reversal of probe generated PC. These observations reveal that the underlying PC mechanism is a combination of the thermoelectric and built-in electric field effects. Our results enhance the understanding of non-equilibrium electron dynamics, electron-electron interactions, and electron-phonon interactions in graphene. They also determine fundamental limits on ultrafast device operation speeds (˜500 GHz) for graphene-based photodetectors.

  19. Changes in cecal microbiota and mucosal gene expression revealed new aspects of epizootic rabbit enteropathy.

    Directory of Open Access Journals (Sweden)

    Christine Bäuerl

    Full Text Available Epizootic Rabbit Enteropathy (ERE is a severe disease of unknown aetiology that mainly affects post-weaning animals. Its incidence can be prevented by antibiotic treatment suggesting that bacterial elements are crucial for the development of the disease. Microbial dynamics and host responses during the disease were studied. Cecal microbiota was characterized in three rabbit groups (ERE-affected, healthy and healthy pretreated with antibiotics, followed by transcriptional analysis of cytokines and mucins in the cecal mucosa and vermix by q-rtPCR. In healthy animals, cecal microbiota with or without antibiotic pretreatment was very similar and dominated by Alistipes and Ruminococcus. Proportions of both genera decreased in ERE rabbits whereas Bacteroides, Akkermansia and Rikenella increased, as well as Clostridium, γ-Proteobacteria and other opportunistic and pathogenic species. The ERE group displayed remarkable dysbiosis and reduced taxonomic diversity. Transcription rate of mucins and inflammatory cytokines was very high in ERE rabbits, except IL-2, and its analysis revealed the existence of two clearly different gene expression patterns corresponding to Inflammatory and (mucin Secretory Profiles. Furthermore, these profiles were associated to different bacterial species, suggesting that they may correspond to different stages of the disease. Other data obtained in this work reinforced the notion that ERE morbidity and mortality is possibly caused by an overgrowth of different pathogens in the gut of animals whose immune defence mechanisms seem not to be adequately responding.

  20. Basic materials and structures aspects for hypersonic transport vehicles (HTV)

    Science.gov (United States)

    Steinheil, E.; Uhse, W.

    A Mach 5 transport design is used to illustrate structural concepts and criteria for materials selections and also key technologies that must be followed in the areas of computational methods, materials and construction methods. Aside from the primary criteria of low weight, low costs, and conceivable risks, a number of additional requirements must be met, including stiffness and strength, corrosion resistance, durability, and a construction adequate for inspection, maintenance and repair. Current aircraft construction requirements are significantly extended for hypersonic vehicles. Additional consideration is given to long-duration temperature resistance of the airframe structure, the integration of large-volume cryogenic fuel tanks, computational tools, structural design, polymer matrix composites, and advanced manufacturing technologies.

  1. Nonlinear aspects of structural fatigue damage assessment and accumulation

    International Nuclear Information System (INIS)

    Leis, B.N.

    1977-01-01

    The present paper reviews a recently developed concept for structural fatigue analysis which is capable of accounting for nonlinearities in both the above noted transformations. It is shown that, for cases where the local stressing and straining is proportional, the multiplicity of initiation sites and mechanisms observed to dominate structural fatigue resistance can be explained in terms of these additional nonlinearities. The ability of current concepts for structural fatigue analysis which account for nonlinear action to handle situaions where nonproportional stressing occurs in fatigue critical locations is next examined. Limitations in the assumptions made in fatigue analysis are shown to essentially preclude the application of present technology to that class of problems. A new approach whereby the present fatigue analysis procedures based on a deformation-type plasticity analysis can be extended to handle the nonproportional cycling by their application on a 'memory event' by 'memory event' basis is postulated and discussed in the context of a simple component

  2. Structural aspects of coaxial oxy-fuel flames

    Science.gov (United States)

    Ditaranto, M.; Sautet, J. C.; Samaniego, J. M.

    Oxy-fuel combustion has been proven to increase thermal efficiency and to have a potential for NOx emission reduction. The study of 25-kW turbulent diffusion flames of natural gas with pure oxygen is undertaken on a coaxial burner with quarl. The structural properties are analysed by imaging the instantaneous reaction zone by OH* chemiluminescence and measuring scalar and velocity profiles. The interaction between the flame front and the shear layers present in the coaxial jets depends on the momentum ratio which dictates the turbulent structure development. Flame length and NOx emission sensitivity to air leaks in the combustion chamber are also investigated.

  3. Nuclear-structure aspects of theoretical neutron physics

    International Nuclear Information System (INIS)

    Soloviev, V.G.

    1976-01-01

    The structure of neutron resonances is studied on the basis of the semimicroscopic nuclear theory. Few-quasiparticle components of the wave functions of neutron resonances are calculated which determine the neutron and radiational strength functions. It is stated that it is necessary to clarify the role of their many-quasiparticle components. The structure of neutron resonances is studied within the framework of the general approach based on the operator form of the wave functions. The role of three-quasiparticle components in the wave functions of neutron resonances is studied and the cases of validity of the valence neutron model are pointed out. It is shown that the experimental information about the structure of neutron resonances is limited to few-quasiparticle components which are of 10 -3 -10 -6 part of the normalization of their wave functions. To study the structure of neutron resonances it is necessary to find the values of many-quasiparticle components of the wave functions. The ways of experimental finding of these components based on the study of γ-transitions between highly excited states are discussed. The fragmentation of single-particle states in deformed nuclei is studied within the framework of the model based on the quasiparticle--phonon interactions. The S-, p-, and α-wave neutron strength functions are determined

  4. Chiral symmetry and nucleon structure: Low energy aspects

    International Nuclear Information System (INIS)

    Weise, W.

    1989-01-01

    The symmetries and currents of QCD at low energy and long wavelength are realized in the form of mesons, rather than quarks and gluons. In this talk I summarize the merits, but also the limits, of chiral non-linear meson theories and their soliton solutions, in descriptions of nucleon structure and the nucleon-nucleon interaction. (orig.)

  5. Structural aspects of crotalic venom proteins modified by ionizing radiation

    International Nuclear Information System (INIS)

    Oliveira, Karina Corleto de

    2010-01-01

    Snake bites are a serious public health problem, especially in subtropical countries. In Brazil, the Ministry of Health notified around 26 000 accidents in 2008. The genus Crotalus (rattlesnakes) accounts for approximately 7% of the total, with a high mortality rate of 72% when untreated with the specific serum, the only effective treatment in case of snake bites. In Brazil, the serum is produced in horses which, despite the large size, have a reduced lifespan due to the high toxicity of the antigen. Ionizing radiation has proven to be an excellent tool for reducing the toxicity of venoms and isolated toxins, resulting in better immunogens for serum production, and contributing to the welfare of serum producing animals. Since the action of gamma radiation on venoms and toxins has not been yet fully clarified from the structural point of view, we proposed in this paper, to characterize two toxins of the species Crotalus durissus terrificus: crotoxin and crotamine. After isolation of the toxins of interest by chromatographic techniques, they were subjected to structural analysis with the application of the following methods: Fluorescence, Circular Dichroism, Differential Calorimetry and Infrared Spectroscopy. These tests showed that both crotamine as crotoxin when subjected to gamma radiation, showed changes in their structural conformation compared with the samples in the native state. Such changes probably occur in the secondary and tertiary structure and may explain the changes on the biological activity of these toxins. (author)

  6. Structural aspects of the evaluation of agent organizations

    NARCIS (Netherlands)

    Grossi, D.; Dignum, F.P.M.; Dignum, V.; Dastani, M.; Royakkers, L.M.M.; Noriega, P.; Vázquez-Salceda, J.; Boella, G.; Boissier, O.; Dignum, V.; Fornara, N.; Matson, E.

    2007-01-01

    A multi-agent system can be analyzed and specified as an organization consisting of roles and their relations. The performance of an organization depends on many factors among which the type of its organizational structure, i.e., the set of relations holding between its roles. This work focuses on

  7. Structure, context, complexity, organization: physical aspects of information and value

    National Research Council Canada - National Science Library

    Eriksson, Karl-Erik; Lindgren, Kristian; Månsson, Bengt Å

    1987-01-01

    ... and of information theory are general enough to play such a role. The authors have been involved in studies of the handling of natural resources in human societies. There we met problems and ideas which led us to the theme of this book: a perspective and a set of concepts, useful for describing and understanding processes in which structure emerges. T...

  8. Two aspects of relevance in structured argumentation: minimality and paraconsistency

    NARCIS (Netherlands)

    Grooters, Diana; Prakken, H.

    2016-01-01

    This paper studies two issues concerning relevance in structured argumentation in the context of the ASPIC+ framework, arising from the combined use of strict and defeasible inference rules. One issue arises if the strict inference rules correspond to classical logic. A longstanding problem is how

  9. Structural aspect on the Slano blato landslide (Slovenia

    Directory of Open Access Journals (Sweden)

    Ladislav Placer

    2008-12-01

    Full Text Available The active landslide Slano blato above Lokavec in the Vipava valley, Slovenia, is a complex phenomenon. The hinterland of the landslide consists of the large fossil block of Mala Gora that slid about 300 m down the slope of Mt. Čaven, and was tilted with respect to the slope. We presume that the corresponding failure surface is concavelyshaped. The block consist in its lower part of Eocene flysch beds and in its upper part of Triassic carbonate rocks that are thrust over the flysch. It is probable that due to gravitational slumping the flysch basement obtained a concave shape, that serves as a catchment structure for retaining the ground water. It slowly percolates throughthe crushed calcarenitic layers in flysch. According to available data the Slano blato was triggered in 1887 by earthworks, and in 2000 by natural erosion processes. The structural characteristics allow the assumption that movement occurs in crushed and weathered flysch beds that are percolated by a steady or periodical supply ofgroundwater from the structural reservoir in the Mala Gora fossil slumped block. Coexistence of the older structural and the younger active weathered material landslides can be observed also at other localities along the thrust front of the Trnovo and Hrušica (Nanos nappe. Especially interesting in this respect are the Razdrto and Strane landslides.

  10. Structural aspects of DNA in its replication and repair

    International Nuclear Information System (INIS)

    Mitra, S.; Pal, B.C.; Foote, R.S.; Bates, R.C.; Bhattacharyya, A.; Snow, E.T.; Wobbe, C.R.; Morse, C.C.; Snyder, C.E.

    1984-01-01

    The research objective of this laboratory is to investigate the structure of DNA, the mechanism of DNA replication and its regulation, and the mechanism and role of repair of the altered DNA in the expression of heritable changes. This research has two broad aims, namely investigation of (a) the regulation of DNA replication in mammals, using parvovirus DNA as a model system and (b) the role of DNA repair in mutagenesis and carcinogenesis induced by simple alkylating mutagens

  11. Do edaphic aspects alter vegetation structures in the Brazilian restinga?

    Directory of Open Access Journals (Sweden)

    Francisco Soares Santos-Filho

    2013-09-01

    Full Text Available The vegetation of the Brazilian restinga (coastal woodland presents a variety of species and different characteristics, encompassing fields, fruit groves and forests on quartzarenic neosols. We hypothesised that the structure of the restinga landscape along the coast of the state of Piauí is influenced by edaphic factors and presents a pattern similar to that of other northeastern restingas. We evaluated three restingas in Piauí, using the quarter method to determine their structure. Composite soil samples were collected to determine their chemical and physical properties. Edaphic variables were correlated with plant species by canonical correspondence analysis (CCA. Phytosociological data for all three areas indicated regenerating vegetation comprising several small individuals, 82.5% of which showed a diameter at ground level < 13 cm. We also observed considerable tillering. In two of the areas, there was a predominance of Fabaceae species, such as Caesalpinia pyramidalis and Copaifera martii. Although the structural characteristics of the restingas studied were similar to those of other northeastern restingas, the former showed lower Shannon diversity indices (2.18-2.44. The CCA indicated that species distribution was influenced by edaphic factors such as pH, aluminium content and amount of organic matter. The restingas studied were similar to others along the Brazilian coast.

  12. Artemin Crystal Structure Reveals Insights into Heparan Sulfate Binding

    Energy Technology Data Exchange (ETDEWEB)

    Silvian,L.; Jin, P.; Carmillo, P.; Boriack-Sjodin, P.; Pelletier, C.; Rushe, M.; Gong, B.; Sah, D.; Pepinsky, B.; Rossomando, A.

    2006-01-01

    Artemin (ART) promotes the growth of developing peripheral neurons by signaling through a multicomponent receptor complex comprised of a transmembrane tyrosine kinase receptor (cRET) and a specific glycosylphosphatidylinositol-linked co-receptor (GFR{alpha}3). Glial cell line-derived neurotrophic factor (GDNF) signals through a similar ternary complex but requires heparan sulfate proteoglycans (HSPGs) for full activity. HSPG has not been demonstrated as a requirement for ART signaling. We crystallized ART in the presence of sulfate and solved its structure by isomorphous replacement. The structure reveals ordered sulfate anions bound to arginine residues in the pre-helix and amino-terminal regions that were organized in a triad arrangement characteristic of heparan sulfate. Three residues in the pre-helix were singly or triply substituted with glutamic acid, and the resulting proteins were shown to have reduced heparin-binding affinity that is partly reflected in their ability to activate cRET. This study suggests that ART binds HSPGs and identifies residues that may be involved in HSPG binding.

  13. Spin-transfer phenomena in layered magnetic structures: Physical phenomena and materials aspects

    International Nuclear Information System (INIS)

    Gruenberg, P.; Buergler, D.E.; Dassow, H.; Rata, A.D.; Schneider, C.M.

    2007-01-01

    During the past 20 years, layered structures consisting of ferromagnetic layers and spacers of various material classes with a thickness of only a few nanometers have revealed a variety of exciting and potentially very useful phenomena not present in bulk material. Representing distinct manifestations of spin-transfer processes, these phenomena may be categorized into interlayer exchange coupling (IEC), giant magnetoresistance (GMR), tunneling magnetoresistance (TMR), and the more recently discovered spin-transfer torque effect leading to current-induced magnetization switching (CIMS) and current-driven magnetization dynamics. These phenomena clearly confer novel material properties on magnetic layered structures with respect to the (magneto-)transport and the magnetostatic as well as magnetodynamic behavior. Here, we will first concentrate on the less well understood aspects of IEC across insulating and semiconducting interlayers and relate the observations to TMR in the corresponding structures. In this context, we will also discuss more recent advances in TMR due to the use of electrodes made from Heusler alloys and the realization of coherent tunneling in epitaxial magnetic tunneling junctions. Finally, we will review our results on CIMS in epitaxial magnetic nanostructures showing that normal and inverse CIMS can occur simultaneously in a single nanopillar device. In all cases discussed, material issues play a major role in the detailed understanding of the spin-transfer effects, in particular in those systems that yield the largest effects and are thus of utmost interest for applications

  14. Selected Aspects of Agro-structural Change within the Alps

    Directory of Open Access Journals (Sweden)

    Thomas Streifeneder

    2009-07-01

    Full Text Available La région couverte par la Convention alpine a connu un recul important des exploitations agricoles (– 40 % entre 1980 et 2000. Des régions stables (Autriche, Suisse côtoient des régions profondément transformées (Italie, Slovénie. Les modifications agrostructurelles ont conduit à des bouleversements majeurs dans les structures de fonctionnement (agrandissement des exploitations, abandon de surface agricole utile, partages diversifiés des types socio-économiques d’exploitations. Cela résulte de divers facteurs, qu’ils soient culturels (l’attachement aux traditions agricoles, l’identification de la société au monde agricole, politico-agricoles (Politique Agricole Commune, OMC ou économiques (opportunités de revenus non-agricoles et fonctionnels (taille des exploitations. Au-delà des différenciations nationales et régionales majeures au sein de l’arc alpin (abandon d’exploitations modéré à fort, les exploitations agricoles affrontent les mêmes enjeux en ce qui concerne les transformations des structures agricoles (ex : abandon d’exploitation et augmentation de la taille des exploitations restantes. En comparaison avec la moyenne à l’échelle alpine de l’évolution du nombre d’exploitations et des surfaces agricoles utiles (1980-2000, on peut observer des tendances modérées (Autriche/Suisse/Allemagne, dynamiques (Italie/Slovénie ou non corrélées (France.The Alpine region registered a substantial abandonment of farms (-40% between 1980 and 2000. Both Alpine regions with a relatively stable situation (AT, CH and regions with significant agricultural changes (IT, SI exist next to each other. The agro-structural change has led to profound changes in operational structures (enlargement of farms, abandonment of utilised agricultural areas, varying shares of socio-economic farm types. This resulted from various cultural (e.g. relatedness to agricultural traditions, identification of the society with

  15. [Max Weber's illness--sociologic aspects of the depressive structure].

    Science.gov (United States)

    Frommer, J; Frommer, S

    1993-05-01

    Between 1897 and 1902 the economist and sociologist Max Weber from Heidelberg suffered from a severe depressive crisis with multiple recurrences of its symptomatology in the following years. The biographic background of the disease process is examined. Questions regarding the specific diagnosis are discussed. Furthermore, his work shows that Weber was indirectly deeply concerned with the cultural, historical and social background conditions of depressive experience and behavior in the context of his study on Protestantic Ethics and the Spirit of Capitalism. Weber's definition of modern society as an iron cage, determined by Occidental Rationalism, shows that this cultural background demands a great amount of role conformity from the individual. Weber's theoretical approach should spark interest in the current psychopathological discussion of the characteristic structural features of a depressed personality.

  16. Metallization of high aspect ratio, out of plane structures

    DEFF Research Database (Denmark)

    Vazquez, Patricia; Dimaki, Maria; Svendsen, Winnie Edith

    2009-01-01

    This work is dedicated to developing a novel three dimensional structure for electrochemical measurements in neuronal studies. The final prototype will allow not only for the study and culture on chip of neuronal cells, but also of brain tissue. The use of out-of-plane electrodes instead of planar...... ones increases the sensitivity of the system and increases the signal-to-noise ratio in the recorded signals, due to the higher availability of surface area. The main bottleneck of the out-of-plane electrode fabrication lies in the metallization process for transforming them into active electrodes......, since the coverage of the side walls of almost vertical pillars is not trivial by standard processes in a clean room facility. This paper will discuss the different steps taken towards this goal and present the results that we have obtained so far....

  17. Memory functions reveal structural properties of gene regulatory networks

    Science.gov (United States)

    Perez-Carrasco, Ruben

    2018-01-01

    Gene regulatory networks (GRNs) control cellular function and decision making during tissue development and homeostasis. Mathematical tools based on dynamical systems theory are often used to model these networks, but the size and complexity of these models mean that their behaviour is not always intuitive and the underlying mechanisms can be difficult to decipher. For this reason, methods that simplify and aid exploration of complex networks are necessary. To this end we develop a broadly applicable form of the Zwanzig-Mori projection. By first converting a thermodynamic state ensemble model of gene regulation into mass action reactions we derive a general method that produces a set of time evolution equations for a subset of components of a network. The influence of the rest of the network, the bulk, is captured by memory functions that describe how the subnetwork reacts to its own past state via components in the bulk. These memory functions provide probes of near-steady state dynamics, revealing information not easily accessible otherwise. We illustrate the method on a simple cross-repressive transcriptional motif to show that memory functions not only simplify the analysis of the subnetwork but also have a natural interpretation. We then apply the approach to a GRN from the vertebrate neural tube, a well characterised developmental transcriptional network composed of four interacting transcription factors. The memory functions reveal the function of specific links within the neural tube network and identify features of the regulatory structure that specifically increase the robustness of the network to initial conditions. Taken together, the study provides evidence that Zwanzig-Mori projections offer powerful and effective tools for simplifying and exploring the behaviour of GRNs. PMID:29470492

  18. Structure and evolutionary aspects of matrix metalloproteinases: a brief overview.

    Science.gov (United States)

    Das, Sudip; Mandal, Malay; Chakraborti, Tapati; Mandal, Amritlal; Chakraborti, Sajal

    2003-11-01

    The matrix metalloproteinases (MMPs) are zinc dependent endopeptidases known for their ability to cleave one or several extracellular matrix (ECM) constituents, as well as non-matrix proteins. They comprise a large family of proteinases that share common structural and functional elements and are products of different genes. All members of this family contain a signal peptide, a propeptide and a catalytic domain. The catalytic domain contains two zinc ions and at least one calcium ion coordinated to various residues. All MMPs, with the exception matrilysin, have a hemopexin/vitronectin-like domain that is connected to the catalytic domain by a hinge or linker region. The hemopexin-like domain influences tissue inhibitor of metalloproteinases (TIMP) binding, the binding of certain substrates, membrane activation, and some proteolytic activities. It has been proposed that the origin of MMPs could be traced to before the emergence of vertebrates from invertebrates. It appears conceivable that the domain assemblies occurred at an early stage of the diversification of different MMPs and that they progressed through the evolutionary process independent of one another, and perhaps parallel to each other.

  19. Aspects of structural landscape of human islet amyloid polypeptide

    Energy Technology Data Exchange (ETDEWEB)

    He, Jianfeng, E-mail: hjf@bit.edu.cn; Dai, Jin, E-mail: daijing491@gmail.com [School of Physics, Beijing Institute of Technology, Beijing 100081 (China); Li, Jing, E-mail: jinglichina@139.com [Institute of Biopharmaceutical Research, Yangtze River Pharmaceutical Group Beijing Haiyan Pharmaceutical Co., Ltd, Beijing 102206 (China); Peng, Xubiao, E-mail: xubiaopeng@gmail.com [Department of Physics and Astronomy, Uppsala University, P.O. Box 803, S-75108 Uppsala (Sweden); Niemi, Antti J., E-mail: Antti.Niemi@physics.uu.se [School of Physics, Beijing Institute of Technology, Beijing 100081 (China); Department of Physics and Astronomy, Uppsala University, P.O. Box 803, S-75108 Uppsala (Sweden); Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, F37200 Tours (France)

    2015-01-28

    The human islet amyloid polypeptide (hIAPP) co-operates with insulin to maintain glycemic balance. It also constitutes the amyloid plaques that aggregate in the pancreas of type-II diabetic patients. We have performed extensive in silico investigations to analyse the structural landscape of monomeric hIAPP, which is presumed to be intrinsically disordered. For this, we construct from first principles a highly predictive energy function that describes a monomeric hIAPP observed in a nuclear magnetic resonance experiment, as a local energy minimum. We subject our theoretical model of hIAPP to repeated heating and cooling simulations, back and forth between a high temperature regime where the conformation resembles a random walker and a low temperature limit where no thermal motions prevail. We find that the final low temperature conformations display a high level of degeneracy, in a manner which is fully in line with the presumed intrinsically disordered character of hIAPP. In particular, we identify an isolated family of α-helical conformations that might cause the transition to amyloidosis, by nucleation.

  20. Mammalian cells exposed to ionizing radiation: structural and biochemical aspects

    International Nuclear Information System (INIS)

    Sabanero, M.; Flores V, L. L.; Azorin V, J. C.; Vallejo, M. A.; Cordova F, T.; Sosa A, M.; Castruita D, J. P.; Barbosa S, G.

    2015-10-01

    Acute or chronic exposure to ionizing radiation is a factor that may be hazardous to health. It has been reported that exposure to low doses of radiation (less than 50 mSv / year) and subsequently exposure to high doses have greater effects in people. However, it is unknown molecular and biochemical level alteration. This study, analyzes the susceptibility of a biological system (HeLa Atcc CCL-2 human cervix cancer cell line) to ionizing radiation (6 and 60 mSv/ 90). Our evaluate multiple variables such as: total protein profile, mitochondrial metabolic activity (XTT assay), cell viability (Trypan blue exclusion assay), cytoskeleton (actin micro filaments), nuclei (D API), genomic DNA. The results indicate, that cells exposed to ionizing radiation structurally show alterations in nuclear phenotype and aneuploidy, further disruption in the tight junctions and consequently on the distribution of actin micro filaments. Similar alterations were observed in cells treated with a genotoxic agent (200μM H 2 O 2 /1 h). In conclusion, this multi-criteria assessment enables precise comparisons of the effects of radiation between any biological systems. However, it is necessary to determine stress markers for integration of the effects of ionizing radiation. (Author)

  1. Mammalian cells exposed to ionizing radiation: structural and biochemical aspects

    Energy Technology Data Exchange (ETDEWEB)

    Sabanero, M.; Flores V, L. L. [Universidad de Guanajuato, Departamento de Biologia, DCNE, Noria Alta s/n, 36250 Guanajuato, Gto. (Mexico); Azorin V, J. C.; Vallejo, M. A.; Cordova F, T.; Sosa A, M. [Universidad de Guanajuato, Departamento de Ingenieria Fisica, DCI, Loma del Bosque 103, Col. Lomas del Campestre, 37150 Leon, Guanajuato (Mexico); Castruita D, J. P. [Universidad de Guadalajara, Departamento de Ecologia, CUCBA, Las Agujas, 45100 Zapopan, Jalisco (Mexico); Barbosa S, G., E-mail: myrna.sabanero@gmail.com [Universidad de Guanajuato, Departamento de Ciencias Medicas, DCS, 20 de Enero No. 929, Col. Obregon, 37000 Leon, Guanajuato (Mexico)

    2015-10-15

    Acute or chronic exposure to ionizing radiation is a factor that may be hazardous to health. It has been reported that exposure to low doses of radiation (less than 50 mSv / year) and subsequently exposure to high doses have greater effects in people. However, it is unknown molecular and biochemical level alteration. This study, analyzes the susceptibility of a biological system (HeLa Atcc CCL-2 human cervix cancer cell line) to ionizing radiation (6 and 60 mSv/ 90). Our evaluate multiple variables such as: total protein profile, mitochondrial metabolic activity (XTT assay), cell viability (Trypan blue exclusion assay), cytoskeleton (actin micro filaments), nuclei (D API), genomic DNA. The results indicate, that cells exposed to ionizing radiation structurally show alterations in nuclear phenotype and aneuploidy, further disruption in the tight junctions and consequently on the distribution of actin micro filaments. Similar alterations were observed in cells treated with a genotoxic agent (200μM H{sub 2}O{sub 2}/1 h). In conclusion, this multi-criteria assessment enables precise comparisons of the effects of radiation between any biological systems. However, it is necessary to determine stress markers for integration of the effects of ionizing radiation. (Author)

  2. Theoretical aspects of electronic structure of high Tc superconductors

    International Nuclear Information System (INIS)

    Gupta, R.P.

    1990-01-01

    Although the mechanism responsible for the high T c superconductivity is still unknown, it is nevertheless clear that superconductivity in hole doped materials depends sensitively on the number of holes, C h , per CuO 2 plane. A correlation between C h and T c has been established. In this paper we present several examples of the critical dependence of the charge transfer and thus the value of C h on the cristallographic characteristics. For example, our electronic structure investigations of YBa 2 Cu 3 O 6.5 using several configurations of the oxygen atoms on the chains show that the order-disorder phenomena of the oxygen atoms play a crucial role on the value of C h and T c . We have also studied the variation of the charge transfer and C h as a function of hydrostatic pressure for several cuprates: La 1.85 Sr 0.15 CuO 4 (ΔT c /Δp ∼ 0.3 - 0.4 K/kbar); YBa 2 Cu 4 O 8 (ΔT c /Δp ∼ 5.5 K/kbar). We show that the values of C h increase under pressure [fr

  3. Structural aspects of elastic deformation of a metallic glass

    International Nuclear Information System (INIS)

    Hufnagel, T. C.; Ott, R. T.; Almer, J.

    2006-01-01

    We report the use of high-energy x-ray scattering to measure strain in a Zr 57 Ti 5 Cu 20 Ni 8 Al 10 bulk metallic glass in situ during uniaxial compression in the elastic regime up to stresses of approximately 60% of the yield stress. The strains extracted in two ways--directly from the normalized scattering data and from the pair correlation functions--are in good agreement with each other for length scales greater than 4 A. The elastic modulus calculated on the basis of this strain is in good agreement with that reported for closely related amorphous alloys based on macroscopic measurements. The strain measured for atoms in the nearest-neighbor shell, however, is smaller than that for more distant shells, and the effective elastic modulus calculated from the strain on this scale is therefore larger, comparable to crystalline alloys of similar composition. These observations are in agreement with previously proposed models in which the nominally elastic deformation of a metallic glass has a significant anelastic component due to atomic rearrangements in topologically unstable regions of the structure. We also observe that the distribution of the atomic-level stresses in the glass becomes more uniform during loading. This implies that the stiffness of metallic glasses may have an entropic contribution, analogous to the entropic contribution in rubber elasticity

  4. Structural and microstructural aspects of asbestos-cement waste vitrification

    Science.gov (United States)

    Iwaszko, Józef; Zawada, Anna; Przerada, Iwona; Lubas, Małgorzata

    2018-04-01

    The main goal of the work was to evaluate the vitrification process of asbestos-cement waste (ACW). A mixture of 50 wt% ACW and 50 wt% glass cullet was melted in an electric furnace at 1400 °C for 90 min and then cast into a steel mold. The vitrified product was subjected to annealing. Optical microscopy, scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FT-IR) and X-ray diffraction (XRD) were used to evaluate the effects of the vitrification. The chemical constitution of the material before and after the vitrification process was also analyzed. It was found that the vitrified product has an amorphous structure in which the components of asbestos-cement waste are incorporated. MIR spectroscopy showed that the absorption bands of chrysotile completely disappeared after the vitrification process. The results of the spectroscopic studies were confirmed by X-ray studies - no diffraction reflections from the chrysotile crystallographic planes were observed. As a result of the treatment, the fibrous asbestos construction, the main cause of its pathogenic properties, completely disappeared. The vitrified material was characterized by higher resistance to ion leaching in an aquatic environment than ACW and a smaller volume of nearly 72% in relation to the apparent volume of the substrates. The research has confirmed the high effectiveness of vitrification in neutralizing hazardous waste containing asbestos and the FT-IR spectroscopy was found to be useful to identify asbestos varieties and visualizing changes caused by the vitrification process. The work also presents the current situation regarding the utilization of asbestos-containing products.

  5. Statistical universals reveal the structures and functions of human music.

    Science.gov (United States)

    Savage, Patrick E; Brown, Steven; Sakai, Emi; Currie, Thomas E

    2015-07-21

    Music has been called "the universal language of mankind." Although contemporary theories of music evolution often invoke various musical universals, the existence of such universals has been disputed for decades and has never been empirically demonstrated. Here we combine a music-classification scheme with statistical analyses, including phylogenetic comparative methods, to examine a well-sampled global set of 304 music recordings. Our analyses reveal no absolute universals but strong support for many statistical universals that are consistent across all nine geographic regions sampled. These universals include 18 musical features that are common individually as well as a network of 10 features that are commonly associated with one another. They span not only features related to pitch and rhythm that are often cited as putative universals but also rarely cited domains including performance style and social context. These cross-cultural structural regularities of human music may relate to roles in facilitating group coordination and cohesion, as exemplified by the universal tendency to sing, play percussion instruments, and dance to simple, repetitive music in groups. Our findings highlight the need for scientists studying music evolution to expand the range of musical cultures and musical features under consideration. The statistical universals we identified represent important candidates for future investigation.

  6. Fine-scaled human genetic structure revealed by SNP microarrays.

    Science.gov (United States)

    Xing, Jinchuan; Watkins, W Scott; Witherspoon, David J; Zhang, Yuhua; Guthery, Stephen L; Thara, Rangaswamy; Mowry, Bryan J; Bulayeva, Kazima; Weiss, Robert B; Jorde, Lynn B

    2009-05-01

    We report an analysis of more than 240,000 loci genotyped using the Affymetrix SNP microarray in 554 individuals from 27 worldwide populations in Africa, Asia, and Europe. To provide a more extensive and complete sampling of human genetic variation, we have included caste and tribal samples from two states in South India, Daghestanis from eastern Europe, and the Iban from Malaysia. Consistent with observations made by Charles Darwin, our results highlight shared variation among human populations and demonstrate that much genetic variation is geographically continuous. At the same time, principal components analyses reveal discernible genetic differentiation among almost all identified populations in our sample, and in most cases, individuals can be clearly assigned to defined populations on the basis of SNP genotypes. All individuals are accurately classified into continental groups using a model-based clustering algorithm, but between closely related populations, genetic and self-classifications conflict for some individuals. The 250K data permitted high-level resolution of genetic variation among Indian caste and tribal populations and between highland and lowland Daghestani populations. In particular, upper-caste individuals from Tamil Nadu and Andhra Pradesh form one defined group, lower-caste individuals from these two states form another, and the tribal Irula samples form a third. Our results emphasize the correlation of genetic and geographic distances and highlight other elements, including social factors that have contributed to population structure.

  7. High aspect ratio lead zirconate titanate tube structures: I. Template assisted fabrication - vacuum infiltration method

    Directory of Open Access Journals (Sweden)

    Vladimír Kovaľ

    2012-03-01

    Full Text Available Polycrystalline Pb(Zr0.52Ti0.48O3 (PZT microtubes are fabricated by a vacuum infiltration method. The method is based on repeated infiltration of precursor solution into macroporous silicon (Si templates at a sub-atmospheric pressure. The pyrolyzed PZT tubes of a 2-µm outer diameter, extending to over 30 µm in length were released from the template using a selective isotropic-pulsed XeF2 reactive ion etching of silicon. Free-standing microtubes, partially anchored at the bottom of the Si template, were then crystallized in pure oxygen atmosphere at 750 °C for 2 min using a rapid thermal annealer. The perovskite phase of the final PZT tubes was confirmed by X-ray diffraction (XRD analysis. The XRD spectrum also revealed a small amount of the pyrochlore phase in the structure and signs of possible fluoride contamination caused most likely by the XeF2 etching process. The surface morphology was examined using scanning electron microscopy. It was demonstrated that the whole surface of the pore walls was conformally coated during the repeated infiltration of templates, resulting in straight tubes with closed tips formed on the opposite ends as replicas of the pore bottoms. These high aspect ratio ferroelectric structures are suggested as building units for developing miniaturized electronic devices, such as memory storage (DRAM trenched capacitors, piezoelectric scanners and actuators, and are of fundamental value for the theory of ferroelectricity in systems with low dimensionality.

  8. Key Techniques on Preparing High Aspect Ratio Micro and Nano Structures

    DEFF Research Database (Denmark)

    Jian, Zhao; Lianhe, Dong; Xiaoli, Zhu

    2016-01-01

    effectively. The mechanism of action between NaCl and HSQ was analyzed. The collapse and adhesion of resist structure due to the effect of gas-liquid interfacial capillary surface tension were suppressed by the CO2 supercritical drying method. Large-area dense nano-structures with the aspect ratio of 12...

  9. Hot embossing of photonic crystal polymer structures with a high aspect ratio

    DEFF Research Database (Denmark)

    Schelb, Mauno; Vannahme, Christoph; Kolew, Alexander

    2011-01-01

    ). A nickel tool for the replication of structures with lateral dimensions of 110 nm and heights of approximately 370 nm is fabricated via electroplating of a nanostructured sample resulting in an aspect ratio of approximately 3.5. The structures are subsequently hot embossed into PMMA and COC substrates....

  10. Structural Aspects, Institutional Aspects, and Actors in the Organizational Field of Textbook Publishing : a case study on high school “Contemporary Society”

    OpenAIRE

    小原, 明恵

    2016-01-01

    The purpose of this paper is to clarify the organizational field of high school “Contemporary Society” textbook publishing using triadic relationship among structure, institutions, and actors as an analytical framework. Firstly, the Course of Study for high school “Contemporary Society” is explained as the institutional aspect of textbook publishing field. Secondly, the structural aspects of textbook publishing industry such as the market size, the number of publishers and textbooks, and the ...

  11. Hurricane Inner-Core Structure as Revealed by GPS Dropwindsondes

    National Research Council Canada - National Science Library

    Leejoice, Robert

    2000-01-01

    New high-resolution information of the vertical thermodynamic and kinematic structure of the hurricane inner-core is now available from aircraft released Global Positioning System (GPS) dropwindsondes...

  12. Structural and dynamical aspects of Streptococcus gordonii FabH through molecular docking and MD simulations.

    Science.gov (United States)

    Shamim, Amen; Abbasi, Sumra Wajid; Azam, Syed Sikander

    2015-07-01

    β-Ketoacyl-ACP-synthase III (FabH or KAS III) has become an attractive target for the development of new antibacterial agents which can overcome the multidrug resistance. Unraveling the fatty acid biosynthesis (FAB) metabolic pathway and understanding structural coordinates of FabH will provide valuable insights to target Streptococcus gordonii for curing oral infection. In this study, we designed inhibitors against therapeutic target FabH, in order to block the FAB pathway. As compared to other targets, FabH has more interactions with other proteins, located on the leading strand with higher codon adaptation index value and associated with lipid metabolism category of COG. Current study aims to gain in silico insights into the structural and dynamical aspect of S. gordonii FabH via molecular docking and molecular dynamics (MD) simulations. The FabH protein is catalytically active in dimerization while it can lock in monomeric state. Current study highlights two residues Pro88 and Leu315 that are close to each other by dimerization. The active site of FabH is composed of the catalytic triad formed by residues Cys112, His249, and Asn279 in which Cys112 is involved in acetyl transfer, while His249 and Asn279 play an active role in decarboxylation. Docking analysis revealed that among the studied compounds, methyl-CoA disulfide has highest GOLD score (82.75), binding affinity (-11 kcal/mol) and exhibited consistently better interactions. During MD simulations, the FabH structure remained stable with the average RMSD value of 1.7 Å and 1.6 Å for undocked protein and docked complex, respectively. Further, crucial hydrogen bonding of the conserved catalytic triad for exhibiting high affinity between the FabH protein and ligand is observed by RDF analysis. The MD simulation results clearly demonstrated that binding of the inhibitor with S. gordonii FabH enhanced the structure and stabilized the dimeric FabH protein. Therefore, the inhibitor has the potential to become

  13. Lee-side flow structures of very low aspect ratio cruciform wing–body configurations

    CSIR Research Space (South Africa)

    Tuling, S

    2013-12-01

    Full Text Available A numerical and experimental investigation was performed to study the dominant flow structures in the lee side of a cruciform wing–body configuration at supersonic speeds in the + orientation. The wings or strakes are of very low aspect ratio...

  14. Structural and quantitative aspects of radical formation after heavy ion bombardment

    Energy Technology Data Exchange (ETDEWEB)

    Dusemund, B; Hoffmann, A K; Weiland, B; Huettermann, J [Klinikum Homburg (Germany). Fachrichtung Biophysik

    1997-09-01

    In this report the authors present a summary of their recent attempts aiming at clarifying some basic structural and quantitative aspects of free radical formation in DNA constituents and in DNA as well as of product analysis from nucleotide model compounds. (orig./MG)

  15. Addressing special structure in the relevance feedback learning problem through aspect-based image search

    NARCIS (Netherlands)

    M.J. Huiskes (Mark)

    2004-01-01

    textabstractIn this paper we focus on a number of issues regarding special structure in the relevance feedback learning problem, most notably the effects of image selection based on partial relevance on the clustering behavior of examples. We propose a simple scheme, aspect-based image search, which

  16. Novel aspects of live intestinal epithelial cell function revealed using a custom time-lapse video microscopy apparatus.

    Science.gov (United States)

    Papetti, Michael; Kozlowski, Piotr

    2018-04-01

    Many aspects of cell physiology, including migration, membrane function, and cell division, are best understood by observing live cell dynamics over time using video microscopy. To probe these phenomena in colon epithelial cells using simple components with a limited budget, we have constructed an inexpensive (PID (proportional-integrative-derivative) controller contained within a 0.077 m 3 insulated acrylic box. Temperature, humidity, pH, and proliferative capacity of colon epithelial cells in this system mimic those in a standard tissue culture incubator for over four days. Our system offers significant advantages over existing cost-prohibitive commercially available and custom-made devices because of its very low cost, use of PID temperature control, lack of reliance on constant infusion of external humidified, heated air or carbon dioxide, ability to directly measure cell culture medium temperature, and combination of exquisite cellular detail with minimal focus drift under physiological conditions for extended periods of time. Using this apparatus, coupled with an inverted microscope equipped with phase contrast optics and a programmable digital camera, we have observed many events in colon epithelial cells not visible by static imaging, including kinetics of normal and abnormal mitoses, dynamic membrane structures, intracellular vesicle movements, and cell migration. © 2018 International Society for Advancement of Cytometry. © 2018 International Society for Advancement of Cytometry.

  17. Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements

    Science.gov (United States)

    Watters, Kyle E; Choudhary, Krishna; Aviran, Sharon; Perry, Keith L

    2018-01-01

    Abstract In single stranded (+)-sense RNA viruses, RNA structural elements (SEs) play essential roles in the infection process from replication to encapsidation. Using selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) and covariation analysis, we explore the structural features of the third genome segment of cucumber mosaic virus (CMV), RNA3 (2216 nt), both in vitro and in plant cell lysates. Comparing SHAPE-Seq and covariation analysis results revealed multiple SEs in the coat protein open reading frame and 3′ untranslated region. Four of these SEs were mutated and serially passaged in Nicotiana tabacum plants to identify biologically selected changes to the original mutated sequences. After passaging, loop mutants showed partial reversion to their wild-type sequence and SEs that were structurally disrupted by mutations were restored to wild-type-like structures via synonymous mutations in planta. These results support the existence and selection of virus open reading frame SEs in the host organism and provide a framework for further studies on the role of RNA structure in viral infection. Additionally, this work demonstrates the applicability of high-throughput chemical probing in plant cell lysates and presents a new method for calculating SHAPE reactivities from overlapping reverse transcriptase priming sites. PMID:29294088

  18. Cocaine Hydrochloride Structure in Solution Revealed by Three Chiroptical Methods

    Czech Academy of Sciences Publication Activity Database

    Fagan, P.; Kocourková, L.; Tatarkovič, M.; Králík, F.; Kuchař, M.; Setnička, V.; Bouř, Petr

    2017-01-01

    Roč. 18, č. 16 (2017), s. 2258-2265 ISSN 1439-4235 R&D Projects: GA ČR(CZ) GA16-05935S; GA MŠk(CZ) LTC17012 Institutional support: RVO:61388963 Keywords : analytical methods * circular dichroism * density functional calculations * Raman spectroscopy * structure elucidation Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 3.075, year: 2016

  19. Structure of Drosophila Oskar reveals a novel RNA binding protein

    Science.gov (United States)

    Yang, Na; Yu, Zhenyu; Hu, Menglong; Wang, Mingzhu; Lehmann, Ruth; Xu, Rui-Ming

    2015-01-01

    Oskar (Osk) protein plays critical roles during Drosophila germ cell development, yet its functions in germ-line formation and body patterning remain poorly understood. This situation contrasts sharply with the vast knowledge about the function and mechanism of osk mRNA localization. Osk is predicted to have an N-terminal LOTUS domain (Osk-N), which has been suggested to bind RNA, and a C-terminal hydrolase-like domain (Osk-C) of unknown function. Here, we report the crystal structures of Osk-N and Osk-C. Osk-N shows a homodimer of winged-helix–fold modules, but without detectable RNA-binding activity. Osk-C has a lipase-fold structure but lacks critical catalytic residues at the putative active site. Surprisingly, we found that Osk-C binds the 3′UTRs of osk and nanos mRNA in vitro. Mutational studies identified a region of Osk-C important for mRNA binding. These results suggest possible functions of Osk in the regulation of stability, regulation of translation, and localization of relevant mRNAs through direct interaction with their 3′UTRs, and provide structural insights into a novel protein–RNA interaction motif involving a hydrolase-related domain. PMID:26324911

  20. Effects of anabolic hormones on structural, metabolic and functional aspects of skeletal muscle

    Directory of Open Access Journals (Sweden)

    Flávio de Oliveira Pires

    2009-01-01

    Full Text Available http://dx.doi.org/10.5007/1980-0037.2009v11n3p350   This study reviewed information regarding the effects of anabolic hormones on strength gain and muscle hypertrophy, emphasizing the physiological mechanisms that may increase muscle strength. Structural, metabolic and functional aspects were analyzed and special attention was paid to the dose-response relationship. The Pubmed database was searched and studies were selected according to relevance and date of publication (last 15 years. The administration of high testosterone doses (~600 mg/week potentiates the effects of strength training, increasing lean body mass, muscle fiber type IIA and IIB cross-sectional area, and the number of myonuclei. There is no evidence of conversion between MHC isoforms. The interaction between testosterone administration and strength training seems to modify some metabolic pathways, increasing protein synthesis, glycogen and ATP-CP muscle stores and improving fat mobilization. Changes in 17-estradiol concentration or in the ACTH-cortisol and insulin-glucagon ratios seem to be associated with these metabolic alterations. Regarding performance, testosterone administration may improve muscle strength by 5-20% depending on the dose used. On the other hand, the effects of growth hormone on the structural and functional aspects of skeletal muscle are not evident, with this hormone more affecting metabolic aspects. However, strictly controlled human studies are necessary to establish the extent of the effects of anabolic hormones on structural, metabolic and functional aspects.

  1. Effects of anabolic hormones on structural, metabolic and functional aspects of skeletal muscle

    Directory of Open Access Journals (Sweden)

    Flávio de Oliveira Pires

    2009-06-01

    Full Text Available This study reviewed information regarding the effects of anabolic hormones on strength gain and muscle hypertrophy, emphasizing the physiological mechanisms that may increase muscle strength. Structural, metabolic and functional aspects were analyzed and special attention was paid to the dose-response relationship. The Pubmed database was searched and studies were selected according to relevance and date of publication (last 15 years. The administration of high testosterone doses (~600 mg/week potentiates the effects of strength training, increasing lean body mass, muscle fiber type IIA and IIB cross-sectional area, and the number of myonuclei. There is no evidence of conversion between MHC isoforms. The interaction between testosterone administration and strength training seems to modify some metabolic pathways, increasing protein synthesis, glycogen and ATP-CP muscle stores and improving fat mobilization. Changes in 17-estradiol concentration or in the ACTH-cortisol and insulin-glucagon ratios seem to be associated with these metabolic alterations. Regarding performance, testosterone administration may improve muscle strength by 5-20% depending on the dose used. On the other hand, the effects of growth hormone on the structural and functional aspects of skeletal muscle are not evident, with this hormone more affecting metabolic aspects. However, strictly controlled human studies are necessary to establish the extent of the effects of anabolic hormones on structural, metabolic and functional aspects.

  2. Predator-guided sampling reveals biotic structure in the bathypelagic.

    Science.gov (United States)

    Benoit-Bird, Kelly J; Southall, Brandon L; Moline, Mark A

    2016-02-24

    We targeted a habitat used differentially by deep-diving, air-breathing predators to empirically sample their prey's distributions off southern California. Fine-scale measurements of the spatial variability of potential prey animals from the surface to 1,200 m were obtained using conventional fisheries echosounders aboard a surface ship and uniquely integrated into a deep-diving autonomous vehicle. Significant spatial variability in the size, composition, total biomass, and spatial organization of biota was evident over all spatial scales examined and was consistent with the general distribution patterns of foraging Cuvier's beaked whales (Ziphius cavirostris) observed in separate studies. Striking differences found in prey characteristics between regions at depth, however, did not reflect differences observed in surface layers. These differences in deep pelagic structure horizontally and relative to surface structure, absent clear physical differences, change our long-held views of this habitat as uniform. The revelation that animals deep in the water column are so spatially heterogeneous at scales from 10 m to 50 km critically affects our understanding of the processes driving predator-prey interactions, energy transfer, biogeochemical cycling, and other ecological processes in the deep sea, and the connections between the productive surface mixed layer and the deep-water column. © 2016 The Author(s).

  3. The interior structure of Ceres as revealed by surface topography

    Science.gov (United States)

    Fu, Roger R.; Ermakov, Anton; Marchi, Simone; Castillo-Rogez, Julie C.; Raymond, Carol A.; Hager, Bradford; Zuber, Maria; King, Scott D.; Bland, Michael T.; De Sanctis, Maria Cristina; Preusker, Frank; Park, Ryan S.; Russell, Christopher T.

    2017-01-01

    Ceres, the largest body in the asteroid belt (940 km diameter), provides a unique opportunity to study the interior structure of a volatile-rich dwarf planet. Variations in a planetary body's subsurface rheology and density affect the rate of topographic relaxation. Preferential attenuation of long wavelength topography (≥150 km) on Ceres suggests that the viscosity of its crust decreases with increasing depth. We present finite element (FE) geodynamical simulations of Ceres to identify the internal structures and compositions that best reproduce its topography as observed by the NASA Dawn mission. We infer that Ceres has a mechanically strong crust with maximum effective viscosity ∼1025 Pa s. Combined with density constraints, this rheology suggests a crustal composition of carbonates or phyllosilicates, water ice, and at least 30 volume percent (vol.%) low-density, high-strength phases most consistent with salt and/or clathrate hydrates. The inference of these crustal materials supports the past existence of a global ocean, consistent with the observed surface composition. Meanwhile, we infer that the uppermost ≥60 km of the silicate-rich mantle is mechanically weak with viscosity <1021 Pa s, suggesting the presence of liquid pore fluids in this region and a low temperature history that avoided igneous differentiation due to late accretion or efficient heat loss through hydrothermal processes.

  4. Shared memories reveal shared structure in neural activity across individuals

    Science.gov (United States)

    Chen, J.; Leong, Y.C.; Honey, C.J.; Yong, C.H.; Norman, K.A.; Hasson, U.

    2016-01-01

    Our lives revolve around sharing experiences and memories with others. When different people recount the same events, how similar are their underlying neural representations? Participants viewed a fifty-minute movie, then verbally described the events during functional MRI, producing unguided detailed descriptions lasting up to forty minutes. As each person spoke, event-specific spatial patterns were reinstated in default-network, medial-temporal, and high-level visual areas. Individual event patterns were both highly discriminable from one another and similar between people, suggesting consistent spatial organization. In many high-order areas, patterns were more similar between people recalling the same event than between recall and perception, indicating systematic reshaping of percept into memory. These results reveal the existence of a common spatial organization for memories in high-level cortical areas, where encoded information is largely abstracted beyond sensory constraints; and that neural patterns during perception are altered systematically across people into shared memory representations for real-life events. PMID:27918531

  5. Revealing the structure of the world airline network

    Science.gov (United States)

    Verma, T.; Araújo, N. A. M.; Herrmann, H. J.

    2014-07-01

    Resilience of most critical infrastructures against failure of elements that appear insignificant is usually taken for granted. The World Airline Network (WAN) is an infrastructure that reduces the geographical gap between societies, both small and large, and brings forth economic gains. With the extensive use of a publicly maintained data set that contains information about airports and alternative connections between these airports, we empirically reveal that the WAN is a redundant and resilient network for long distance air travel, but otherwise breaks down completely due to removal of short and apparently insignificant connections. These short range connections with moderate number of passengers and alternate flights are the connections that keep remote parts of the world accessible. It is surprising, insofar as there exists a highly resilient and strongly connected core consisting of a small fraction of airports (around 2.3%) together with an extremely fragile star-like periphery. Yet, in spite of their relevance, more than 90% of the world airports are still interconnected upon removal of this core. With standard and unconventional removal measures we compare both empirical and topological perceptions for the fragmentation of the world. We identify how the WAN is organized into different classes of clusters based on the physical proximity of airports and analyze the consequence of this fragmentation.

  6. Priming paradigm reveals harmonic structure processing in congenital amusia.

    Science.gov (United States)

    Tillmann, Barbara; Gosselin, Nathalie; Bigand, Emmanuel; Peretz, Isabelle

    2012-09-01

    Deficits for pitch structure processing in congenital amusia has been mostly reported for melodic stimuli and explicit judgments. The present study investigated congenital amusia with harmonic stimuli and a priming task. Amusic and control participants performed a speeded phoneme discrimination task on sung chord sequences. The target phoneme was sung either on a functionally important chord (tonic chord, referred to as "related target") or a less important one (subdominant chord, referred to as "less-related target"). Correct response times were faster when the target phoneme was sung on tonic chords rather than on subdominant chords, and this effect was less pronounced, albeit significant, in amusic participants. These data report for the first time a deficit in congenital amusia for chord processing, but also provide evidence that, despite this deficit, amusic individuals have internalized sophisticated syntactic-like functions of chords in the Western tonal musical system. This finding suggests that thanks to this musical knowledge, amusic individuals could develop expectancies for musical events, and, presumably, follow the tension-relaxation schemas in Western tonal music, which also influence emotional responses to music. Copyright © 2012 Elsevier Srl. All rights reserved.

  7. Probabilistic diffusion tractography reveals improvement of structural network in musicians.

    Directory of Open Access Journals (Sweden)

    Jianfu Li

    Full Text Available PURPOSE: Musicians experience a large amount of information transfer and integration of complex sensory, motor, and auditory processes when training and playing musical instruments. Therefore, musicians are a useful model in which to investigate neural adaptations in the brain. METHODS: Here, based on diffusion-weighted imaging, probabilistic tractography was used to determine the architecture of white matter anatomical networks in musicians and non-musicians. Furthermore, the features of the white matter networks were analyzed using graph theory. RESULTS: Small-world properties of the white matter network were observed in both groups. Compared with non-musicians, the musicians exhibited significantly increased connectivity strength in the left and right supplementary motor areas, the left calcarine fissure and surrounding cortex and the right caudate nucleus, as well as a significantly larger weighted clustering coefficient in the right olfactory cortex, the left medial superior frontal gyrus, the right gyrus rectus, the left lingual gyrus, the left supramarginal gyrus, and the right pallidum. Furthermore, there were differences in the node betweenness centrality in several regions. However, no significant differences in topological properties were observed at a global level. CONCLUSIONS: We illustrated preliminary findings to extend the network level understanding of white matter plasticity in musicians who have had long-term musical training. These structural, network-based findings may indicate that musicians have enhanced information transmission efficiencies in local white matter networks that are related to musical training.

  8. Structural Aspects LiNbO3 Nanoparticles and Their Ferromagnetic Properties

    Science.gov (United States)

    Diaz-Moreno, Carlos A.; Farias-Mancilla, Rurik; Elizalde-Galindo, Jose T.; González-Hernández, Jesus; Hurtado-Macias, Abel; Bahena, Daniel; José-Yacamán, Miguel; Ramos, Manuel

    2014-01-01

    We present a solid-state synthesis of ferromagnetic lithium niobate nanoparticles (LiNbO3) and their corresponding structural aspects. In order to investigate the effect of heat treatments, two batches of samples with a heat-treated (HT) and non-heat-treated (nHT) reduction at 650 °C in 5% of hydrogen/argon were considered to investigate the multiferroic properties and their corresponding structural aspects; using magnetometry and scanning transmission electron microscopy (STEM). Results indicate the existence of ferromagnetic domains with a magnetic moment per unit cell of 5.24 × 10−3 μB; caused mainly due to voids and defects on the nanoparticle surface, as confirmed by STEM measurements. PMID:28788242

  9. Some structural aspects that are relevant for synthesis of planetary gear trains

    Energy Technology Data Exchange (ETDEWEB)

    Rajasri, I. [Pathfinder Engineering College, Hanamkonda (India); Gupta, A.V.S.S.K.S. [JNTU, Hyderabad (India); Rao, Y.V.D. [BITS-Pilani. Dept. of Mechanical Engineering, Hyderabad (India)

    2012-07-01

    Gear Trains are typically used in various mechanisms including wind turbines and robots to transmit specified motion and/or torque between two or more shafts and wind turbines need drives and overdrives that amplify the speed of turbine shaft and provide high speed at generator shaft. Planetary gear trains (PGT) are compact, easy to build and operate. Therefore PGTs are most suitable for such drives including over drives. Graph theory used in synthesis of the PGTs is also useful to identify various possible structural aspects of the PGTs. Generation of PGTs is followed by the test for isomorphism in PGTs generated. In this context various structural aspects relevant for the synthesis of PGTs is described. (Author)

  10. Electronic Health Record in Occupational Medicine: Specific Aspects and Requirements of Data Structuring and Standardization

    Directory of Open Access Journals (Sweden)

    Dorin TRIFF

    2009-07-01

    Full Text Available The service of occupational medicine of a specific economic agent, as integrated part of the System of Labor Health and Safety, requires efficient, well-organized information management through standardized and computerized data processing and exploitation. Legal requirements and practical aspects of information management in occupational medicine trigger necessary operational modifications in the Electronic Health File. The goal of the paper is to present basic requirements of structuring the electronic health file and the necessary standards in recording specific data.

  11. Sustainability of transport structures - some aspects of the nonlinear reliability assessment

    Science.gov (United States)

    Pukl, Radomír; Sajdlová, Tereza; Strauss, Alfred; Lehký, David; Novák, Drahomír

    2017-09-01

    Efficient techniques for both nonlinear numerical analysis of concrete structures and advanced stochastic simulation methods have been combined in order to offer an advanced tool for assessment of realistic behaviour, failure and safety assessment of transport structures. The utilized approach is based on randomization of the non-linear finite element analysis of the structural models. Degradation aspects such as carbonation of concrete can be accounted in order predict durability of the investigated structure and its sustainability. Results can serve as a rational basis for the performance and sustainability assessment based on advanced nonlinear computer analysis of the structures of transport infrastructure such as bridges or tunnels. In the stochastic simulation the input material parameters obtained from material tests including their randomness and uncertainty are represented as random variables or fields. Appropriate identification of material parameters is crucial for the virtual failure modelling of structures and structural elements. Inverse analysis using artificial neural networks and virtual stochastic simulations approach is applied to determine the fracture mechanical parameters of the structural material and its numerical model. Structural response, reliability and sustainability have been investigated on different types of transport structures made from various materials using the above mentioned methodology and tools.

  12. Different methods to alter surface morphology of high aspect ratio structures

    Energy Technology Data Exchange (ETDEWEB)

    Leber, M., E-mail: moritz.leber@utah.edu [Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT (United States); Shandhi, M.M.H. [Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT (United States); Hogan, A. [Blackrock Microsystems, Salt Lake City, UT (United States); Solzbacher, F. [Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT (United States); Bhandari, R.; Negi, S. [Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT (United States); Blackrock Microsystems, Salt Lake City, UT (United States)

    2016-03-01

    Graphical abstract: Surface engineering of high aspect ratio silicon structures. - Highlights: • Multiple roughening techniques for high aspect ratio devices were investigated. • Modification of surface morphology of high aspect ratio silicon devices (1:15). • Decrease of 76% in impedance proves significant increase in surface area. - Abstract: In various applications such as neural prostheses or solar cells, there is a need to alter the surface morphology of high aspect ratio structures so that the real surface area is greater than geometrical area. The change in surface morphology enhances the devices functionality. One of the applications of altering the surface morphology is of neural implants such as the Utah electrode array (UEA) that communicate with single neurons by charge injection induced stimulation or by recording electrical neural signals. For high selectivity between single cells of the nervous system, the electrode surface area is required to be as small as possible, while the impedance is required to be as low as possible for good signal to noise ratios (SNR) during neural recording. For stimulation, high charge injection and charge transfer capacities of the electrodes are required, which increase with the electrode surface. Traditionally, researchers have worked with either increasing the roughness of the existing metallization (platinum grey, black) or other materials such as Iridium Oxide and PEDOT. All of these previously investigated methods lead to more complicated metal deposition processes that are difficult to control and often have a critical impact on the mechanical properties of the metal films. Therefore, a modification of the surface underneath the electrode's coating will increase its surface area while maintaining the standard and well controlled metal deposition process. In this work, the surfaces of the silicon micro-needles were engineered by creating a defined microstructure on the electrodes surface using several

  13. Simultaneous fabrication of very high aspect ratio positive nano- to milliscale structures.

    Science.gov (United States)

    Chen, Long Qing; Chan-Park, Mary B; Zhang, Qing; Chen, Peng; Li, Chang Ming; Li, Sai

    2009-05-01

    A simple and inexpensive technique for the simultaneous fabrication of positive (i.e., protruding), very high aspect (>10) ratio nanostructures together with micro- or millistructures is developed. The method involves using residual patterns of thin-film over-etching (RPTO) to produce sub-micro-/nanoscale features. The residual thin-film nanopattern is used as an etching mask for Si deep reactive ion etching. The etched Si structures are further reduced in size by Si thermal oxidation to produce amorphous SiO(2), which is subsequently etched away by HF. Two arrays of positive Si nanowalls are demonstrated with this combined RPTO-SiO(2)-HF technique. One array has a feature size of 150 nm and an aspect ratio of 26.7 and another has a feature size of 50 nm and an aspect ratio of 15. No other parallel reduction technique can achieve such a very high aspect ratio for 50-nm-wide nanowalls. As a demonstration of the technique to simultaneously achieve nano- and milliscale features, a simple Si nanofluidic master mold with positive features with dimensions varying continuously from 1 mm to 200 nm and a highest aspect ratio of 6.75 is fabricated; the narrow 200-nm section is 4.5 mm long. This Si master mold is then used as a mold for UV embossing. The embossed open channels are then closed by a cover with glue bonding. A high aspect ratio is necessary to produce unblocked closed channels after the cover bonding process of the nanofluidic chip. The combined method of RPTO, Si thermal oxidation, and HF etching can be used to make complex nanofluidic systems and nano-/micro-/millistructures for diverse applications.

  14. Architectural and structural engineering aspects of protective design for nuclear power plants against terrorist attack

    International Nuclear Information System (INIS)

    Musacchio, J.M.; Rozen, A.

    1987-01-01

    This paper presents the results of several threat studies which have been performed, provides collective data on costs, and discusses, in a general sense, architectural/structural aspects of passive protection design measures which have been developed and utilized at several nuclear power plants. By combining relevant architectural and structural measures in the standard design, it is possible to substantially reduce the vulnerability of nuclear power plants to terrorist attack and the estimated damage to a manageable level with a minimal investment. (orig./HP)

  15. Predicting the Proteins of Angomonas deanei, Strigomonas culicis and Their Respective Endosymbionts Reveals New Aspects of the Trypanosomatidae Family

    Science.gov (United States)

    Motta, Maria Cristina Machado; Martins, Allan Cezar de Azevedo; de Souza, Silvana Sant’Anna; Catta-Preta, Carolina Moura Costa; Silva, Rosane; Klein, Cecilia Coimbra; de Almeida, Luiz Gonzaga Paula; de Lima Cunha, Oberdan; Ciapina, Luciane Prioli; Brocchi, Marcelo; Colabardini, Ana Cristina; de Araujo Lima, Bruna; Machado, Carlos Renato; de Almeida Soares, Célia Maria; Probst, Christian Macagnan; de Menezes, Claudia Beatriz Afonso; Thompson, Claudia Elizabeth; Bartholomeu, Daniella Castanheira; Gradia, Daniela Fiori; Pavoni, Daniela Parada; Grisard, Edmundo C.; Fantinatti-Garboggini, Fabiana; Marchini, Fabricio Klerynton; Rodrigues-Luiz, Gabriela Flávia; Wagner, Glauber; Goldman, Gustavo Henrique; Fietto, Juliana Lopes Rangel; Elias, Maria Carolina; Goldman, Maria Helena S.; Sagot, Marie-France; Pereira, Maristela; Stoco, Patrícia H.; de Mendonça-Neto, Rondon Pessoa; Teixeira, Santuza Maria Ribeiro; Maciel, Talles Eduardo Ferreira; de Oliveira Mendes, Tiago Antônio; Ürményi, Turán P.; de Souza, Wanderley; Schenkman, Sergio; de Vasconcelos, Ana Tereza Ribeiro

    2013-01-01

    Endosymbiont-bearing trypanosomatids have been considered excellent models for the study of cell evolution because the host protozoan co-evolves with an intracellular bacterium in a mutualistic relationship. Such protozoa inhabit a single invertebrate host during their entire life cycle and exhibit special characteristics that group them in a particular phylogenetic cluster of the Trypanosomatidae family, thus classified as monoxenics. In an effort to better understand such symbiotic association, we used DNA pyrosequencing and a reference-guided assembly to generate reads that predicted 16,960 and 12,162 open reading frames (ORFs) in two symbiont-bearing trypanosomatids, Angomonas deanei (previously named as Crithidia deanei) and Strigomonas culicis (first known as Blastocrithidia culicis), respectively. Identification of each ORF was based primarily on TriTrypDB using tblastn, and each ORF was confirmed by employing getorf from EMBOSS and Newbler 2.6 when necessary. The monoxenic organisms revealed conserved housekeeping functions when compared to other trypanosomatids, especially compared with Leishmania major. However, major differences were found in ORFs corresponding to the cytoskeleton, the kinetoplast, and the paraflagellar structure. The monoxenic organisms also contain a large number of genes for cytosolic calpain-like and surface gp63 metalloproteases and a reduced number of compartmentalized cysteine proteases in comparison to other TriTryp organisms, reflecting adaptations to the presence of the symbiont. The assembled bacterial endosymbiont sequences exhibit a high A+T content with a total of 787 and 769 ORFs for the Angomonas deanei and Strigomonas culicis endosymbionts, respectively, and indicate that these organisms hold a common ancestor related to the Alcaligenaceae family. Importantly, both symbionts contain enzymes that complement essential host cell biosynthetic pathways, such as those for amino acid, lipid and purine/pyrimidine metabolism

  16. Predicting the proteins of Angomonas deanei, Strigomonas culicis and their respective endosymbionts reveals new aspects of the trypanosomatidae family.

    Directory of Open Access Journals (Sweden)

    Maria Cristina Machado Motta

    Full Text Available Endosymbiont-bearing trypanosomatids have been considered excellent models for the study of cell evolution because the host protozoan co-evolves with an intracellular bacterium in a mutualistic relationship. Such protozoa inhabit a single invertebrate host during their entire life cycle and exhibit special characteristics that group them in a particular phylogenetic cluster of the Trypanosomatidae family, thus classified as monoxenics. In an effort to better understand such symbiotic association, we used DNA pyrosequencing and a reference-guided assembly to generate reads that predicted 16,960 and 12,162 open reading frames (ORFs in two symbiont-bearing trypanosomatids, Angomonas deanei (previously named as Crithidia deanei and Strigomonas culicis (first known as Blastocrithidia culicis, respectively. Identification of each ORF was based primarily on TriTrypDB using tblastn, and each ORF was confirmed by employing getorf from EMBOSS and Newbler 2.6 when necessary. The monoxenic organisms revealed conserved housekeeping functions when compared to other trypanosomatids, especially compared with Leishmania major. However, major differences were found in ORFs corresponding to the cytoskeleton, the kinetoplast, and the paraflagellar structure. The monoxenic organisms also contain a large number of genes for cytosolic calpain-like and surface gp63 metalloproteases and a reduced number of compartmentalized cysteine proteases in comparison to other TriTryp organisms, reflecting adaptations to the presence of the symbiont. The assembled bacterial endosymbiont sequences exhibit a high A+T content with a total of 787 and 769 ORFs for the Angomonas deanei and Strigomonas culicis endosymbionts, respectively, and indicate that these organisms hold a common ancestor related to the Alcaligenaceae family. Importantly, both symbionts contain enzymes that complement essential host cell biosynthetic pathways, such as those for amino acid, lipid and purine

  17. Revealing the Structural Complexity of Component Interactions of Topic-Specific PCK when Planning to Teach

    Science.gov (United States)

    Mavhunga, Elizabeth

    2018-04-01

    Teaching pedagogical content knowledge (PCK) at a topic-specific level requires clarity on the content-specific nature of the components employed, as well as the specific features that bring about the desirable depth in teacher explanations. Such understanding is often hazy; yet, it influences the nature of teacher tasks and learning opportunities afforded to pre-service teachers in a teaching program. The purpose of this study was twofold: firstly, to illuminate the emerging complexity when content-specific components of PCK interact when planning to teach a chemistry topic; and secondly, to identify the kinds of teacher tasks that promote the emergence of such complexity. Data collected were content representations (CoRes) in chemical equilibrium accompanied by expanded lesson outlines from 15 pre-service teachers in their final year of study towards a first degree in teaching (B Ed). The analysis involved extraction of episodes that exhibited component interaction by using a qualitative in-depth analysis method. The results revealed the structure in which the components of PCK in a topic interact among each other to be linear, interwoven, or a combination of the two. The interwoven interactions contained multiple components that connected explanations on different aspects of a concept, all working in a complementary manner. The most sophisticated component interactions emerged from teacher tasks on descriptions of a lesson sequence and a summary of a lesson. Recommendations in this study highlight core practices for making pedagogical transformation of topic content knowledge more accessible.

  18. Superposed ruptile deformational events revealed by field and VOM structural analysis

    Science.gov (United States)

    Kumaira, Sissa; Guadagnin, Felipe; Keller Lautert, Maiara

    2017-04-01

    Virtual outcrop models (VOM) is becoming an important application in the analysis of geological structures due to the possibility of obtaining the geometry and in some cases kinematic aspects of analyzed structures in a tridimensional photorealistic space. These data are used to gain quantitative information on the deformational features which coupled with numeric models can assist in understands deformational processes. Old basement units commonly register superposed deformational events either ductile or ruptile along its evolution. The Porongos Belt, located at southern Brazil, have a complex deformational history registering at least five ductile and ruptile deformational events. In this study, we presents a structural analysis of a quarry in the Porongos Belt, coupling field and VOM structural information to understand process involved in the last two deformational events. Field information was acquired using traditional structural methods for analysis of ruptile structures, such as the descriptions, drawings, acquisition of orientation vectors and kinematic analysis. VOM was created from the image-based modeling method through photogrammetric data acquisition and orthorectification. Photogrammetric data acquisition was acquired using Sony a3500 camera and a total of 128 photographs were taken from ca. 10-20 m from the outcrop in different orientations. Thirty two control point coordinates were acquired using a combination of RTK dGPS surveying and total station work, providing a precision of few millimeters for x, y and z. Photographs were imported into the Photo Scan software to create a 3D dense point cloud from structure from-motion algorithm, which were triangulated and textured to generate the VOM. VOM was georreferenced (oriented and scaled) using the ground control points, and later analyzed in OpenPlot software to extract structural information. Data was imported in Wintensor software to obtain tensor orientations, and Move software to process and

  19. Search and rescue in collapsed structures: engineering and social science aspects.

    Science.gov (United States)

    El-Tawil, Sherif; Aguirre, Benigno

    2010-10-01

    This paper discusses the social science and engineering dimensions of search and rescue (SAR) in collapsed buildings. First, existing information is presented on factors that influence the behaviour of trapped victims, particularly human, physical, socioeconomic and circumstantial factors. Trapped victims are most often discussed in the context of structural collapse and injuries sustained. Most studies in this area focus on earthquakes as the type of disaster that produces the most extensive structural damage. Second, information is set out on the engineering aspects of urban search and rescue (USAR) in the United States, including the role of structural engineers in USAR operations, training and certification of structural specialists, and safety and general procedures. The use of computational simulation to link the engineering and social science aspects of USAR is discussed. This could supplement training of local SAR groups and USAR teams, allowing them to understand better the collapse process and how voids form in a rubble pile. A preliminary simulation tool developed for this purpose is described. © 2010 The Author(s). Journal compilation © Overseas Development Institute, 2010.

  20. Structural analysis of reinforced concrete structures under monotonous and cyclic loadings: numerical aspects

    International Nuclear Information System (INIS)

    Lepretre, C.; Millard, A.; Nahas, G.

    1989-01-01

    The structural analysis of reinforced concrete structures is usually performed either by means of simplified methods of strength of materials type i.e. global methods, or by means of detailed methods of continuum mechanics type, i.e. local methods. For this second type, some constitutive models are available for concrete and rebars in a certain number of finite element systems. These models are often validated on simple homogeneous tests. Therefore, it is important to appraise the validity of the results when applying them to the analysis of a reinforced concrete structure, in order to be able to make correct predictions of the actual behaviour, under normal and faulty conditions. For this purpose, some tests have been performed at I.N.S.A. de Lyon on reinforced concrete beams, subjected to monotonous and cyclic loadings, in order to generate reference solutions to be compared with the numerical predictions given by two finite element systems: - CASTEM, developed by C.E.A./.D.E.M.T. - ELEFINI, developed by I.N.S.A. de Lyon

  1. Ligand induced structural isomerism in phosphine coordinated gold clusters revealed by ion mobility mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Ligare, Marshall R.; Baker, Erin M.; Laskin, Julia; Johnson, Grant E.

    2017-01-01

    Structural isomerism in ligated gold clusters is revealed using electrospray ionization ion mobility spectrometry mass spectrometry. Phosphine ligated Au8 clusters are shown to adopt more “extended” type structures with increasing exchange of methyldiphenylphosphine (MePPh2) for triphenylphosphine (PPh3). These ligand-dependant structure-property relationships are critical to applications of clusters in catalysis.

  2. Microscopic silicon-based lateral high-aspect-ratio structures for thin film conformality analysis

    International Nuclear Information System (INIS)

    Gao, Feng; Arpiainen, Sanna; Puurunen, Riikka L.

    2015-01-01

    Film conformality is one of the major drivers for the interest in atomic layer deposition (ALD) processes. This work presents new silicon-based microscopic lateral high-aspect-ratio (LHAR) test structures for the analysis of the conformality of thin films deposited by ALD and by other chemical vapor deposition means. The microscopic LHAR structures consist of a lateral cavity inside silicon with a roof supported by pillars. The cavity length (e.g., 20–5000 μm) and cavity height (e.g., 200–1000 nm) can be varied, giving aspect ratios of, e.g., 20:1 to 25 000:1. Film conformality can be analyzed with the microscopic LHAR by several means, as demonstrated for the ALD Al 2 O 3 and TiO 2 processes from Me 3 Al/H 2 O and TiCl 4 /H 2 O. The microscopic LHAR test structures introduced in this work expose a new parameter space for thin film conformality investigations expected to prove useful in the development, tuning and modeling of ALD and other chemical vapor deposition processes

  3. Structural aspects of some hydrobenzofuran neolignans; Aspectos estruturais de algumas neolignanas hidrobenzofuranicas

    Energy Technology Data Exchange (ETDEWEB)

    Yoshida, Massayoshi, E-mail: myoshida@iq.usp.br [Universidade de Sao Paulo (IQ/USP), SP (Brazil). Inst. de Quimica; Centro de Biotecnologia da Amazonia, Manaus, AM (Brazil)

    2012-07-01

    The neolignans are defined as dimers of allylphenol and propenylphenol between itself or crossed, whose bond does not occur by the 8-8' carbons like lignans. This review centered on stereochemical aspects of the hydrobenzofuran type, a widespread skeleton among neolignans. The chemical structures established based on spectrometric data are registered in the literature. The absolute configurations reported previously were determined by chiroptical techniques. Some chemical transformations with neolignans, performed in previous studies, afforded products which are accumulated in other vegetal species and contributed to assign the unknown stereochemistry of these natural compounds. Possible biosynthetic pathways are also proposed. (author)

  4. Modeling and characterization of dielectrophoretically structured piezoelectric composites using piezoceramic particle inclusions with high aspect ratios

    Science.gov (United States)

    van den Ende, D. A.; Maier, R. A.; van Neer, P. L. M. J.; van der Zwaag, S.; Randall, C. A.; Groen, W. A.

    2013-01-01

    In this work, the piezoelectric properties at high electric fields of dielectrophoretically aligned PZT—polymer composites containing high aspect ratio particles (such as short fibers) are presented. Polarization and strain as a function of electric field are evaluated. The properties of the composites are compared to those of PZT-polymer composites with equiaxed particles, continuous PZT fiber-polymer composites, and bulk PZT ceramics. From high-field polarization and strain measurements, the effective field dependent permittivity and piezoelectric charge constant in the poling direction are determined for dielectrophoresis structured PZT-polymer composites, continuous PZT fiber-polymer composites, and bulk PZT ceramics. The changes in dielectric properties of the inclusions and the matrix at high fields influence the dielectric and piezoelectric properties of the composites. It is found that the permittivity and piezoelectric charge constants increase towards a maximum at an applied field of around 2.5-5 kV/mm. The electric field at which the maximum occurs depends on the aspect ratio and degree of alignment of the inclusions. Experimental values of d33 at low and high applied fields are compared to a model describing the composites as a continuous polymer matrix containing PZT particles of various aspect ratios arranged into chains. Thickness mode coupling factors were determined from measured impedance data using fitted equivalent circuit model simulations. The relatively high piezoelectric strain constants, voltage constants, and thickness coupling factors indicate that such aligned short fiber composites could be useful as flexible large area transducers.

  5. Social cognitive aspects of the participation in workplace health promotion as revealed by the theory of planned behavior.

    Science.gov (United States)

    Röttger, Stefan; Maier, Johanna; Krex-Brinkmann, Larissa; Kowalski, Jens T; Krick, Annika; Felfe, Jörg; Stein, Michael

    2017-12-01

    Health-promoting efforts strongly depend on individual cognitions such as attitudes as well as social cognitive aspects of the work environment such as leadership and support. Using the theory of planned behavior (TPB) as a theoretical frame, participation behavior of employees in courses offered by the workplace health promotion (WHP) program of the German Armed Forces was investigated. Social cognitive aspects of the work environment, such as leadership behaviors by setting an example or optimizing organization of work, were included in the TPB components of subjective norm and perceived behavioral control, which allowed for an investigation of the specific effects of leadership on WHP participation. A survey study with N=1385 members of the German Armed Forces was conducted in 2015 in Germany. Results showed that perceived behavioral control and attitudes towards WHP were the strongest predictors for WHP participation. While subjective norm was positively related to attitudes, it had a slightly negative effect on intention to participate in WHP activities. These findings suggest that the most effective way for leadership to increase WHP participation is to enhance perceived behavioral control. Quite contrary, creating a positive subjective norm regarding WHP participation may even result in psychological reactance. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. The relationship between sociosexuality and aspects of body image in men and women: a structural equation modeling approach.

    Science.gov (United States)

    Rammsayer, Thomas H; Troche, Stefan J

    2013-10-01

    The present study investigated the association between individual differences in sociosexual orientation and four aspects of body image in 156 male and 136 female students. While men were characterized by a less restricted sociosexual orientation, higher self-perceived physical attractiveness, and more pronounced self-rated physical assertiveness, women placed more emphasis on accentuation of body presentation. Structural equation modeling revealed significant positive relationships between sociosexual attitudes and physical attractiveness and accentuation of body presentation as well as between sociosexual behavior and physical attractiveness for the total sample. When introducing sex as a grouping variable, the attitudinal and behavioral components of sociosexuality were reliably related to both physical attractiveness and accentuation of body presentation as two aspects of body image in men, but not in women. Furthermore, our findings suggest that accentuation of body presentation represents a goal-directed behavior in men to increase the likelihood of having uncommitted sex but serves additional functions widely unrelated to unrestrictive sociosexual behavior in women.

  7. Load assumption for fatigue design of structures and components counting methods, safety aspects, practical application

    CERN Document Server

    Köhler, Michael; Pötter, Kurt; Zenner, Harald

    2017-01-01

    Understanding the fatigue behaviour of structural components under variable load amplitude is an essential prerequisite for safe and reliable light-weight design. For designing and dimensioning, the expected stress (load) is compared with the capacity to withstand loads (fatigue strength). In this process, the safety necessary for each particular application must be ensured. A prerequisite for ensuring the required fatigue strength is a reliable load assumption. The authors describe the transformation of the stress- and load-time functions which have been measured under operational conditions to spectra or matrices with the application of counting methods. The aspects which must be considered for ensuring a reliable load assumption for designing and dimensioning are discussed in detail. Furthermore, the theoretical background for estimating the fatigue life of structural components is explained, and the procedures are discussed for numerous applications in practice. One of the prime intentions of the authors ...

  8. Problematic Alcohol Use and Problem Gambling: Associations to Structural and Functional aspects of Social Ties in a Finnish Population Sample

    Directory of Open Access Journals (Sweden)

    Nordmyr Johanna

    2016-09-01

    Full Text Available AIMS – This study aims to explore associations between structural and functional aspects of social networks and relationships (here labelled social ties among individuals exhibiting problematic alcohol use and problem gambling, respectively.

  9. The Contradictions and Compartmentalizing the Interactions between Integrated Business Structures: Aspect of Branding

    Directory of Open Access Journals (Sweden)

    Nifatova Olena M.

    2017-04-01

    Full Text Available The article is aimed at identifying contradictions and developing a compartmentalizing as to the interaction between integrated business structures, taking into consideration the branding approach to management. The main specific features and contradictions that arise in the process of integration in the domestic market of mergers and acquisitions have been allocated. The contradictions identified were systematized and substantiated at three economic levels: macro-, meso-, and microeconomic. A compartmentalizing of the business units interaction in a merge or an acquisition process has been proposed. This compartmentalizing takes account of the branding aspect through the introduction of «brands interaction» – cluster interaction, circular interaction, holding interaction, linear interaction, which enhances the scientific view of exploring the problem of business units interaction in the process of the formations becoming integrated. The development of a compartmentalizing as to the interaction between integrated business structures, taking into consideration the branding approach to management, would provide a more effective use of the fundamental nature of branding as synergistic force in terms of the system of integration of business structures at the current stage of development of the national economy. Further development of branding issues in this sphere will have a significant impact on the functioning of the integrated business structures with the participation of Ukrainian companies.

  10. Some aspects of the chemistry of fast reactor fuel, structural material and decontamination

    International Nuclear Information System (INIS)

    Ganesan, V.

    2012-01-01

    The chemistry of materials pertaining to fast reactors is both fascinating and challenging considering the nature of materials involved such as the fuel, coolant, control and shielding materials in addition to the interactions between the structural materials and the fuel/coolant depending on the nature and conditions involved. The different chemical forms of fuel materials, the need to operate up to high burnups with consequent interactions of the fuel with clad materials, the need to close the fuel cycle by recovery of the fuel materials from spent fuels for refabrication and the necessity to manage the waste, throw a host of challenges which make their study scientifically interesting and technologically important. The use of liquid sodium as coolant in fast reactor heat transport systems combined with its inherent chemical reactivity opens up an interesting branch of chemistry involving liquid sodium especially in contact with structural materials during normal operation of the reactor and with fuels in the event of fuel pin failure. The phenomenon of sodium wetting and the associated corrosion of structural materials in contact with it combined with the need to carryout decontamination of such materials make it interesting to examine and evaluate their suitability for reuse without compromising on their structural integrity. Boron being the material of choice for control and shielding applications in fast reactors with varying isotopic enrichment and the technological challenge to produce large quantities of boron carbide makes it unique. Some of these aspects are addressed in this paper. (author)

  11. Fabrication of high-aspect-ratio nano structures using a nano x-ray shadow mask

    International Nuclear Information System (INIS)

    Kim, Yong Chul; Lee, Seung S

    2008-01-01

    This paper describes a novel method for the fabrication of high-aspect-ratio nano structures (HAR-nano structures) using a nano x-ray shadow mask and deep x-ray lithography (DXRL). The nano x-ray shadow mask is fabricated by depositing an x-ray absorber layer (Au, 3 µm) onto the back side of a nano shadow mask. The nano shadow mask is produced with nano-sized apertures whose dimensions are reduced to several tens of nanometers by the accumulation of low-stress silicon nitride (Si x N y ) using the LPCVD process on the shadow mask. A shadow mask containing apertures with a size of 1 µm is fabricated on a bulk micromachined Si x N y membrane. The thickness of an absorber layer must be in the range of several tens of micrometers in order to obtain a contrast of more than 100 for the conventional DXRL process at the Pohang Light Source (PLS). However, a 3 µm thick absorber layer can provide a sufficient contrast if the modified DXRL of the central beam-stop method is used, which blocks high-energy x-rays. A nano shadow mask with 30 nm sized apertures is fabricated and a nano x-ray shadow mask with 250 nm sized apertures is fabricated by depositing a 3 µm thick absorber layer on a nano shadow mask with 500 nm sized apertures. HAR-nano structures (circles with a diameter of 420 nm and lines with a width of 274 nm) with aspect ratios of over 10:1 on a 3.2 µm SU-8 are successfully fabricated by using the nano x-ray shadow mask and the central beam-stop method

  12. The structural and content aspects of abstracts versus bodies of full text journal articles are different.

    Science.gov (United States)

    Cohen, K Bretonnel; Johnson, Helen L; Verspoor, Karin; Roeder, Christophe; Hunter, Lawrence E

    2010-09-29

    An increase in work on the full text of journal articles and the growth of PubMedCentral have the opportunity to create a major paradigm shift in how biomedical text mining is done. However, until now there has been no comprehensive characterization of how the bodies of full text journal articles differ from the abstracts that until now have been the subject of most biomedical text mining research. We examined the structural and linguistic aspects of abstracts and bodies of full text articles, the performance of text mining tools on both, and the distribution of a variety of semantic classes of named entities between them. We found marked structural differences, with longer sentences in the article bodies and much heavier use of parenthesized material in the bodies than in the abstracts. We found content differences with respect to linguistic features. Three out of four of the linguistic features that we examined were statistically significantly differently distributed between the two genres. We also found content differences with respect to the distribution of semantic features. There were significantly different densities per thousand words for three out of four semantic classes, and clear differences in the extent to which they appeared in the two genres. With respect to the performance of text mining tools, we found that a mutation finder performed equally well in both genres, but that a wide variety of gene mention systems performed much worse on article bodies than they did on abstracts. POS tagging was also more accurate in abstracts than in article bodies. Aspects of structure and content differ markedly between article abstracts and article bodies. A number of these differences may pose problems as the text mining field moves more into the area of processing full-text articles. However, these differences also present a number of opportunities for the extraction of data types, particularly that found in parenthesized text, that is present in article bodies

  13. Aspect has a greater impact on alpine soil bacterial community structure than elevation.

    Science.gov (United States)

    Wu, Jieyun; Anderson, Barbara J; Buckley, Hannah L; Lewis, Gillian; Lear, Gavin

    2017-03-01

    Gradients in environmental conditions, including climate factors and resource availability, occur along mountain inclines, providing a 'natural laboratory' to explore their combined impacts on microbial distributions. Conflicting spatial patterns observed across elevation gradients in soil bacterial community structure suggest that they are driven by various interacting factors at different spatial scales. Here, we investigated the relative impacts of non-resource (e.g. soil temperature, pH) and resource conditions (e.g. soil carbon and nitrogen) on the biogeography of soil bacterial communities across broad (i.e. along a 1500 m mountain elevation gradient) and fine sampling scales (i.e. along sunny and shady aspects of a mountain ridge). Our analysis of 16S rRNA gene data confirmed that when sampling across distances of soil pH. These findings highlight the need to incorporate knowledge of multiple factors, including site aspect and soil pH for the appropriate use of elevation gradients as a proxy to explore the impacts of climate change on microbial community composition. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. The vortex structure and flux creep within superconducting permanent-magnet high aspect-ratio discs

    International Nuclear Information System (INIS)

    Watson, J.H.P.; Younas, I.

    1997-01-01

    Inhomogeneous type II superconducting discs magnetized by an applied field will retain some magnetization when field is switched off so the superconducting disc will behave as a permanent magnet after flux creep has reduced to a low value.This paper examines the superconducting vortex structure within superconducting permanent-magnet high aspect-ratio discs which is consistent with the calculated magnetic field distribution.The discs, with radius R, have the axis along the z-direction and the mid-plane of the disc corresponds to z = 0. These discs with large aspect ratios in the remnant state have a region between radius r l and R where the magnetic field is reversed. Surrounding the line r = r l and z = 0 there is a region where H cl which is in the Meissner state. Near r l the vortex lines are strongly curved. For radii r l vortex lines creep to larger values of r. For radii r > r l vortex lines creep to smaller values of r, meet at r l with vortex lines of opposite sign and form a continuous loop which decreases in size and is finally annihilated in the Meissner region. Flux creep induces lossless currents in the Meissner region. (author)

  15. Scale for positive aspects of caregiving experience: development, reliability, and factor structure.

    Science.gov (United States)

    Kate, N; Grover, S; Kulhara, P; Nehra, R

    2012-06-01

    OBJECTIVE. To develop an instrument (Scale for Positive Aspects of Caregiving Experience [SPACE]) that evaluates positive caregiving experience and assess its psychometric properties. METHODS. Available scales which assess some aspects of positive caregiving experience were reviewed and a 50-item questionnaire with a 5-point rating was constructed. In all, 203 primary caregivers of patients with severe mental disorders were asked to complete the questionnaire. Internal consistency, test-retest reliability, cross-language reliability, split-half reliability, and face validity were evaluated. Principal component factor analysis was run to assess the factorial validity of the scale. RESULTS. The scale developed as part of the study was found to have good internal consistency, test-retest reliability, cross-language reliability, split-half reliability, and face validity. Principal component factor analysis yielded a 4-factor structure, which also had good test-retest reliability and cross-language reliability. There was a strong correlation between the 4 factors obtained. CONCLUSION. The SPACE developed as part of this study has good psychometric properties.

  16. Simulation and Measurement of Neuroelectrodes' Characteristics with Integrated High Aspect Ratio Nano Structures

    Directory of Open Access Journals (Sweden)

    Christoph Nick

    2015-07-01

    Full Text Available Improving the interface between electrodes and neurons has been the focus of research for the last decade. Neuroelectrodes should show small geometrical surface area and low impedance for measuring and high charge injection capacities for stimulation. Increasing the electrochemically active surface area by using nanoporous electrode material or by integrating nanostructures onto planar electrodes is a common approach to improve this interface. In this paper a simulation approach for neuro electrodes' characteristics with integrated high aspect ratio nano structures based on a point-contact-model is presented. The results are compared with experimental findings conducted with real nanostructured microelectrodes. In particular, effects of carbon nanotubes and gold nanowires integrated onto microelectrodes are described. Simulated and measured impedance properties are presented and its effects onto the transfer function between the neural membrane potential and the amplifier output signal are studied based on the point-contact-model. Simulations show, in good agreement with experimental results, that electrode impedances can be dramatically reduced by the integration of high aspect ratio nanostructures such as gold nanowires and carbon nanotubes. This lowers thermal noise and improves the signal-to-noise ratio for measuring electrodes. It also may increase the adhesion of cells to the substrate and thus increase measurable signal amplitudes.

  17. Structural, Chemical and Biological Aspects of Antioxidants for Strategies Against Metal and Metalloid Exposure

    Directory of Open Access Journals (Sweden)

    Swaran J. S. Flora

    2009-01-01

    Full Text Available Oxidative stress contributes to the pathophysiology of exposure to heavy metals/metalloid. Beneficial renal effects of some medications, such as chelation therapy depend at least partially on the ability to alleviate oxidative stress. The administration of various natural or synthetic antioxidants has been shown to be of benefit in the prevention and attenuation of metal induced biochemical alterations. These include vitamins, N-acetylcysteine, α-lipoic acid, melatonin, dietary flavonoids and many others. Human studies are limited in this regard. Under certain conditions, surprisingly, the antioxidant supplements may exhibit pro-oxidant properties and even worsen metal induced toxic damage. To date, the evidence is insufficient to recommend antioxidant supplements in subject with exposure to metals. Prospective, controlled clinical trials on safety and effectiveness of different therapeutic antioxidant strategies either individually or in combination with chelating agent are indispensable. The present review focuses on structural, chemical and biological aspects of antioxidants particularly related to their chelating properties.

  18. Structural design aspects of magnetic coils for a linear theta-pinch hybrid reactor

    International Nuclear Information System (INIS)

    Bartholomew, R.J.

    1976-02-01

    The structural design aspects of a linear theta-pinch hybrid reactor (LTPHR) are centered in the solenoidal adiabatic compression coil (ACC) which must support the high magnetic pulse forces that tend to expand the coil and separate the leads. The structural model is represented by the theory of elasticity solution to a thick-walled cylinder. Dynamic amplification (or attenuation) is considered by a shock spectrum technique. A composite material is postulated, where the conductor material for each strand is clad with a high-strength stainless steel with insulation considered. Yield strength (for isolated-pulse operation) and endurance limit (for repetitive-pulse operation) for the high-strength steel impose magnetic field strength constraints on the coil design. These constraints are combined in an overall energy balance calculation that includes neutronic considerations to determine an optimum ACC design. The computer code ENBAL was used to incorporate neutronic, electrical, and structural constraints into the overall energy balance of the LTPHR. The lead separation problem is solved by designing spaced clamps to hold the leads together over great distances

  19. Topology optimization aided structural design: Interpretation, computational aspects and 3D printing.

    Science.gov (United States)

    Kazakis, Georgios; Kanellopoulos, Ioannis; Sotiropoulos, Stefanos; Lagaros, Nikos D

    2017-10-01

    Construction industry has a major impact on the environment that we spend most of our life. Therefore, it is important that the outcome of architectural intuition performs well and complies with the design requirements. Architects usually describe as "optimal design" their choice among a rather limited set of design alternatives, dictated by their experience and intuition. However, modern design of structures requires accounting for a great number of criteria derived from multiple disciplines, often of conflicting nature. Such criteria derived from structural engineering, eco-design, bioclimatic and acoustic performance. The resulting vast number of alternatives enhances the need for computer-aided architecture in order to increase the possibility of arriving at a more preferable solution. Therefore, the incorporation of smart, automatic tools in the design process, able to further guide designer's intuition becomes even more indispensable. The principal aim of this study is to present possibilities to integrate automatic computational techniques related to topology optimization in the phase of intuition of civil structures as part of computer aided architectural design. In this direction, different aspects of a new computer aided architectural era related to the interpretation of the optimized designs, difficulties resulted from the increased computational effort and 3D printing capabilities are covered here in.

  20. Aspergillus niger biofilms for celulasas production: some structural and physiological aspects

    Directory of Open Access Journals (Sweden)

    Gretty K. Villena

    2013-06-01

    Full Text Available Aspergillus niger biofilms developed on polyester cloth were evaluated considering two aspects related to the growth on surfaces: structure and physiological behavior focused on cellulase production. The biofilm structure was assessed by using electron scanning microphotographs from inoculation and adsorption to 120 h growth. The microphotographs show that biofilm formation can be divided into three phases: 1 Adhesion, which is strongly increased by Aspergillus spore hydrophobicity; 2 Initial growth and development phase from spore germination, that begins 4 to 10 h after inoculation and continues up to 24 h when almost all available surface has been colonized; 3 Maturation phase in which biomass density is highly increased from 48 h after inoculation until 120 h growth when an internal channel organization that assures medium flow through biofilm is clearly evident as it is frequently reported for bacterial biofilms.Biofilm cellulolytic enzyme activity and productivity were also evaluated, being up to 40% and 55%, respectively, higher than that attained by freely suspended cultures. These results are in agreement with the behavior of most surface living microorganisms, which generally show a higher metabolic activity because of a differential gene expression. This work is a first attempt to understand the structure and physiology of industrial filamentous fungal biofilms as a response to the scarce available information in comparison with the vast and detailed information related to bacterial and pathogenic yeast biofilms.

  1. A Reformulation of the Dual Career Conceptual Model for Analysis in an Organizational Scope: Revealing new Aspects

    Directory of Open Access Journals (Sweden)

    Heliani Berlato

    2017-01-01

    Full Text Available Couples who live a dual career, in general, are characterized by their continuing professional engagement and their desire for personal growth together. It is a synergy between career aspirations and family sphere, so that they co-exist; reflecting nowadays, a challenge for people who seek to live this duality. Not exempt from it, it is possible to understand the need for management models of people who are in harmony with the desires of dual career couples who are part of organizations. If in the 1980s the existence of dual career couples was not so common in Brazil, nowadays organizations increasingly receive these couples, which impacts the need for people management models to keep up with these social changes. Therefore, the model recognizes that the personal dimension (impacts on the organizational context cannot be avoided, and also that other factors affect both spheres (personal and organizational when referring to the normative roles that permeate these areas. The main intention of this essay is to construct a theoretical model of dual career to consider the factor - organization, as vital to understand (and accept the need to consider other dimensions on the dual career analytical perspective. The first evidences of dual career studies in Brazil revealed that the look at this movement only from the individual's margin is limited. This way, to consider the existence of other dimensions and consequently the influences they may cause, favors an expansion of the perspective, and also brings a detailing about the external factors (organization, society and culture that influence the dual career couple. To consider that this couple, as well as having personal challenges in the relationship between work and family, is subject to the culture that regulates their roles (men and women and that directly influences how organizations will handle that topic reveals the merit of this study. This, in turn, draws attention to the organizational sphere

  2. Exotic nuclei: another aspect of nuclear structure; Les noyaux exotiques: un autre regard sur la structure nucleaire

    Energy Technology Data Exchange (ETDEWEB)

    Dobaczewski, J [Warsaw Univ., Institute of Theoretical Physics (Poland); Blumenfeld, Y; Flocard, H; Garcia Borge, M J; Nowacki, F; Rombouts, S; Theisen, Ch; Marques, F M; Lacroix, D; Dessagne, P; Gaeggeler, H

    2002-07-01

    This document gathers the lectures made at the Joliot Curie international summer school in 2002 whose theme that year was exotic nuclei. There were 11 contributions whose titles are: 1) interactions, symmetry breaking and effective fields from quarks to nuclei; 2) status and perspectives for the study of exotic nuclei: experimental aspects; 3) the pairing interaction and the N = Z nuclei; 4) borders of stability region and exotic decays; 5) shell structure of nuclei: from stability to decay; 6) variational approach of system with a few nucleons; 7) from heavy to super-heavy nuclei; 8) halos, molecules and multi-neutrons; 9) macroscopic approaches for fusion reactions; 10) beta decay: a tool for spectroscopy; 11) the gas phase chemistry of super-heavy elements.

  3. High Potential Source for Biomass Degradation Enzyme Discovery and Environmental Aspects Revealed through Metagenomics of Indian Buffalo Rumen

    Directory of Open Access Journals (Sweden)

    K. M. Singh

    2014-01-01

    Full Text Available The complex microbiomes of the rumen functions as an effective system for plant cell wall degradation, and biomass utilization provide genetic resource for degrading microbial enzymes that could be used in the production of biofuel. Therefore the buffalo rumen microbiota was surveyed using shot gun sequencing. This metagenomic sequencing generated 3.9 GB of sequences and data were assembled into 137270 contiguous sequences (contigs. We identified potential 2614 contigs encoding biomass degrading enzymes including glycoside hydrolases (GH: 1943 contigs, carbohydrate binding module (CBM: 23 contigs, glycosyl transferase (GT: 373 contigs, carbohydrate esterases (CE: 259 contigs, and polysaccharide lyases (PE: 16 contigs. The hierarchical clustering of buffalo metagenomes demonstrated the similarities and dissimilarity in microbial community structures and functional capacity. This demonstrates that buffalo rumen microbiome was considerably enriched in functional genes involved in polysaccharide degradation with great prospects to obtain new molecules that may be applied in the biofuel industry.

  4. Application of a new dual localization-affinity purification tag reveals novel aspects of protein kinase biology in Aspergillus nidulans.

    Science.gov (United States)

    De Souza, Colin P; Hashmi, Shahr B; Osmani, Aysha H; Osmani, Stephen A

    2014-01-01

    Filamentous fungi occupy critical environmental niches and have numerous beneficial industrial applications but devastating effects as pathogens and agents of food spoilage. As regulators of essentially all biological processes protein kinases have been intensively studied but how they regulate the often unique biology of filamentous fungi is not completely understood. Significant understanding of filamentous fungal biology has come from the study of the model organism Aspergillus nidulans using a combination of molecular genetics, biochemistry, cell biology and genomic approaches. Here we describe dual localization-affinity purification (DLAP) tags enabling endogenous N or C-terminal protein tagging for localization and biochemical studies in A. nidulans. To establish DLAP tag utility we endogenously tagged 17 protein kinases for analysis by live cell imaging and affinity purification. Proteomic analysis of purifications by mass spectrometry confirmed association of the CotA and NimXCdk1 kinases with known binding partners and verified a predicted interaction of the SldABub1/R1 spindle assembly checkpoint kinase with SldBBub3. We demonstrate that the single TOR kinase of A. nidulans locates to vacuoles and vesicles, suggesting that the function of endomembranes as major TOR cellular hubs is conserved in filamentous fungi. Comparative analysis revealed 7 kinases with mitotic specific locations including An-Cdc7 which unexpectedly located to mitotic spindle pole bodies (SPBs), the first such localization described for this family of DNA replication kinases. We show that the SepH septation kinase locates to SPBs specifically in the basal region of apical cells in a biphasic manner during mitosis and again during septation. This results in gradients of SepH between G1 SPBs which shift along hyphae as each septum forms. We propose that SepH regulates the septation initiation network (SIN) specifically at SPBs in the basal region of G1 cells and that localized gradients

  5. Segment polarity gene expression in a myriapod reveals conserved and diverged aspects of early head patterning in arthropods.

    Science.gov (United States)

    Janssen, Ralf

    2012-09-01

    Arthropods show two kinds of developmental mode. In the so-called long germ developmental mode (as exemplified by the fly Drosophila), all segments are formed almost simultaneously from a preexisting field of cells. In contrast, in the so-called short germ developmental mode (as exemplified by the vast majority of arthropods), only the anterior segments are patterned similarly as in Drosophila, and posterior segments are added in a single or double segmental periodicity from a posterior segment addition zone (SAZ). The addition of segments from the SAZ is controlled by dynamic waves of gene activity. Recent studies on a spider have revealed that a similar dynamic process, involving expression of the segment polarity gene (SPG) hedgehog (hh), is involved in the formation of the anterior head segments. The present study shows that in the myriapod Glomeris marginata the early expression of hh is also in a broad anterior domain, but this domain corresponds only to the ocular and antennal segment. It does not, like in spiders, represent expression in the posterior adjacent segment. In contrast, the anterior hh pattern is conserved in Glomeris and insects. All investigated myriapod SPGs and associated factors are expressed with delay in the premandibular (tritocerebral) segment. This delay is exclusively found in insects and myriapods, but not in chelicerates, crustaceans and onychophorans. Therefore, it may represent a synapomorphy uniting insects and myriapods (Atelocerata hypothesis), contradicting the leading opinion that suggests a sister relationship of crustaceans and insects (Pancrustacea hypothesis). In Glomeris embryos, the SPG engrailed is first expressed in the mandibular segment. This feature is conserved in representatives of all arthropod classes suggesting that the mandibular segment may have a special function in anterior patterning.

  6. Calorimetric Studies and Structural Aspects of Ionic Liquids in Designing Sorption Materials for Thermal Energy Storage.

    Science.gov (United States)

    Brünig, Thorge; Krekić, Kristijan; Bruhn, Clemens; Pietschnig, Rudolf

    2016-11-02

    The thermal properties of a series of twenty-four ionic liquids (ILs) have been determined by isothermal titration calorimetry (ITC) with the aim of simulating processes involving water sorption. For eleven water-free ILs, the molecular structures have been determined by X-ray crystallography in the solid state, which have been used to derive the molecular volumes of the ionic components of the ILs. Moreover, the structures reveal a high prevalence of hydrogen bonding in these compounds. A relationship between the molecular volumes and the experimentally determined energies of dilution could be established. The highest energies of dilution observed in this series were obtained for the acetate-based ILs, which underlines their potential as working fluids in sorption-based thermal energy storage systems. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Powder X-ray diffraction studies of structural and kinetic aspects of polymorphism

    International Nuclear Information System (INIS)

    Chan, F.C.

    1999-01-01

    Polymorphism is a poorly understood phenomenon that is of considerable technological interest to the pharmaceutical industry. The polymorph selected can influence the bioavailability, processing and stability of the pharmaceutical dosage form. In this study structural, kinetic and thermodynamics aspects of polymorphism and polymorphic phase transformations have been examined using powder X-ray diffraction (PXRD). The compound sulphathiazole is a well-studied model in the investigation of polymorphism and crystal growth. There are five known polymorphic forms and the structure of form V was unknown until this study. The difficulty has been that it has not been possibly to prepare crystals of appropriate size and quality for single crystal diffraction. Furthermore, structure solution from powder data for organic molecules is almost impossible. Despite the challenge the structure of sulphathiazole form V have been solved ab initio from powder data using direct methods. With 16 non-hydrogen atoms in the molecule and two molecules in the asymmetric unit, this structure represents a significant advance in terms of the complexity of an organic structure solved from PXRD data. The structural data should be invaluable for rationalizing experimental observations and the development of theoretical ideas regarding polymorphism and crystal growth. The second part of the study, has examined kinetics of polymorphic phase transformations as a function of pressure combined with temperature using real-time synchrotron PXRD. The significance of pressure arises from the fact that phase transitions can be induced in pharmaceuticals during tabletting. The phase transformation behaviour of rubidium iodide (chosen as a simple test model) has been investigated as a function of isobaric pressure at ambient and elevated temperatures. The kinetics have been characterized by using the Johnson-Melil-Avrami equation. The effect of successive cycling across the transition pressure was also

  8. Aspects of the design and structural analysis of the prestressed cast iron nuclear reactor pressure vessel

    International Nuclear Information System (INIS)

    Thomas, R.G.

    1978-09-01

    The development of the prestressed cast iron nuclear reactor pressure vessel up to the present time is reviewed, and the current status is outlined of the techniques used for its structural analysis. Details of the manufacturing processes involved in the production of the castings, and problems of inspecting them to the standards required for a nuclear application are discussed. A method for the detailed modelling of the cast iron segments is proposed, using the finite element technique with plate bending elements, and criteria for obtaining accurate results are derived. The application of the technique to the analysis of a single cast segment situated in the wall of a PCIPV has enabled an accurate determination of the stress field to be made. Account is taken of the effect of the vessel displacements on the tendon stresses at normal vault pressure and at high overpressure. Studies by this method of several different casting designs have identified favourable features, which have been incorporated into an optimised design. The sensitivity of the structure to a machining error in a casting and to the failure or removal of circumferential and axial tendons is examined, making use of axisymmetric and three-dimensional global finite element solutions to provide boundary conditions for detailed local analyses. Some aspects of the economics of the cast iron reactor pressure vessel are discussed, and recommendations are made for further research in areas relevant to the assessment of the reliability of the vessel. (author)

  9. Bosch-like method for creating high aspect ratio poly(methyl methacrylate) (PMMA) structures

    KAUST Repository

    Haiducu, Marius

    2012-02-02

    This paper presents a method for etching millimetre-deep trenches in commercial grade PMMA using deep-UV at 254 nm. The method is based on consecutive cycles of irradiation and development of the exposed areas, respectively. The exposure segment is performed using an inexpensive, in-house built irradiation box while the development part is accomplished using an isopropyl alcohol (IPA):H2O developer. The method was tested and characterized by etching various dimension square test structures in commercial grade, mirrored acrylic. The undercut of the sidewalls due to the uncollimated nature of the irradiation light was dramatically alleviated by using a honeycomb metallic grid in between the irradiation source and the acrylic substrate and by rotating the latter using a direct current (DC) motor-driven stage. By using an extremely affordable set-up and non-toxic, environmentally friendly materials and substances, this process represents an excellent alternative to microfabricating microfluidic devices in particular and high aspect ratio structures in general using PMMA as substrate. © 2012 SPIE.

  10. Revealing the correlation between real-space structure and chiral magnetic order at the atomic scale

    Science.gov (United States)

    Hauptmann, Nadine; Dupé, Melanie; Hung, Tzu-Chao; Lemmens, Alexander K.; Wegner, Daniel; Dupé, Bertrand; Khajetoorians, Alexander A.

    2018-03-01

    We image simultaneously the geometric, the electronic, and the magnetic structures of a buckled iron bilayer film that exhibits chiral magnetic order. We achieve this by combining spin-polarized scanning tunneling microscopy and magnetic exchange force microscopy (SPEX) to independently characterize the geometric as well as the electronic and magnetic structures of nonflat surfaces. This new SPEX imaging technique reveals the geometric height corrugation of the reconstruction lines resulting from strong strain relaxation in the bilayer, enabling the decomposition of the real-space from the electronic structure at the atomic level and the correlation with the resultant spin-spiral ground state. By additionally utilizing adatom manipulation, we reveal the chiral magnetic ground state of portions of the unit cell that were not previously imaged with spin-polarized scanning tunneling microscopy alone. Using density functional theory, we investigate the structural and electronic properties of the reconstructed bilayer and identify the favorable stoichiometry regime in agreement with our experimental result.

  11. Hydra meiosis reveals unexpected conservation of structural synaptonemal complex proteins across metazoans

    OpenAIRE

    Fraune, Johanna; Alsheimer, Manfred; Volff, Jean-Nicolas; Busch, Karoline; Fraune, Sebastian; Bosch, Thomas C. G.; Benavente, Ricardo

    2012-01-01

    The synaptonemal complex (SC) is a key structure of meiosis, mediating the stable pairing (synapsis) of homologous chromosomes during prophase I. Its remarkable tripartite structure is evolutionarily well conserved and can be found in almost all sexually reproducing organisms. However, comparison of the different SC protein components in the common meiosis model organisms Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, and Mus musculus revealed...

  12. Characterization of dermal plates from armored catfish Pterygoplichthys pardalis reveals sandwich-like nanocomposite structure.

    Science.gov (United States)

    Ebenstein, Donna; Calderon, Carlos; Troncoso, Omar P; Torres, Fernando G

    2015-05-01

    Dermal plates from armored catfish are bony structures that cover their body. In this paper we characterized structural, chemical, and nanomechanical properties of the dermal plates from the Amazonian fish Pterygoplichthys pardalis. Analysis of the morphology of the plates using scanning electron microscopy (SEM) revealed that the dermal plates have a sandwich-like structure composed of an inner porous matrix surrounded by two external dense layers. This is different from the plywood-like laminated structure of elasmoid fish scales but similar to the structure of osteoderms found in the dermal armour of some reptiles and mammals. Chemical analysis performed using Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC) and X-ray diffraction (XRD) results revealed similarities between the composition of P. pardalis plates and the elasmoid fish scales of Arapaima gigas. Reduced moduli of P. pardalis plates measured using nanoindentation were also consistent with reported values for A. gigas scales, but further revealed that the dermal plate is an anisotropic and heterogeneous material, similar to many other fish scales and osteoderms. It is postulated that the sandwich-like structure of the dermal plates provides a lightweight and tough protective layer. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Crystal structure of a small heat-shock protein from Xylella fastidiosa reveals a distinct high-order structure.

    Science.gov (United States)

    Fonseca, Emanuella Maria Barreto; Scorsato, Valéria; Dos Santos, Marcelo Leite; Júnior, Atilio Tomazini; Tada, Susely Ferraz Siqueira; Dos Santos, Clelton Aparecido; de Toledo, Marcelo Augusto Szymanski; de Souza, Anete Pereira; Polikarpov, Igor; Aparicio, Ricardo

    2017-04-01

    Citrus variegated chlorosis is a disease that attacks economically important citrus plantations and is caused by the plant-pathogenic bacterium Xylella fastidiosa. In this work, the structure of a small heat-shock protein from X. fastidiosa (XfsHSP17.9) is reported. The high-order structures of small heat-shock proteins from other organisms are arranged in the forms of double-disc, hollow-sphere or spherical assemblies. Unexpectedly, the structure reported here reveals a high-order architecture forming a nearly square cavity.

  14. Analyzing the structural aspects of Isoprenoid biosynthesis pathway proteins in Ocimum species

    Directory of Open Access Journals (Sweden)

    Muktesh Chandra

    2017-10-01

    Full Text Available Generally thought that the extremely diverse array of secondary metabolites observed within Ocimum species defends against a comparable diverse array of biotic pests, pathogens and herbivores encountered around its natural range. Along with defense the diverse array of secondary metabolite also leads to the therapeutic and remedial property which justifies Ocimum as natural medicinal and aromatic casket. Many of the defense compounds, aroma compounds and medicinal derivatives are secondary metabolites isolated from trichome glands, mainly consist of terpenoids as well as phenylpropanoids. Various pathways fabricating these compounds are known viz. mevalonate pathway (MVA, phenylpropanoid pathway and MEP pathways. The enzyme cascade responsible for various secondary metabolites, need to be explored in various aspects. Here we had studied the MVA pathway enzymes in O. basilicum and O. gratissimum to figure out variations in enzyme structures due to speciation. Hence, in depth analysis of the transcriptome of O. basilicum and O. gratissimum, varrying in qualitative and quantitative aspects of essential oil were carried out. The transcriptome data from NCBI server was assembled using bioinformatic approaches. nr database at NCBI repository used for annotation, which assigned 60% contigs to known functions. Contigs corresponding to Mevalonate pathway enzymes are isolated using perl pipelines developed in our lab, which were further assembled using CLC workbench to remove redundancy and make larger stretch of sequence. Blastx of these larger sequences assigned them function and they are mapped to validated sequences to make full length. Data from both species led us to overall seven enzymes (total 14 of MVA pathway. These enzymes are studied in detail for various physio-chemical properties, steriochemical properties and motif/domain for protein-protein interaction (PPI study. Homolog models of all enzymes were predicted, against templates from RCSB

  15. 5-HT2C Receptor Structures Reveal the Structural Basis of GPCR Polypharmacology

    DEFF Research Database (Denmark)

    Peng, Yao; Mccorvy, John D.; Harpsøe, Kasper

    2018-01-01

    Drugs frequently require interactions with multiple targets—via a process known as polypharmacology—to achieve their therapeutic actions. Currently, drugs targeting several serotonin receptors, including the 5-HT2C receptor, are useful for treating obesity, drug abuse, and schizophrenia. The comp...... the structural basis of polypharmacology at canonical GPCRs and illustrates how understanding characteristic patterns of ligand-receptor interaction and activation may ultimately facilitate drug design at multiple GPCRs....

  16. Structural fragment clustering reveals novel structural and functional motifs in α-helical transmembrane proteins

    Directory of Open Access Journals (Sweden)

    Vassilev Boris

    2010-04-01

    Full Text Available Abstract Background A large proportion of an organism's genome encodes for membrane proteins. Membrane proteins are important for many cellular processes, and several diseases can be linked to mutations in them. With the tremendous growth of sequence data, there is an increasing need to reliably identify membrane proteins from sequence, to functionally annotate them, and to correctly predict their topology. Results We introduce a technique called structural fragment clustering, which learns sequential motifs from 3D structural fragments. From over 500,000 fragments, we obtain 213 statistically significant, non-redundant, and novel motifs that are highly specific to α-helical transmembrane proteins. From these 213 motifs, 58 of them were assigned to function and checked in the scientific literature for a biological assessment. Seventy percent of the motifs are found in co-factor, ligand, and ion binding sites, 30% at protein interaction interfaces, and 12% bind specific lipids such as glycerol or cardiolipins. The vast majority of motifs (94% appear across evolutionarily unrelated families, highlighting the modularity of functional design in membrane proteins. We describe three novel motifs in detail: (1 a dimer interface motif found in voltage-gated chloride channels, (2 a proton transfer motif found in heme-copper oxidases, and (3 a convergently evolved interface helix motif found in an aspartate symporter, a serine protease, and cytochrome b. Conclusions Our findings suggest that functional modules exist in membrane proteins, and that they occur in completely different evolutionary contexts and cover different binding sites. Structural fragment clustering allows us to link sequence motifs to function through clusters of structural fragments. The sequence motifs can be applied to identify and characterize membrane proteins in novel genomes.

  17. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.

    Science.gov (United States)

    Ding, Yiliang; Tang, Yin; Kwok, Chun Kit; Zhang, Yu; Bevilacqua, Philip C; Assmann, Sarah M

    2014-01-30

    RNA structure has critical roles in processes ranging from ligand sensing to the regulation of translation, polyadenylation and splicing. However, a lack of genome-wide in vivo RNA structural data has limited our understanding of how RNA structure regulates gene expression in living cells. Here we present a high-throughput, genome-wide in vivo RNA structure probing method, structure-seq, in which dimethyl sulphate methylation of unprotected adenines and cytosines is identified by next-generation sequencing. Application of this method to Arabidopsis thaliana seedlings yielded the first in vivo genome-wide RNA structure map at nucleotide resolution for any organism, with quantitative structural information across more than 10,000 transcripts. Our analysis reveals a three-nucleotide periodic repeat pattern in the structure of coding regions, as well as a less-structured region immediately upstream of the start codon, and shows that these features are strongly correlated with translation efficiency. We also find patterns of strong and weak secondary structure at sites of alternative polyadenylation, as well as strong secondary structure at 5' splice sites that correlates with unspliced events. Notably, in vivo structures of messenger RNAs annotated for stress responses are poorly predicted in silico, whereas mRNA structures of genes related to cell function maintenance are well predicted. Global comparison of several structural features between these two categories shows that the mRNAs associated with stress responses tend to have more single-strandedness, longer maximal loop length and higher free energy per nucleotide, features that may allow these RNAs to undergo conformational changes in response to environmental conditions. Structure-seq allows the RNA structurome and its biological roles to be interrogated on a genome-wide scale and should be applicable to any organism.

  18. The crystal structures of EAP domains from Staphylococcus aureus reveal an unexpected homology to bacterial superantigens.

    Science.gov (United States)

    Geisbrecht, Brian V; Hamaoka, Brent Y; Perman, Benjamin; Zemla, Adam; Leahy, Daniel J

    2005-04-29

    The Eap (extracellular adherence protein) of Staphylococcus aureus functions as a secreted virulence factor by mediating interactions between the bacterial cell surface and several extracellular host proteins. Eap proteins from different Staphylococcal strains consist of four to six tandem repeats of a structurally uncharacterized domain (EAP domain). We have determined the three-dimensional structures of three different EAP domains to 1.8, 2.2, and 1.35 A resolution, respectively. These structures reveal a core fold that is comprised of an alpha-helix lying diagonally across a five-stranded, mixed beta-sheet. Comparison of EAP domains with known structures reveals an unexpected homology with the C-terminal domain of bacterial superantigens. Examination of the structure of the superantigen SEC2 bound to the beta-chain of a T-cell receptor suggests a possible ligand-binding site within the EAP domain (Fields, B. A., Malchiodi, E. L., Li, H., Ysern, X., Stauffacher, C. V., Schlievert, P. M., Karjalainen, K., and Mariuzza, R. (1996) Nature 384, 188-192). These results provide the first structural characterization of EAP domains, relate EAP domains to a large class of bacterial toxins, and will guide the design of future experiments to analyze EAP domain structure/function relationships.

  19. Hydra meiosis reveals unexpected conservation of structural synaptonemal complex proteins across metazoans.

    Science.gov (United States)

    Fraune, Johanna; Alsheimer, Manfred; Volff, Jean-Nicolas; Busch, Karoline; Fraune, Sebastian; Bosch, Thomas C G; Benavente, Ricardo

    2012-10-09

    The synaptonemal complex (SC) is a key structure of meiosis, mediating the stable pairing (synapsis) of homologous chromosomes during prophase I. Its remarkable tripartite structure is evolutionarily well conserved and can be found in almost all sexually reproducing organisms. However, comparison of the different SC protein components in the common meiosis model organisms Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, and Mus musculus revealed no sequence homology. This discrepancy challenged the hypothesis that the SC arose only once in evolution. To pursue this matter we focused on the evolution of SYCP1 and SYCP3, the two major structural SC proteins of mammals. Remarkably, our comparative bioinformatic and expression studies revealed that SYCP1 and SYCP3 are also components of the SC in the basal metazoan Hydra. In contrast to previous assumptions, we therefore conclude that SYCP1 and SYCP3 form monophyletic groups of orthologous proteins across metazoans.

  20. High-aspect-ratio, silicon oxide-enclosed pillar structures in microfluidic liquid chromatography.

    Science.gov (United States)

    Taylor, Lisa C; Lavrik, Nickolay V; Sepaniak, Michael J

    2010-11-15

    The present paper discusses the ability to separate chemical species using high-aspect-ratio, silicon oxide-enclosed pillar arrays. These miniaturized chromatographic systems require smaller sample volumes, experience less flow resistance, and generate superior separation efficiency over traditional packed bed liquid chromatographic columns, improvements controlled by the increased order and decreased pore size of the systems. In our distinctive fabrication sequence, plasma-enhanced chemical vapor deposition (PECVD) of silicon oxide is used to alter the surface and structural properties of the pillars for facile surface modification while improving the pillar mechanical stability and increasing surface area. The separation behavior of model compounds within our pillar systems indicated an unexpected hydrophobic-like separation mechanism. The effects of organic modifier, ionic concentration, and pressure-driven flow rate were studied. A decrease in the organic content of the mobile phase increased peak resolution while detrimentally effecting peak shape. A resolution of 4.7 (RSD = 3.7%) was obtained for nearly perfect Gaussian shaped peaks, exhibiting plate heights as low as 1.1 and 1.8 μm for fluorescein and sulforhodamine B, respectively. Contact angle measurements and DART mass spectrometry analysis indicate that our employed elastomeric soft bonding technique modifies pillar properties, creating a fortuitous stationary phase. This discovery provides evidence supporting the ability to easily functionalize PECVD oxide surfaces by gas-phase reactions.

  1. Recommendations on basic requirements for intensive care units: structural and organizational aspects.

    Science.gov (United States)

    Valentin, Andreas; Ferdinande, Patrick

    2011-10-01

    To provide guidance and recommendations for the planning or renovation of intensive care units (ICUs) with respect to the specific characteristics relevant to organizational and structural aspects of intensive care medicine. The Working Group on Quality Improvement (WGQI) of the European Society of Intensive Care Medicine (ESICM) identified the basic requirements for ICUs by a comprehensive literature search and an iterative process with several rounds of consensus finding with the participation of 47 intensive care physicians from 23 countries. The starting point of this process was an ESICM recommendation published in 1997 with the need for an updated version. The document consists of operational guidelines and design recommendations for ICUs. In the first part it covers the definition and objectives of an ICU, functional criteria, activity criteria, and the management of equipment. The second part deals with recommendations with respect to the planning process, floorplan and connections, accommodation, fire safety, central services, and the necessary communication systems. This document provides a detailed framework for the planning or renovation of ICUs based on a multinational consensus within the ESICM.

  2. Structural and topological aspects of borophosphate glasses and their relation to physical properties

    DEFF Research Database (Denmark)

    Hermansen, Christian; Youngman, R.E.; Wang, J.

    2015-01-01

    We establish a topological model of alkali borophosphate and calcium borophosphate glasses that describes both the effect of the network formers and network modifiers on physical properties. We show that the glass transition temperature (Tg), Vickers hardness (HV), liquid fragility (m) and isobaric....... The origin of the effect of the type of network modifying oxide on Tg, HV, m and ΔCp of calcium borophosphate glasses is revealed in terms of the modifying ion sub-network. The same topological principles quantitatively explain the significant differences in physical properties between the alkali...... and the calcium borophosphate glasses. This work has implications for quantifying structure-property relations in complex glass forming systems containing several types of network forming and modifying oxides....

  3. Some Aspects of Structural Modeling of Damage Accumulation and Fracture Processes in Metal Structures at Low Temperature

    Directory of Open Access Journals (Sweden)

    Valeriy Lepov

    2016-01-01

    Full Text Available The problem of brittle fracture of structures at low temperature conditions connected to damage accumulation and ductile-brittle transition in metals. The data for locomotive tire contact impact fatigue and spalling are presented. The results of experimental testing showed the impact toughness drop at low temperature. The internal friction method was applied to revealing of the mechanism of dislocation microstructure changes during the low temperature ductile-brittle transition. It has been shown for the first time that the transition is not connected to interatomic interactions but stipulated by thermofluctuation on nucleus such as microcracks and by their further growth and coalescence. From now on, the proposed mechanism would be used for theoretical and numerical modeling of damage accumulation and fracture in materials.

  4. Leaf colleters in Tontelea micrantha (Celastraceae, Salacioideae): ecological, morphological and structural aspects.

    Science.gov (United States)

    Mercadante-Simões, Maria Olívia; Paiva, Elder Antônio Sousa

    2013-08-01

    The colleter secretion can be useful to protect plants of Cerrado (Brazilian savanna) biome during the long and pronounced dry season. This study describes the presence of colleters in Tontelea micrantha and represents the first record of these structures in Celastraceae. To investigate colleter structure and their secretory processes, young leaves were collected, fixed, and processed according to conventional techniques for light, and electron microscopy. Colleters were observed at the marginal teeth on the leaf. They produce mucilaginous secretions that spread over the leaf surface. After secretory phase, colleters abscise. The secretory epithelium is uniseriate and composed of elongated cells whose dense cytoplasm is rich in organelles. The ultrastructure of the secretory cells is compatible with the pectin-rich secretion. Observations of the young leaves surface revealed the presence of superficial hydrophilic secretion films that appeared to have the function of maintaining the water status of those organs. Copyright © 2013 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  5. Broken symmetry within crystallographic super-spaces: structural and dynamical aspects

    International Nuclear Information System (INIS)

    Mariette, Celine

    2013-01-01

    Aperiodic crystals have the property to possess long range order without translational symmetry. These crystals are described within the formalism of super-space crystallography. In this manuscript, we will focus on symmetry breaking which take place in such crystallographic super-space groups, considering the prototype family of n-alkane/urea. Studies performed by X-ray diffraction using synchrotron sources reveal multiple structural solutions implying or not changes of the dimension of the super-space. Once the characterization of the order parameter and of the symmetry breaking is done, we present the critical pre-transitional phenomena associated to phase transitions of group/subgroup types. Coherent neutron scattering and inelastic X-ray scattering allow a dynamical analysis of different kind of excitations in these materials (phonons, phasons). The inclusion compounds with short guest molecules (alkane C n H 2n+2 , n varying from 7 to 13) show at room temperature unidimensional 'liquid-like' phases. The dynamical disorder along the incommensurate direction of these materials generates new structural solutions at low temperature (inter-modulated monoclinic composite, commensurate lock-in). (author) [fr

  6. Cryogenic EBSD reveals structure of directionally solidified ice–polymer composite

    International Nuclear Information System (INIS)

    Donius, Amalie E.; Obbard, Rachel W.; Burger, Joan N.; Hunger, Philipp M.; Baker, Ian; Doherty, Roger D.; Wegst, Ulrike G.K.

    2014-01-01

    Despite considerable research efforts on directionally solidified or freeze-cast materials in recent years, little fundamental knowledge has been gained that links model with experiment. In this contribution, the cryogenic characterization of directionally solidified polymer solutions illustrates, how powerful cryo-scanning electron microscopy combined with electron backscatter diffraction is for the structural characterization of ice–polymer composite materials. Under controlled sublimation, the freeze-cast polymer scaffold structure is revealed and imaged with secondary electrons. Electron backscatter diffraction fabric analysis shows that the ice crystals, which template the polymer scaffold and create the lamellar structure, have a-axes oriented parallel to the direction of solidification and the c-axes perpendicular to it. These results indicate the great potential of both cryo-scanning electron microscopy and cryo-electron backscatter diffraction in gaining fundamental knowledge of structure–property–processing correlations. - Highlights: • Cryo-SEM of freeze-cast polymer solution reveals an ice-templated structure. • Cryo-EBSD reveals the ice crystal a-axis to parallel the solidification direction. • The honeycomb-like polymer phase favors columnar ridges only on one side. • Combining cryo-SEM with EBSD links solidification theory with experiment

  7. Cryogenic EBSD reveals structure of directionally solidified ice–polymer composite

    Energy Technology Data Exchange (ETDEWEB)

    Donius, Amalie E., E-mail: amalie.donius@gmail.com [Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 (United States); Department of Materials Science and Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104 (United States); Obbard, Rachel W., E-mail: Rachel.W.Obbard@dartmouth.edu [Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 (United States); Burger, Joan N., E-mail: ridge.of.the.ancients@gmail.com [Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 (United States); Department of Materials Science and Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104 (United States); Hunger, Philipp M., E-mail: philipp.m.hunger@gmail.com [Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 (United States); Department of Materials Science and Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104 (United States); Baker, Ian, E-mail: Ian.Baker@dartmouth.edu [Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 (United States); Doherty, Roger D., E-mail: dohertrd@drexel.edu [Department of Materials Science and Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104 (United States); Wegst, Ulrike G.K., E-mail: ulrike.wegst@dartmouth.edu [Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH 03755 (United States)

    2014-07-01

    Despite considerable research efforts on directionally solidified or freeze-cast materials in recent years, little fundamental knowledge has been gained that links model with experiment. In this contribution, the cryogenic characterization of directionally solidified polymer solutions illustrates, how powerful cryo-scanning electron microscopy combined with electron backscatter diffraction is for the structural characterization of ice–polymer composite materials. Under controlled sublimation, the freeze-cast polymer scaffold structure is revealed and imaged with secondary electrons. Electron backscatter diffraction fabric analysis shows that the ice crystals, which template the polymer scaffold and create the lamellar structure, have a-axes oriented parallel to the direction of solidification and the c-axes perpendicular to it. These results indicate the great potential of both cryo-scanning electron microscopy and cryo-electron backscatter diffraction in gaining fundamental knowledge of structure–property–processing correlations. - Highlights: • Cryo-SEM of freeze-cast polymer solution reveals an ice-templated structure. • Cryo-EBSD reveals the ice crystal a-axis to parallel the solidification direction. • The honeycomb-like polymer phase favors columnar ridges only on one side. • Combining cryo-SEM with EBSD links solidification theory with experiment.

  8. Selected aspects of GDP value and structure development in sub-Saharan Africa

    Directory of Open Access Journals (Sweden)

    Luboš Smutka

    2011-01-01

    Full Text Available Africa belongs to the poorest regions of the world. This statement may be applied especially to its sub-Saharan part. The paper analyses some basic structural characteristics related to the economic development of sub-Saharan region. The article reveals existing differences between countries and regions of sub-Saharan Africa and analyses key problems which influence economic development of individual states. An emphasis is placed on analysing an unsuitable GDP structure and on external economic relations which affect this structure. Results of an investigation show that the GDP of sub-Saharan countries is to a large extend generated by the primary sector of their economies, which is dominant in the total GDP value and its position is continuously strengthening due to a high dynamics of its growth. Having regard to the external environment, there can be stated that the foreign trade has contributed to the GDP growth of the whole region only to a limited degree (this does not apply to all countries seen as individuals. The integration process in sub-Saharan Africa may be characterized as questionable. Many integration groupings are operating in the region, but their influence on economic growth is limited due a low potential for mutual cooperation based on specialisation and use of comparative advantages. The economies of sub-Saharan countries are very sensitive to changes in their external economic environment. In this regard, there is important to highlight the very strong sensitivity of the GDP in the sub-Saharan region in relation to the World GDP (mainly to European and US GDP because both regions belong to the most important trading partners of Africa as a whole.

  9. A structural homologue of colipase in black mamba venom revealed by NMR floating disulphide bridge analysis.

    Science.gov (United States)

    Boisbouvier, J; Albrand, J P; Blackledge, M; Jaquinod, M; Schweitz, H; Lazdunski, M; Marion, D

    1998-01-01

    The solution structure of mamba intestinal toxin 1 (MIT1), isolated from Dendroaspis polylepis polylepis venom, has been determined. This molecule is a cysteine-rich polypeptide exhibiting no recognised family membership. Resistance to MIT1 to classical specific endoproteases produced contradictory NMR and biochemical information concerning disulphide-bridge topology. We have used distance restraints allowing ambiguous partners between S atoms in combination with NMR-derived structural information, to correctly determine the disulphide-bridge topology. The resultant solution structure of MIT1, determined to a resolution of 0.5 A, reveals an unexpectedly similar global fold with respect to colipase, a protein involved in fatty acid digestion. Colipase exhibits an analogous resistance to endoprotease activity, indicating for the first time the possible topological origins of this biochemical property. The biochemical and structural homology permitted us to propose a mechanically related digestive function for MIT1 and provides novel information concerning snake venom protein evolution. Copyright 1998 Academic Press.

  10. Quantitative image analysis reveals distinct structural transitions during aging in Caenorhabditis elegans tissues.

    Science.gov (United States)

    Johnston, Josiah; Iser, Wendy B; Chow, David K; Goldberg, Ilya G; Wolkow, Catherine A

    2008-07-30

    Aging is associated with functional and structural declines in many body systems, even in the absence of underlying disease. In particular, skeletal muscles experience severe declines during aging, a phenomenon termed sarcopenia. Despite the high incidence and severity of sarcopenia, little is known about contributing factors and development. Many studies focus on functional aspects of aging-related tissue decline, while structural details remain understudied. Traditional approaches for quantifying structural changes have assessed individual markers at discrete intervals. Such approaches are inadequate for the complex changes associated with aging. An alternative is to consider changes in overall morphology rather than in specific markers. We have used this approach to quantitatively track tissue architecture during adulthood and aging in the C. elegans pharynx, the neuromuscular feeding organ. Using pattern recognition to analyze aged-grouped pharynx images, we identified discrete step-wise transitions between distinct morphologies. The morphology state transitions were maintained in mutants with pharynx neurotransmission defects, although the pace of the transitions was altered. Longitudinal measurements of pharynx function identified a predictive relationship between mid-life pharynx morphology and function at later ages. These studies demonstrate for the first time that adult tissues undergo distinct structural transitions reflecting postdevelopmental events. The processes that underlie these architectural changes may contribute to increased disease risk during aging, and may be targets for factors that alter the aging rate. This work further demonstrates that pattern analysis of an image series offers a novel and generally accessible approach for quantifying morphological changes and identifying structural biomarkers.

  11. Phylogeographic analysis reveals significant spatial genetic structure of Incarvillea sinensis as a product of mountain building

    Directory of Open Access Journals (Sweden)

    Chen Shaotian

    2012-04-01

    Full Text Available Abstract Background Incarvillea sinensis is widely distributed from Southwest China to Northeast China and in the Russian Far East. The distribution of this species was thought to be influenced by the uplift of the Qinghai-Tibet Plateau and Quaternary glaciation. To reveal the imprints of geological events on the spatial genetic structure of Incarvillea sinensis, we examined two cpDNA segments ( trnH- psbA and trnS- trnfM in 705 individuals from 47 localities. Results A total of 16 haplotypes was identified, and significant genetic differentiation was revealed (GST =0.843, NST = 0.975, P  Conclusions The results revealed that the uplift of the Qinghai-Tibet Plateau likely resulted in the significant divergence between the lineage in the eastern Qinghai-Tibet Plateau and the other one outside this area. The diverse niches in the eastern Qinghai-Tibet Plateau created a wide spectrum of habitats to accumulate and accommodate new mutations. The features of genetic diversity of populations outside the eastern Qinghai-Tibet Plateau seemed to reveal the imprints of extinction during the Glacial and the interglacial and postglacial recolonization. Our study is a typical case of the significance of the uplift of the Qinghai-Tibet Plateau and the Quaternary Glacial in spatial genetic structure of eastern Asian plants, and sheds new light on the evolution of biodiversity in the Qinghai-Tibet Plateau at the intraspecies level.

  12. Ionic core–shell dendrimers with a polycationic core: structural aspects and host–guest binding properties

    NARCIS (Netherlands)

    van de Coevering, R.; Bruijnincx, P.C.A.; Lutz, M.; Spek, A.L.; van Koten, G.; Klein Gebbink, R.J.M.

    2007-01-01

    The structural aspects and host–guest binding properties of ionic core–shell dendrimers [1]Br8 and [2]Br4, which bear a polycationic core and a neutral shell of Fréchet-type poly(benzyl aryl ether) dendrons, have been investigated by means of dendritic wedges [3]Br2 and [4]Br, that resemble one of

  13. General aspects of slip from technique in the construction of containment structure of the Narora Atomic Power Station

    International Nuclear Information System (INIS)

    Tilak, M.M.

    1975-01-01

    The paper describes one of the modern techniques of construction methods, i.e. use of slip form technique. Important features in adopting the above technique and its impact on construction aspects and design parameters in respect of containment structure are briefly discussed. (author)

  14. Eigenspaces of networks reveal the overlapping and hierarchical community structure more precisely

    International Nuclear Information System (INIS)

    Ma, Xiaoke; Gao, Lin; Yong, Xuerong

    2010-01-01

    Identifying community structure is fundamental for revealing the structure–functionality relationship in complex networks, and spectral algorithms have been shown to be powerful for this purpose. In a traditional spectral algorithm, each vertex of a network is embedded into a spectral space by making use of the eigenvectors of the adjacency matrix or Laplacian matrix of the graph. In this paper, a novel spectral approach for revealing the overlapping and hierarchical community structure of complex networks is proposed by not only using the eigenvalues and eigenvectors but also the properties of eigenspaces of the networks involved. This gives us a better characterization of community. We first show that the communicability between a pair of vertices can be rewritten in term of eigenspaces of a network. An agglomerative clustering algorithm is then presented to discover the hierarchical communities using the communicability matrix. Finally, these overlapping vertices are discovered with the corresponding eigenspaces, based on the fact that the vertices more densely connected amongst one another are more likely to be linked through short cycles. Compared with the traditional spectral algorithms, our algorithm can identify both the overlapping and hierarchical community without increasing the time complexity O(n 3 ), where n is the size of the network. Furthermore, our algorithm can also distinguish the overlapping vertices from bridges. The method is tested by applying it to some computer-generated and real-world networks. The experimental results indicate that our algorithm can reveal community structure more precisely than the traditional spectral approaches

  15. Structural design aspects of innovative designs under development in the current US Liquid Metal-Cooled Reactor program

    International Nuclear Information System (INIS)

    Seidensticker, R.W.

    1986-01-01

    The US Liquid Metal-Cooled Reactor (LMR) program has been restructured and is now focussed on the development of innovative plant designs which emphasize shorter construction times, increased use of passive, inherently safe features, cost-competitiveness with LWR plants, and minimization of safety-related systems. These changes have a considerable effect on the structural design aspects of the LMR plant. These structural problems and their solutions now under study form the main focus of this paper. (orig.)

  16. Bacterial vaginosis (clue cell-positive discharge) : diagnostic, ultra-structural and therapeutic aspects

    NARCIS (Netherlands)

    W.I. van der Meijden (Willem)

    1987-01-01

    textabstractThis thesis deals with several aspects of (abnormal) vaginal discharge, focusing especially on clue cell-positive discharge (bacterial vaginosis, nonspecific vaginitis). It reports data on epidemiology and clinical features, pathogenesis, and treatment of this vaginal disease entity,

  17. Structural characterisation of Tpx from Yersinia pseudotuberculosis reveals insights into the binding of salicylidene acylhydrazide compounds.

    Directory of Open Access Journals (Sweden)

    Mads Gabrielsen

    Full Text Available Thiol peroxidase, Tpx, has been shown to be a target protein of the salicylidene acylhydrazide class of antivirulence compounds. In this study we present the crystal structures of Tpx from Y. pseudotuberculosis (ypTpx in the oxidised and reduced states, together with the structure of the C61S mutant. The structures solved are consistent with previously solved atypical 2-Cys thiol peroxidases, including that for "forced" reduced states using the C61S mutant. In addition, by investigating the solution structure of ypTpx using small angle X-ray scattering (SAXS, we have confirmed that reduced state ypTpx in solution is a homodimer. The solution structure also reveals flexibility around the dimer interface. Notably, the conformational changes observed between the redox states at the catalytic triad and at the dimer interface have implications for substrate and inhibitor binding. The structural data were used to model the binding of two salicylidene acylhydrazide compounds to the oxidised structure of ypTpx. Overall, the study provides insights into the binding of the salicylidene acylhydrazides to ypTpx, aiding our long-term strategy to understand the mode of action of this class of compounds.

  18. Crystal structure analysis reveals functional flexibility in the selenocysteine-specific tRNA from mouse.

    Directory of Open Access Journals (Sweden)

    Oleg M Ganichkin

    Full Text Available Selenocysteine tRNAs (tRNA(Sec exhibit a number of unique identity elements that are recognized specifically by proteins of the selenocysteine biosynthetic pathways and decoding machineries. Presently, these identity elements and the mechanisms by which they are interpreted by tRNA(Sec-interacting factors are incompletely understood.We applied rational mutagenesis to obtain well diffracting crystals of murine tRNA(Sec. tRNA(Sec lacking the single-stranded 3'-acceptor end ((ΔGCCARNA(Sec yielded a crystal structure at 2.0 Å resolution. The global structure of (ΔGCCARNA(Sec resembles the structure of human tRNA(Sec determined at 3.1 Å resolution. Structural comparisons revealed flexible regions in tRNA(Sec used for induced fit binding to selenophosphate synthetase. Water molecules located in the present structure were involved in the stabilization of two alternative conformations of the anticodon stem-loop. Modeling of a 2'-O-methylated ribose at position U34 of the anticodon loop as found in a sub-population of tRNA(Secin vivo showed how this modification favors an anticodon loop conformation that is functional during decoding on the ribosome. Soaking of crystals in Mn(2+-containing buffer revealed eight potential divalent metal ion binding sites but the located metal ions did not significantly stabilize specific structural features of tRNA(Sec.We provide the most highly resolved structure of a tRNA(Sec molecule to date and assessed the influence of water molecules and metal ions on the molecule's conformation and dynamics. Our results suggest how conformational changes of tRNA(Sec support its interaction with proteins.

  19. TreeNetViz: revealing patterns of networks over tree structures.

    Science.gov (United States)

    Gou, Liang; Zhang, Xiaolong Luke

    2011-12-01

    Network data often contain important attributes from various dimensions such as social affiliations and areas of expertise in a social network. If such attributes exhibit a tree structure, visualizing a compound graph consisting of tree and network structures becomes complicated. How to visually reveal patterns of a network over a tree has not been fully studied. In this paper, we propose a compound graph model, TreeNet, to support visualization and analysis of a network at multiple levels of aggregation over a tree. We also present a visualization design, TreeNetViz, to offer the multiscale and cross-scale exploration and interaction of a TreeNet graph. TreeNetViz uses a Radial, Space-Filling (RSF) visualization to represent the tree structure, a circle layout with novel optimization to show aggregated networks derived from TreeNet, and an edge bundling technique to reduce visual complexity. Our circular layout algorithm reduces both total edge-crossings and edge length and also considers hierarchical structure constraints and edge weight in a TreeNet graph. These experiments illustrate that the algorithm can reduce visual cluttering in TreeNet graphs. Our case study also shows that TreeNetViz has the potential to support the analysis of a compound graph by revealing multiscale and cross-scale network patterns. © 2011 IEEE

  20. Structural characterization of Helicobacter pylori dethiobiotin synthetase reveals differences between family members

    Energy Technology Data Exchange (ETDEWEB)

    Porebski, Przemyslaw J.; Klimecka, Maria; Chruszcz, Maksymilian; Nicholls, Robert A.; Murzyn, Krzysztof; Cuff, Marianne E.; Xu, Xiaohui; Cymborowski, Marcin; Murshudov, Garib N.; Savchenko, Alexei; Edwards, Aled; Minor, Wladek (MCSG); (UV); (MRC)

    2012-07-11

    Dethiobiotin synthetase (DTBS) is involved in the biosynthesis of biotin in bacteria, fungi, and plants. As humans lack this pathway, DTBS is a promising antimicrobial drug target. We determined structures of DTBS from Helicobacter pylori (hpDTBS) bound with cofactors and a substrate analog, and described its unique characteristics relative to other DTBS proteins. Comparison with bacterial DTBS orthologs revealed considerable structural differences in nucleotide recognition. The C-terminal region of DTBS proteins, which contains two nucleotide-recognition motifs, differs greatly among DTBS proteins from different species. The structure of hpDTBS revealed that this protein is unique and does not contain a C-terminal region containing one of the motifs. The single nucleotide-binding motif in hpDTBS is similar to its counterpart in GTPases; however, isothermal titration calorimetry binding studies showed that hpDTBS has a strong preference for ATP. The structural determinants of ATP specificity were assessed with X-ray crystallographic studies of hpDTBS-ATP and hpDTBS-GTP complexes. The unique mode of nucleotide recognition in hpDTBS makes this protein a good target for H. pylori-specific inhibitors of the biotin synthesis pathway.

  1. The asymmetrical structure of Golgi apparatus membranes revealed by in situ atomic force microscope.

    Directory of Open Access Journals (Sweden)

    Haijiao Xu

    Full Text Available The Golgi apparatus has attracted intense attentions due to its fascinating morphology and vital role as the pivot of cellular secretory pathway since its discovery. However, its complex structure at the molecular level remains elusive due to limited approaches. In this study, the structure of Golgi apparatus, including the Golgi stack, cisternal structure, relevant tubules and vesicles, were directly visualized by high-resolution atomic force microscope. We imaged both sides of Golgi apparatus membranes and revealed that the outer leaflet of Golgi membranes is relatively smooth while the inner membrane leaflet is rough and covered by dense proteins. With the treatment of methyl-β-cyclodextrin and Triton X-100, we confirmed the existence of lipid rafts in Golgi apparatus membrane, which are mostly in the size of 20 nm -200 nm and appear irregular in shape. Our results may be of significance to reveal the structure-function relationship of the Golgi complex and pave the way for visualizing the endomembrane system in mammalian cells at the molecular level.

  2. Structure of Human GIVD Cytosolic Phospholipase A2 Reveals Insights into Substrate Recognition

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Hui; Klein, Michael G.; Snell, Gyorgy; Lane, Weston; Zou, Hua; Levin, Irena; Li, Ke; Sang, Bi-Ching (Takeda Cali)

    2016-07-01

    Cytosolic phospholipases A2 (cPLA2s) consist of a family of calcium-sensitive enzymes that function to generate lipid second messengers through hydrolysis of membrane-associated glycerophospholipids. The GIVD cPLA2 (cPLA2δ) is a potential drug target for developing a selective therapeutic agent for the treatment of psoriasis. Here, we present two X-ray structures of human cPLA2δ, capturing an apo state, and in complex with a substrate-like inhibitor. Comparison of the apo and inhibitor-bound structures reveals conformational changes in a flexible cap that allows the substrate to access the relatively buried active site, providing new insight into the mechanism for substrate recognition. The cPLA2δ structure reveals an unexpected second C2 domain that was previously unrecognized from sequence alignments, placing cPLA2δ into the class of membrane-associated proteins that contain a tandem pair of C2 domains. Furthermore, our structures elucidate novel inter-domain interactions and define three potential calcium-binding sites that are likely important for regulation and activation of enzymatic activity. These findings provide novel insights into the molecular mechanisms governing cPLA2's function in signal transduction.

  3. Structural view of the helicase reveals that Zika virus uses a conserved mechanism for unwinding RNA.

    Science.gov (United States)

    Li, Lei; Wang, Jin; Jia, Zhihui; Shaw, Neil

    2018-04-01

    Recent studies suggest a link between infection by Zika virus (ZIKV) and the development of neurological complications. The lack of ZIKV-specific therapeutics has alarmed healthcare professionals worldwide. Here, crystal structures of apo and AMPPNP- and Mn 2+ -bound forms of the essential helicase of ZIKV refined to 1.78 and 1.3 Å resolution, respectively, are reported. The structures reveal a conserved trimodular topology of the helicase. ATP and Mn 2+ are tethered between two RecA-like domains by conserved hydrogen-bonding interactions. The binding of ligands induces the movement of backbone Cα and side-chain atoms. Numerous solvent molecules are observed in the vicinity of the AMPPNP, suggesting a role in catalysis. These high-resolution structures could be useful for the design of inhibitors targeting the helicase of ZIKV for the treatment of infections caused by ZIKV.

  4. Rhabdovirus matrix protein structures reveal a novel mode of self-association.

    Directory of Open Access Journals (Sweden)

    Stephen C Graham

    2008-12-01

    Full Text Available The matrix (M proteins of rhabdoviruses are multifunctional proteins essential for virus maturation and budding that also regulate the expression of viral and host proteins. We have solved the structures of M from the vesicular stomatitis virus serotype New Jersey (genus: Vesiculovirus and from Lagos bat virus (genus: Lyssavirus, revealing that both share a common fold despite sharing no identifiable sequence homology. Strikingly, in both structures a stretch of residues from the otherwise-disordered N terminus of a crystallographically adjacent molecule is observed binding to a hydrophobic cavity on the surface of the protein, thereby forming non-covalent linear polymers of M in the crystals. While the overall topology of the interaction is conserved between the two structures, the molecular details of the interactions are completely different. The observed interactions provide a compelling model for the flexible self-assembly of the matrix protein during virion morphogenesis and may also modulate interactions with host proteins.

  5. Instability and associated roll structure of Marangoni convection in high Prandtl number liquid bridge with large aspect ratio

    Science.gov (United States)

    Yano, T.; Nishino, K.; Kawamura, H.; Ueno, I.; Matsumoto, S.

    2015-02-01

    This paper reports the experimental results on the instability and associated roll structures (RSs) of Marangoni convection in liquid bridges formed under the microgravity environment on the International Space Station. The geometry of interest is high aspect ratio (AR = height/diameter ≥ 1.0) liquid bridges of high Prandtl number fluids (Pr = 67 and 207) suspended between coaxial disks heated differentially. The unsteady flow field and associated RSs were revealed with the three-dimensional particle tracking velocimetry. It is found that the flow field after the onset of instability exhibits oscillations with azimuthal mode number m = 1 and associated RSs traveling in the axial direction. The RSs travel in the same direction as the surface flow (co-flow direction) for 1.00 ≤ AR ≤ 1.25 while they travel in the opposite direction (counter-flow direction) for AR ≥ 1.50, thus showing the change of traveling directions with AR. This traveling direction for AR ≥ 1.50 is reversed to the co-flow direction when the temperature difference between the disks is increased to the condition far beyond the critical one. This change of traveling directions is accompanied by the increase of the oscillation frequency. The characteristics of the RSs for AR ≥ 1.50, such as the azimuthal mode of oscillation, the dimensionless oscillation frequency, and the traveling direction, are in reasonable agreement with those of the previous sounding rocket experiment for AR = 2.50 and those of the linear stability analysis of an infinite liquid bridge.

  6. Structure insight of GSDMD reveals the basis of GSDMD autoinhibition in cell pyroptosis.

    Science.gov (United States)

    Kuang, Siyun; Zheng, Jun; Yang, Hui; Li, Suhua; Duan, Shuyan; Shen, Yanfang; Ji, Chaoneng; Gan, Jianhua; Xu, Xue-Wei; Li, Jixi

    2017-10-03

    Recent findings have revealed that the protein gasdermin D (GSDMD) plays key roles in cell pyroptosis. GSDMD binds lipids and forms pore structures to induce pyroptosis upon microbial infection and associated danger signals. However, detailed structural information for GSDMD remains unknown. Here, we report the crystal structure of the C-terminal domain of human GSDMD (GSDMD-C) at 2.64-Å resolution. The first loop on GSDMD-C inserts into the N-terminal domain (GSDMD-N), which helps stabilize the conformation of the full-length GSDMD. Substitution of this region by a short linker sequence increased levels of cell death. Mutants F283A and F283R can increase protein heterogeneity in vitro and are capable of undergoing cell pyroptosis in 293T cells. The small-angle X-ray-scattering envelope of human GSDMD is consistent with the modeled GSDMD structure and mouse GSDMA3 structure, which suggests that GSDMD adopts an autoinhibited conformation in solution. The positive potential surface of GSDMD-N covered by GSDMD-C is exposed after being released from the autoinhibition state and can form high-order oligomers via a charge-charge interaction. Furthermore, by mapping different regions of GSDMD, we determined that one short segment is sufficient to kill bacteria in vitro and can efficiently inhibit cell growth in Escherichia coli and Mycobacterium Smegmatis These findings reveal that GSDMD-C acts as an auto-inhibition executor and GSDMD-N could form pore structures via a charge-charge interaction upon cleavage by caspases during cell pyroptosis.

  7. Framework to model neutral particle flux in convex high aspect ratio structures using one-dimensional radiosity

    Science.gov (United States)

    Manstetten, Paul; Filipovic, Lado; Hössinger, Andreas; Weinbub, Josef; Selberherr, Siegfried

    2017-02-01

    We present a computationally efficient framework to compute the neutral flux in high aspect ratio structures during three-dimensional plasma etching simulations. The framework is based on a one-dimensional radiosity approach and is applicable to simulations of convex rotationally symmetric holes and convex symmetric trenches with a constant cross-section. The framework is intended to replace the full three-dimensional simulation step required to calculate the neutral flux during plasma etching simulations. Especially for high aspect ratio structures, the computational effort, required to perform the full three-dimensional simulation of the neutral flux at the desired spatial resolution, conflicts with practical simulation time constraints. Our results are in agreement with those obtained by three-dimensional Monte Carlo based ray tracing simulations for various aspect ratios and convex geometries. With this framework we present a comprehensive analysis of the influence of the geometrical properties of high aspect ratio structures as well as of the particle sticking probability on the neutral particle flux.

  8. Structure in nascent carbon nanotubes revealed by spatially resolved Raman spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Landois, Périne [CEA, IRAMIS, SPAM, Laboratoire Francis Perrin (CNRS URA 2453), 91191 Gif-sur-Yvette (France); Laboratoire de Physique des Solides, UMR CNRS 8502, Université Paris Sud 11, 91405 Orsay (France); Pinault, Mathieu [CEA, IRAMIS, SPAM, Laboratoire Francis Perrin (CNRS URA 2453), 91191 Gif-sur-Yvette (France); Huard, Mickaël [Laboratoire de Physique des Solides, UMR CNRS 8502, Université Paris Sud 11, 91405 Orsay (France); Reita, Valérie [Univ. Grenoble Alpes, Inst NEEL, F-38042 Grenoble (France); CNRS, Inst NEEL, F-38042 Grenoble (France); Rouzière, Stéphan; Launois, Pascale [Laboratoire de Physique des Solides, UMR CNRS 8502, Université Paris Sud 11, 91405 Orsay (France); Mayne-L' Hermite, Martine [CEA, IRAMIS, SPAM, Laboratoire Francis Perrin (CNRS URA 2453), 91191 Gif-sur-Yvette (France); Bendiab, Nedjma, E-mail: nedjma.bendiab@grenoble.cnrs.fr [Univ. Grenoble Alpes, Inst NEEL, F-38042 Grenoble (France); CNRS, Inst NEEL, F-38042 Grenoble (France)

    2014-10-01

    The understanding of carbon nanotube (CNT) growth is crucial for the control of their production. In particular, the identification of structural changes of carbon possibly occurring near the catalyst particle in the very early stages of their formation is of high interest. In this study, samples of nascent CNT obtained during nucleation step and samples of vertically aligned CNT obtained during growth step are analysed by combined spatially resolved Raman spectroscopy and X-ray diffraction measurements. Spatially resolved Raman spectroscopy reveals that iron-based phases and carbon phases are co-localized at the same position, and indicates that sp{sup 2} carbon nucleates preferentially on iron-based particles during this nucleation step. Depth scan Raman spectroscopy analysis, performed on nascent CNT, highlights that carbon structural organisation is significantly changing from defective graphene layers surrounding the iron-based particles at their base up to multi-walled nanotube structures in the upper part of iron-based particles. - Highlights: • Spatial co-localization of iron and carbon structures in nascent carbon nanotubes • Imaging local carbon structure changes along catalyst particles by Raman spectroscopy. • In nascent nanotubes, significant structural changes occur along catalyst particle.

  9. 11th International Conference on Clustering Aspects of Nuclear Structure and Dynamics

    International Nuclear Information System (INIS)

    2017-01-01

    Preface The 11 th edition of the International Conference on Clustering Aspects of Nuclear Structure and Dynamics (CLUSTER‘16) was held in Napoli, Italy, on May 23-27 2016. All the Conference Sessions took place in the magnificent Complesso Monumentale dei Ss. Marcellino e Festo , located in the Historical Centre of Naples. This is one of the most prestigious building complexes of the Federico II University of Naples, the main home institution of the organizers, together with the Istituto Nazionale di Fisica Nucleare (Naples division). This building is 500 years old; in the XVIII century, it was reshaped by Luigi Vanvitelli, a famous architect of the pre-Neoclassical period in Italy, designer of the prestigious Royal Palace in the near town of Caserta. The site of Plenary Sessions was the Church of Ss. Marcellino e Festo , where all the participants were surrounded by the Baroque frescoes by Belisario Corenzio and, among the others, the paintings of Battistello Caracciolo, Massimo Stanzione, Giuseppe Simonelli and Francesco De Mura, important artists of the late Baroque period in South Italy. The sites of Parallel Sessions were two halls in the arcade of the S. Marcellino cloister: this gave the opportunity to the participants to enjoy the beauty of the architecture of the cloister with its fountains, gardens, sculptures. As organizers of the Conference, our main aims were: (1) to provide an excellent programme, with the expectation to be a reference point for the Nuclear Cluster Physics in the next four years; (2) to assure a very relaxing stay to the participants, allowing them to explore the bounty of artistic, and also culinary, masterpieces that Naples offers to its guests. The first point was assured by all the conveners that, with their excellent talks, gave a very precise and complete overview of the most recent achievements on Nuclear Cluster Physics, both from the experimental and theoretical point of view. We are indebted with the International

  10. Chromosomal structures and repetitive sequences divergence in Cucumis species revealed by comparative cytogenetic mapping.

    Science.gov (United States)

    Zhang, Yunxia; Cheng, Chunyan; Li, Ji; Yang, Shuqiong; Wang, Yunzhu; Li, Ziang; Chen, Jinfeng; Lou, Qunfeng

    2015-09-25

    Differentiation and copy number of repetitive sequences affect directly chromosome structure which contributes to reproductive isolation and speciation. Comparative cytogenetic mapping has been verified an efficient tool to elucidate the differentiation and distribution of repetitive sequences in genome. In present study, the distinct chromosomal structures of five Cucumis species were revealed through genomic in situ hybridization (GISH) technique and comparative cytogenetic mapping of major satellite repeats. Chromosome structures of five Cucumis species were investigated using GISH and comparative mapping of specific satellites. Southern hybridization was employed to study the proliferation of satellites, whose structural characteristics were helpful for analyzing chromosome evolution. Preferential distribution of repetitive DNAs at the subtelomeric regions was found in C. sativus, C hystrix and C. metuliferus, while majority was positioned at the pericentromeric heterochromatin regions in C. melo and C. anguria. Further, comparative GISH (cGISH) through using genomic DNA of other species as probes revealed high homology of repeats between C. sativus and C. hystrix. Specific satellites including 45S rDNA, Type I/II, Type III, Type IV, CentM and telomeric repeat were then comparatively mapped in these species. Type I/II and Type IV produced bright signals at the subtelomeric regions of C. sativus and C. hystrix simultaneously, which might explain the significance of their amplification in the divergence of Cucumis subgenus from the ancient ancestor. Unique positioning of Type III and CentM only at the centromeric domains of C. sativus and C. melo, respectively, combining with unique southern bands, revealed rapid evolutionary patterns of centromeric DNA in Cucumis. Obvious interstitial telomeric repeats were observed in chromosomes 1 and 2 of C. sativus, which might provide evidence of the fusion hypothesis of chromosome evolution from x = 12 to x = 7 in

  11. Quantitative image analysis reveals distinct structural transitions during aging in Caenorhabditis elegans tissues.

    Directory of Open Access Journals (Sweden)

    Josiah Johnston

    2008-07-01

    Full Text Available Aging is associated with functional and structural declines in many body systems, even in the absence of underlying disease. In particular, skeletal muscles experience severe declines during aging, a phenomenon termed sarcopenia. Despite the high incidence and severity of sarcopenia, little is known about contributing factors and development. Many studies focus on functional aspects of aging-related tissue decline, while structural details remain understudied. Traditional approaches for quantifying structural changes have assessed individual markers at discrete intervals. Such approaches are inadequate for the complex changes associated with aging. An alternative is to consider changes in overall morphology rather than in specific markers. We have used this approach to quantitatively track tissue architecture during adulthood and aging in the C. elegans pharynx, the neuromuscular feeding organ. Using pattern recognition to analyze aged-grouped pharynx images, we identified discrete step-wise transitions between distinct morphologies. The morphology state transitions were maintained in mutants with pharynx neurotransmission defects, although the pace of the transitions was altered. Longitudinal measurements of pharynx function identified a predictive relationship between mid-life pharynx morphology and function at later ages. These studies demonstrate for the first time that adult tissues undergo distinct structural transitions reflecting postdevelopmental events. The processes that underlie these architectural changes may contribute to increased disease risk during aging, and may be targets for factors that alter the aging rate. This work further demonstrates that pattern analysis of an image series offers a novel and generally accessible approach for quantifying morphological changes and identifying structural biomarkers.

  12. Three-dimensional structure of a schistosome serpin revealing an unusual configuration of the helical subdomain

    Energy Technology Data Exchange (ETDEWEB)

    Granzin, Joachim [Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich (Germany); Huang, Ying; Topbas, Celalettin [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Huang, Wenying [Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Wu, Zhiping [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Misra, Saurav [Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Hazen, Stanley L. [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Blanton, Ronald E. [Department of Infectious Diseases, Case Western Reserve University, Cleveland, OH 44190 (United States); Lee, Xavier [Department of Cell Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195 (United States); Weiergräber, Oliver H., E-mail: o.h.weiergraeber@fz-juelich.de [Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich (Germany)

    2012-06-01

    The crystal structure of ShSPI, a serpin from the blood fluke S. haematobium, reveals some peculiar features of the helical subdomain which have not been observed previously in the serpin superfamily. Parasitic organisms are constantly challenged by the defence mechanisms of their respective hosts, which often depend on serine protease activities. Consequently, protease inhibitors such as those belonging to the serpin superfamily have emerged as protective elements that support the survival of the parasites. This report describes the crystal structure of ShSPI, a serpin from the trematode Schistosoma haematobium. The protein is exposed on the surface of invading cercaria as well as of adult worms, suggesting its involvement in the parasite–host interaction. While generally conforming to the well established serpin fold, the structure reveals several distinctive features, mostly concerning the helical subdomain of the protein. It is proposed that these peculiarities are related to the unique biological properties of a small serpin subfamily which is conserved among pathogenic schistosomes.

  13. Biomaterials from blends of fluoropolymers and corn starch—implant and structural aspects

    Energy Technology Data Exchange (ETDEWEB)

    Pereira, João D.A.S. [Faculdade de Ciências e Tecnologia, UNESP Univ Estadual Paulista, 19060-900 Presidente Prudente, SP, Brazil. (Brazil); Condensed Matter Physics Department, CellMat Laboratory, Faculty of Science, University of Valladolid, Valladolid Spain (Spain); Camargo, Regina C.T.; Filho, José C.S.C.; Alves, Neri [Faculdade de Ciências e Tecnologia, UNESP Univ Estadual Paulista, 19060-900 Presidente Prudente, SP, Brazil. (Brazil); Rodriguez-Perez, Miguel A. [Condensed Matter Physics Department, CellMat Laboratory, Faculty of Science, University of Valladolid, Valladolid Spain (Spain); Constantino, Carlos J.L., E-mail: case@fct.unesp.br [Faculdade de Ciências e Tecnologia, UNESP Univ Estadual Paulista, 19060-900 Presidente Prudente, SP, Brazil. (Brazil)

    2014-03-01

    The development of polymeric blends to be used as matrices for bone regeneration is a hot topic nowadays. In this article we report on the blends composed by corn starch and poly(vinylidene fluoride), PVDF, or poly(vinylidene fluoride-trifluoroethylene), P(VDF-TrFE), to obtain biocompatible materials. Blends were produced by compressing/annealing and chemically/structurally characterized by micro-Raman scattering and Fourier transform infrared (FTIR) absorption spectroscopies, dynamic mechanical analysis (DMA) and scanning electron microscopy (SEM), besides in vivo study to evaluate the tissue response. Vibrational spectroscopy reveals no chemical interaction between the polymers and starch, absence of material degradation due to compressing/annealing process or organism implantation, and maintenance of α and ferroelectric crystalline phases of PVDF and P(VDF-TrFE), respectively. As a consequence of absence of interaction between polymers and starch, it was possible to identify by SEM each material, with starch acting as filler. Elastic modulus (E′) obtained from DMA measurement, independent of the material proportion used in blends, reaches values close to those of cancellous bone. Finally, the in vivo study in animals shows that the blends, regardless of the composition, were tolerated by cancellous bone. - Highlights: • Spectroscopy shows no chemical interaction between the polymers and starch. • It was possible to identify by SEM each material, with starch acting as filler. • The modulus of elasticity (E′) reaches values close to those of cancellous bone. • In vivo study in animals shows that the blends were tolerated by cancellous bone. • Cell aggregates present at outside region of implanted samples suggest bone healing.

  14. Biomaterials from blends of fluoropolymers and corn starch—implant and structural aspects

    International Nuclear Information System (INIS)

    Pereira, João D.A.S.; Camargo, Regina C.T.; Filho, José C.S.C.; Alves, Neri; Rodriguez-Perez, Miguel A.; Constantino, Carlos J.L.

    2014-01-01

    The development of polymeric blends to be used as matrices for bone regeneration is a hot topic nowadays. In this article we report on the blends composed by corn starch and poly(vinylidene fluoride), PVDF, or poly(vinylidene fluoride-trifluoroethylene), P(VDF-TrFE), to obtain biocompatible materials. Blends were produced by compressing/annealing and chemically/structurally characterized by micro-Raman scattering and Fourier transform infrared (FTIR) absorption spectroscopies, dynamic mechanical analysis (DMA) and scanning electron microscopy (SEM), besides in vivo study to evaluate the tissue response. Vibrational spectroscopy reveals no chemical interaction between the polymers and starch, absence of material degradation due to compressing/annealing process or organism implantation, and maintenance of α and ferroelectric crystalline phases of PVDF and P(VDF-TrFE), respectively. As a consequence of absence of interaction between polymers and starch, it was possible to identify by SEM each material, with starch acting as filler. Elastic modulus (E′) obtained from DMA measurement, independent of the material proportion used in blends, reaches values close to those of cancellous bone. Finally, the in vivo study in animals shows that the blends, regardless of the composition, were tolerated by cancellous bone. - Highlights: • Spectroscopy shows no chemical interaction between the polymers and starch. • It was possible to identify by SEM each material, with starch acting as filler. • The modulus of elasticity (E′) reaches values close to those of cancellous bone. • In vivo study in animals shows that the blends were tolerated by cancellous bone. • Cell aggregates present at outside region of implanted samples suggest bone healing

  15. The structure of Plasmodium falciparum serine hydroxymethyltransferase reveals a novel redox switch that regulates its activities

    Energy Technology Data Exchange (ETDEWEB)

    Chitnumsub, Penchit; Ittarat, Wanwipa; Jaruwat, Aritsara; Noytanom, Krittikar [National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120 (Thailand); Amornwatcharapong, Watcharee [Mahidol University, Bangkok (Thailand); Pornthanakasem, Wichai [National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120 (Thailand); Chaiyen, Pimchai [Mahidol University, Bangkok (Thailand); Yuthavong, Yongyuth; Leartsakulpanich, Ubolsree [National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120 (Thailand)

    2014-06-01

    The crystal structure of P. falciparum SHMT revealed snapshots of an intriguing disulfide/sulfhydryl switch controlling the functional activity. Plasmodium falciparum serine hydroxymethyltransferase (PfSHMT), an enzyme in the dTMP synthesis cycle, is an antimalarial target because inhibition of its expression or function has been shown to be lethal to the parasite. As the wild-type enzyme could not be crystallized, protein engineering of residues on the surface was carried out. The surface-engineered mutant PfSHMT-F292E was successfully crystallized and its structure was determined at 3 Å resolution. The PfSHMT-F292E structure is a good representation of PfSHMT as this variant revealed biochemical properties similar to those of the wild type. Although the overall structure of PfSHMT is similar to those of other SHMTs, unique features including the presence of two loops and a distinctive cysteine pair formed by Cys125 and Cys364 in the tetrahydrofolate (THF) substrate binding pocket were identified. These structural characteristics have never been reported in other SHMTs. Biochemical characterization and mutation analysis of these two residues confirm that they act as a disulfide/sulfhydryl switch to regulate the THF-dependent catalytic function of the enzyme. This redox switch is not present in the human enzyme, in which the cysteine pair is absent. The data reported here can be further exploited as a new strategy to specifically disrupt the activity of the parasite enzyme without interfering with the function of the human enzyme.

  16. The structure of Plasmodium falciparum serine hydroxymethyltransferase reveals a novel redox switch that regulates its activities

    International Nuclear Information System (INIS)

    Chitnumsub, Penchit; Ittarat, Wanwipa; Jaruwat, Aritsara; Noytanom, Krittikar; Amornwatcharapong, Watcharee; Pornthanakasem, Wichai; Chaiyen, Pimchai; Yuthavong, Yongyuth; Leartsakulpanich, Ubolsree

    2014-01-01

    The crystal structure of P. falciparum SHMT revealed snapshots of an intriguing disulfide/sulfhydryl switch controlling the functional activity. Plasmodium falciparum serine hydroxymethyltransferase (PfSHMT), an enzyme in the dTMP synthesis cycle, is an antimalarial target because inhibition of its expression or function has been shown to be lethal to the parasite. As the wild-type enzyme could not be crystallized, protein engineering of residues on the surface was carried out. The surface-engineered mutant PfSHMT-F292E was successfully crystallized and its structure was determined at 3 Å resolution. The PfSHMT-F292E structure is a good representation of PfSHMT as this variant revealed biochemical properties similar to those of the wild type. Although the overall structure of PfSHMT is similar to those of other SHMTs, unique features including the presence of two loops and a distinctive cysteine pair formed by Cys125 and Cys364 in the tetrahydrofolate (THF) substrate binding pocket were identified. These structural characteristics have never been reported in other SHMTs. Biochemical characterization and mutation analysis of these two residues confirm that they act as a disulfide/sulfhydryl switch to regulate the THF-dependent catalytic function of the enzyme. This redox switch is not present in the human enzyme, in which the cysteine pair is absent. The data reported here can be further exploited as a new strategy to specifically disrupt the activity of the parasite enzyme without interfering with the function of the human enzyme

  17. Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis.

    Science.gov (United States)

    Iwata-Otsubo, Aiko; Lin, Jer-Young; Gill, Navdeep; Jackson, Scott A

    2016-05-01

    Cowpea (Vigna unguiculata (L.) Walp) is an important legume, particularly in developing countries. However, little is known about its genome or chromosome structure. We used molecular cytogenetics to characterize the structure of pachytene chromosomes to advance our knowledge of chromosome and genome organization of cowpea. Our data showed that cowpea has highly distinct chromosomal structures that are cytologically visible as brightly DAPI-stained heterochromatic regions. Analysis of the repetitive fraction of the cowpea genome present at centromeric and pericentromeric regions confirmed that two retrotransposons are major components of pericentromeric regions and that a 455-bp tandem repeat is found at seven out of 11 centromere pairs in cowpea. These repeats likely evolved after the divergence of cowpea from common bean and form chromosomal structure unique to cowpea. The integration of cowpea genetic and physical chromosome maps reveals potential regions of suppressed recombination due to condensed heterochromatin and a lack of pairing in a few chromosomal termini. This study provides fundamental knowledge on cowpea chromosome structure and molecular cytogenetics tools for further chromosome studies.

  18. Crystal structure of Clostridium botulinum whole hemagglutinin reveals a huge triskelion-shaped molecular complex.

    Science.gov (United States)

    Amatsu, Sho; Sugawara, Yo; Matsumura, Takuhiro; Kitadokoro, Kengo; Fujinaga, Yukako

    2013-12-06

    Clostridium botulinum HA is a component of the large botulinum neurotoxin complex and is critical for its oral toxicity. HA plays multiple roles in toxin penetration in the gastrointestinal tract, including protection from the digestive environment, binding to the intestinal mucosal surface, and disruption of the epithelial barrier. At least two properties of HA contribute to these roles: the sugar-binding activity and the barrier-disrupting activity that depends on E-cadherin binding of HA. HA consists of three different proteins, HA1, HA2, and HA3, whose structures have been partially solved and are made up mainly of β-strands. Here, we demonstrate structural and functional reconstitution of whole HA and present the complete structure of HA of serotype B determined by x-ray crystallography at 3.5 Å resolution. This structure reveals whole HA to be a huge triskelion-shaped molecule. Our results suggest that whole HA is functionally and structurally separable into two parts: HA1, involved in recognition of cell-surface carbohydrates, and HA2-HA3, involved in paracellular barrier disruption by E-cadherin binding.

  19. The unique N-terminal zinc finger of synaptotagmin-like protein 4 reveals FYVE structure.

    Science.gov (United States)

    Miyamoto, Kazuhide; Nakatani, Arisa; Saito, Kazuki

    2017-12-01

    Synaptotagmin-like protein 4 (Slp4), expressed in human platelets, is associated with dense granule release. Slp4 is comprised of the N-terminal zinc finger, Slp homology domain, and C2 domains. We synthesized a compact construct (the Slp4N peptide) corresponding to the Slp4 N-terminal zinc finger. Herein, we have determined the solution structure of the Slp4N peptide by nuclear magnetic resonance (NMR). Furthermore, experimental, chemical modification of Cys residues revealed that the Slp4N peptide binds two zinc atoms to mediate proper folding. NMR data showed that eight Cys residues coordinate zinc atoms in a cross-brace fashion. The Simple Modular Architecture Research Tool database predicted the structure of Slp4N as a RING finger. However, the actual structure of the Slp4N peptide adopts a unique C 4 C 4 -type FYVE fold and is distinct from a RING fold. To create an artificial RING finger (ARF) with specific ubiquitin-conjugating enzyme (E2)-binding capability, cross-brace structures with eight zinc-ligating residues are needed as the scaffold. The cross-brace structure of the Slp4N peptide could be utilized as the scaffold for the design of ARFs. © 2017 The Protein Society.

  20. The structure of Lactococcus lactis thioredoxin reductase reveals molecular features of photo-oxidative damage

    DEFF Research Database (Denmark)

    Skjoldager, Nicklas; Bang, Maria Blanner; Rykær, Martin

    2017-01-01

    The NADPH-dependent homodimeric flavoenzyme thioredoxin reductase (TrxR) provides reducing equivalents to thioredoxin, a key regulator of various cellular redox processes. Crystal structures of photo-inactivated thioredoxin reductase (TrxR) from the Gram-positive bacterium Lactococcus lactis have...... been determined. These structures reveal novel molecular features that provide further insight into the mechanisms behind the sensitivity of this enzyme toward visible light. We propose that a pocket on the si-face of the isoalloxazine ring accommodates oxygen that reacts with photo-excited FAD...... thus be a widespread feature among bacterial TrxR with the described characteristics, which affords applications in clinical photo-therapy of drug-resistant bacteria....

  1. Structure of Prokaryotic Polyamine Deacetylase Reveals Evolutionary Functional Relationships with Eukaryotic Histone Deacetylases

    Energy Technology Data Exchange (ETDEWEB)

    P Lombardi; H Angell; D Whittington; E Flynn; K Rajashankar; D Christianson

    2011-12-31

    Polyamines are a ubiquitous class of polycationic small molecules that can influence gene expression by binding to nucleic acids. Reversible polyamine acetylation regulates nucleic acid binding and is required for normal cell cycle progression and proliferation. Here, we report the structures of Mycoplana ramosa acetylpolyamine amidohydrolase (APAH) complexed with a transition state analogue and a hydroxamate inhibitor and an inactive mutant complexed with two acetylpolyamine substrates. The structure of APAH is the first of a histone deacetylase-like oligomer and reveals that an 18-residue insert in the L2 loop promotes dimerization and the formation of an 18 {angstrom} long 'L'-shaped active site tunnel at the dimer interface, accessible only to narrow and flexible substrates. The importance of dimerization for polyamine deacetylase function leads to the suggestion that a comparable dimeric or double-domain histone deacetylase could catalyze polyamine deacetylation reactions in eukaryotes.

  2. Crystal structure of the Alcanivorax borkumensis YdaH transporter reveals an unusual topology

    Science.gov (United States)

    Bolla, Jani Reddy; Su, Chih-Chia; Delmar, Jared A.; Radhakrishnan, Abhijith; Kumar, Nitin; Chou, Tsung-Han; Long, Feng; Rajashankar, Kanagalaghatta R.; Yu, Edward W.

    2015-04-01

    The potential of the folic acid biosynthesis pathway as a target for the development of antibiotics has been clinically validated. However, many pathogens have developed resistance to these antibiotics, prompting a re-evaluation of potential drug targets within the pathway. The ydaH gene of Alcanivorax borkumensis encodes an integral membrane protein of the AbgT family of transporters for which no structural information was available. Here we report the crystal structure of A. borkumensis YdaH, revealing a dimeric molecule with an architecture distinct from other families of transporters. YdaH is a bowl-shaped dimer with a solvent-filled basin extending from the cytoplasm to halfway across the membrane bilayer. Each subunit of the transporter contains nine transmembrane helices and two hairpins that suggest a plausible pathway for substrate transport. Further analyses also suggest that YdaH could act as an antibiotic efflux pump and mediate bacterial resistance to sulfonamide antimetabolite drugs.

  3. Revealing Abrupt and Spontaneous Ruptures of Protein Native Structure under picoNewton Compressive Force Manipulation.

    Science.gov (United States)

    Chowdhury, S Roy; Cao, Jin; He, Yufan; Lu, H Peter

    2018-03-27

    Manipulating protein conformations for exploring protein structure-function relationship has shown great promise. Although protein conformational changes under pulling force manipulation have been extensively studied, protein conformation changes under a compressive force have not been explored quantitatively. The latter is even more biologically significant and relevant in revealing protein functions in living cells associated with protein crowdedness, distribution fluctuations, and cell osmotic stress. Here we report our experimental observations on abrupt ruptures of protein native structures under compressive force, demonstrated and studied by single-molecule AFM-FRET spectroscopic nanoscopy. Our results show that the protein ruptures are abrupt and spontaneous events occurred when the compressive force reaches a threshold of 12-75 pN, a force amplitude accessible from thermal fluctuations in a living cell. The abrupt ruptures are sensitive to local environment, likely a general and important pathway of protein unfolding in living cells.

  4. Disrupted topological organization of structural networks revealed by probabilistic diffusion tractography in Tourette syndrome children.

    Science.gov (United States)

    Wen, Hongwei; Liu, Yue; Rekik, Islem; Wang, Shengpei; Zhang, Jishui; Zhang, Yue; Peng, Yun; He, Huiguang

    2017-08-01

    Tourette syndrome (TS) is a childhood-onset neurobehavioral disorder. Although previous TS studies revealed structural abnormalities in distinct corticobasal ganglia circuits, the topological alterations of the whole-brain white matter (WM) structural networks remain poorly understood. Here, we used diffusion MRI probabilistic tractography and graph theoretical analysis to investigate the topological organization of WM networks in 44 drug-naive TS children and 41 age- and gender-matched healthy children. The WM networks were constructed by estimating inter-regional connectivity probability and the topological properties were characterized using graph theory. We found that both TS and control groups showed an efficient small-world organization in WM networks. However, compared to controls, TS children exhibited decreased global and local efficiency, increased shortest path length and small worldness, indicating a disrupted balance between local specialization and global integration in structural networks. Although both TS and control groups showed highly similar hub distributions, TS children exhibited significant decreased nodal efficiency, mainly distributed in the default mode, language, visual, and sensorimotor systems. Furthermore, two separate networks showing significantly decreased connectivity in TS group were identified using network-based statistical (NBS) analysis, primarily composed of the parieto-occipital cortex, precuneus, and paracentral lobule. Importantly, we combined support vector machine and multiple kernel learning frameworks to fuse multiple levels of network topological features for classification of individuals, achieving high accuracy of 86.47%. Together, our study revealed the disrupted topological organization of structural networks related to pathophysiology of TS, and the discriminative topological features for classification are potential quantitative neuroimaging biomarkers for clinical TS diagnosis. Hum Brain Mapp 38:3988-4008, 2017

  5. Agarose Gel Electrophoresis Reveals Structural Fluidity of a Phage T3 DNA Packaging Intermediate

    Science.gov (United States)

    Serwer, Philip; Wright, Elena T.

    2012-01-01

    We find a new aspect of DNA packaging-associated structural fluidity for phage T3 capsids. The procedure is (1) glutaraldehyde cross-linking of in vivo DNA packaging intermediates for stabilization of structure and then (2) determining of effective radius by two-dimensional agarose gel electrophoresis (2d-AGE). The intermediates are capsids with incompletely packaged DNA (ipDNA) and without an external DNA segment; these intermediates are called ipDNA-capsids. We initially increase production of ipDNA-capsids by raising NaCl concentration during in vivo DNA packaging. By 2d-AGE, we find a new state of contracted shell for some particles of one previously identified ipDNA-capsid. The contracted shell-state is found when ipDNA length/mature DNA length (F) is above 0.17, but not at lower F. Some contracted-shell ipDNA-capsids have the phage tail; others do not. The contracted-shell ipDNA-capsids are explained by premature DNA maturation cleavage that makes accessible a contracted-shell intermediate of a cycle of the T3 DNA packaging motor. The analysis of ipDNA-capsids, rather than intermediates with uncleaved DNA, provides a simplifying strategy for a complete biochemical analysis of in vivo DNA packaging. PMID:22222979

  6. Agarose gel electrophoresis reveals structural fluidity of a phage T3 DNA packaging intermediate.

    Science.gov (United States)

    Serwer, Philip; Wright, Elena T

    2012-01-01

    We find a new aspect of DNA packaging-associated structural fluidity for phage T3 capsids. The procedure is (i) glutaraldehyde cross-linking of in vivo DNA packaging intermediates for the stabilization of structure and then (ii) determining effective radius by two-dimensional agarose gel electrophoresis (2D-AGE). The intermediates are capsids with incompletely packaged DNA (ipDNA) and without an external DNA segment; these intermediates are called ipDNA-capsids. We initially increase the production of ipDNA-capsids by raising NaCl concentration during in vivo DNA packaging. By 2D-AGE, we find a new state of contracted shell for some particles of one previously identified ipDNA-capsid. The contracted shell-state is found when the ipDNA length/mature DNA length (F) is above 0.17, but not at lower F. Some contracted-shell ipDNA-capsids have the phage tail; others do not. The contracted-shell ipDNA-capsids are explained by premature DNA maturation cleavage that makes accessible a contracted-shell intermediate of a cycle of the T3 DNA packaging motor. The analysis of ipDNA-capsids, rather than intermediates with uncleaved DNA, provides a simplifying strategy for a complete biochemical analysis of in vivo DNA packaging. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Nanoscale stiffness topography reveals structure and mechanics of the transport barrier in intact nuclear pore complexes

    Science.gov (United States)

    Bestembayeva, Aizhan; Kramer, Armin; Labokha, Aksana A.; Osmanović, Dino; Liashkovich, Ivan; Orlova, Elena V.; Ford, Ian J.; Charras, Guillaume; Fassati, Ariberto; Hoogenboom, Bart W.

    2015-01-01

    The nuclear pore complex (NPC) is the gate for transport between the cell nucleus and the cytoplasm. Small molecules cross the NPC by passive diffusion, but molecules larger than ∼5 nm must bind to nuclear transport receptors to overcome a selective barrier within the NPC. Although the structure and shape of the cytoplasmic ring of the NPC are relatively well characterized, the selective barrier is situated deep within the central channel of the NPC and depends critically on unstructured nuclear pore proteins, and is therefore not well understood. Here, we show that stiffness topography with sharp atomic force microscopy tips can generate nanoscale cross-sections of the NPC. The cross-sections reveal two distinct structures, a cytoplasmic ring and a central plug structure, which are consistent with the three-dimensional NPC structure derived from electron microscopy. The central plug persists after reactivation of the transport cycle and resultant cargo release, indicating that the plug is an intrinsic part of the NPC barrier. Added nuclear transport receptors accumulate on the intact transport barrier and lead to a homogenization of the barrier stiffness. The observed nanomechanical properties in the NPC indicate the presence of a cohesive barrier to transport and are quantitatively consistent with the presence of a central condensate of nuclear pore proteins in the NPC channel.

  8. The Structure of Neurexin 1[alpha] Reveals Features Promoting a Role as Synaptic Organizer

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Fang; Venugopal, Vandavasi; Murray, Beverly; Rudenko, Gabby (Michigan)

    2014-10-02

    {alpha}-Neurexins are essential synaptic adhesion molecules implicated in autism spectrum disorder and schizophrenia. The {alpha}-neurexin extracellular domain consists of six LNS domains interspersed by three EGF-like repeats and interacts with many different proteins in the synaptic cleft. To understand how {alpha}-neurexins might function as synaptic organizers, we solved the structure of the neurexin 1{alpha} extracellular domain (n1{alpha}) to 2.65 {angstrom}. The L-shaped molecule can be divided into a flexible repeat I (LNS1-EGF-A-LNS2), a rigid horseshoe-shaped repeat II (LNS3-EGF-B-LNS4) with structural similarity to so-called reelin repeats, and an extended repeat III (LNS5-EGF-B-LNS6) with controlled flexibility. A 2.95 {angstrom} structure of n1{alpha} carrying splice insert SS3 in LNS4 reveals that SS3 protrudes as a loop and does not alter the rigid arrangement of repeat II. The global architecture imposed by conserved structural features enables {alpha}-neurexins to recruit and organize proteins in distinct and variable ways, influenced by splicing, thereby promoting synaptic function.

  9. Structure and Evolution of the Lunar Procellarum Region as Revealed by GRAIL Gravity Data

    Science.gov (United States)

    Andrews-Hanna, Jeffrey C.; Besserer, Jonathan; Head, James W., III; Howett, Carly J. A.; Kiefer, Walter S.; Lucey, Paul J.; McGovern, Patrick J.; Melosh, H. Jay; Neumann, Gregory A.; Phillips, Roger J.; hide

    2014-01-01

    The Procellarum region is a broad area on the nearside of the Moon that is characterized by low elevations, thin crust, and high surface concentrations of the heat-producing elements uranium, thorium, and potassium. The Procellarum region has been interpreted as an ancient impact basin approximately 3200 km in diameter, though supporting evidence at the surface would have been largely obscured as a result of the great antiquity and poor preservation of any diagnostic features. Here we use data from the Gravity Recovery and Interior Laboratory (GRAIL) mission to examine the subsurface structure of Procellarum. The Bouguer gravity anomalies and gravity gradients reveal a pattern of narrow linear anomalies that border the Procellarum region and are interpreted to be the frozen remnants of lava-filled rifts and the underlying feeder dikes that served as the magma plumbing system for much of the nearside mare volcanism. The discontinuous surface structures that were earlier interpreted as remnants of an impact basin rim are shown in GRAIL data to be a part of this continuous set of quasi-rectangular border structures with angular intersections, contrary to the expected circular or elliptical shape of an impact basin. The spatial pattern of magmatic-tectonic structures bounding Procellarum is consistent with their formation in response to thermal stresses produced by the differential cooling of the province relative to its surroundings, coupled with magmatic activity driven by the elevated heat flux in the region.

  10. Structure of a Spumaretrovirus Gag Central Domain Reveals an Ancient Retroviral Capsid.

    Directory of Open Access Journals (Sweden)

    Neil J Ball

    2016-11-01

    Full Text Available The Spumaretrovirinae, or foamy viruses (FVs are complex retroviruses that infect many species of monkey and ape. Despite little sequence homology, FV and orthoretroviral Gag proteins perform equivalent functions, including genome packaging, virion assembly, trafficking and membrane targeting. However, there is a paucity of structural information for FVs and it is unclear how disparate FV and orthoretroviral Gag molecules share the same function. To probe the functional overlap of FV and orthoretroviral Gag we have determined the structure of a central region of Gag from the Prototype FV (PFV. The structure comprises two all α-helical domains NtDCEN and CtDCEN that although they have no sequence similarity, we show they share the same core fold as the N- (NtDCA and C-terminal domains (CtDCA of archetypal orthoretroviral capsid protein (CA. Moreover, structural comparisons with orthoretroviral CA align PFV NtDCEN and CtDCEN with NtDCA and CtDCA respectively. Further in vitro and functional virological assays reveal that residues making inter-domain NtDCEN-CtDCEN interactions are required for PFV capsid assembly and that intact capsid is required for PFV reverse transcription. These data provide the first information that relates the Gag proteins of Spuma and Orthoretrovirinae and suggests a common ancestor for both lineages containing an ancient CA fold.

  11. The Structure of the MAP2K MEK6 Reveals an Autoinhibitory Dimer

    Energy Technology Data Exchange (ETDEWEB)

    Min, Xiaoshan; Akella, Radha; He, Haixia; Humphreys, John M.; Tsutakawa, Susan E.; Lee, Seung-Jae; Tainer, John A.; Cobb, Melanie H.; Goldsmith, Elizabeth J.

    2009-07-13

    MAP2Ks are dual-specificity protein kinases functioning at the center of three-tiered MAP kinase modules. The structure of the kinase domain of the MAP2K MEK6 with phosphorylation site mimetic aspartic acid mutations (MEK6/{Delta}N/DD) has been solved at 2.3 {angstrom} resolution. The structure reveals an autoinhibited elongated ellipsoidal dimer. The enzyme adopts an inactive conformation, based upon structural queues, despite the phosphomimetic mutations. Gel filtration and small-angle X-ray scattering analysis confirm that the crystallographically observed ellipsoidal dimer is a feature of MEK6/{Delta}N/DD and full-length unphosphorylated wild-type MEK6 in solution. The interface includes the phosphate binding ribbon of each subunit, part of the activation loop, and a rare 'arginine stack' between symmetry-related arginine residues in the N-terminal lobe. The autoinhibited structure likely confers specificity on active MAP2Ks. The dimer may also serve the function in unphosphorylated MEK6 of preventing activation loop phosphorylation by inappropriate kinases.

  12. Structure of a Spumaretrovirus Gag Central Domain Reveals an Ancient Retroviral Capsid

    Science.gov (United States)

    Dutta, Moumita; Pollard, Dominic J.; Goldstone, David C.; Ramos, Andres; Müllers, Erik; Stirnnagel, Kristin; Stanke, Nicole; Lindemann, Dirk; Taylor, William R.; Rosenthal, Peter B.

    2016-01-01

    The Spumaretrovirinae, or foamy viruses (FVs) are complex retroviruses that infect many species of monkey and ape. Despite little sequence homology, FV and orthoretroviral Gag proteins perform equivalent functions, including genome packaging, virion assembly, trafficking and membrane targeting. However, there is a paucity of structural information for FVs and it is unclear how disparate FV and orthoretroviral Gag molecules share the same function. To probe the functional overlap of FV and orthoretroviral Gag we have determined the structure of a central region of Gag from the Prototype FV (PFV). The structure comprises two all α-helical domains NtDCEN and CtDCEN that although they have no sequence similarity, we show they share the same core fold as the N- (NtDCA) and C-terminal domains (CtDCA) of archetypal orthoretroviral capsid protein (CA). Moreover, structural comparisons with orthoretroviral CA align PFV NtDCEN and CtDCEN with NtDCA and CtDCA respectively. Further in vitro and functional virological assays reveal that residues making inter-domain NtDCEN—CtDCEN interactions are required for PFV capsid assembly and that intact capsid is required for PFV reverse transcription. These data provide the first information that relates the Gag proteins of Spuma and Orthoretrovirinae and suggests a common ancestor for both lineages containing an ancient CA fold. PMID:27829070

  13. A Butterfly in the Making: Revealing the Near-Infrared Structure of Hubble 12

    Science.gov (United States)

    Hora, Joseph L.; Latter, William B.

    1996-01-01

    We present deep narrowband near-IR images and moderate resolution spectra of the young planetary nebula Hubble 12. These data are the first to show clearly the complex structure for this important planetary nebula. Images were obtained at lambda = 2.12, 2.16, and 2.26 micron. The lambda = 2.12 Am image reveals the bipolar nature of the nebula, as well as complex structure near the central star in the equatorial region. The images show an elliptical region of emission, which may indicate a ring or a cylindrical source structure. This structure is possibly related to the mechanism that is producing the bipolar flow. The spectra show the nature of several distinct components. The central object is dominated by recombination lines of H I and He I. The core is not a significant source of molecular hydrogen emission. The east position in the equatorial region is rich in lines of ultraviolet-excited fluorescent H2. A spectrum of part of the central region shows strong [Fe II] emission, which might indicate the presence of shocks.

  14. Diverse binding site structures revealed in homology models of polyreactive immunoglobulins

    Science.gov (United States)

    Ramsland, Paul A.; Guddat, Luke W.; Edmundson, Allen B.; Raison, Robert L.

    1997-09-01

    We describe here computer-assisted homology models of the combiningsite structure of three polyreactive immunoglobulins. Template-based modelsof Fv (VL-VH) fragments were derived forthe surface IgM expressed by the malignant CD5 positive B cells from threepatients with chronic lymphocytic leukaemia (CLL). The conserved frameworkregions were constructed using crystal coordinates taken from highlyhomologous human variable domain structures (Pot and Hil). Complementaritydetermining regions (CDRs) were predicted by grafting loops, taken fromknown immunoglobulin structures, onto the Fv framework models. The CDRtemplates were chosen, where possible, to be of the same length and of highresidue identity or similarity. LCDR1, 2 and 3 as well as HCDR1 and 2 forthe Fv were constructed using this strategy. For HCDR3 prediction, adatabase containing the Cartesian coordinates of 30 of these loops wascompiled from unliganded antibody X-ray crystallographic structures and anHCDR3 of the same length as that of the B CLL Fv was selected as a template.In one case (Yar), the resulting HCDR3 model gave unfavourable interactionswhen incorporated into the Fv model. This HCDR3 was therefore modelled usingan alternative strategy of construction of the loop stems, using apreviously described HCDR3 conformation (Pot), followed by chain closurewith a β-turn. The template models were subjected to positionalrefinement using energy minimisation and molecular dynamics simulations(X-PLOR). An electrostatic surface description (GRASP) did not reveal acommon structural feature within the binding sites of the three polyreactiveFv. Thus, polyreactive immunoglobulins may recognise similar and multipleantigens through a diverse array of binding site structures.

  15. Comparison of S. cerevisiae F-BAR domain structures reveals a conserved inositol phosphate binding site

    Science.gov (United States)

    Moravcevic, Katarina; Alvarado, Diego; Schmitz, Karl R.; Kenniston, Jon A.; Mendrola, Jeannine M.; Ferguson, Kathryn M.; Lemmon, Mark A.

    2015-01-01

    SUMMARY F-BAR domains control membrane interactions in endocytosis, cytokinesis, and cell signaling. Although generally thought to bind curved membranes containing negatively charged phospholipids, numerous functional studies argue that differences in lipid-binding selectivities of F-BAR domains are functionally important. Here, we compare membrane-binding properties of the S. cerevisiae F-BAR domains in vitro and in vivo. Whereas some F-BAR domains (such as Bzz1p and Hof1p F-BARs) bind equally well to all phospholipids, the F-BAR domain from the RhoGAP Rgd1p preferentially binds phosphoinositides. We determined X-ray crystal structures of F-BAR domains from Hof1p and Rgd1p, the latter bound to an inositol phosphate. The structures explain phospholipid-binding selectivity differences, and reveal an F-BAR phosphoinositide binding site that is fully conserved in a mammalian RhoGAP called Gmip, and is partly retained in certain other F-BAR domains. Our findings reveal previously unappreciated determinants of F-BAR domain lipid-binding specificity, and provide a basis for its prediction from sequence. PMID:25620000

  16. Structure of the human protein kinase MPSK1 reveals an atypical activation loop architecture.

    Science.gov (United States)

    Eswaran, Jeyanthy; Bernad, Antonio; Ligos, Jose M; Guinea, Barbara; Debreczeni, Judit E; Sobott, Frank; Parker, Sirlester A; Najmanovich, Rafael; Turk, Benjamin E; Knapp, Stefan

    2008-01-01

    The activation segment of protein kinases is structurally highly conserved and central to regulation of kinase activation. Here we report an atypical activation segment architecture in human MPSK1 comprising a beta sheet and a large alpha-helical insertion. Sequence comparisons suggested that similar activation segments exist in all members of the MPSK1 family and in MAST kinases. The consequence of this nonclassical activation segment on substrate recognition was studied using peptide library screens that revealed a preferred substrate sequence of X-X-P/V/I-phi-H/Y-T*-N/G-X-X-X (phi is an aliphatic residue). In addition, we identified the GTPase DRG1 as an MPSK1 interaction partner and specific substrate. The interaction domain in DRG1 was mapped to the N terminus, leading to recruitment and phosphorylation at Thr100 within the GTPase domain. The presented data reveal an atypical kinase structural motif and suggest a role of MPSK1 regulating DRG1, a GTPase involved in regulation of cellular growth.

  17. Altered brain structural networks in attention deficit/hyperactivity disorder children revealed by cortical thickness.

    Science.gov (United States)

    Liu, Tian; Chen, Yanni; Li, Chenxi; Li, Youjun; Wang, Jue

    2017-07-04

    This study investigated the cortical thickness and topological features of human brain anatomical networks related to attention deficit/hyperactivity disorder. Data were collected from 40 attention deficit/hyperactivity disorder children and 40 normal control children. Interregional correlation matrices were established by calculating the correlations of cortical thickness between all pairs of cortical regions (68 regions) of the whole brain. Further thresholds were applied to create binary matrices to construct a series of undirected and unweighted graphs, and global, local, and nodal efficiencies were computed as a function of the network cost. These experimental results revealed abnormal cortical thickness and correlations in attention deficit/hyperactivity disorder, and showed that the brain structural networks of attention deficit/hyperactivity disorder subjects had inefficient small-world topological features. Furthermore, their topological properties were altered abnormally. In particular, decreased global efficiency combined with increased local efficiency in attention deficit/hyperactivity disorder children led to a disorder-related shift of the network topological structure toward regular networks. In addition, nodal efficiency, cortical thickness, and correlation analyses revealed that several brain regions were altered in attention deficit/hyperactivity disorder patients. These findings are in accordance with a hypothesis of dysfunctional integration and segregation of the brain in patients with attention deficit/hyperactivity disorder and provide further evidence of brain dysfunction in attention deficit/hyperactivity disorder patients by observing cortical thickness on magnetic resonance imaging.

  18. EXPLORATORY DATA ANALYSIS AND MULTIVARIATE STRATEGIES FOR REVEALING MULTIVARIATE STRUCTURES IN CLIMATE DATA

    Directory of Open Access Journals (Sweden)

    2016-12-01

    Full Text Available This paper is on data analysis strategy in a complex, multidimensional, and dynamic domain. The focus is on the use of data mining techniques to explore the importance of multivariate structures; using climate variables which influences climate change. Techniques involved in data mining exercise vary according to the data structures. The multivariate analysis strategy considered here involved choosing an appropriate tool to analyze a process. Factor analysis is introduced into data mining technique in order to reveal the influencing impacts of factors involved as well as solving for multicolinearity effect among the variables. The temporal nature and multidimensionality of the target variables is revealed in the model using multidimensional regression estimates. The strategy of integrating the method of several statistical techniques, using climate variables in Nigeria was employed. R2 of 0.518 was obtained from the ordinary least square regression analysis carried out and the test was not significant at 5% level of significance. However, factor analysis regression strategy gave a good fit with R2 of 0.811 and the test was significant at 5% level of significance. Based on this study, model building should go beyond the usual confirmatory data analysis (CDA, rather it should be complemented with exploratory data analysis (EDA in order to achieve a desired result.

  19. Structural and functional analysis of cyclin D1 reveals p27 and substrate inhibitor binding requirements.

    Science.gov (United States)

    Liu, Shu; Bolger, Joshua K; Kirkland, Lindsay O; Premnath, Padmavathy N; McInnes, Campbell

    2010-12-17

    An alternative strategy for inhibition of the cyclin dependent kinases (CDKs) in antitumor drug discovery is afforded through the substrate recruitment site on the cyclin positive regulatory subunit. Critical CDK substrates such as the Rb and E2F families must undergo cyclin groove binding before phosphorylation, and hence inhibitors of this interaction also block substrate specific kinase activity. This approach offers the potential to generate highly selective and cell cycle specific CDK inhibitors and to reduce the inhibition of transcription mediated through CDK7 and 9, commonly observed with ATP competitive compounds. While highly potent peptide and small molecule inhibitors of CDK2/cyclin A, E substrate recruitment have been reported, little information has been generated on the determinants of inhibitor binding to the cyclin groove of the CDK4/cyclin D1 complex. CDK4/cyclin D is a validated anticancer drug target and continues to be widely pursued in the development of new therapeutics based on cell cycle blockade. We have therefore investigated the structural basis for peptide binding to its cyclin groove and have examined the features contributing to potency and selectivity of inhibitors. Peptidic inhibitors of CDK4/cyclin D of pRb phosphorylation have been synthesized, and their complexes with CDK4/cyclin D1 crystal structures have been generated. Based on available structural information, comparisons of the cyclin grooves of cyclin A2 and D1 are presented and provide insights into the determinants for peptide binding and the basis for differential binding and inhibition. In addition, a complex structure has been generated in order to model the interactions of the CDKI, p27(KIP)¹, with cyclin D1. This information has been used to shed light onto the endogenous inhibition of CDK4 and also to identify unique aspects of cyclin D1 that can be exploited in the design of cyclin groove based CDK inhibitors. Peptidic and nonpeptidic compounds have been

  20. Different measures of structural similarity tap different aspects of visual object processing

    DEFF Research Database (Denmark)

    Gerlach, Christian

    2017-01-01

    The structural similarity of objects has been an important variable in explaining why some objects are easier to categorize at a superordinate level than to individuate, and also why some patients with brain injury have more difficulties in recognizing natural (structurally similar) objects than...... artifacts (structurally distinct objects). In spite of its merits as an explanatory variable, structural similarity is not a unitary construct, and it has been operationalized in different ways. Furthermore, even though measures of structural similarity have been successful in explaining task and category-effects...

  1. Crystal structure of aspartame anhydrate from powder diffraction data. Structural aspects of the dehydration process of aspartame

    NARCIS (Netherlands)

    Guguta, C.; Meekes, H.L.M.; Gelder, R. de

    2006-01-01

    Aspartame has three pseudo-polymorphic forms, two hydrates and a hemi-hydrate, for which crystal structures were determined from single-crystal diffraction data. This paper presents the crystal structure of the anhydrate, which was obtained by dehydrating the hemi-hydrate. The crystal structure of

  2. Sacrificial structures for deep reactive ion etching of high-aspect ratio kinoform silicon x-ray lenses

    DEFF Research Database (Denmark)

    Stöhr, Frederik; Michael-Lindhard, Jonas; Hübner, Jörg

    2015-01-01

    This article describes the realization of complex high-aspect ratio silicon structures with feature dimensions from 100 lm to 100nm by deep reactive ion etching using the Bosch process. As the exact shape of the sidewall profiles can be crucial for the proper functioning of a device, the authors...... of the sacrificial structures was accomplished by thermal oxidation and subsequent selective wet etching. The effects of the dimensions and relative placement of sacrificial walls and pillars on the etching result were determined through systematic experiments. The authors applied this process for exact sidewall...

  3. Three-dimensional Crustal Structure beneath the Tibetan Plateau Revealed by Multi-scale Gravity Analysis

    Science.gov (United States)

    Xu, C.; Luo, Z.; Sun, R.; Li, Q.

    2017-12-01

    The Tibetan Plateau, the largest and highest plateau on Earth, was uplifted, shorten and thicken by the collision and continuous convergence of the Indian and Eurasian plates since 50 million years ago, the Eocene epoch. Fine three-dimensional crustal structure of the Tibetan Plateau is helpful in understanding the tectonic development. At present, the ordinary method used for revealing crustal structure is seismic method, which is inhibited by poor seismic station coverage, especially in the central and western plateau primarily due to the rugged terrain. Fortunately, with the implementation of satellite gravity missions, gravity field models have demonstrated unprecedented global-scale accuracy and spatial resolution, which can subsequently be employed to study the crustal structure of the entire Tibetan Plateau. This study inverts three-dimensional crustal density and Moho topography of the Tibetan Plateau from gravity data using multi-scale gravity analysis. The inverted results are in agreement with those provided by the previous works. Besides, they can reveal rich tectonic development of the Tibetan Plateau: (1) The low-density channel flow can be observed from the inverted crustal density; (2) The Moho depth in the west is deeper than that in the east, and the deepest Moho, which is approximately 77 km, is located beneath the western Qiangtang Block; (3) The Moho fold, the directions of which are in agreement with the results of surface movement velocities estimated from Global Positioning System, exists clearly on the Moho topography.This study is supported by the National Natural Science Foundation of China (Grant No. 41504015), the China Postdoctoral Science Foundation (Grant No. 2015M572146), and the Surveying and Mapping Basic Research Programme of the National Administration of Surveying, Mapping and Geoinformation (Grant No. 15-01-08).

  4. X-ray structure reveals a new class and provides insight into evolution of alkaline phosphatases.

    Directory of Open Access Journals (Sweden)

    Subhash C Bihani

    Full Text Available The alkaline phosphatase (AP is a bi-metalloenzyme of potential applications in biotechnology and bioremediation, in which phosphate monoesters are nonspecifically hydrolysed under alkaline conditions to yield inorganic phosphate. The hydrolysis occurs through an enzyme intermediate in which the catalytic residue is phosphorylated. The reaction, which also requires a third metal ion, is proposed to proceed through a mechanism of in-line displacement involving a trigonal bipyramidal transition state. Stabilizing the transition state by bidentate hydrogen bonding has been suggested to be the reason for conservation of an arginine residue in the active site. We report here the first crystal structure of alkaline phosphatase purified from the bacterium Sphingomonas. sp. Strain BSAR-1 (SPAP. The crystal structure reveals many differences from other APs: 1 the catalytic residue is a threonine instead of serine, 2 there is no third metal ion binding pocket, and 3 the arginine residue forming bidentate hydrogen bonding is deleted in SPAP. A lysine and an aspargine residue, recruited together for the first time into the active site, bind the substrate phosphoryl group in a manner not observed before in any other AP. These and other structural features suggest that SPAP represents a new class of APs. Because of its direct contact with the substrate phosphoryl group, the lysine residue is proposed to play a significant role in catalysis. The structure is consistent with a mechanism of in-line displacement via a trigonal bipyramidal transition state. The structure provides important insights into evolutionary relationships between members of AP superfamily.

  5. Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance.

    Science.gov (United States)

    Martin, Michael D; Zimmer, Elizabeth A; Olsen, Morten T; Foote, Andrew D; Gilbert, M Thomas P; Brush, Grace S

    2014-04-01

    Invasive plants provide ample opportunity to study evolutionary shifts that occur after introduction to novel environments. However, although genetic characters pre-dating introduction can be important determinants of later success, large-scale investigations of historical genetic structure have not been feasible. Common ragweed (Ambrosia artemisiifolia L.) is an invasive weed native to North America that is known for its allergenic pollen. Palynological records from sediment cores indicate that this species was uncommon before European colonization of North America, and ragweed populations expanded rapidly as settlers deforested the landscape on a massive scale, later becoming an aggressive invasive with populations established globally. Towards a direct comparison of genetic structure now and during intense anthropogenic disturbance of the late 19th century, we sampled 45 natural populations of common ragweed across its native range as well as historical herbarium specimens collected up to 140 years ago. Bayesian clustering analyses of 453 modern and 473 historical samples genotyped at three chloroplast spacer regions and six nuclear microsatellite loci reveal that historical ragweed's spatial genetic structure mirrors both the palaeo-record of Ambrosia pollen deposition and the historical pattern of agricultural density across the landscape. Furthermore, for unknown reasons, this spatial genetic pattern has changed substantially in the intervening years. Following on previous work relating morphology and genetic expression between plants collected from eastern North America and Western Europe, we speculate that the cluster associated with humans' rapid transformation of the landscape is a likely source of these aggressive invasive populations. © 2014 John Wiley & Sons Ltd.

  6. X-ray CT Scanning Reveals Long-Term Copper Pollution Effects on Functional Soil Structure

    DEFF Research Database (Denmark)

    Naveed, Muhammad; Møldrup, Per; Homstrup, Martin

    Soil structure plays the main role in the ability of the soil to fulfill essential soil functions such as the root growth, rate of water infiltration and retention, transport of gaseous and chemicals/pollutants through the soil. Soil structure is a dynamic soil property and affected by various...... factors such as soil type, land use, and soil contamination. In this study, we quantified the soil structure using X-ray CT scanning and revealed the effect of a long history of Copper (Cu) pollution on it. A fallow field at Hygum Denmark provides this opportunity as it had a long history of Copper...... sulphate contamination in a gradient with Cu content varies from 21 mg kg-1 to 3837 mg kg-1. Total 20 intact soil columns (diameter of 10 cm and height of 8 cm) were sampled at five locations along the Cu-gradient from a depth of 5 to 15 cm below surface level. The soil columns were scanned at a voxel...

  7. Patterned biofilm formation reveals a mechanism for structural heterogeneity in bacterial biofilms.

    Science.gov (United States)

    Gu, Huan; Hou, Shuyu; Yongyat, Chanokpon; De Tore, Suzanne; Ren, Dacheng

    2013-09-03

    Bacterial biofilms are ubiquitous and are the major cause of chronic infections in humans and persistent biofouling in industry. Despite the significance of bacterial biofilms, the mechanism of biofilm formation and associated drug tolerance is still not fully understood. A major challenge in biofilm research is the intrinsic heterogeneity in the biofilm structure, which leads to temporal and spatial variation in cell density and gene expression. To understand and control such structural heterogeneity, surfaces with patterned functional alkanthiols were used in this study to obtain Escherichia coli cell clusters with systematically varied cluster size and distance between clusters. The results from quantitative imaging analysis revealed an interesting phenomenon in which multicellular connections can be formed between cell clusters depending on the size of interacting clusters and the distance between them. In addition, significant differences in patterned biofilm formation were observed between wild-type E. coli RP437 and some of its isogenic mutants, indicating that certain cellular and genetic factors are involved in interactions among cell clusters. In particular, autoinducer-2-mediated quorum sensing was found to be important. Collectively, these results provide missing information that links cell-to-cell signaling and interaction among cell clusters to the structural organization of bacterial biofilms.

  8. Crystal Structure of Homo Sapiens PTD012 Reveals a Zinc-Containing Hydrolase Fold

    Energy Technology Data Exchange (ETDEWEB)

    Manjasetty,B.; Bussow, K.; Fieber-ErdMan, M.; Roske, Y.; Gobam, J.; Scheich, C.; Gotz, F.; Niesen, F.; Heinemann, U.

    2006-01-01

    The human protein PTD012 is the longer product of an alternatively spliced gene and was described to be localized in the nucleus. The X-ray structure analysis at 1.7 Angstroms resolution of PTD012 through SAD phasing reveals a monomeric protein and a novel fold. The shorter splice form was also studied and appears to be unfolded and non-functional. The structure of PTD012 displays an {alpha}{beta}{beta}{alpha} four-layer topology. A metal ion residing between the central {beta}-sheets is partially coordinated by three histidine residues. X-ray absorption near-edge structure (XANES) analysis identifies the PTD012-bound ion as Zn{sup 2+}. Tetrahedral coordination of the ion is completed by the carboxylate oxygen atom of an acetate molecule taken up from the crystallization buffer. The binding of Zn{sup 2+} to PTD012 is reminiscent of zinc-containing enzymes such as carboxypeptidase, carbonic anhydrase, and {beta}-lactamase. Biochemical assays failed to demonstrate any of these enzyme activities in PTD012. However, PTD012 exhibits ester hydrolase activity on the substrate p-nitrophenyl acetate.

  9. Crystal structure of the Haemophilus influenzae Hap adhesin reveals an intercellular oligomerization mechanism for bacterial aggregation

    Science.gov (United States)

    Meng, Guoyu; Spahich, Nicole; Kenjale, Roma; Waksman, Gabriel; St Geme, Joseph W

    2011-01-01

    Bacterial biofilms are complex microbial communities that are common in nature and are being recognized increasingly as an important determinant of bacterial virulence. However, the structural determinants of bacterial aggregation and eventual biofilm formation have been poorly defined. In Gram-negative bacteria, a major subgroup of extracellular proteins called self-associating autotransporters (SAATs) can mediate cell–cell adhesion and facilitate biofilm formation. In this study, we used the Haemophilus influenzae Hap autotransporter as a prototype SAAT to understand how bacteria associate with each other. The crystal structure of the H. influenzae HapS passenger domain (harbouring the SAAT domain) was determined to 2.2 Å by X-ray crystallography, revealing an unprecedented intercellular oligomerization mechanism for cell–cell interaction. The C-terminal SAAT domain folds into a triangular-prism-like structure that can mediate Hap–Hap dimerization and higher degrees of multimerization through its F1–F2 edge and F2 face. The intercellular multimerization can give rise to massive buried surfaces that are required for overcoming the repulsive force between cells, leading to bacterial cell–cell interaction and formation of complex microcolonies. PMID:21841773

  10. Time-Resolved Soft X-ray Diffraction Reveals Transient Structural Distortions of Ternary Liquid Crystals

    Directory of Open Access Journals (Sweden)

    Klaus Mann

    2009-11-01

    Full Text Available Home-based soft X-ray time-resolved scattering experiments with nanosecond time resolution (10 ns and nanometer spatial resolution were carried out at a table top soft X-ray plasma source (2.2–5.2 nm. The investigated system was the lyotropic liquid crystal C16E7/paraffin/glycerol/formamide/IR 5. Usually, major changes in physical, chemical, and/or optical properties of the sample occur as a result of structural changes and shrinking morphology. Here, these effects occur as a consequence of the energy absorption in the sample upon optical laser excitation in the IR regime. The liquid crystal shows changes in the structural response within few hundred nanoseconds showing a time decay of 182 ns. A decrease of the Bragg peak diffracted intensity of 30% and a coherent macroscopic movement of the Bragg reflection are found as a response to the optical pump. The Bragg reflection movement is established to be isotropic and diffusion controlled (1 μs. Structural processes are analyzed in the Patterson analysis framework of the time-varying diffraction peaks revealing that the inter-lamellar distance increases by 2.7 Å resulting in an elongation of the coherently expanding lamella crystallite. The present studies emphasize the possibility of applying TR-SXRD techniques for studying the mechanical dynamics of nanosystems.

  11. The enzymes of biotin dependent CO2 metabolism: What structures reveal about their reaction mechanisms

    Science.gov (United States)

    Waldrop, Grover L; Holden, Hazel M; Maurice, Martin St

    2012-01-01

    Biotin is the major cofactor involved in carbon dioxide metabolism. Indeed, biotin-dependent enzymes are ubiquitous in nature and are involved in a myriad of metabolic processes including fatty acid synthesis and gluconeogenesis. The cofactor, itself, is composed of a ureido ring, a tetrahydrothiophene ring, and a valeric acid side chain. It is the ureido ring that functions as the CO2 carrier. A complete understanding of biotin-dependent enzymes is critically important for translational research in light of the fact that some of these enzymes serve as targets for anti-obesity agents, antibiotics, and herbicides. Prior to 1990, however, there was a dearth of information regarding the molecular architectures of biotin-dependent enzymes. In recent years there has been an explosion in the number of three-dimensional structures reported for these proteins. Here we review our current understanding of the structures and functions of biotin-dependent enzymes. In addition, we provide a critical analysis of what these structures have and have not revealed about biotin-dependent catalysis. PMID:22969052

  12. Repeated Structural Imaging Reveals Nonlinear Progression of Experience-Dependent Volume Changes in Human Motor Cortex.

    Science.gov (United States)

    Wenger, Elisabeth; Kühn, Simone; Verrel, Julius; Mårtensson, Johan; Bodammer, Nils Christian; Lindenberger, Ulman; Lövdén, Martin

    2017-05-01

    Evidence for experience-dependent structural brain change in adult humans is accumulating. However, its time course is not well understood, as intervention studies typically consist of only 2 imaging sessions (before vs. after training). We acquired up to 18 structural magnetic resonance images over a 7-week period while 15 right-handed participants practiced left-hand writing and drawing. After 4 weeks, we observed increases in gray matter of both left and right primary motor cortices relative to a control group; 3 weeks later, these differences were no longer reliable. Time-series analyses revealed that gray matter in the primary motor cortices expanded during the first 4 weeks and then partially renormalized, in particular in the right hemisphere, despite continued practice and increasing task proficiency. Similar patterns of expansion followed by partial renormalization are also found in synaptogenesis, cortical map plasticity, and maturation, and may qualify as a general principle of structural plasticity. Research on human brain plasticity needs to encompass more than 2 measurement occasions to capture expansion and potential renormalization processes over time. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  13. The structure of the TFIIH p34 subunit reveals a von Willebrand factor A like fold.

    Directory of Open Access Journals (Sweden)

    Dominik R Schmitt

    Full Text Available RNA polymerase II dependent transcription and nucleotide excision repair are mediated by a multifaceted interplay of subunits within the general transcription factor II H (TFIIH. A better understanding of the molecular structure of TFIIH is the key to unravel the mechanism of action of this versatile protein complex within these vital cellular processes. The importance of this complex becomes further evident in the context of severe diseases like xeroderma pigmentosum, Cockayne's syndrome and trichothiodystrophy, that arise from single point mutations in TFIIH subunits. Here we describe the structure of the p34 subunit of the TFIIH complex from the eukaryotic thermophilic fungus Chaetomium thermophilum. The structure revealed that p34 contains a von Willebrand Factor A (vWA like domain, a fold which is generally known to be involved in protein-protein interactions. Within TFIIH p34 strongly interacts with p44, a positive regulator of the helicase XPD. Putative protein-protein interfaces are analyzed and possible binding sites for the p34-p44 interaction suggested.

  14. Genetic structure of South African Nguni (Zulu) sheep populations reveals admixture with exotic breeds.

    Science.gov (United States)

    Selepe, Mokhethi Matthews; Ceccobelli, Simone; Lasagna, Emiliano; Kunene, Nokuthula Winfred

    2018-01-01

    The population of Zulu sheep is reported to have declined by 7.4% between 2007 and 2011 due to crossbreeding. There is insufficient information on the genetic diversity of the Zulu sheep populations in the different area of KwaZulu Natal where they are reared. The study investigated genetic variation and genetic structure within and among eight Zulu sheep populations using 26 microsatellite markers. In addition, Damara, Dorper and South African Merino breeds were included to assess the genetic relationship between these breeds and the Zulu sheep. The results showed that there is considerable genetic diversity among the Zulu sheep populations (expected heterozygosity ranging from 0.57 to 0.69) and the level of inbreeding was not remarkable. The structure analysis results revealed that Makhathini Research Station and UNIZULU research station share common genetic structure, while three populations (Nongoma, Ulundi and Nquthu) had some admixture with the exotic Dorper breed. Thus, there is a need for sustainable breeding and conservation programmes to control the gene flow, in order to stop possible genetic dilution of the Zulu sheep.

  15. Genetic structure of South African Nguni (Zulu sheep populations reveals admixture with exotic breeds.

    Directory of Open Access Journals (Sweden)

    Mokhethi Matthews Selepe

    Full Text Available The population of Zulu sheep is reported to have declined by 7.4% between 2007 and 2011 due to crossbreeding. There is insufficient information on the genetic diversity of the Zulu sheep populations in the different area of KwaZulu Natal where they are reared. The study investigated genetic variation and genetic structure within and among eight Zulu sheep populations using 26 microsatellite markers. In addition, Damara, Dorper and South African Merino breeds were included to assess the genetic relationship between these breeds and the Zulu sheep. The results showed that there is considerable genetic diversity among the Zulu sheep populations (expected heterozygosity ranging from 0.57 to 0.69 and the level of inbreeding was not remarkable. The structure analysis results revealed that Makhathini Research Station and UNIZULU research station share common genetic structure, while three populations (Nongoma, Ulundi and Nquthu had some admixture with the exotic Dorper breed. Thus, there is a need for sustainable breeding and conservation programmes to control the gene flow, in order to stop possible genetic dilution of the Zulu sheep.

  16. Thermal, structural, and fabrication aspects of diamond windows for high power synchrotron x-ray beamlines

    International Nuclear Information System (INIS)

    Khounsary, A.M.; Phillips, W.

    1992-01-01

    Recent advances in chemical vapor deposition (CVD) technology have made it possible to produce thin free-standing diamond foils that can be used as the window material in high heat load, synchrotron beamlines. Numerical simulations suggest that these windows can offer an attractive and at times the only altemative to beryllium windows for use in third generation x-ray synchrotron radiation beamlines. Utilization, design, and fabrication aspects of diamond windows for high heat load x-ray beamlines are discussed, as are the microstructure characteristics bearing on diamond's performance in this role. Analytic and numerical results are also presented to provide a basis for the design and testing of such windows

  17. Integrated analysis of multiple data sources reveals modular structure of biological networks

    International Nuclear Information System (INIS)

    Lu Hongchao; Shi Baochen; Wu Gaowei; Zhang Yong; Zhu Xiaopeng; Zhang Zhihua; Liu Changning; Zhao, Yi; Wu Tao; Wang Jie; Chen Runsheng

    2006-01-01

    It has been a challenging task to integrate high-throughput data into investigations of the systematic and dynamic organization of biological networks. Here, we presented a simple hierarchical clustering algorithm that goes a long way to achieve this aim. Our method effectively reveals the modular structure of the yeast protein-protein interaction network and distinguishes protein complexes from functional modules by integrating high-throughput protein-protein interaction data with the added subcellular localization and expression profile data. Furthermore, we take advantage of the detected modules to provide a reliably functional context for the uncharacterized components within modules. On the other hand, the integration of various protein-protein association information makes our method robust to false-positives, especially for derived protein complexes. More importantly, this simple method can be extended naturally to other types of data fusion and provides a framework for the study of more comprehensive properties of the biological network and other forms of complex networks

  18. Integration of community structure data reveals observable effects below sediment guideline thresholds in a large estuary

    KAUST Repository

    Tremblay, Louis A.

    2017-04-07

    The sustainable management of estuarine and coastal ecosystems requires robust frameworks due to the presence of multiple physical and chemical stressors. In this study, we assessed whether ecological health decline, based on community structure composition changes along a pollution gradient, occurred at levels below guideline threshold values for copper, zinc and lead. Canonical analysis of principal coordinates (CAP) was used to characterise benthic communities along a metal contamination gradient. The analysis revealed changes in benthic community distribution at levels below the individual guideline values for the three metals. These results suggest that field-based measures of ecological health analysed with multivariate tools can provide additional information to single metal guideline threshold values to monitor large systems exposed to multiple stressors.

  19. Upper crustal structure of Madeira Island revealed from ambient noise tomography

    Science.gov (United States)

    Matos, Catarina; Silveira, Graça; Matias, Luís; Caldeira, Rita; Ribeiro, M. Luísa; Dias, Nuno A.; Krüger, Frank; Bento dos Santos, Telmo

    2015-06-01

    We present the first image of the Madeira upper crustal structure, using ambient seismic noise tomography. 16 months of ambient noise, recorded in a dense network of 26 seismometers deployed across Madeira, allowed reconstructing Rayleigh wave Green's functions between receivers. Dispersion analysis was performed in the short period band from 1.0 to 4.0 s. Group velocity measurements were regionalized to obtain 2D tomographic images, with a lateral resolution of 2.0 km in central Madeira. Afterwards, the dispersion curves, extracted from each cell of the 2D group velocity maps, were inverted as a function of depth to obtain a 3D shear wave velocity model of the upper crust, from the surface to a depth of 2.0 km. The obtained 3D velocity model reveals features throughout the island that correlates well with surface geology and island evolution.

  20. High-speed atomic force microscopy reveals structural dynamics of α -synuclein monomers and dimers

    Science.gov (United States)

    Zhang, Yuliang; Hashemi, Mohtadin; Lv, Zhengjian; Williams, Benfeard; Popov, Konstantin I.; Dokholyan, Nikolay V.; Lyubchenko, Yuri L.

    2018-03-01

    α-Synuclein (α-syn) is the major component of the intraneuronal inclusions called Lewy bodies, which are the pathological hallmark of Parkinson's disease. α-Syn is capable of self-assembly into many different species, such as soluble oligomers and fibrils. Even though attempts to resolve the structures of the protein have been made, detailed understanding about the structures and their relationship with the different aggregation steps is lacking, which is of interest to provide insights into the pathogenic mechanism of Parkinson's disease. Here we report the structural flexibility of α-syn monomers and dimers in an aqueous solution environment as probed by single-molecule time-lapse high-speed AFM. In addition, we present the molecular basis for the structural transitions using discrete molecular dynamics (DMD) simulations. α-Syn monomers assume a globular conformation, which is capable of forming tail-like protrusions over dozens of seconds. Importantly, a globular monomer can adopt fully extended conformations. Dimers, on the other hand, are less dynamic and show a dumbbell conformation that experiences morphological changes over time. DMD simulations revealed that the α-syn monomer consists of several tightly packed small helices. The tail-like protrusions are also helical with a small β-sheet, acting as a "hinge". Monomers within dimers have a large interfacial interaction area and are stabilized by interactions in the non-amyloid central (NAC) regions. Furthermore, the dimer NAC-region of each α-syn monomer forms a β-rich segment. Moreover, NAC-regions are located in the hydrophobic core of the dimer.

  1. Revealing the Linkage Network Dynamic Structures of Chinese Maritime Ports through Automatic Information System Data

    Directory of Open Access Journals (Sweden)

    Hongchu Yu

    2017-10-01

    Full Text Available Marine economic cooperation has emerged as a major theme in this era of globalization; hence, maritime network connectivity and dynamics have attracted more and more attention. Port construction and maritime route improvements increase maritime trade and thus facilitate economic viability and resource sustainability. This paper reveals the regional dimension of inter-port linkage dynamic structure of Chinese maritime ports from a complex multilayer perspective that is meaningful for strategic forecasting and regional long-term economic development planning. In this research, Automatic Information System (AIS-derived traffic flows were used to construct a maritime network and subnetworks based on the geographical locations of ports. The linkage intensity between subnetworks, the linkage tightness within subnetworks, the spatial isolation between high-intensity backbones and tight skeleton networks, and a linkage concentration index for each port were calculated. The ports, in turn, were analyzed based on these network attributes. This study analyzed the external competitiveness and internal cohesion of each subnetwork. The results revealed problems in port management and planning, such as unclear divisions in port operations. More critically, weak complementary relationships between the backbone and skeleton networks among the ports reduce connectivity and must be strengthened. This research contributes to the body of work supporting strategic decision-making for future development.

  2. Collagen I self-assembly: revealing the developing structures that generate turbidity.

    Science.gov (United States)

    Zhu, Jieling; Kaufman, Laura J

    2014-04-15

    Type I collagen gels are routinely used in biophysical studies and bioengineering applications. The structural and mechanical properties of these fibrillar matrices depend on the conditions under which collagen fibrillogenesis proceeds, and developing a fuller understanding of this process will enhance control over gel properties. Turbidity measurements have long been the method of choice for monitoring developing gels, whereas imaging methods are regularly used to visualize fully developed gels. In this study, turbidity and confocal reflectance microscopy (CRM) were simultaneously employed to track collagen fibrillogenesis and reconcile the information reported by the two techniques, with confocal fluorescence microscopy (CFM) used to supplement information about early events in fibrillogenesis. Time-lapse images of 0.5 mg/ml, 1.0 mg/ml, and 2.0 mg/ml acid-solubilized collagen I gels forming at 27°C, 32°C, and 37°C were collected. It was found that in situ turbidity measured in a scanning transmittance configuration was interchangeable with traditional turbidity measurements using a spectrophotometer. CRM and CFM were employed to reveal the structures responsible for the turbidity that develops during collagen self-assembly. Information from CRM and transmittance images was collapsed into straightforward single variables; total intensity in CRM images tracked turbidity development closely for all collagen gels investigated, and the two techniques were similarly sensitive to fibril number and dimension. Complementary CRM, CFM, and in situ turbidity measurements revealed that fibril and network formation occurred before substantial turbidity was present, and the majority of increasing turbidity during collagen self-assembly was due to increasing fibril thickness. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  3. Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds.

    Science.gov (United States)

    Onzima, R B; Upadhyay, M R; Mukiibi, R; Kanis, E; Groenen, M A M; Crooijmans, R P M A

    2018-02-01

    Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium-density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (H O ) and expected (H E ) heterozygosity across breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub-structuring among the breeds. Principal components separated Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f 4 statistics revealed gene flow from Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within-breed diversity and heterozygote advantage in crossbreeding schemes. © 2018 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.

  4. Some structural aspects of language are more stable than others: a comparison of seven methods.

    Directory of Open Access Journals (Sweden)

    Dan Dediu

    Full Text Available Understanding the patterns and causes of differential structural stability is an area of major interest for the study of language change and evolution. It is still debated whether structural features have intrinsic stabilities across language families and geographic areas, or if the processes governing their rate of change are completely dependent upon the specific context of a given language or language family. We conducted an extensive literature review and selected seven different approaches to conceptualising and estimating the stability of structural linguistic features, aiming at comparing them using the same dataset, the World Atlas of Language Structures. We found that, despite profound conceptual and empirical differences between these methods, they tend to agree in classifying some structural linguistic features as being more stable than others. This suggests that there are intrinsic properties of such structural features influencing their stability across methods, language families and geographic areas. This finding is a major step towards understanding the nature of structural linguistic features and their interaction with idiosyncratic, lineage- and area-specific factors during language change and evolution.

  5. Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity.

    Science.gov (United States)

    Kouno, Takahide; Silvas, Tania V; Hilbert, Brendan J; Shandilya, Shivender M D; Bohn, Markus F; Kelch, Brian A; Royer, William E; Somasundaran, Mohan; Kurt Yilmaz, Nese; Matsuo, Hiroshi; Schiffer, Celia A

    2017-04-28

    Nucleic acid editing enzymes are essential components of the immune system that lethally mutate viral pathogens and somatically mutate immunoglobulins, and contribute to the diversification and lethality of cancers. Among these enzymes are the seven human APOBEC3 deoxycytidine deaminases, each with unique target sequence specificity and subcellular localization. While the enzymology and biological consequences have been extensively studied, the mechanism by which APOBEC3s recognize and edit DNA remains elusive. Here we present the crystal structure of a complex of a cytidine deaminase with ssDNA bound in the active site at 2.2 Å. This structure not only visualizes the active site poised for catalysis of APOBEC3A, but pinpoints the residues that confer specificity towards CC/TC motifs. The APOBEC3A-ssDNA complex defines the 5'-3' directionality and subtle conformational changes that clench the ssDNA within the binding groove, revealing the architecture and mechanism of ssDNA recognition that is likely conserved among all polynucleotide deaminases, thereby opening the door for the design of mechanistic-based therapeutics.

  6. Sleep-dependent consolidation patterns reveal insights into episodic memory structure.

    Science.gov (United States)

    Oyanedel, Carlos N; Sawangjit, Anuck; Born, Jan; Inostroza, Marion

    2018-05-18

    Episodic memory formation is considered a genuinely hippocampal function. Its study in rodents has relied on two different task paradigms, i.e. the so called "what-where-when" (WW-When) task and "what-where-which" (WW-Which) task. The WW-When task aims to assess the memory for an episode as an event bound into its context defined by spatial and distinct temporal information, the WW-Which task lacks the temporal component and introduces, instead, an "occasion setter" marking the broader contextual configuration in which the event occurred. Whether both tasks measure episodic memory in an equivalent manner in terms of recollection has been controversially discussed. Here, we compared in two groups of rats the consolidating effects of sleep on episodic-like memory between both task paradigms. Sampling and test phases were separated by a 90-min morning retention interval which did or did not allow for spontaneous sleep. Results show that sleep is crucial for the consolidation of the memory on both tasks. However, consolidating effects of sleep were stronger for the WW-Which than WW-When task. Comparing performance during the post-sleep test phase revealed that WW-When memory only gradually emerged during the 3-min test period whereas WW-Which memory was readily expressed already from the first minute onward. Separate analysis of the temporal and spatial components of WW-When performance showed that the delayed episodic memory on this task originated from the temporal component which also did not emerge until the third minute of the test phase, whereas the spatial component already showed up in the first minute. In conclusion, sleep differentially affects consolidation on the two episodic-like memory tasks, with the delayed expression of WW-When memory after sleep resulting from preferential coverage of temporal aspects by this task. Copyright © 2018. Published by Elsevier Inc.

  7. Molecular dynamics simulations revealed structural differences among WRKY domain-DNA interaction in barley (Hordeum vulgare).

    Science.gov (United States)

    Pandey, Bharati; Grover, Abhinav; Sharma, Pradeep

    2018-02-12

    The WRKY transcription factors are a class of DNA-binding proteins involved in diverse plant processes play critical roles in response to abiotic and biotic stresses. Genome-wide divergence analysis of WRKY gene family in Hordeum vulgare provided a framework for molecular evolution and functional roles. So far, the crystal structure of WRKY from barley has not been resolved; moreover, knowledge of the three-dimensional structure of WRKY domain is pre-requisites for exploring the protein-DNA recognition mechanisms. Homology modelling based approach was used to generate structures for WRKY DNA binding domain (DBD) and its variants using AtWRKY1 as a template. Finally, the stability and conformational changes of the generated model in unbound and bound form was examined through atomistic molecular dynamics (MD) simulations for 100 ns time period. In this study, we investigated the comparative binding pattern of WRKY domain and its variants with W-box cis-regulatory element using molecular docking and dynamics (MD) simulations assays. The atomic insight into WRKY domain exhibited significant variation in the intermolecular hydrogen bonding pattern, leading to the structural anomalies in the variant type and differences in the DNA-binding specificities. Based on the MD analysis, residual contribution and interaction contour, wild-type WRKY (HvWRKY46) were found to interact with DNA through highly conserved heptapeptide in the pre- and post-MD simulated complexes, whereas heptapeptide interaction with DNA was missing in variants (I and II) in post-MD complexes. Consequently, through principal component analysis, wild-type WRKY was also found to be more stable by obscuring a reduced conformational space than the variant I (HvWRKY34). Lastly, high binding free energy for wild-type and variant II allowed us to conclude that wild-type WRKY-DNA complex was more stable relative to variants I. The results of our study revealed complete dynamic and structural information

  8. Preliminary aspects concerning phytoplankton structure in the Balta Mare – Carja 1 fish farm

    Directory of Open Access Journals (Sweden)

    Maria FETECAU

    2010-08-01

    Full Text Available The present paper presents information on the structure and the dynamics of the water ecosystem’s phytoplankton of the Carja 1 fish farm - Vaslui County, carps and Asian cyprinids are grown ascommon fish. To establish the structure and the dynamics of the phytoplankton, two samples from 6 stations were taken in the spring and in the autumn, using of a Garmin GPS 7- type navigation system.When analysing the number of individuals and the algae species present in the phytoplankton’s structure, one can notice the low development level of the vegetable plankton. From the quantity point of view, one can notice the numerical abundance of the clorophyceae in all the analysed samples. The dominant species were: Scenedesmus acuminatus, Scenedesmus quadricauda, Tetrastrum staurogenieforme. The small number of species and algae specimens determined in the phytoplankton’s structure emphasizes the reduced level of trophicity and biodiversity of the analysed ecosystem.

  9. Aspects of Structure and Dynamics at a Refugee Centre in Denmark

    DEFF Research Database (Denmark)

    Mackrill, Thomas Edward

    1996-01-01

    This article presents an empirical analysis that is part of a practice research project carried out at a Danish Red Cross refugee centre in Copenhagen. It focuses on the relation between the individual refugee and the receiving institution. It points out how the organizational structure...... of a particular refugee centre enables discord between refugees and centre workers as well as among the centre staff. It analyses some of the dynamics of the conflicts that are facilitated by the structure...

  10. The structure and institutions: a regional aspect of interaction in the economic system

    Directory of Open Access Journals (Sweden)

    Leonid Stepanovich Tarasevich

    2014-09-01

    Full Text Available In the article with the help of two-sector model of the economic system, the interaction of national and regional economy is investigated. This interaction is observed from the position of development of material structure and institutions. As the key structural parameter of an economy, the proportion between sector of excess resources and sector of scarce resources is taken. The situation when sector of excess resources prevails over sector of scarce resources forms structural conditions for the creation of the market institutions. If a sector of excess resources is smaller than a sector of scarce resources, the conditions for the emergence of institutions of government regulation are formed. Two cases are analyzed: the first one concerns the situation of a simple national economy consisting of 2 provisory regions. The second is the case of the national economy consisting of many regions. The authors show that material structure of a total combination of regions defines institutions of the market or state regulation for the national economy as a whole. The institutions formed at the level of the national economy, can support or resist the development of structure of the region. The conditions are observed under which united institutions of the national economy contradict a development of structure of the individual region.

  11. Under-explored aspects of structural adjustment: Growing inequalities among women and implications for feminist movements

    DEFF Research Database (Denmark)

    Hiranandani, Vanmala Sunder

    2008-01-01

    , privatization of the public sector and exposing domestic industries to foreign market competition. Contrary to promised benefits, SAPs have resulted in escalating poverty and inequality, deteriorating health, education and housing conditions, and degradation of the environment. Women in ‘developing countries...... that can thwart neo-liberal and concomitant fundamentalist forces. With a focus on India, the essay highlights the escalating disparities among women that have remained under-researched, and accentuates the need to investigate the repercussions of these egregious inequities for feminist organizations.......’ have faced the major brunt as SAPs have transformed crucial aspects of their lives. While the outcomes of SAPs for women have been well-documented, most extant literature views women as a homogenous group ignoring differential impacts of economic reforms across class, caste, religion and other social...

  12. Electrical properties of transparent CNT and ITO coatings on PET substrate including nano-structural aspects

    Science.gov (United States)

    Park, Joung-Man; Wang, Zuo-Jia; Kwon, Dong-Jun; Gu, Ga-Young; Lawrence DeVries, K.

    2013-01-01

    Ultraviolet (UV)-visible spectra and surface resistance measurement were used to investigate optical transmittance and conductive properties of carbon nanotube (CNT) and indium tin oxide (ITO) coated polyethylene terephthalate (PET) substrates. Conductive CNT and ITO coatings were successfully fabricated on PET by a spray-coating method. Thin coatings of both materials exhibited good conductivity and transparency. Changes in electrical and optical properties of the coatings were studied as a function of the coating suspension concentration. Interfacial durability of the coatings on PET substrates was also investigated under fatigue and bending loads. CNT coated substrates, with high aspect ratios, exhibited no detectable change in surface resistance up to 2000 cyclic loadings, whereas the ITO coated substrates exhibited a substantial increase in surface resistance at 1000 loading cycles. This change in resistance is attributed to a reduction in the number and effectiveness of the electrical contact points due to the inherent brittle nature of ITO.

  13. Organization aspect

    NARCIS (Netherlands)

    Grefen, P.W.P.J.; Mehandjiev, N.; Mehandjiev, N.; Grefen, P.W.P.J.

    2010-01-01

    Following the BOAT framework discussed in Chapter 1, this chapter describes the organization aspect of the CrossWork approach. It shows how the business requirements identified in the previous chapter can be fulfilled by dynamic organization structures and business processes in Networks of

  14. Revealing the structure and dust content of debris disks on solar systems scales with GPI

    Science.gov (United States)

    Duchene, Gaspard; Fitzgerald, Michael P.; Kalas, Paul; Graham, James R.; Arriaga, Pauline; Bruzzone, Sebastian; Chen, Christine; Dawson, Rebekah Ilene; Dong, Ruobing; Draper, Zachary; Esposito, Thomas; Follette, Katherine; Hung, Li-Wei; Lawler, Samantha; Metchev, Stanimir; Millar-Blanchaer, Max; Murray-Clay, Ruth; Perrin, Marshall D.; Rameau, Julien; Wang, Jason; Wolff, Schuyler; Macintosh, Bruce; GPIES Team

    2016-01-01

    High contrast scattered light images offer the best prospect to assess the detailed geometry and structure of dusty debris disks. In turn, such images can yield profound insight on the architecture of the underlying planetary system as dust grains respond to the gravitational pull of planetary bodies. A new generation of extreme adaptive optics systems now enables an unprecedented exploration of circumstellar disks on solar system scales. Here we review the new science derived from over a dozen debris disks imaged with the Gemini Planet Imager (GPI) as part of the GPI Exoplanet Survey (GPIES). In addition to its exquisite imaging capability, GPI's polarimetric mode provides invaluable insight on the dust content of each disk, in most cases for the very first time. These early results typically reveal narrow belts of material with evacuated regions roughly 50-100 AU in radius, subtle asymmetries in structure and high degree of linear polarization. We will provide an overview of the disk observations made during the GPIES campaign to date and will discuss in more detail some of the most remarkable systems.This work is supported by grants NSF AST-0909188, -1411868, -1413718; NASA NNX-15AD95G, -14AJ80G, -11AD21G; and the NExSS research network.

  15. Rich club analysis in the Alzheimer's disease connectome reveals a relatively undisturbed structural core network.

    Science.gov (United States)

    Daianu, Madelaine; Jahanshad, Neda; Nir, Talia M; Jack, Clifford R; Weiner, Michael W; Bernstein, Matt A; Thompson, Paul M

    2015-08-01

    Diffusion imaging can assess the white matter connections within the brain, revealing how neural pathways break down in Alzheimer's disease (AD). We analyzed 3-Tesla whole-brain diffusion-weighted images from 202 participants scanned by the Alzheimer's Disease Neuroimaging Initiative-50 healthy controls, 110 with mild cognitive impairment (MCI) and 42 AD patients. From whole-brain tractography, we reconstructed structural brain connectivity networks to map connections between cortical regions. We tested whether AD disrupts the "rich club" - a network property where high-degree network nodes are more interconnected than expected by chance. We calculated the rich club properties at a range of degree thresholds, as well as other network topology measures including global degree, clustering coefficient, path length, and efficiency. Network disruptions predominated in the low-degree regions of the connectome in patients, relative to controls. The other metrics also showed alterations, suggesting a distinctive pattern of disruption in AD, less pronounced in MCI, targeting global brain connectivity, and focusing on more remotely connected nodes rather than the central core of the network. AD involves severely reduced structural connectivity; our step-wise rich club coefficients analyze points to disruptions predominantly in the peripheral network components; other modalities of data are needed to know if this indicates impaired communication among non rich club regions. The highly connected core was relatively preserved, offering new evidence on the neural basis of progressive risk for cognitive decline. © 2015 Wiley Periodicals, Inc.

  16. Some aspects of the reliability-based design of reactor containment structures

    International Nuclear Information System (INIS)

    Schueller, G.I.

    1975-01-01

    It is generally recognized that the load which a structure is likely to experience during its design life as well as its resistance are to be represented by random variables. A rational design procedure for reactor containment structures can therefore only be carried out within a probabilistic framework. Internal load conditions caused by system failure such as loss-of-coolant accident, pressure loads etc., and external load conditions caused for instance by impact due to aircraft crashes, external pressure waves and natural hazards such as earthquakes, floods, hurricanes are described by extreme value distributions of the Fisher-Tippett types. Statistical and physical arguments are given to support their application. The occurrence of these rare events with respect to time is modeled by a Poisson process. The yield strength of the containment structure for both steel (liner) and reinforced concrete shells is also modeled by extreme value distributions (of the smallest values). The failure criterion considered here is that of collapse determined by plastic yieldline formation. A failure mechanism as considered here describes a particular regime of plastic line formation. The probability of failure of a structure under a single load application of load types likely to occur during the design life of the structure is to be determined by integrating over all possible mechanisms. Finally Freudenthal's reliability function is utilized to combine the information derived above so that a containment design for given design lifes and reliabilities is possible. (orig.) [de

  17. Biophysical investigation of type A PutAs reveals a conserved core oligomeric structure

    Energy Technology Data Exchange (ETDEWEB)

    Korasick, David A. [Department of Biochemistry, University of Missouri, Columbia MO USA; Singh, Harkewal [Department of Chemistry, University of Missouri, Columbia MO USA; Pemberton, Travis A. [Department of Chemistry, University of Missouri, Columbia MO USA; Luo, Min [Department of Chemistry, University of Missouri, Columbia MO USA; Dhatwalia, Richa [Department of Chemistry, University of Missouri, Columbia MO USA; Tanner, John J. [Department of Biochemistry, University of Missouri, Columbia MO USA; Department of Chemistry, University of Missouri, Columbia MO USA

    2017-08-01

    Many enzymes form homooligomers, yet the functional significance of self-association is seldom obvious. Herein, we examine the connection between oligomerization and catalytic function for proline utilization A (PutA) enzymes. PutAs are bifunctional enzymes that catalyze both reactions of proline catabolism. Type A PutAs are the smallest members of the family, possessing a minimal domain architecture consisting of N-terminal proline dehydrogenase and C-terminal l-glutamate-γ-semialdehyde dehydrogenase modules. Type A PutAs form domain-swapped dimers, and in one case (Bradyrhizobium japonicum PutA), two of the dimers assemble into a ring-shaped tetramer. Whereas the dimer has a clear role in substrate channeling, the functional significance of the tetramer is unknown. To address this question, we performed structural studies of four-type A PutAs from two clades of the PutA tree. The crystal structure of Bdellovibrio bacteriovorus PutA covalently inactivated by N-propargylglycine revealed a fold and substrate-channeling tunnel similar to other PutAs. Small-angle X-ray scattering (SAXS) and analytical ultracentrifugation indicated that Bdellovibrio PutA is dimeric in solution, in contrast to the prediction from crystal packing of a stable tetrameric assembly. SAXS studies of two other type A PutAs from separate clades also suggested that the dimer predominates in solution. To assess whether the tetramer of B. japonicum PutA is necessary for catalytic function, a hot spot disruption mutant that cleanly produces dimeric protein was generated. The dimeric variant exhibited kinetic parameters similar to the wild-type enzyme. These results implicate the domain-swapped dimer as the core structural and functional unit of type A PutAs.

  18. Glycan structure of Gc Protein-derived Macrophage Activating Factor as revealed by mass spectrometry.

    Science.gov (United States)

    Borges, Chad R; Rehder, Douglas S

    2016-09-15

    Disagreement exists regarding the O-glycan structure attached to human vitamin D binding protein (DBP). Previously reported evidence indicated that the O-glycan of the Gc1S allele product is the linear core 1 NeuNAc-Gal-GalNAc-Thr trisaccharide. Here, glycan structural evidence is provided from glycan linkage analysis and over 30 serial glycosidase-digestion experiments which were followed by analysis of the intact protein by electrospray ionization mass spectrometry (ESI-MS). Results demonstrate that the O-glycan from the Gc1F protein is the same linear trisaccharide found on the Gc1S protein and that the hexose residue is galactose. In addition, the putative anti-cancer derivative of DBP known as Gc Protein-derived Macrophage Activating Factor (GcMAF, which is formed by the combined action of β-galactosidase and neuraminidase upon DBP) was analyzed intact by ESI-MS, revealing that the activating E. coli β-galactosidase cleaves nothing from the protein-leaving the glycan structure of active GcMAF as a Gal-GalNAc-Thr disaccharide, regardless of the order in which β-galactosidase and neuraminidase are applied. Moreover, glycosidase digestion results show that α-N-Acetylgalactosamindase (nagalase) lacks endoglycosidic function and only cleaves the DBP O-glycan once it has been trimmed down to a GalNAc-Thr monosaccharide-precluding the possibility of this enzyme removing the O-glycan trisaccharide from cancer-patient DBP in vivo. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. Structural Characterization of Maize SIRK1 Kinase Domain Reveals an Unusual Architecture of the Activation Segment

    Directory of Open Access Journals (Sweden)

    Bruno Aquino

    2017-05-01

    Full Text Available Kinases are primary regulators of plant metabolism and excellent targets for plant breeding. However, most kinases, including the abundant receptor-like kinases (RLK, have no assigned role. SIRK1 is a leucine-rich repeat receptor-like kinase (LRR-RLK, the largest family of RLK. In Arabidopsis thaliana, SIRK1 (AtSIRK1 is phosphorylated after sucrose is resupplied to sucrose-starved seedlings and it modulates the sugar response by phosphorylating several substrates. In maize, the ZmSIRK1 expression is altered in response to drought stress. In neither Arabidopsis nor in maize has the function of SIRK1 been completely elucidated. As a first step toward the biochemical characterization of ZmSIRK1, we obtained its recombinant kinase domain, demonstrated that it binds AMP-PNP, a non-hydrolysable ATP-analog, and solved the structure of ZmSIRK1- AMP-PNP co-crystal. The ZmSIRK1 crystal structure revealed a unique conformation for the activation segment. In an attempt to find inhibitors for ZmSIRK1, we screened a focused small molecule library and identified six compounds that stabilized ZmSIRK1 against thermal melt. ITC analysis confirmed that three of these compounds bound to ZmSIRK1 with low micromolar affinity. Solving the 3D structure of ZmSIRK1-AMP-PNP co-crystal provided information on the molecular mechanism of ZmSIRK1 activity. Furthermore, the identification of small molecules that bind this kinase can serve as initial backbone for development of new potent and selective ZmSIRK1 antagonists.

  20. Cyberlexicography in LSP: New Aspects of Components and Structures in the Dictionary

    DEFF Research Database (Denmark)

    Laursen, Anne Lise; Duvå, Grete

    2005-01-01

    In the pre-electronic days the structure of a dictionary was discussed within pre-established frames, the controversial part being - more or less - how much information to include and in which order. Electronic devices offer a much wider set of possibilities within which no obvious pattern seems...... to have been established. In this paper, we shall focus on the strengths and weaknesses of a number of existing electronic dictionaries, and we shall make some suggestions as to how to reach an optimum and how to change the components and the structures of the internet dictionary accordingly....

  1. Steric structure and thermodynamic aspects of Dy3+ complexes with aminobenzoic acids in aqueous solutions

    International Nuclear Information System (INIS)

    Kondrashina, Yu.G.; Mustafina, A.R.; Vul'fson, S.G.

    1994-01-01

    Stability and structure of dysprosium(3) aminobenzoate complexes with molar ratios Dy:L 1:1 and 1:2 (HL-aminobenzoic acid) in aqueous solutions are determined on the basis of pH-metric and paramagnetic birefringence data. The increase of conjugation effect in the series of benzoic, meta- ortho-, and para-aminobenzoic acid results in the increase of stability of 1:1 and 1:2 complexes. Features of the structure and coordination of ligands in dysprosium complexes with meta-, ortho-, and para-aminobenzoic acid are considered. 11 refs.; 4 figs.; 2 tabs

  2. Revealing Students' Cognitive Structure about Physical and Chemical Change: Use of a Word Association Test

    Science.gov (United States)

    Yildirir, Hasene Esra; Demirkol, Hatice

    2018-01-01

    The current study aimed at examining the utility of a word association test in revealing students' cognitive structure in a specific chemistry topic through a word association test. The participants were 153 6th graders in a western Turkish city. The results revealed that the word association test serves a useful purpose in exploring the students'…

  3. Main aspects of the design of a support structure of a LMFBR with particular reference to the explosive accident consequences

    International Nuclear Information System (INIS)

    Giuliano, V.; Lazzeri, L.

    1977-01-01

    The aim of this paper is a review of the main aspects of the design of a support structure of a LMFBR tank, with particular reference to the analysis of the non-linear dynamic behaviour of the structure in the plastic range under the effect of an explosive accident within the tank. The structure is composed by a L-shaped flange, which supports the tank, connected by means of nine square beams to a rigid box-type ring, fixed to the concrete. The plug of the tank is connected to the L-shaped figure by means of a group of SS bars. The non-linear dynamic analysis of the explosive accident has been carried out on a lumped mass model, with elastic-plastic elements which simulate main components of the support structure and tank. The impulsive load connected to the explosive accident has been modelled (on the basis of extensive comparative studies carried out) as two triangular pressure impulses acting on the plug and on the botton of the tank. A large amount of results, which describe displacements, velocities and accelerations of the plug, of the tank, and of the support structure, together with the forces and stresses acting on the main structural components are presented and discussed, with particular reference to the influence of the various parameters involved in the analysis. (Auth.)

  4. Associations between structural quality aspects and process quality in Dutch early childhood education and care settings

    NARCIS (Netherlands)

    Slot, P.L.; Leseman, P.P.M.; Verhagen, J.; Mulder, H.

    2015-01-01

    The relationship between structural quality and process quality in early childhood education and care (ECEC) has been addressed in several studies. However, the findings are not conclusive. The present study was conducted in the Netherlands, which has a strongly regulated mid-quality ECEC system

  5. What do children know and understand about universal gravitation? Structural and developmental aspects

    NARCIS (Netherlands)

    Frappart, S.; Raijmakers, M.; Frède, V.

    2014-01-01

    Children's understanding of universal gravitation starts at an early age but changes until adulthood, which makes it an interesting topic for studying the development and structure of knowledge. Children's understanding of gravitation was tested for a variety of contexts and across a wide age range

  6. New Biochemical Pathway for Biphenyl Degradation in Plants: Structural, Mechanistic and Biotechnological Aspects

    International Nuclear Information System (INIS)

    Pacios, L. F.; Campos, V. M.; Merino, I.; Gomez, L.

    2009-01-01

    Polychlorinated biphenyls (PVBs) and other structurally-related xenobiotics are amongst the most relevant organic pollutants known today. while some bacterial species can metabolize PCBs, with varying efficiency, no catabolic pathways have yet been described in plants. This is so despite the great potential of (at least some) plant species for soil and groundwater decontamination, a technology known as phyto remediation. (Author)

  7. Structural and Functional Aspects of the Sensor Histidine Kinase PrrB from Mycobacterium tuberculosis

    DEFF Research Database (Denmark)

    Nowak, E.; Panjikar, S.; Morth, J.P.

    2006-01-01

    We describe the solution structures of two- and three-domain constructs of the sensor histidine kinase PrrB from Mycobacterium tuberculosis, which allow us to locate the HAMP linker relative to the ATP binding and dimerization domains. We show that the three-domain construct is active both...

  8. Conformational aspects of dibenzo-tetroxecin: A structural, Raman spectroscopic and computational study

    Science.gov (United States)

    Gordon, Keith C.; McAdam, C. John; Moratti, Stephen C.; Shillito, Georgina E.; Simpson, Jim

    2017-10-01

    Crystalline dibenzo-tetroxecin (I) has been prepared from a reaction between catechol and dichloromethane and its molecular and crystal structure, together with the Raman spectrum of the material in the solid state and in solution, is reported. The molecular structure shows the molecule adopts an anti or stepped conformation. Density functional theory (DFT) optimisation and frequency calculations using the B3LYP functional with the 6-31G(d) basis set showed the presence of syn- and anti-conformers of (I), with the anti-conformer predicted to be the lower in energy by 13.6 kJ mol-1. The vibrational frequencies and relative Raman intensities of the anti-conformer are well modelled by the DFT calculations. The bond lengths and angles obtained for the anti-conformer are also in good agreement with the crystal structure. The crystal structure of (I) is stabilised by intermolecular Csbnd H⋯O hydrogen bonds that generate a three dimensional network.

  9. Reliability of photogrammetry in the evaluation of the postural aspects of individuals with structural scoliosis.

    Science.gov (United States)

    Saad, Karen Ruggeri; Colombo, Alexandra Siqueira; Ribeiro, Ana Paula; João, Sílvia Maria Amado

    2012-04-01

    The purpose of this study was to investigate the reliability of photogrammetry in the measurement of the postural deviations in individuals with idiopathic scoliosis. Twenty participants with scoliosis (17 women and three men), with a mean age of 23.1 ± 9 yrs, were photographed from the posterior and lateral views. The postural aspects were measured with CorelDRAW software. High inter-rater and test-retest reliability indices were found. It was observed that with more severity of scoliosis, greater were the variations between the thoracic kyphosis and lumbar lordosis measures obtained by the same examiner from the left lateral view photographs. A greater body mass index (BMI) was associated with greater variability of the trunk rotation measures obtained by two independent examiners from the right, lateral view (r = 0.656; p = 0.002). The severity of scoliosis was also associated with greater inter-rater variability measures of trunk rotation obtained from the left, lateral view (r = 0.483; p = 0.036). Photogrammetry demonstrated to be a reliable method for the measurement of postural deviations from the posterior and lateral views of individuals with idiopathic scoliosis and could be complementarily employed for the assessment procedures, which could reduce the number of X-rays used for the follow-up assessments of these individuals. Copyright © 2011 Elsevier Ltd. All rights reserved.

  10. Structural aspects of cold-formed steel section designed as U-shape composite beam

    Science.gov (United States)

    Saggaff, Anis; Tahir, Mahmood Md.; Azimi, Mohammadamin; Alhajri, T. M.

    2017-11-01

    Composite beam construction usually associated with old-style Hot-Rolled Steel Section (HRSS) has proven to act much better in compare with Cold-Formed Steel Section (CFSS) sections due to thicker section. Due, it's getting popular to replace HRSS with CFSS in some aspects as a composite beam. The advantages such as lightweight, cost effective and easy to install have contributed to the apply CFSS as a preferred construction material for composite beam. There is a few technical data available regarding the application of the usage of CFSS as a composite system, despite the potentials use for residential and light-weight industrial constructions. This paper presents an experimental tests results which have been conducted using CFSS as composite beam. Composite action of CFSS arranged as double beam with Self-Compacting Concrete (SCC) slab are integrated together with bolted shear connectors were used. A full-scale test comprised of 3 proposed composite beam specimens with bolted shear connector spaced at 300 mm interval of grade 8.8 was using single nut with washer on flange of CFS, cast to the slab and loaded until failed. The test show that the bolted shear connector yielded better capacity of ultimate strength and ultimate moment for the proposed composite beam. It can be concluded that, bolted shear connectors of 16 mm in diameter performed better than the other diameter size of bolted shear connectors.

  11. Northern Bobwhite (Colinus virginianus Mitochondrial Population Genomics Reveals Structure, Divergence, and Evidence for Heteroplasmy.

    Directory of Open Access Journals (Sweden)

    Yvette A Halley

    Full Text Available Herein, we evaluated the concordance of population inferences and conclusions resulting from the analysis of short mitochondrial fragments (i.e., partial or complete D-Loop nucleotide sequences versus complete mitogenome sequences for 53 bobwhites representing six ecoregions across TX and OK (USA. Median joining (MJ haplotype networks demonstrated that analyses performed using small mitochondrial fragments were insufficient for estimating the true (i.e., complete mitogenome haplotype structure, corresponding levels of divergence, and maternal population history of our samples. Notably, discordant demographic inferences were observed when mismatch distributions of partial (i.e., partial D-Loop versus complete mitogenome sequences were compared, with the reduction in mitochondrial genomic information content observed to encourage spurious inferences in our samples. A probabilistic approach to variant prediction for the complete bobwhite mitogenomes revealed 344 segregating sites corresponding to 347 total mutations, including 49 putative nonsynonymous single nucleotide variants (SNVs distributed across 12 protein coding genes. Evidence of gross heteroplasmy was observed for 13 bobwhites, with 10 of the 13 heteroplasmies involving one moderate to high frequency SNV. Haplotype network and phylogenetic analyses for the complete bobwhite mitogenome sequences revealed two divergent maternal lineages (dXY = 0.00731; FST = 0.849; P < 0.05, thereby supporting the potential for two putative subspecies. However, the diverged lineage (n = 103 variants almost exclusively involved bobwhites geographically classified as Colinus virginianus texanus, which is discordant with the expectations of previous geographic subspecies designations. Tests of adaptive evolution for functional divergence (MKT, frequency distribution tests (D, FS and phylogenetic analyses (RAxML provide no evidence for positive selection or hybridization with the sympatric scaled quail

  12. Electronic transport properties aspects and structure of polymer-fullerene based organic semiconductors for photovoltaic devices

    International Nuclear Information System (INIS)

    Adamopoulos, G.; Heiser, T.; Giovanella, U.; Ould-Saad, S.; Wetering, K.I. van de; Brochon, C.; Zorba, T.; Paraskevopoulos, K.M.; Hadziioannou, G.

    2006-01-01

    A series of polystyrene (PS) and fullerene (C 60 ) based thin films containing from 23 to 60 wt.% in fullerene were investigated. Initially, the films were characterised by Fourier Transform Infrared Spectroscopy (FTIR) spectroscopy where the characteristic absorption bands of both the fullerene and the polystyrene were revealed. The additional characteristic absorption bands due the grafted fullerene to polystyrene were revealed as well. The relative peak intensities provided with qualitative information of the films stoichiometry in terms of the fullerene's amount that was grafted to polystyrene. The optical properties of the films were investigated by spectroscopic ellipsometry (SE). It was found that the increase of the fullerene's amount that was grafted to polystyrene results in an increase of the absorption coefficient α, refractive index n, extinction coefficient k as well as in the dielectric constant ε ∝ within the range between 2.4 and 2.8 for the lower and higher fullerene content, respectively. The films' J-V characteristics, of the space charge limited current (SCLC) behaviour, showed increased currents with increasing the fullerene's content. The electron mobility was extracted and found to increase with increasing the fullerene amount, from 4 x 10 -9 cm 2 /V s to 2 x 10 -7 cm 2 /V s

  13. Electronic transport properties aspects and structure of polymer-fullerene based organic semiconductors for photovoltaic devices

    Energy Technology Data Exchange (ETDEWEB)

    Adamopoulos, G. [Laboratoire d' Ingenierie des Polymeres pour les Hautes Technologies (L.I.P.H.T.), Ecole Europeenne Chimie Polymeres Materiaux (E.C.P.M.), 25 Rue Becquerel, 67087 Strasbourg Cedex 02 (France)]. E-mail: geo_adamo@yahoo.fr; Heiser, T. [Institut d' Electronique du Solide et des Systemes (IN.E.S.S.), CNRS/ULP, 23 Rue du Loess, BP 20, 67037 Strasbourg Cedex 02 (France); Giovanella, U. [Laboratoire d' Ingenierie des Polymeres pour les Hautes Technologies (L.I.P.H.T.), Ecole Europeenne Chimie Polymeres Materiaux (E.C.P.M.), 25 Rue Becquerel, 67087 Strasbourg Cedex 02 (France); Ould-Saad, S. [Laboratoire d' Ingenierie des Polymeres pour les Hautes Technologies (L.I.P.H.T.), Ecole Europeenne Chimie Polymeres Materiaux (E.C.P.M.), 25 Rue Becquerel, 67087 Strasbourg Cedex 02 (France); Wetering, K.I. van de [Laboratoire d' Ingenierie des Polymeres pour les Hautes Technologies (L.I.P.H.T.), Ecole Europeenne Chimie Polymeres Materiaux (E.C.P.M.), 25 Rue Becquerel, 67087 Strasbourg Cedex 02 (France); Brochon, C. [Laboratoire d' Ingenierie des Polymeres pour les Hautes Technologies (L.I.P.H.T.), Ecole Europeenne Chimie Polymeres Materiaux (E.C.P.M.), 25 Rue Becquerel, 67087 Strasbourg Cedex 02 (France); Zorba, T. [Physics Department, Solid State Physics Section, Aristotle University of Thessaloniki, 54124 Thessaloniki (Greece); Paraskevopoulos, K.M. [Physics Department, Solid State Physics Section, Aristotle University of Thessaloniki, 54124 Thessaloniki (Greece); Hadziioannou, G. [Laboratoire d' Ingenierie des Polymeres pour les Hautes Technologies (L.I.P.H.T.), Ecole Europeenne Chimie Polymeres Materiaux (E.C.P.M.), 25 Rue Becquerel, 67087 Strasbourg Cedex 02 (France)

    2006-07-26

    A series of polystyrene (PS) and fullerene (C{sub 60}) based thin films containing from 23 to 60 wt.% in fullerene were investigated. Initially, the films were characterised by Fourier Transform Infrared Spectroscopy (FTIR) spectroscopy where the characteristic absorption bands of both the fullerene and the polystyrene were revealed. The additional characteristic absorption bands due the grafted fullerene to polystyrene were revealed as well. The relative peak intensities provided with qualitative information of the films stoichiometry in terms of the fullerene's amount that was grafted to polystyrene. The optical properties of the films were investigated by spectroscopic ellipsometry (SE). It was found that the increase of the fullerene's amount that was grafted to polystyrene results in an increase of the absorption coefficient {alpha}, refractive index n, extinction coefficient k as well as in the dielectric constant {epsilon} {sub {proportional_to}} within the range between 2.4 and 2.8 for the lower and higher fullerene content, respectively. The films' J-V characteristics, of the space charge limited current (SCLC) behaviour, showed increased currents with increasing the fullerene's content. The electron mobility was extracted and found to increase with increasing the fullerene amount, from 4 x 10{sup -9} cm{sup 2}/V s to 2 x 10{sup -7} cm{sup 2}/V s.

  14. Sequence, structure and function relationships in flaviviruses as assessed by evolutive aspects of its conserved non-structural protein domains.

    Science.gov (United States)

    da Fonseca, Néli José; Lima Afonso, Marcelo Querino; Pedersolli, Natan Gonçalves; de Oliveira, Lucas Carrijo; Andrade, Dhiego Souto; Bleicher, Lucas

    2017-10-28

    Flaviviruses are responsible for serious diseases such as dengue, yellow fever, and zika fever. Their genomes encode a polyprotein which, after cleavage, results in three structural and seven non-structural proteins. Homologous proteins can be studied by conservation and coevolution analysis as detected in multiple sequence alignments, usually reporting positions which are strictly necessary for the structure and/or function of all members in a protein family or which are involved in a specific sub-class feature requiring the coevolution of residue sets. This study provides a complete conservation and coevolution analysis on all flaviviruses non-structural proteins, with results mapped on all well-annotated available sequences. A literature review on the residues found in the analysis enabled us to compile available information on their roles and distribution among different flaviviruses. Also, we provide the mapping of conserved and coevolved residues for all sequences currently in SwissProt as a supplementary material, so that particularities in different viruses can be easily analyzed. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Structural aspects of magnetic fluid stabilization in aqueous agarose solutions

    Energy Technology Data Exchange (ETDEWEB)

    Nagornyi, A.V. [Joint Institute for Nuclear Research, Dubna (Russian Federation); Taras Shevchenko National University of Kyiv, Kyiv (Ukraine); Petrenko, V.I., E-mail: vip@nf.jinr.ru [Joint Institute for Nuclear Research, Dubna (Russian Federation); Taras Shevchenko National University of Kyiv, Kyiv (Ukraine); Avdeev, M.V. [Joint Institute for Nuclear Research, Dubna (Russian Federation); Yelenich, O.V.; Solopan, S.O.; Belous, A.G. [V.I.Vernadsky Institute of General and Inorganic Chemistry of the Ukrainian NAS, Kyiv (Ukraine); Gruzinov, A.Yu. [National Research Centre “Kurchatov Institute”, Moscow (Russian Federation); Ivankov, O.I. [Joint Institute for Nuclear Research, Dubna (Russian Federation); Institute for Safety Problems of Nuclear Power Plants of the Ukrainian NAS, Kyiv (Ukraine); Bulavin, L.A. [Taras Shevchenko National University of Kyiv, Kyiv (Ukraine); Institute for Safety Problems of Nuclear Power Plants of the Ukrainian NAS, Kyiv (Ukraine)

    2017-06-01

    Structure characterization of magnetic fluids (MFs) synthesized by three different methods in aqueous solutions of agarose was done by means of small-angle neutron (SANS) and synchrotron X-ray scattering (SAXS). The differences in the complex aggregation observed in the studied magnetic fluids were related to different stabilizing procedures of the three kinds of MFs. The results of the analysis of the scattering (mean size of single polydisperse magnetic particles, fractal dimensions of the aggregates) are consistent with the data of transmission electron microscopy (TEM). - Highlights: • MFs synthesized by three different methods in agarose solution were studied. • all MFs are agglomerated colloidal systems whose structures are nevertheless stable in time. • differences in the complex aggregation were observed in the studied magnetic fluids. • results of the SAXS and SANS analysis are consistent with TEM data.

  16. Structural aspects of the nucleolus and its associated heterochromatin in neurons

    International Nuclear Information System (INIS)

    Pessacq, T.P.; Vidal Rioja, L.A.

    1975-01-01

    The study of the structure of the nucleolus has received considerable attention in recent years. Most data have been provided by a number of electromicroscopical studies which to some extent are confirmatory of the previous opticomicroscopical findings of Estable and Sotelo (1951, 1952, 1955), Davis (1960), Altmann, Stoecker, and Thoenes (1963), O'Donell (1961), Lettre, and Siebs (1961), Bernhard, Bauer, Gropp, Haguenau and Oberling (1955) among others. In a recent work Melker (1970) points out the existence in neurons of a mammal of a particular arrangement of the nucleolus and its associated chromatin very similar to that already established in avian neurons (Pessacq 1969). The research reported here adds some new structural facts on nucleolar-heterochromatinic rapports which although recognizable in a great variety of cellular types appears with schematic clearness only in a limited number of highly specialized cells of some species. (auth.)

  17. Synthesis, structural and luminescent aspect of Tb3+ doped Sr2SnO4 phosphor

    International Nuclear Information System (INIS)

    Taikar, Deepak R.

    2016-01-01

    A novel green emitting, Tb 3+ doped Sr 2 SnO 4 phosphor was synthesized by the co-precipitation method and its photoluminescence characterization was performed. Sr 2 SnO 4 has an ordered tetragonal K 2 NiF 4 -type structure with space group I4/mmm. The structure of Sr 2 SnO 4 consists of SnO 6 octahedra. From the structure of Sr 2 SnO 4 , it was observed that the sites of Sn 4+ ions have inverse symmetry while the Sr 2+ ions have the low symmetry. X-ray powder diffraction (XRD) analysis confirmed the formation of Sr 2 SnO 4 :Tb 3+ . Photoluminescence measurements showed that the phosphor exhibited bright green emission at about 543 nm attributed to 5 D 4 à 7 F 5 transition of Tb 3+ ion under UV excitation. The emission spectra did not exhibit conventional blue emission peaks of Tb 3+ ions due to 5 D 3 → 7 F J transitions in the spectral region 350-470 nm. The excitation spectra indicate that this compound may be useful as a lamp phosphor. (author)

  18. Structural aspects of crotoxin modified by ionizing radiation; Aspectos estruturais da crotoxina modificada pela radiacao ionizante

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Karina Corleto de; Albero, Felipe Guimaraes; Zezell, Denise Maria; Spencer, Patrick Jack; Nascimento, Nanci do, E-mail: kcorleto@usp.b [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2010-03-15

    Ionizing radiation has proven to be an excellent tool for reducing the toxicity of venoms and isolated toxins, resulting in better immunogens for serum production, the only effective treatment in case of snake bites, and contributing to the welfare of serum-producing animals. Since the action of gamma radiation of venoms and toxins has not been yet fully clarified from the structural point of view, we proposed in this paper, to characterize the crotoxin, a venom protein of the species Crotalus durissus terrificus by Circular Dichroism (CD) and Infrared Spectroscopy (FTIR) techniques. After chromatographic techniques, crotoxin was irradiated with 2.0 kGy ({sup 60}Co source). The CD spectra obtained of native and irradiated crotoxin solutions showed changes between the samples in characteristic regions of -sheet and-helix . The Infrared analyse showed expressive changes in the spectra of the native and irradiated crotoxin (amide I band region). These tests showed that crotoxin when subjected to gamma radiation, showed changes in their structural conformation compared with the samples in the native state. Such changes probably occur in the secondary structure and may explain its neurotoxic activity loss. (author)

  19. Structural aspects of catalytic mechanisms of endonucleases and their binding to nucleic acids

    Energy Technology Data Exchange (ETDEWEB)

    Zhukhlistova, N. E.; Balaev, V. V.; Lyashenko, A. V.; Lashkov, A. A., E-mail: alashkov83@gmail.com [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2012-05-15

    Endonucleases (EC 3.1) are enzymes of the hydrolase class that catalyze the hydrolytic cleavage of deoxyribonucleic and ribonucleic acids at any region of the polynucleotide chain. Endonucleases are widely used both in biotechnological processes and in veterinary medicine as antiviral agents. Medical applications of endonucleases in human cancer therapy hold promise. The results of X-ray diffraction studies of the spatial organization of endonucleases and their complexes and the mechanism of their action are analyzed and generalized. An analysis of the structural studies of this class of enzymes showed that the specific binding of enzymes to nucleic acids is characterized by interactions with nitrogen bases and the nucleotide backbone, whereas the nonspecific binding of enzymes is generally characterized by interactions only with the nucleic-acid backbone. It should be taken into account that the specificity can be modulated by metal ions and certain low-molecular-weight organic compounds. To test the hypotheses about specific and nonspecific nucleic-acid-binding proteins, it is necessary to perform additional studies of atomic-resolution three-dimensional structures of enzyme-nucleic-acid complexes by methods of structural biology.

  20. Some aspects of floor spectra of 1DOF nonlinear primary structures

    International Nuclear Information System (INIS)

    Politopoulos, I.; Feau, C.

    2007-01-01

    In this paper the influence of the nonlinear behaviour of the primary structure on floor spectra is investigated by means of simple models. The general trends of floor spectra for different types of nonlinear behaviour of one degree of freedom (1DOF) primary structure are shown and we point out their common futures and their differences. A special attention is given to the cases of elastoplastic and nonlinear elastic behaviours and methods to determine an equivalent linear oscillator are proposed. The properties (frequency and damping) of this equivalent linear oscillator are quite different from the properties of equivalent linear oscillators commonly considered in practice. In particular, in the case of elastoplastic behaviour, there is no frequency shift and damping is smaller than assumed by other methods commonly used. In the case of nonlinear elastic behaviour, the concept of an equivalent frequency which is a random variable is used. Finally, a design floor spectrum of primary structures, exhibiting energy dissipating nonlinear behaviour is proposed. (authors)

  1. Evaluation Aspects of Building Structures Reconstructed After a Failure or Catastrophe

    Science.gov (United States)

    Krentowski, Janusz R.; Knyziak, Piotr

    2017-10-01

    The article presents the characteristics of several steel structures, among others modernized industrial dye house, school sports hall, truck repair workshop, that have been rebuilt after a disaster or a catastrophe. The structures were analyzed in detail, and the evaluation and reconstruction processes were described. The emergencies that occurred during exploitation of the buildings were the result of multiple mistakes: incorrectly defined intervals between inspections, errors during periodic inspections, incorrect repair work recommendations. The concepts of reinforcement work implemented by the authors, enabling the long-term future failure-free operation of the objects, were presented. Recommendations for monitoring of the facilities, applied after reinforcement or reconstruction, have been formulated. The methodology for the implementation of specialized investigations, such as geodetic, optical, geological, chemical strength tests, both destructive and non-destructive, has been defined. The need to determine the limit values of deformations, deflections, damage or other faults of structural elements and the entire rebuilt facilities, as well as defining conditions for objects’ withdrawal from operation in subsequent exceptional situations was indicated.

  2. Some physical problems in biology: Aspects of the origin and structure of the first cell

    International Nuclear Information System (INIS)

    Chela Flores, J.

    1995-01-01

    A review is presented within the framework of the theory of evolution, after it has been extrapolated from the population level to the cellular and molecular levels. From Darwin's seminal and persuasive insight - the theory of common descent - we assume, with him, that ''probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed''. We are now aware that his primordial cell may have been a protocyanobacterium, but it has often been called 'a last universal ancestor', a 'breakthrough organism', or a 'progenote', a term introduced by Woese which has gained wide acceptance. Strictly speaking, in the 'intermediate period', ranging from the first living cell to the progenote, life may have evolved in the absence of significant diversity, effectively as a single phylum, incorporating organisms whose genetic systems were already based on DNA. Earlier still, prior to the encapsulation of nucleic acids in microspheres, evolution may already have been at work on RNA molecules (the 'RNA world'). This takes our discussion into the period of chemical evolution, a concept first put forward by Oparin, whose principal merit is to have formulated the underlying problem in clear scientific terms. This review does not attempt to be comprehensive. It is mainly devoted to the discussion of certain concepts that may have played a relevant role in the pathway that led to the origin and evolution of the progenote. We do not dwell on the main events of the intermediate period. The topic that we have chosen to include are: the origin of chirality of protein amino acids, the origin of translation, and the origin of the genome. We conclude with some comments on one further aspect of the evolutionary process - the development of biodiversity - by considering the origin of the first eukaryotic cell, an event which, according to the fossil record, may have preceded the evolutionary radiation in the early

  3. Growth Aspects, Structural and Optical Properties of 2-aminopyridinium 2,4 Dinitrophenolate Single Crystal

    Directory of Open Access Journals (Sweden)

    S. Reena Devi

    2017-06-01

    Full Text Available Organic single crystal of 2-aminopyridinium 2,4-dinitrophenolate single crystal was grown by slow evaporation technique. The cell parameters and space group (P were determined from single X-ray diffraction analysis. HRXRD studies ascertained the crystalline quality. UV-Visible and PL spectral studies revealed the emission in red region, transparency (75% cutoff wavelength around 440 nm respectively. The laser damage threshold of grown crystal was estimated by using Nd:YAG laser beam and these results were mutually related with specific heat capacity of the grown crystal. The third-order nonlinear optical parameters were estimated by Z-scan technique which is useful for optical applications.

  4. Interplay of protein and DNA structure revealed in simulations of the lac operon.

    Directory of Open Access Journals (Sweden)

    Luke Czapla

    Full Text Available The E. coli Lac repressor is the classic textbook example of a protein that attaches to widely spaced sites along a genome and forces the intervening DNA into a loop. The short loops implicated in the regulation of the lac operon suggest the involvement of factors other than DNA and repressor in gene control. The molecular simulations presented here examine two likely structural contributions to the in-vivo looping of bacterial DNA: the distortions of the double helix introduced upon association of the highly abundant, nonspecific nucleoid protein HU and the large-scale deformations of the repressor detected in low-resolution experiments. The computations take account of the three-dimensional arrangements of nucleotides and amino acids found in crystal structures of DNA with the two proteins, the natural rest state and deformational properties of protein-free DNA, and the constraints on looping imposed by the conformation of the repressor and the orientation of bound DNA. The predicted looping propensities capture the complex, chain-length-dependent variation in repression efficacy extracted from gene expression studies and in vitro experiments and reveal unexpected chain-length-dependent variations in the uptake of HU, the deformation of repressor, and the folding of DNA. Both the opening of repressor and the presence of HU, at levels approximating those found in vivo, enhance the probability of loop formation. HU affects the global organization of the repressor and the opening of repressor influences the levels of HU binding to DNA. The length of the loop determines whether the DNA adopts antiparallel or parallel orientations on the repressor, whether the repressor is opened or closed, and how many HU molecules bind to the loop. The collective behavior of proteins and DNA is greater than the sum of the parts and hints of ways in which multiple proteins may coordinate the packaging and processing of genetic information.

  5. Biochemistry and structural studies of kynurenine 3-monooxygenase reveal allosteric inhibition by Ro 61-8048.

    Science.gov (United States)

    Gao, Jingjing; Yao, Licheng; Xia, Tingting; Liao, Xuebin; Zhu, Deyu; Xiang, Ye

    2018-04-01

    The human kynurenine 3-monooxygenase (hKMO) is a potential therapeutic target for neurodegenerative and neurologic disorders. Inhibition of KMO by Ro 61-8048, a potent, selective, and the most widely used inhibitor of KMO, was shown effective in various models of neurodegenerative or neurologic disorders. However, the molecular basis of hKMO inhibition by Ro 61-8048 is not clearly understood. Here, we report biochemistry studies on hKMO and crystal structures of an hKMO homolog, pfKMO from Pseudomonas fluorescens, in complex with the substrate l-kynurenine and Ro 61-8048. We found that the C-terminal ∼110 aa are essential for the enzymatic activity of hKMO and the homologous C-terminal region of pfKMO folds into a distinct, all-α-helical domain, which associates with the N-terminal catalytic domain to form a unique tunnel in proximity to the substrate-binding pocket. The tunnel binds the Ro 61-8048 molecule, which fills most of the tunnel, and Ro 61-8048 is hydrogen bonded with several completely conserved residues, including an essential catalytic residue. Modification of Ro 61-8048 and biochemical studies of the modified Ro 61-8048 derivatives suggested that Ro 61-8048 inhibits the enzyme in an allosteric manner by affecting the conformation of the essential catalytic residue and by blocking entry of the substrate or product release. The unique binding sites distinguish Ro 61-8048 as a noncompetitive and highly selective inhibitor from other competitive inhibitors, which should facilitate further optimization of Ro 61-8048 and the development of new inhibitory drugs to hKMO.-Gao, J., Yao, L., Xia, T., Liao, X., Zhu, D., Xiang, Y. Biochemistry and structural studies of kynurenine 3-monooxygenase reveal allosteric inhibition by Ro 61-8048.

  6. Interplay of protein and DNA structure revealed in simulations of the lac operon.

    Science.gov (United States)

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

    2013-01-01

    The E. coli Lac repressor is the classic textbook example of a protein that attaches to widely spaced sites along a genome and forces the intervening DNA into a loop. The short loops implicated in the regulation of the lac operon suggest the involvement of factors other than DNA and repressor in gene control. The molecular simulations presented here examine two likely structural contributions to the in-vivo looping of bacterial DNA: the distortions of the double helix introduced upon association of the highly abundant, nonspecific nucleoid protein HU and the large-scale deformations of the repressor detected in low-resolution experiments. The computations take account of the three-dimensional arrangements of nucleotides and amino acids found in crystal structures of DNA with the two proteins, the natural rest state and deformational properties of protein-free DNA, and the constraints on looping imposed by the conformation of the repressor and the orientation of bound DNA. The predicted looping propensities capture the complex, chain-length-dependent variation in repression efficacy extracted from gene expression studies and in vitro experiments and reveal unexpected chain-length-dependent variations in the uptake of HU, the deformation of repressor, and the folding of DNA. Both the opening of repressor and the presence of HU, at levels approximating those found in vivo, enhance the probability of loop formation. HU affects the global organization of the repressor and the opening of repressor influences the levels of HU binding to DNA. The length of the loop determines whether the DNA adopts antiparallel or parallel orientations on the repressor, whether the repressor is opened or closed, and how many HU molecules bind to the loop. The collective behavior of proteins and DNA is greater than the sum of the parts and hints of ways in which multiple proteins may coordinate the packaging and processing of genetic information.

  7. Ribosome•RelA structures reveal the mechanism of stringent response activation

    Science.gov (United States)

    Loveland, Anna B; Bah, Eugene; Madireddy, Rohini; Zhang, Ying; Brilot, Axel F; Grigorieff, Nikolaus; Korostelev, Andrei A

    2016-01-01

    Stringent response is a conserved bacterial stress response underlying virulence and antibiotic resistance. RelA/SpoT-homolog proteins synthesize transcriptional modulators (p)ppGpp, allowing bacteria to adapt to stress. RelA is activated during amino-acid starvation, when cognate deacyl-tRNA binds to the ribosomal A (aminoacyl-tRNA) site. We report four cryo-EM structures of E. coli RelA bound to the 70S ribosome, in the absence and presence of deacyl-tRNA accommodating in the 30S A site. The boomerang-shaped RelA with a wingspan of more than 100 Å wraps around the A/R (30S A-site/RelA-bound) tRNA. The CCA end of the A/R tRNA pins the central TGS domain against the 30S subunit, presenting the (p)ppGpp-synthetase domain near the 30S spur. The ribosome and A/R tRNA are captured in three conformations, revealing hitherto elusive states of tRNA engagement with the ribosomal decoding center. Decoding-center rearrangements are coupled with the step-wise 30S-subunit 'closure', providing insights into the dynamics of high-fidelity tRNA decoding. DOI: http://dx.doi.org/10.7554/eLife.17029.001 PMID:27434674

  8. Multilocus genotypic data reveal high genetic diversity and low population genetic structure of Iranian indigenous sheep

    International Nuclear Information System (INIS)

    Vahidi, S.M.F.; Faruque, M.O.; Falahati Anbaran, M.; Afraz, F.; Mousavi, S.M.; Boettcher, P.; Joost, S.; Han, J.L.; Colli, L.; Periasamy, K.; Negrini, R.; Ajmone-Marsan, P.

    2016-01-01

    Full text: Iranian livestock diversity is still largely unexplored, in spite of the interest in the populations historically reared in this country located near the Fertile Crescent, a major livestock domestication centre. In this investigation, the genetic diversity and differentiation of 10 Iranian indigenous fat-tailed sheep breeds were investigated using 18 microsatellite markers. Iranian breeds were found to host a high level of diversity. This conclusion is substantiated by the large number of alleles observed across loci (average 13.83, range 7–22) and by the high within-breed expected heterozygosity (average 0.75, range 0.72–0.76). Iranian sheep have a low level of genetic differentiation, as indicated by the analysis of molecular variance, which allocated a very small proportion (1.67%) of total variation to the between-population component, and by the small fixation index (FST = 0.02). Both Bayesian clustering and principal coordinates analysis revealed the absence of a detectable genetic structure. Also, no isolation by distance was observed through comparison of genetic and geographical distances. In spite of high within-breed variation, signatures of inbreeding were detected by the FIS indices, which were positive in all and statistically significant in three breeds. Possible factors explaining the patterns observed, such as considerable gene flow and inbreeding probably due to anthropogenic activities in the light of population management and conservation programmes are discussed. (author)

  9. Changes in chromatin structure during the aging of cell cultures as revealed by differential scanning calorimetry

    International Nuclear Information System (INIS)

    Almagor, M.; Cole, R.D.

    1989-01-01

    Nuclei from cultured human cells were examined by differential scanning calorimetry. Their melting profiles revealed four structural transitions at 60, 76, 88, and 105 degrees C (transitions I-IV, respectively). In immortalized (i.e., tumor) cell cultures and in normal cell cultures of low passage number, melting profiles were dominated by the 105 degrees C transition (transition IV), but in vitro aging of normal and Werner syndrome cells was associated with a marked decrease in transition IV followed by an increase in transition III at the expense of transition IV. At intermediate times in the aging process, much DNA melted at a temperature range (95-102 degrees C) intermediate between transitions III and IV, and this is consistent with the notion that aging of cell cultures is accompanied by an increase in single-strand character of the DNA. Calorimetric changes were observed in the melting profile of nuclei from UV-irradiated tumor cells that resembled the age-induced intermediate melting of chromatin. It is suggested that aging is accompanied by an increase in single-stranded character of the DNA in chromatin, which lowers its melting temperature, followed by strand breaks in the DNA that destroy its supercoiling potential

  10. Revealing the velocity structure of the filamentary nebula in NGC 1275 in its entirety

    Science.gov (United States)

    Gendron-Marsolais, M.; Hlavacek-Larrondo, J.; Martin, T. B.; Drissen, L.; McDonald, M.; Fabian, A. C.; Edge, A. C.; Hamer, S. L.; McNamara, B.; Morrison, G.

    2018-05-01

    We have produced for the first time a detailed velocity map of the giant filamentary nebula surrounding NGC 1275, the Perseus cluster's brightest galaxy, and revealed a previously unknown rich velocity structure across the entire nebula. These new observations were obtained with the optical imaging Fourier transform spectrometer SITELLE at CFHT. With its wide field of view (˜11'×11'), SITELLE is the only integral field unit spectroscopy instrument able to cover the 80 kpc×55 kpc (3.8'×2.6') large nebula in NGC 1275. Our analysis of these observations shows a smooth radial gradient of the [N II]λ6583/Hα line ratio, suggesting a change in the ionization mechanism and source across the nebula. The velocity map shows no visible general trend or rotation, indicating that filaments are not falling uniformly onto the galaxy, nor being uniformly pulled out from it. Comparison between the physical properties of the filaments and Hitomi measurements of the X-ray gas dynamics in Perseus are also explored.

  11. Multilayer Stochastic Block Models Reveal the Multilayer Structure of Complex Networks

    Directory of Open Access Journals (Sweden)

    Toni Vallès-Català

    2016-03-01

    Full Text Available In complex systems, the network of interactions we observe between systems components is the aggregate of the interactions that occur through different mechanisms or layers. Recent studies reveal that the existence of multiple interaction layers can have a dramatic impact in the dynamical processes occurring on these systems. However, these studies assume that the interactions between systems components in each one of the layers are known, while typically for real-world systems we do not have that information. Here, we address the issue of uncovering the different interaction layers from aggregate data by introducing multilayer stochastic block models (SBMs, a generalization of single-layer SBMs that considers different mechanisms of layer aggregation. First, we find the complete probabilistic solution to the problem of finding the optimal multilayer SBM for a given aggregate-observed network. Because this solution is computationally intractable, we propose an approximation that enables us to verify that multilayer SBMs are more predictive of network structure in real-world complex systems.

  12. Combined techniques for characterising pasta structure reveals how the gluten network slows enzymic digestion rate.

    Science.gov (United States)

    Zou, Wei; Sissons, Mike; Gidley, Michael J; Gilbert, Robert G; Warren, Frederick J

    2015-12-01

    The aim of the present study is to characterise the influence of gluten structure on the kinetics of starch hydrolysis in pasta. Spaghetti and powdered pasta were prepared from three different cultivars of durum semolina, and starch was also purified from each cultivar. Digestion kinetic parameters were obtained through logarithm-of-slope analysis, allowing identification of sequential digestion steps. Purified starch and semolina were digested following a single first-order rate constant, while pasta and powdered pasta followed two sequential first-order rate constants. Rate coefficients were altered by pepsin hydrolysis. Confocal microscopy revealed that, following cooking, starch granules were completely swollen for starch, semolina and pasta powder samples. In pasta, they were completely swollen in the external regions, partially swollen in the intermediate region and almost intact in the pasta strand centre. Gluten entrapment accounts for sequential kinetic steps in starch digestion of pasta; the compact microstructure of pasta also reduces digestion rates. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Structural Studies Reveal the Functional Modularity of the Scc2-Scc4 Cohesin Loader

    Directory of Open Access Journals (Sweden)

    William C.H. Chao

    2015-08-01

    Full Text Available The remarkable accuracy of eukaryotic cell division is partly maintained by the cohesin complex acting as a molecular glue to prevent premature sister chromatid separation. The loading of cohesin onto chromosomes is catalyzed by the Scc2-Scc4 loader complex. Here, we report the crystal structure of Scc4 bound to the N terminus of Scc2 and show that Scc4 is a tetratricopeptide repeat (TPR superhelix. The Scc2 N terminus adopts an extended conformation and is entrapped by the core of the Scc4 superhelix. Electron microscopy (EM analysis reveals that the Scc2-Scc4 loader complex comprises three domains: a head, body, and hook. Deletion studies unambiguously assign the Scc2N-Scc4 as the globular head domain, whereas in vitro cohesin loading assays show that the central body and the hook domains are sufficient to catalyze cohesin loading onto circular DNA, but not chromatinized DNA in vivo, suggesting a possible role for Scc4 as a chromatin adaptor.

  14. Revealing the Interface Structure and Bonding Mechanism of Coupling Agent Treated WPC

    Directory of Open Access Journals (Sweden)

    Jiuping Rao

    2018-03-01

    Full Text Available This paper presents the interfacial optimisation of wood plastic composites (WPC based on recycled wood flour and polyethylene by employing maleated and silane coupling agents. The effect of the incorporation of the coupling agents on the variation of chemical structure of the composites were investigated by Attenuated total reflectance-Fourier Transform Infrared spectroscopy (ATR-FTIR and Solid state 13C Nuclear Magnetic Resonance spectroscopy (NMR analyses. The results revealed the chemical reactions that occurred between the coupling agents and raw materials, which thus contributed to the enhancement of compatibility and interfacial adhesion between the constituents of WPC. NMR results also indicated that there existed the transformation of crystalline cellulose to an amorphous state during the coupling agent treatments, reflecting the inferior resonance of crystalline carbohydrates. Fluorescence Microscope (FM and Scanning Electron Microscope (SEM analyses showed the improvements of wood particle dispersion and wettability, compatibility of the constituents, and resin penetration, and impregnation of the composites after the coupling agent treatments. The optimised interface of the composites was attributed to interdiffusion, electrostatic adhesion, chemical reactions, and mechanical interlocking bonding mechanisms.

  15. Structure-guided mutational analysis reveals the functional requirements for product specificity of DOT1 enzymes.

    Science.gov (United States)

    Dindar, Gülcin; Anger, Andreas M; Mehlhorn, Christine; Hake, Sandra B; Janzen, Christian J

    2014-11-12

    DOT1 enzymes are conserved methyltransferases that catalyse the methylation of lysine 79 on histone H3 (H3K79). Most eukaryotes contain one DOT1 enzyme, whereas African trypanosomes have two homologues, DOT1A and DOT1B, with different enzymatic activities. DOT1A mediates mono- and dimethylation of H3K76, the homologue of H3K79 in other organisms, whereas DOT1B additionally catalyses H3K76 trimethylation. However, it is unclear how these different enzymatic activities are achieved. Here we employ a trypanosomal nucleosome reconstitution system and structure-guided homology modelling to identify critical residues within and outside the catalytic centre that modulate product specificity. Exchange of these residues transfers the product specificity from one enzyme to the other, and reveals the existence of distinct regulatory domains adjacent to the catalytic centre. Our study provides the first evidence that a few crucial residues in DOT1 enzymes are sufficient to catalyse methyl-state-specific reactions. These results might also have far-reaching consequences for the functional understanding of homologous enzymes in higher eukaryotes.

  16. Structures of the NLRP14 pyrin domain reveal a conformational switch mechanism regulating its molecular interactions

    International Nuclear Information System (INIS)

    Eibl, Clarissa; Hessenberger, Manuel; Wenger, Julia; Brandstetter, Hans

    2014-01-01

    Pyrin domains (PYDs) recruit downstream effector molecules in NLR signalling. A specific charge-relay system suggests a the formation of a signalling complex involving a PYD dimer. The cytosolic tripartite NLR receptors serve as important signalling platforms in innate immunity. While the C-terminal domains act as sensor and activation modules, the N-terminal death-like domain, e.g. the CARD or pyrin domain, is thought to recruit downstream effector molecules by homotypic interactions. Such homotypic complexes have been determined for all members of the death-domain superfamily except for pyrin domains. Here, crystal structures of human NLRP14 pyrin-domain variants are reported. The wild-type protein as well as the clinical D86V mutant reveal an unexpected rearrangement of the C-terminal helix α6, resulting in an extended α5/6 stem-helix. This reordering mediates a novel symmetric pyrin-domain dimerization mode. The conformational switching is controlled by a charge-relay system with a drastic impact on protein stability. How the identified charge relay allows classification of NLRP receptors with respect to distinct recruitment mechanisms is discussed

  17. Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids.

    Science.gov (United States)

    Schmitz, Alexander; Fischer, Sabine C; Mattheyer, Christian; Pampaloni, Francesco; Stelzer, Ernst H K

    2017-03-03

    Three-dimensional multicellular aggregates such as spheroids provide reliable in vitro substitutes for tissues. Quantitative characterization of spheroids at the cellular level is fundamental. We present the first pipeline that provides three-dimensional, high-quality images of intact spheroids at cellular resolution and a comprehensive image analysis that completes traditional image segmentation by algorithms from other fields. The pipeline combines light sheet-based fluorescence microscopy of optically cleared spheroids with automated nuclei segmentation (F score: 0.88) and concepts from graph analysis and computational topology. Incorporating cell graphs and alpha shapes provided more than 30 features of individual nuclei, the cellular neighborhood and the spheroid morphology. The application of our pipeline to a set of breast carcinoma spheroids revealed two concentric layers of different cell density for more than 30,000 cells. The thickness of the outer cell layer depends on a spheroid's size and varies between 50% and 75% of its radius. In differently-sized spheroids, we detected patches of different cell densities ranging from 5 × 10 5 to 1 × 10 6  cells/mm 3 . Since cell density affects cell behavior in tissues, structural heterogeneities need to be incorporated into existing models. Our image analysis pipeline provides a multiscale approach to obtain the relevant data for a system-level understanding of tissue architecture.

  18. Structural aspects of the distinct biochemical properties of glutaredoxin 2 from Saccharomyces cerevisiae

    Energy Technology Data Exchange (ETDEWEB)

    Discola, Karen Fulan; Cussiol, Jose Renato Rosa; Monteiro, Gisele; Soares Netto, Luis Eduardo [Universidade de Sao Paulo (IB/USP), SP (Brazil). Inst. de Biociencias. Dept. de Genetica e Biologia Evolutiva; Oliveira, Marcos Antonio de [Universidade Estadual Paulista (DB/UNESP), Sao Vicente, SP (Brazil). Dept. de Biologia; Barcena, Jose Antonio; Porras, Pablo; Padilla, Carmen Alicia [Universidad de Cordoba (Spain). Dept. de Bioquimica y Biologia Molecular; Guimaraes, Beatriz Gomes [Synchrotron SOLEIL, Saint-Aubin (France)

    2009-07-01

    Glutaredoxins (Grxs) are small thiol-dependent oxidoreductases with disulfide reductase activity endowed by at least one cysteine at their active sites. Although Grxs are implicated in many cellular processes. including protein folding and protection against reactive oxygen species, few of their targets are known. In the yeast Saccharomyces cerevisiae, eight Grxs isoforms were identified (ScGrx 1-8). Two of them (ScGrx 1-2) are dithioic possessing a conserved Cys-Pro-Tyr-Cys motif. In spite of the fact that ScGrx1 and ScGrx2 share 85% of aminoacid sequence similarity, we have shown that ScGrx2 is fifteen times more active as oxidoreductase than ScGrx1. In an attempt to better understand the mechanisms and differences between yeast dithiol Grxs activities, we elucidated the crystallographic structures of ScGrx2 in the oxidized state and of the ScGrx2-C30S mutant with a glutathionyl mixed disulfide at resolutions of 2.05 and 1.91 A, respectively. Comparisons among these structures and those available for ScGrx1 provided insights into the remarkable functional divergence between these enzymes. We hypothesize that the substitutions of Ser23 and Gln52 in SeGrx1 by Ala23 and Glu52 in ScGrx2 can modify the capability of the active site C-terminal cysteine to attack the mixed disulfide between the N-terminal active site cysteine and the glutathione molecule. Mutagenesis studies supported this hypothesis. The observed structural and functional differences between ScGrx1 and ScGrx2 may reflect variations in substrate specificity and non-redundant biological functions. (author)

  19. Aspects of Dzyaloshinskii-Moriya Interaction in Two Dimensional Magnetic Structures

    Science.gov (United States)

    Kundu, Anirban

    Research on topologically protected chiral magnetic structures such as magnetic domain walls (DWs) and skyrmions, have gained extensive interest because of their possible applications in magnetic data storage industries. The recently observed chiral DW structures in ultrathin ferromagnetic lms with perpendicular magnetic anisotropy has been attributed to the presence of a strong Dzyaloshinskii-Moriya interaction (DMI). In this thesis, the DMI mediated by the conduction electrons in two dimensional magnetic systems such as magnetic thin lms or at the interfaces between two magnetic materials has been studied. I calculate the Ruderman-Kittel- Kasuya-Yosida (RKKY) type indirect exchange coupling between two magnetic moments at nite temperature using the free electron band. At high temperature, the coupling strength decays with distance faster than the coupling at zero temperature but the period of oscillation remains same. However, the free electron band alone could not produce DMI. In the next step, I show addition of Rashba spin-orbit coupling (RSOC) with the spin-polarized conduction electron band produces the DMI between two magnetic ions. The essential feature of this DMI is: the coupling strength increases with the strength of RSOC, but decreases signi cantly with the Heisenberg exchange coupling. The DMI calculated with this model well explains the possibility of preferred Neel or Bloch DW structures with specifc chirality. In addition: I study switching of magnetization with ultrafast laser pulse by inverse Faraday e ect (IFE) where an optically induced non-equilibrium orbital momentum generates an e ective magnetic eld via spin-orbit coupling for magnetization switching. I calculate the magnitude of induced orbital moment for the generic itinerant band and show that magnitude is not large enough to make the switching by a single pulse, however, switching could be possible if multiple pulses are applied to the material.

  20. Structural aspects of the distinct biochemical properties of glutaredoxin 2 from Saccharomyces cerevisiae

    International Nuclear Information System (INIS)

    Discola, Karen Fulan; Cussiol, Jose Renato Rosa; Monteiro, Gisele; Soares Netto, Luis Eduardo

    2009-01-01

    Glutaredoxins (Grxs) are small thiol-dependent oxidoreductases with disulfide reductase activity endowed by at least one cysteine at their active sites. Although Grxs are implicated in many cellular processes. including protein folding and protection against reactive oxygen species, few of their targets are known. In the yeast Saccharomyces cerevisiae, eight Grxs isoforms were identified (ScGrx 1-8). Two of them (ScGrx 1-2) are dithioic possessing a conserved Cys-Pro-Tyr-Cys motif. In spite of the fact that ScGrx1 and ScGrx2 share 85% of aminoacid sequence similarity, we have shown that ScGrx2 is fifteen times more active as oxidoreductase than ScGrx1. In an attempt to better understand the mechanisms and differences between yeast dithiol Grxs activities, we elucidated the crystallographic structures of ScGrx2 in the oxidized state and of the ScGrx2-C30S mutant with a glutathionyl mixed disulfide at resolutions of 2.05 and 1.91 A, respectively. Comparisons among these structures and those available for ScGrx1 provided insights into the remarkable functional divergence between these enzymes. We hypothesize that the substitutions of Ser23 and Gln52 in SeGrx1 by Ala23 and Glu52 in ScGrx2 can modify the capability of the active site C-terminal cysteine to attack the mixed disulfide between the N-terminal active site cysteine and the glutathione molecule. Mutagenesis studies supported this hypothesis. The observed structural and functional differences between ScGrx1 and ScGrx2 may reflect variations in substrate specificity and non-redundant biological functions. (author)

  1. Molecular Aspects of Structure, Gating, and Physiology of pH-Sensitive Background K2P and Kir K+-Transport Channels

    Science.gov (United States)

    Sepúlveda, Francisco V.; Pablo Cid, L.; Teulon, Jacques; Niemeyer, María Isabel

    2015-01-01

    K+ channels fulfill roles spanning from the control of excitability to the regulation of transepithelial transport. Here we review two groups of K+ channels, pH-regulated K2P channels and the transport group of Kir channels. After considering advances in the molecular aspects of their gating based on structural and functional studies, we examine their participation in certain chosen physiological and pathophysiological scenarios. Crystal structures of K2P and Kir channels reveal rather unique features with important consequences for the gating mechanisms. Important tasks of these channels are discussed in kidney physiology and disease, K+ homeostasis in the brain by Kir channel-equipped glia, and central functions in the hearing mechanism in the inner ear and in acid secretion by parietal cells in the stomach. K2P channels fulfill a crucial part in central chemoreception probably by virtue of their pH sensitivity and are central to adrenal secretion of aldosterone. Finally, some unorthodox behaviors of the selectivity filters of K2P channels might explain their normal and pathological functions. Although a great deal has been learned about structure, molecular details of gating, and physiological functions of K2P and Kir K+-transport channels, this has been only scratching at the surface. More molecular and animal studies are clearly needed to deepen our knowledge. PMID:25540142

  2. Three-layered models of Ganymede and Callisto - compositions, structures, and aspects of evolution

    International Nuclear Information System (INIS)

    Mueller, S.; Mckinnon, W.B.

    1988-01-01

    The structural models presently defined for Ganymede and Callisto, which encompass a pure-ice upper layer, a mixed ice/rock lower mantle, and a rock core, incorporate three alternative rock component candidates representing various degrees of silicate hydration and oxidation. The three-layered model facilitates close study of the radius increase required for the internal differentiation of an ice-rock satellite; such expansion is determined to be most significant early in the process, and less so as differentiation approaches completion. The probability of postaccretional melting due to radiogenic heating is calculated. 78 references

  3. Aspects of gene structure and functional regulation of the isozymes of Na,K-ATPase

    DEFF Research Database (Denmark)

    Jorgensen, P.L.

    2001-01-01

    genomes, the genes of four alpha-subunit and at least three beta-subunit isoforms of Na,K-ATPase are identified and two gamma-subunits are expressed in kidney. The isoforms combine in a number of Na,K-ATPase isozymes that are expressed in a tissue and cell specific manner. Models of the molecular...... mechanism of regulation of these isozymes have become more reliable due to progress in understanding the three-dimensional protein structure and conformational transitions mediating transfer of energy from the P-domain to intramembrane Na+ and K+ binding sites....

  4. Structural and functional aspects of the multidrug efflux pump AcrB.

    Science.gov (United States)

    Eicher, Thomas; Brandstätter, Lorenz; Pos, Klaas M

    2009-08-01

    The tripartite efflux system AcrA/AcrB/TolC is the main pump in Escherichia coli for the efflux of multiple antibiotics, dyes, bile salts and detergents. The inner membrane component AcrB is central to substrate recognition and energy transduction and acts as a proton/drug antiporter. Recent structural studies show that homotrimeric AcrB can adopt different monomer conformations representing consecutive states in an allosteric functional rotation transport cycle. The conformational changes create an alternate access drug transport tunnel including a hydrophobic substrate binding pocket in one of the cycle intermediates.

  5. Intercalation and structural aspects of macroRAFT agents into MgAl layered double hydroxides

    Directory of Open Access Journals (Sweden)

    Dessislava Kostadinova

    2016-12-01

    Full Text Available Increasing attention has been devoted to the design of layered double hydroxide (LDH-based hybrid materials. In this work, we demonstrate the intercalation by anion exchange process of poly(acrylic acid (PAA and three different hydrophilic random copolymers of acrylic acid (AA and n-butyl acrylate (BA with molar masses ranging from 2000 to 4200 g mol−1 synthesized by reversible addition-fragmentation chain transfer (RAFT polymerization, into LDH containing magnesium(II and aluminium(III intralayer cations and nitrates as counterions (MgAl-NO3 LDH. At basic pH, the copolymer chains (macroRAFT agents carry negative charges which allowed the establishment of electrostatic interactions with the LDH interlayer and their intercalation. The resulting hybrid macroRAFT/LDH materials displayed an expanded interlamellar domain compared to pristine MgAl-NO3 LDH from 1.36 nm to 2.33 nm. Depending on the nature of the units involved into the macroRAFT copolymer (only AA or AA and BA, the intercalation led to monolayer or bilayer arrangements within the interlayer space. The macroRAFT intercalation and the molecular structure of the hybrid phases were further characterized by Fourier transform infrared (FTIR and solid-state 13C, 1H and 27Al nuclear magnetic resonance (NMR spectroscopies to get a better description of the local structure.

  6. Nuclear structure and nuclear reaction aspects of Faessler and Greiner's rotation-vibration coupling theory

    International Nuclear Information System (INIS)

    Aspelund, O.

    In the nuclear structure part, the foundations of Faessler and Greiner's rotation-vibration coupling theory are reviewed, whereafter an alternative derivation of Faessler and Greiner's Hamiltonian is presented. A non-spherical quadrupole phonon number N is defined and used in the matrix elements reported for odd-even/even-odd nuclei. These matrix elements are shown to evince oblate-prolate effects that can be exploited for assessing the signs of quadrupole deformations. In the nuclear reaction part, the wave functions emerging from the structure part are applied in a complete and consistent description of elastic and inelastic particle scattering, one-nucleon transfer, and particle/γ-ray angular correlations. The intentions are to demonstrate that anomolous angular distributions and 1=2 j-effects observed in one-nucleon transfer are interrelated phenomena, that can be satisfactorily explained in terms of the elementary vibrational excitation modes inherent in Faessler and Greiner's theory. The latter is regarded as a non-spherical approach to the theory of the quadrupole component of the nuclear potential energy surface. (Auth.)

  7. Crystal structure studies with the Paris-Edinburgh cell: Neutron scattering aspects

    Science.gov (United States)

    Loveday, J. S.; Wilson, R. M.; Nelmes, R. J.; Besson, J. M.; Klotz, S.; Hamel, G.; Hull, S.

    1994-07-01

    The count rates achieved in neutron powder diffraction experiments create difficulties for high-pressure experiments because large sample volumes (˜100 mm3) must be used. Until recently it has been difficult to build suitable pressure cells with such large volumes and hence the maximum pressure for neutron diffraction has remained at the relatively low value of 3 GPa. We have now developed a pressure cell (the Paris-Edinburgh cell) which is capable of exceeding 10 GPa with a sample volume of ˜100 mm3 for use at the U.K. spallation source ISIS. Considerable effort has been devoted to the opimization of the cell, shielding, and detector geometry to enable the best possible data to be recorded. Finite-element calculations to correct for the systematic errors introduced by the attenuation of the pressure-cell materials have been developed and tested. As a result of this work we are now able to obtain accurate structural data to ˜12 GPa and recent studies of phase IV of ND3, the behaviour of the O-D bondlength in D2O ice VIII, and the structural pressure dependence of B4C illustrate the importance of the extension of neutron-diffraction studies to such pressures.

  8. Nearest-Neighbor Interactions and Their Influence on the Structural Aspects of Dipeptides

    Directory of Open Access Journals (Sweden)

    Gunajyoti Das

    2013-01-01

    Full Text Available In this theoretical study, the role of the side chain moiety of C-terminal residue in influencing the structural and molecular properties of dipeptides is analyzed by considering a series of seven dipeptides. The C-terminal positions of the dipeptides are varied with seven different amino acid residues, namely. Val, Leu, Asp, Ser, Gln, His, and Pyl while their N-terminal positions are kept constant with Sec residues. Full geometry optimization and vibrational frequency calculations are carried out at B3LYP/6-311++G(d,p level in gas and aqueous phase. The stereo-electronic effects of the side chain moieties of C-terminal residues are found to influence the values of Φ and Ω dihedrals, planarity of the peptide planes, and geometry around the C7   α-carbon atoms of the dipeptides. The gas phase intramolecular H-bond combinations of the dipeptides are similar to those in aqueous phase. The theoretical vibrational spectra of the dipeptides reflect the nature of intramolecular H-bonds existing in the dipeptide structures. Solvation effects of aqueous environment are evident on the geometrical parameters related to the amide planes, dipole moments, HOMOLUMO energy gaps as well as thermodynamic stability of the dipeptides.

  9. ASPECTS REGARDING THE ORGANIZATIONAL STRUCTURE, QUALITY AND PERFORMANCE OF SPORT IN HIGHER EDUCATION IN ROMANIA

    Directory of Open Access Journals (Sweden)

    Sorin BUHAȘ

    2017-12-01

    Full Text Available This study addresses sport in higher education in rel ation to its organization structure, quality and sports performance. We have studied documents, normative acts and the way in which certain decisional factors involved in higher education sports activities are organized. The lack of a concrete strategy inthis respect, renders the information sources to be relatively limited. Particularly, our research was based on scientific documentation, historical method and document analysis. There is a small number of legitimated athletes related to the number of higher education students. Higher education sport is a non-functional system, it cannot generate a representative number of participants in the National University Championships, and the international representation is not a natural consequence of the internal competition. Therefore, it is imperative for higher education sports to be the foundation of performance sports. This involves changing both the approach to this phenomenon and its organizational structure. Also, the development of human resources and sports infrastructure are essential conditions for the development ofsports activity.

  10. Aspects of structural health and condition monitoring of offshore wind turbines.

    Science.gov (United States)

    Antoniadou, I; Dervilis, N; Papatheou, E; Maguire, A E; Worden, K

    2015-02-28

    Wind power has expanded significantly over the past years, although reliability of wind turbine systems, especially of offshore wind turbines, has been many times unsatisfactory in the past. Wind turbine failures are equivalent to crucial financial losses. Therefore, creating and applying strategies that improve the reliability of their components is important for a successful implementation of such systems. Structural health monitoring (SHM) addresses these problems through the monitoring of parameters indicative of the state of the structure examined. Condition monitoring (CM), on the other hand, can be seen as a specialized area of the SHM community that aims at damage detection of, particularly, rotating machinery. The paper is divided into two parts: in the first part, advanced signal processing and machine learning methods are discussed for SHM and CM on wind turbine gearbox and blade damage detection examples. In the second part, an initial exploration of supervisor control and data acquisition systems data of an offshore wind farm is presented, and data-driven approaches are proposed for detecting abnormal behaviour of wind turbines. It is shown that the advanced signal processing methods discussed are effective and that it is important to adopt these SHM strategies in the wind energy sector.

  11. The static structure factor of liquid 4He: some new aspects

    International Nuclear Information System (INIS)

    Khalil, K.Y.

    1986-08-01

    The thesis is concerned with three complementary problems. The first deals with a new interpretation of the elusive nature of the roton. This is motivated by the observation that the 'rotonic' minimum in the dispersion curve, which is intimately related to the principal peak of the static structure factor, is a common feature not only for He II but also for He I and almost all other condensed systems. The second problem concerns the precise asymptotic behaviour of the pair correlation function for liquid sup 4 He, whose Fourier transform is essentially the long-wavelength liquid structure factor. The third problem deals with the implications of this new formulation as related to Bose-Einstein condensation and superfluidity, as well as to other physical properties of the system. The thesis concludes with a partial list of open problems and with two possible extensions, including a complete development of an exceedingly simple method for determining the second virial coefficient of the sup 4 He gas over a wide temperature range. 122 refs., 2 figs., 5 tabs. (A.M.H)

  12. STRUCTURAL ASPECTS OF STRONG INHIBITION AND ROLE OF SCAFFOLD FOR SERINE PROTEASE INHIBITORS

    Directory of Open Access Journals (Sweden)

    Jhimli Dasgupta

    2011-12-01

    Full Text Available Canonical serine protease inhibitors inhibit their cognate enzymes by binding tightly at the enzyme active site in a substrate-like manner, being cleaved extremely slowly compared to a true substrate. They interact with cognate enzymes through P3-P2 region of the inhibitory loop while the scaffold hardly makes any contact. Neighbouring scaffolding residues like arginine or asparagine shape-up the inhibitory loop and religate the cleaved scissile bond. The specificity of the inhibitor can be altered by mutating the hyper solvent accessible P1 residue without changing loop-scaffold interactions. To understand the loop-scaffold compatibility, we prepared three chimeric proteins ECIL-WCIS , ETIL-WCIS , and STIL-WCIS , where the inhibitory loops of ECI, ETI, and STI were placed on the scaffold of their homologue WCI. Results showed that although ECIL-WCIS and STIL-WCIS behave like inhibitors, ETIL-WCIS behaves like a substrate. Crystal structure of ETIL-WCIS and its comparison with ETI indicated that three novel scaffolding residues Trp88, Arg74, and Tyr113 in ETI act as barrier to confine the inhibitory loop to canonical conformation. Absence of this barrier in the scaffold of WCI makes the inhibitory loop flexible in ETIL-WCIS leading to a loss of canonical conformation, explaining its substrate-like behaviour. Furthermore, complex structures of the inhibitors with their cognate enzymes indicate that rigidification of the inhibitory loop at the enzyme active site is necessary for efficient inhibition.

  13. Fundamental aspects of the structural and electrolyte properties of Li2OHCl from simulations and experiment

    Science.gov (United States)

    Howard, Jason; Hood, Zachary D.; Holzwarth, N. A. W.

    2017-12-01

    Solid-state electrolytes that are compatible with high-capacity electrodes are expected to enable the next generation of batteries. As a promising example, Li2OHCl was reported to have good ionic conductivity and to be compatible with a lithium metal anode even at temperatures above 100 ∘C . In this work, we explore the fundamental properties of Li2OHCl by comparing simulations and experiments. Using calculations based on density functional theory, including both static and dynamic contributions through the quasiharmonic approximation, we model a tetragonal ground state, which is not observed experimentally. An ordered orthorhombic low-temperature phase was also simulated, agreeing with experimental structural analysis of the pristine electrolyte at room temperature. In addition, comparison of the ordered structures with simulations of the disordered cubic phase provide insight into the mechanisms associated with the experimentally observed abrupt increase in ionic conductivity as the system changes from its ordered orthorhombic to its disordered cubic phase. A large Haven ratio for the disordered cubic phase is inferred from the computed tracer diffusion coefficient and measured ionic conductivity, suggesting highly correlated motions of the mobile Li ions in the cubic phase of Li2OHCl . We find that the OH bond orientations participate in gating the Li ion motions which might partially explain the predicted Li-Li correlations.

  14. Aspects of structural health and condition monitoring of offshore wind turbines

    Science.gov (United States)

    Antoniadou, I.; Dervilis, N.; Papatheou, E.; Maguire, A. E.; Worden, K.

    2015-01-01

    Wind power has expanded significantly over the past years, although reliability of wind turbine systems, especially of offshore wind turbines, has been many times unsatisfactory in the past. Wind turbine failures are equivalent to crucial financial losses. Therefore, creating and applying strategies that improve the reliability of their components is important for a successful implementation of such systems. Structural health monitoring (SHM) addresses these problems through the monitoring of parameters indicative of the state of the structure examined. Condition monitoring (CM), on the other hand, can be seen as a specialized area of the SHM community that aims at damage detection of, particularly, rotating machinery. The paper is divided into two parts: in the first part, advanced signal processing and machine learning methods are discussed for SHM and CM on wind turbine gearbox and blade damage detection examples. In the second part, an initial exploration of supervisor control and data acquisition systems data of an offshore wind farm is presented, and data-driven approaches are proposed for detecting abnormal behaviour of wind turbines. It is shown that the advanced signal processing methods discussed are effective and that it is important to adopt these SHM strategies in the wind energy sector. PMID:25583864

  15. Structural and Cohersion Funds: Theoretical and Statistical Aspects in Romania and EU

    Directory of Open Access Journals (Sweden)

    Iulian Viorel BRAŞOVEANU

    2011-06-01

    Full Text Available The paper approaches structural and cohesion funds for the financial perspective 2007-2013. The article describes briefly the evolution of regional development policy, the financial allocations, the impact of EU funds within cohesion policy, legal and institutional framework in Romania, and the institutions which are responsible for the management of EU funds. In Romania, the absorption of structural and cohesion funds is still a problem due to high rejection rate and the existing problems in procuring their own funds by the beneficiaries, such as beneficiary’s contribution, starting the project and covering the non-eligible expenditures. Romanian authorities should increase the absorption rate on transport sector and other sectors where absorption is a problem. Access to Social and Cohesion Funds represents for Romania an opportunity to develop balanced regions, to modernize transportation and environmental infrastructure to support rural development, employment opportunities for labor market, and to promote social policies to increase living standards. Romania has to consider “Life Long Learning” as a priority in the development of the human resources. Less bureaucracy is necessary for a normal development of procedures for refund claims. Also, it is necessary to shorten the time for reimbursement and to simplify related procedures. By increasing the amounts reimbursed, the authorities would increase the possibility to use EU funds more quickly. Preventive control can eliminate situations of default of non-eligible expenditure.

  16. The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function

    International Nuclear Information System (INIS)

    Das, Debanu; Finn, Robert D.; Carlton, Dennis; Miller, Mitchell D.; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L.; Bakolitsa, Constantina; Chen, Connie; Chiu, Hsiu-Ju; Chiu, Michelle; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Ellrott, Kyle; Ernst, Dustin; Farr, Carol L.; Feuerhelm, Julie; Grant, Joanna C.; Grzechnik, Anna; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Krishna, S. Sri; Kumar, Abhinav; Marciano, David; McMullan, Daniel; Morse, Andrew T.; Nigoghossian, Edward; Nopakun, Amanda; Okach, Linda; Puckett, Christina; Reyes, Ron; Rife, Christopher L.; Sefcovic, Natasha; Tien, Henry J.; Trame, Christine B.; Bedem, Henry van den; Weekes, Dana; Wooten, Tiffany; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

    2010-01-01

    The crystal structure of the BVU2987 gene product from B. vulgatus (UniProt A6L4L1) reveals that members of the new Pfam family PF11396 (domain of unknown function; DUF2874) are similar to β-lactamase inhibitor protein and YpmB. Proteins that contain the DUF2874 domain constitute a new Pfam family PF11396. Members of this family have predominantly been identified in microbes found in the human gut and oral cavity. The crystal structure of one member of this family, BVU2987 from Bacteroides vulgatus, has been determined, revealing a β-lactamase inhibitor protein-like structure with a tandem repeat of domains. Sequence analysis and structural comparisons reveal that BVU2987 and other DUF2874 proteins are related to β-lactamase inhibitor protein, PepSY and SmpA-OmlA proteins and hence are likely to function as inhibitory proteins

  17. Financial aspects of a seismic base isolation system for a steel high-rack structure

    Directory of Open Access Journals (Sweden)

    Kilar, V.

    2013-12-01

    Full Text Available The paper deals with the effects and costs of implementing a base isolation system for the mitigation of the seismic risk of an existing steel rack structure. Different realistic distributions of the payload mass and occupancy levels, which form different plan asymmetric variants, have been analysed. The results obtained by the pushover analysis (N2 method are presented as top floor envelopes and as plastic hinge damage patterns. In the presented cost study, the cost of the implementation of the proposed base isolation system is compared with the estimated costs of structural repairs to the damaged structural members of the superstructure, as well as with estimated expenses of the downtime period. The results have shown that base isolation is, in general, not economically feasible for lower ground motion intensities, whereas it could be of great benefit in the case of moderate and high intensities, especially if the downtime period is taken into account.El presente artículo trata sobre los efectos y costes de implementación de un sistema de aislamiento en cimentación para la mitigación del riesgo sísmico de la estructura de un bastidor de acero en altura prexistente. Se han analizado diferentes distribuciones realistas de la masa contribuyente y de los niveles de ocupación, conformando diferentes variantes asimétricas en planta. Se presentan los resultados obtenidos mediante el método N2 (análisis estático incremental no lineal como envolventes de las plantas superiores y como patrones de deterioro en estado plástico. En el estudio de costos presentado, el coste de implementación del sistema de aislamiento propuesto se compara con los costes estimados de reparación de los elementos superestructurales y los costes derivados del período de desocupación. Los resultados muestran que, en general, el aislamiento en la base no resulta viable económicamente para movimientos de baja intensidad, pero puede ser muy beneficioso en el caso de

  18. Entanglement beyond tensor product structure: algebraic aspects of quantum non-separability

    International Nuclear Information System (INIS)

    Derkacz, Łukasz; Gwóźdź, Marek; Jakóbczyk, Lech

    2012-01-01

    An algebraic approach to quantum non-separability is applied to the case of two qubits. It is based on the partition of the algebra of observables into independent subalgebras and the tensor product structure of the Hilbert space is not exploited. Even in this simple case, such a general formulation has some advantages. Using algebraic formalism, we can explicitly show the relativity of the notion of entanglement to the observables measured in the system and characterize separable and non-separable pure states. As a universal measure of non-separability of pure states, we propose to take the so-called total correlation. This quantity depends on the state as well as on the algebraic partition. Its numerical value is given by the norm of the corresponding correlation matrix. (paper)

  19. True strain-temperature diagram and structural aspects of molybdenum fracture

    International Nuclear Information System (INIS)

    Vasil'ev, A.D.; Gornaya, I.D.; Moiseev, V.F.; Pechkovskij, Eh.P.; Ponomarev, S.S.; Trefilov, V.I.

    1982-01-01

    For the purpose of studying the regularities of tough fracture of polycrystal molybdenum and explaining characteristic types of uniaxial tensile fractures in the 100-1000 deq C temperature range it is suggested for the first time to use the true strain-temperature (TST) diagram which combines a diagram of structural states and temperature dependence of a number of critical strains reflecting the dynamics of emergence and development of micro-non continuities in a tension specimen. It is shown that in the polycrystal molybdenum the basic parameters controlling the course and the magnitude of separate strain stages as well as the transition to fracture are the strain hardening coefficient and the elasticity limit relation to the strain hardening coefficient at the first stage (homoo.eneous dislocations distribution stage). The TST diagram permits also to explain the following phenomena: the nature of cold brittleness upper temperature, the observed change of fracture mechanisms with the temperature increase, the fracture surface origin

  20. Selected aspects in the structure of beta-delayed particle spectra

    International Nuclear Information System (INIS)

    Honkanen, J.; Aeystoe, J.; Eskola, K.

    1986-01-01

    Some weak beta-delayed particle emitters in the T z =-3/2, -1, -1/2, +1/2 and +5/2 series are reviewed. Selected features of the delayed particle emission are discussed in terms of experimental delayed particle data and (p,γ), (p,p') and (p,n) reaction data. Experimental beta transition strengths are compared with the existing complete shell-model calculations for the sd-shell nuclei. The effect of the Gamow-Teller giant resonance on the structure of the delayed particle spectra is considered. The correlation between the widths of two decay channels, protons and alpha particles, and the preceeding beta decay is studied in the case of the 40 Sc decay. (orig.)

  1. Aspects of second-order analysis of structured inhomogeneous spatio-temporal processes

    DEFF Research Database (Denmark)

    Møller, Jesper; Ghorbani, Mohammad

    2012-01-01

    Statistical methodology for spatio-temporal point processes is in its infancy. We consider second-order analysis based on pair correlation functions and K-functions for general inhomogeneous spatio-temporal point processes and for inhomogeneous spatio-temporal Cox processes. Assuming spatio......-temporal separability of the intensity function, we clarify different meanings of second-order spatio-temporal separability. One is second-order spatio-temporal independence and relates to log-Gaussian Cox processes with an additive covariance structure of the underlying spatio-temporal Gaussian process. Another...... concerns shot-noise Cox processes with a separable spatio-temporal covariance density. We propose diagnostic procedures for checking hypotheses of second-order spatio-temporal separability, which we apply on simulated and real data....

  2. Main aspects of the design of a support structure of a LMFBR with particular reference to the explosive accident consequences

    International Nuclear Information System (INIS)

    Giuliano, V.; Lazzeri, L.

    1977-01-01

    The aim of this paper is a review of the main aspects of the design of a support structure of a LMFBR tank, with particular reference to the analysis of the non-linear dynamic behavior of the structure in the plastic range under the effect of an explosive accident within the tank. The structure is composed by a L-shaped flange, which supports the tank, connected by means of nine square beams to a rigid box-type ring, fixed to the concrete. The plug of the tank is connected to the L-shaped flange by means of a group of SS bars. The non-linear dynamic analysis of the explosive accident has been carried out on a lumped mass model, with elastic-plastic elements which simulate main components of the support structure and tank. The impulsive load connected to the explosive accident has been modelled (on the basis of extensive comparative studies carried out) as two triangular pressure impulses has been the object of a parametric evaluation. The dynamic transient on the support structure during and after the explosive accident for each couple of pressure impulses has been analyzed by means of modified version of the NON SAP code running on a CDC 7600 computer. A large amount of results, which describe displacements, velocities and accelerations of the plug, of the tank, and of the support structure, together with the forces and stresses acting on the main structural components are presented and discussed, with particular reference to the influence of the various parameters involved in the analysis

  3. Fundamental structural aspects and features in the bioengineering of the gas exchangers: comparative perspectives.

    Science.gov (United States)

    Maina, J N

    2002-01-01

    Over its life, an organism's survival and success are determined by the inventory of vital adaptations that its progenitors have creatively appropriated, devised and harnessed along the evolutionary pathway. Such conserved attributes provide the armamentarium necessary for withstanding the adverse effects of natural selection. Refinements of the designs of the respiratory organs have been critical for survival and phylogenetic advancement of animal life. Gas exchangers have changed in direct response to the respiratory needs of whole organisms in different environmental states and conditions. Nowhere else is the dictum that in biology 'there are no rules but only necessities' more manifest than in the evolutionary biology of the gas exchangers. The constructions have been continually fashioned and refined to meet specific needs. Solutions to common respiratory needs have been typified by profound structural convergence. Over the evolutionary continuum, as shifts in environmental situations occurred, infinitely many designs should theoretically have emerged. Moreover, without specific selective pressures and preference for certain designs, considering that there are only two naturally occurring respirable fluid media (air and water), air-lungs, water-lungs, air-gills and water-gills would have formed to similar extents. Factors such as body size, phylogenetic level of development, respiratory medium utilized and habitats occupied have permutatively prescribed the design of the gas exchangers. The construction of the modern gas exchangers has eventuated through painstaking cost-benefit analysis. Trade-offs and compromises have decreed only a limited number of structurally feasible and functionally competent outcomes. The morphological congruity (analogy) of the gas exchangers indicates that similar selective pressures have compelled the designs. Solutions to metabolic demands for molecular O2 have only differed in details. Passive physical diffusion, for example, is

  4. Vertical Subsurface Flow Mixing and Horizontal Anisotropy in Coarse Fluvial Aquifers: Structural Aspects

    Science.gov (United States)

    Huggenberger, P.; Huber, E.

    2014-12-01

    Detailed descriptions of the subsurface heterogeneities in coarse fluvial aquifer gravel often lack in concepts to distinguish between the essence and the noise of a permeability structure and the ability to extrapolate site specific hydraulic information at the tens to several hundred meters scale. At this scale the heterogeneity strongly influences the anisotropies of the flow field and the mixing processes in groundwater. However, in many hydrogeological models the complexity of natural systems is oversimplified. Understanding the link between the dynamics of the surface processes of braided-river systems and the resulting subsurface sedimentary structures is the key to characterizing the complexity of horizontal and vertical mixing processes in groundwater. From the different depositional elements of coarse braided-river systems, the largest permeability contrasts can be observed in the scour-fills. Other elements (e.g. different types of gravel sheets) show much smaller variabilities and could be considered as a kind of matrix. Field experiments on the river Tagliamento (Northeast Italy) based on morphological observation and ground-penetrating radar (GPR) surveys, as well as outcrop analyses of gravel pit exposures (Switzerland) allowed us to define the shape, sizes, spatial distribution and preservation potential of scour-fills. In vertical sections (e.g. 2D GPR data, vertical outcrop), the spatial density of remnant erosional bounding surfaces of scours is an indicator for the dynamics of the braided-river system (lateral mobility of the active floodplain, rate of sediment net deposition and spatial distribution of the confluence scours). In case of combined low aggradation rate and low lateral mobility the deposits may be dominated by a complex overprinting of scour-fills. The delineation of the erosional bounding surfaces, that are coherent over the survey area, is based on the identification of angular discontinuities of the reflectors. Fence diagrams

  5. Framework for Structural Online Health Monitoring of Aging and Degradation of Secondary Systems due to some Aspects of Erosion

    Energy Technology Data Exchange (ETDEWEB)

    Gribok, Andrei [Idaho National Lab. (INL), Idaho Falls, ID (United States); Patnaik, Sobhan [Idaho National Lab. (INL), Idaho Falls, ID (United States); Williams, Christian [Idaho National Lab. (INL), Idaho Falls, ID (United States); Pattanaik, Marut [Idaho National Lab. (INL), Idaho Falls, ID (United States); Kanakala, Raghunath [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2016-09-01

    This report describes the current state of research related to critical aspects of erosion and selected aspects of degradation of secondary components in nuclear power plants. The report also proposes a framework for online health monitoring of aging and degradation of secondary components. The framework consists of an integrated multi-sensor modality system which can be used to monitor different piping configurations under different degradation conditions. The report analyses the currently known degradation mechanisms and available predictive models. Based on this analysis, the structural health monitoring framework is proposed. The Light Water Reactor Sustainability Program began to evaluate technologies that could be used to perform online monitoring of piping and other secondary system structural components in commercial NPPs. These online monitoring systems have the potential to identify when a more detailed inspection is needed using real-time measurements, rather than at a pre-determined inspection interval. This transition to condition-based, risk informed automated maintenance will contribute to a significant reduction of operations and maintenance costs that account for the majority of nuclear power generation costs. There is unanimous agreement between industry experts and academic researchers that identifying and prioritizing inspection locations in secondary piping systems (for example, in raw water piping or diesel piping) would eliminate many excessive in-service inspections. The proposed structural health monitoring framework takes aim at answering this challenge by combining long-range guided wave technologies with other monitoring techniques, which can significantly increase the inspection length and pinpoint the locations that degraded the most. More widely, the report suggests research efforts aimed at developing, validating, and deploying online corrosion monitoring techniques for complex geometries, which are pervasive in NPPs.

  6. Framework for Structural Online Health Monitoring of Aging and Degradation of Secondary Systems due to some Aspects of Erosion

    International Nuclear Information System (INIS)

    Gribok, Andrei; Patnaik, Sobhan; Williams, Christian; Pattanaik, Marut; Kanakala, Raghunath

    2016-01-01

    This report describes the current state of research related to critical aspects of erosion and selected aspects of degradation of secondary components in nuclear power plants. The report also proposes a framework for online health monitoring of aging and degradation of secondary components. The framework consists of an integrated multi-sensor modality system which can be used to monitor different piping configurations under different degradation conditions. The report analyses the currently known degradation mechanisms and available predictive models. Based on this analysis, the structural health monitoring framework is proposed. The Light Water Reactor Sustainability Program began to evaluate technologies that could be used to perform online monitoring of piping and other secondary system structural components in commercial NPPs. These online monitoring systems have the potential to identify when a more detailed inspection is needed using real-time measurements, rather than at a pre-determined inspection interval. This transition to condition-based, risk informed automated maintenance will contribute to a significant reduction of operations and maintenance costs that account for the majority of nuclear power generation costs. There is unanimous agreement between industry experts and academic researchers that identifying and prioritizing inspection locations in secondary piping systems (for example, in raw water piping or diesel piping) would eliminate many excessive in-service inspections. The proposed structural health monitoring framework takes aim at answering this challenge by combining long-range guided wave technologies with other monitoring techniques, which can significantly increase the inspection length and pinpoint the locations that degraded the most. More widely, the report suggests research efforts aimed at developing, validating, and deploying online corrosion monitoring techniques for complex geometries, which are pervasive in NPPs.

  7. STRUCTURAL AND STRATEGIC ASPECTS OF PROFESSIONALLY ORIENTED SPEECH OF A PSYCHOLOGIST MEDIATOR

    Directory of Open Access Journals (Sweden)

    Iryna Levchyk

    2016-12-01

    Full Text Available The article presents characteristic speech patterns of psychologist-mediator on the basis of five staged model of his professional speech behavior that involves the following five speech activities: introductory talks with the conflict parties; clarifying of the parties’ positions; finding the optimal solution to the problem; persuasion in the legality of a compromise; execution of the agreement between the parties. Each of these stages of the mediation process in terms of mental and speech activities of a specialist have been analyzed and subsequently the structure of mediator’s communication has been derived. The concept of a "strategy of verbal behavior" considering professional activity of a psychologist-mediator has been described in terms of its correlation with the type of negotiation behaviors of disputants. The basic types of opponents’ behavior in negotiations ‒ namely avoidance, concession, denial, aggression have been specified. The compliance of strategy of speech of mediator’s behavior to his chosen style of mediation has been discovered. The tactics and logic of mediator’s speech behavior according to the stages of mediation conversation have been determined. It has been found out that the mediator’s tactics implies application of specific professional speech skills to conduct a dialogue in accordance with the chosen strategy as well as emotional and verbal reaction of conflict sides in the process of communication.

  8. Materials and structural aspects of advanced gas-turbine helicopter engines

    Science.gov (United States)

    Freche, J. C.; Acurio, J.

    1979-01-01

    Advances in materials, coatings, turbine cooling technology, structural and design concepts, and component-life prediction of helicopter gas-turbine-engine components are presented. Stationary parts including the inlet particle separator, the front frame, rotor tip seals, vanes and combustors and rotating components - compressor blades, disks, and turbine blades - are discussed. Advanced composite materials are considered for the front frame and compressor blades, prealloyed powder superalloys will increase strength and reduce costs of disks, the oxide dispersion strengthened alloys will have 100C higher use temperature in combustors and vanes than conventional superalloys, ceramics will provide the highest use temperature of 1400C for stator vanes and 1370C for turbine blades, and directionally solidified eutectics will afford up to 50C temperature advantage at turbine blade operating conditions. Coatings for surface protection at higher surface temperatures and design trends in turbine cooling technology are discussed. New analytical methods of life prediction such as strain gage partitioning for high temperature prediction, fatigue life, computerized prediction of oxidation resistance, and advanced techniques for estimating coating life are described.

  9. Characterization and anti-settlement aspects of surface micro-structures from Cancer pagurus

    International Nuclear Information System (INIS)

    Sullivan, T; Regan, F; McGuinness, K; Connor, N E O’

    2014-01-01

    Tuning surface and material properties to inhibit or prevent settlement and attachment of microorganisms is of interest for applications such as antifouling technologies. Here, optimization of nano- and microscale structures on immersed surfaces can be utilized to improve cell removal while reducing adhesion strength and the likelihood of initial cellular attachment. Engineered surfaces capable of controlling cellular behaviour under natural conditions are challenging to design due to the diversity of attaching cell types in environments such as marine waters, where many variations in cell shape, size and adhesion strategy exist. Nevertheless, understanding interactions between a cell and a potential substrate for adhesion, including topographically driven settlement cues, offers a route to designing surfaces capable of controlling cell settlement. Biomimetic design of artificial surfaces, based upon microscale features from natural surfaces, can be utilized as model surfaces to understand cell–surface interactions. The microscale surface features of the carapace from the crustacean Cancer pagurus has been previously found to influence the rate of attachment of particular organisms when compared to smooth controls. However, the nature of microscale topographic features from C. pagurus have not been examined in sufficient detail to allow design of biomimetic surfaces. In this work, the spatial distribution, chemical composition, size and shape descriptors of microscale surface features from C. pagurus are characterized in detail for the first time. Additionally, the influence of topography from C. pagurus on the settlement of marine diatoms is examined under field conditions. (paper)

  10. Modification of graphite structure by irradiation, revealed by thermal oxidation. Examination by electronic microscopy

    International Nuclear Information System (INIS)

    Rouaud, Michel

    1969-01-01

    Based on the analysis of images obtained by electronic microscopy, this document reports the comparative study of the action of neutrons on three different graphites: a natural one (Ticonderoga) and two pyrolytic ones (Carbone-Lorraine and Raytheon). The approach is based on the modification of features of thermal oxidation of graphites by dry air after irradiation. Different corrosion features are identified. The author states that there seems to be a relationship between the number and shape of these features, and defects existing on the irradiated graphite before oxidation. For low doses, the feature aspect varies with depth at which oxidation occurs. For higher doses, the aspect remains the same [fr

  11. A Tri-Oceanic Perspective: DNA Barcoding Reveals Geographic Structure and Cryptic Diversity in Canadian Polychaetes

    Science.gov (United States)

    Carr, Christina M.; Hardy, Sarah M.; Brown, Tanya M.; Macdonald, Tara A.; Hebert, Paul D. N.

    2011-01-01

    Background Although polychaetes are one of the dominant taxa in marine communities, their distributions and taxonomic diversity are poorly understood. Recent studies have shown that many species thought to have broad distributions are actually a complex of allied species. In Canada, 12% of polychaete species are thought to occur in Atlantic, Arctic, and Pacific Oceans, but the extent of gene flow among their populations has not been tested. Methodology/Principal Findings Sequence variation in a segment of the mitochondrial cytochrome c oxidase I (COI) gene was employed to compare morphological versus molecular diversity estimates, to examine gene flow among populations of widespread species, and to explore connectivity patterns among Canada's three oceans. Analysis of 1876 specimens, representing 333 provisional species, revealed 40 times more sequence divergence between than within species (16.5% versus 0.38%). Genetic data suggest that one quarter of previously recognized species actually include two or more divergent lineages, indicating that richness in this region is currently underestimated. Few species with a tri-oceanic distribution showed genetic cohesion. Instead, large genetic breaks occur between Pacific and Atlantic-Arctic lineages, suggesting their long-term separation. High connectivity among Arctic and Atlantic regions and low connectivity with the Pacific further supports the conclusion that Canadian polychaetes are partitioned into two distinct faunas. Conclusions/Significance Results of this study confirm that COI sequences are an effective tool for species identification in polychaetes, and suggest that DNA barcoding will aid the recognition of species overlooked by the current taxonomic system. The consistent geographic structuring within presumed widespread species suggests that historical range fragmentation during the Pleistocene ultimately increased Canadian polychaete diversity and that the coastal British Columbia fauna played a minor

  12. Rangewide genetic analysis of Lesser Prairie-Chicken reveals population structure, range expansion, and possible introgression

    Science.gov (United States)

    Oyler-McCance, Sara J.; DeYoung, Randall W; Fike, Jennifer; Hagen, Christian A.; Johnson, Jeff A.; Larsson, Lena C.; Patten, Michael

    2016-01-01

    The distribution of the Lesser Prairie-Chicken (Tympanuchus pallidicinctus) has been markedly reduced due to loss and fragmentation of habitat. Portions of the historical range, however, have been recolonized and even expanded due to planting of conservation reserve program (CRP) fields that provide favorable vegetation structure for Lesser Prairie-Chickens. The source population(s) feeding the range expansion is unknown, yet has resulted in overlap between Lesser and Greater Prairie-Chickens (T. cupido) increasing the potential for hybridization. Our objectives were to characterize connectivity and genetic diversity among populations, identify source population(s) of recent range expansion, and examine hybridization with the Greater Prairie-Chicken. We analyzed 640 samples from across the range using 13 microsatellites. We identified three to four populations corresponding largely to ecoregions. The Shinnery Oak Prairie and Sand Sagebrush Prairie represented genetically distinct populations (F ST > 0.034 and F ST > 0.023 respectively). The Shortgrass/CRP Mosaic and Mixed Grass ecoregions appeared admixed (F ST = 0.009). Genetic diversity was similar among ecoregions and N e ranged from 142 (95 % CI 99–236) for the Shortgrass/CRP Mosaic to 296 (95 % CI 233–396) in the Mixed Grass Prairie. No recent migration was detected among ecoregions, except asymmetric dispersal from both the Mixed Grass Prairie and to a lesser extent the Sand Sagebrush Prairie north into adjacent Shortgrass/CRP Mosaic (m = 0.207, 95 % CI 0.116–0.298, m = 0.097, 95 % CI 0.010–0.183, respectively). Indices investigating potential hybridization in the Shortgrass/CRP Mosaic revealed that six of the 13 individuals with hybrid phenotypes were significantly admixed suggesting hybridization. Continued monitoring of diversity within and among ecoregions is warranted as are actions promoting genetic connectivity and range expansion.

  13. A tri-oceanic perspective: DNA barcoding reveals geographic structure and cryptic diversity in Canadian polychaetes.

    Directory of Open Access Journals (Sweden)

    Christina M Carr

    Full Text Available Although polychaetes are one of the dominant taxa in marine communities, their distributions and taxonomic diversity are poorly understood. Recent studies have shown that many species thought to have broad distributions are actually a complex of allied species. In Canada, 12% of polychaete species are thought to occur in Atlantic, Arctic, and Pacific Oceans, but the extent of gene flow among their populations has not been tested.Sequence variation in a segment of the mitochondrial cytochrome c oxidase I (COI gene was employed to compare morphological versus molecular diversity estimates, to examine gene flow among populations of widespread species, and to explore connectivity patterns among Canada's three oceans. Analysis of 1876 specimens, representing 333 provisional species, revealed 40 times more sequence divergence between than within species (16.5% versus 0.38%. Genetic data suggest that one quarter of previously recognized species actually include two or more divergent lineages, indicating that richness in this region is currently underestimated. Few species with a tri-oceanic distribution showed genetic cohesion. Instead, large genetic breaks occur between Pacific and Atlantic-Arctic lineages, suggesting their long-term separation. High connectivity among Arctic and Atlantic regions and low connectivity with the Pacific further supports the conclusion that Canadian polychaetes are partitioned into two distinct faunas.Results of this study confirm that COI sequences are an effective tool for species identification in polychaetes, and suggest that DNA barcoding will aid the recognition of species overlooked by the current taxonomic system. The consistent geographic structuring within presumed widespread species suggests that historical range fragmentation during the Pleistocene ultimately increased Canadian polychaete diversity and that the coastal British Columbia fauna played a minor role in Arctic recolonization following deglaciation

  14. Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing.

    Science.gov (United States)

    Zhang, Yanying; Yang, Qingsong; Ling, Juan; Van Nostrand, Joy D; Shi, Zhou; Zhou, Jizhong; Dong, Junde

    2017-01-01

    Diazotrophic communities make an essential contribution to the productivity through providing new nitrogen. However, knowledge of the roles that both mangrove tree species and geochemical parameters play in shaping mangove rhizosphere diazotrophic communities is still elusive. Here, a comprehensive examination of the diversity and structure of microbial communities in the rhizospheres of three mangrove species, Rhizophora apiculata , Avicennia marina , and Ceriops tagal , was undertaken using high - throughput sequencing of the 16S rRNA and nifH genes. Our results revealed a great diversity of both the total microbial composition and the diazotrophic composition specifically in the mangrove rhizosphere. Deltaproteobacteria and Gammaproteobacteria were both ubiquitous and dominant, comprising an average of 45.87 and 86.66% of total microbial and diazotrophic communities, respectively. Sulfate-reducing bacteria belonging to the Desulfobacteraceae and Desulfovibrionaceae were the dominant diazotrophs. Community statistical analyses suggested that both mangrove tree species and additional environmental variables played important roles in shaping total microbial and potential diazotroph communities in mangrove rhizospheres. In contrast to the total microbial community investigated by analysis of 16S rRNA gene sequences, most of the dominant diazotrophic groups identified by nifH gene sequences were significantly different among mangrove species. The dominant diazotrophs of the family Desulfobacteraceae were positively correlated with total phosphorus, but negatively correlated with the nitrogen to phosphorus ratio. The Pseudomonadaceae were positively correlated with the concentration of available potassium, suggesting that diazotrophs potentially play an important role in biogeochemical cycles, such as those of nitrogen, phosphorus, sulfur, and potassium, in the mangrove ecosystem.

  15. Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing

    Directory of Open Access Journals (Sweden)

    Yanying Zhang

    2017-10-01

    Full Text Available Diazotrophic communities make an essential contribution to the productivity through providing new nitrogen. However, knowledge of the roles that both mangrove tree species and geochemical parameters play in shaping mangove rhizosphere diazotrophic communities is still elusive. Here, a comprehensive examination of the diversity and structure of microbial communities in the rhizospheres of three mangrove species, Rhizophora apiculata, Avicennia marina, and Ceriops tagal, was undertaken using high-throughput sequencing of the 16S rRNA and nifH genes. Our results revealed a great diversity of both the total microbial composition and the diazotrophic composition specifically in the mangrove rhizosphere. Deltaproteobacteria and Gammaproteobacteria were both ubiquitous and dominant, comprising an average of 45.87 and 86.66% of total microbial and diazotrophic communities, respectively. Sulfate-reducing bacteria belonging to the Desulfobacteraceae and Desulfovibrionaceae were the dominant diazotrophs. Community statistical analyses suggested that both mangrove tree species and additional environmental variables played important roles in shaping total microbial and potential diazotroph communities in mangrove rhizospheres. In contrast to the total microbial community investigated by analysis of 16S rRNA gene sequences, most of the dominant diazotrophic groups identified by nifH gene sequences were significantly different among mangrove species. The dominant diazotrophs of the family Desulfobacteraceae were positively correlated with total phosphorus, but negatively correlated with the nitrogen to phosphorus ratio. The Pseudomonadaceae were positively correlated with the concentration of available potassium, suggesting that diazotrophs potentially play an important role in biogeochemical cycles, such as those of nitrogen, phosphorus, sulfur, and potassium, in the mangrove ecosystem.

  16. Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota.

    Science.gov (United States)

    Bulgarelli, Davide; Rott, Matthias; Schlaeppi, Klaus; Ver Loren van Themaat, Emiel; Ahmadinejad, Nahal; Assenza, Federica; Rauf, Philipp; Huettel, Bruno; Reinhardt, Richard; Schmelzer, Elmon; Peplies, Joerg; Gloeckner, Frank Oliver; Amann, Rudolf; Eickhorst, Thilo; Schulze-Lefert, Paul

    2012-08-02

    The plant root defines the interface between a multicellular eukaryote and soil, one of the richest microbial ecosystems on Earth. Notably, soil bacteria are able to multiply inside roots as benign endophytes and modulate plant growth and development, with implications ranging from enhanced crop productivity to phytoremediation. Endophytic colonization represents an apparent paradox of plant innate immunity because plant cells can detect an array of microbe-associated molecular patterns (also known as MAMPs) to initiate immune responses to terminate microbial multiplication. Several studies attempted to describe the structure of bacterial root endophytes; however, different sampling protocols and low-resolution profiling methods make it difficult to infer general principles. Here we describe methodology to characterize and compare soil- and root-inhabiting bacterial communities, which reveals not only a function for metabolically active plant cells but also for inert cell-wall features in the selection of soil bacteria for host colonization. We show that the roots of Arabidopsis thaliana, grown in different natural soils under controlled environmental conditions, are preferentially colonized by Proteobacteria, Bacteroidetes and Actinobacteria, and each bacterial phylum is represented by a dominating class or family. Soil type defines the composition of root-inhabiting bacterial communities and host genotype determines their ribotype profiles to a limited extent. The identification of soil-type-specific members within the root-inhabiting assemblies supports our conclusion that these represent soil-derived root endophytes. Surprisingly, plant cell-wall features of other tested plant species seem to provide a sufficient cue for the assembly of approximately 40% of the Arabidopsis bacterial root-inhabiting microbiota, with a bias for Betaproteobacteria. Thus, this root sub-community may not be Arabidopsis-specific but saprophytic bacteria that would naturally be found

  17. Structural and functional aspects of trypsin–gold nanoparticle interactions: An experimental investigation

    Energy Technology Data Exchange (ETDEWEB)

    Nidhin, Marimuthu [Department of Chemistry, Amity School of Applied Sciences, Center for Nanoscience and Technology, Amity University Haryana Amity Education Valley, Gurgaon, Haryana 122413 (India); Ghosh, Debasree [Department of Nanotechnology, Amity School of Applied Sciences, Center for Nanoscience and Technology, Amity University Haryana Amity Education Valley, Gurgaon, Haryana 122413 (India); Yadav, Himanshu; Yadav, Nitu [Department of Chemistry, Amity School of Applied Sciences, Center for Nanoscience and Technology, Amity University Haryana Amity Education Valley, Gurgaon, Haryana 122413 (India); Majumder, Sudip, E-mail: sudip22m@gmail.com [Department of Chemistry, Amity School of Applied Sciences, Center for Nanoscience and Technology, Amity University Haryana Amity Education Valley, Gurgaon, Haryana 122413 (India)

    2015-12-15

    Highlights: • Trypsin undergoes activation on incubation with gold nanoparticles. • Enhanced activity depends on the stoichiometry of the mixture. • Higher concentration of nanoparticles damage stability and conformation of trypsin. • Gold nanoparticles undergo morphological change on incubation with trypsin. - Abstract: Trypsin (Trp) is arguably the most important member of the serine proteases. Constructs made up of gold nanoparticles (GNP) with trypsin have been known to exhibit increased efficiency and stability in various experiments. Here we report simple Trp–GNP constructs mixed in different trypsin-to-GNP ratios which exhibit higher efficiencies in biochemical assay, varying resistance to autolysis and higher ability in cell trypsinization. Trp–GNP constructs in different trypsin-to-GNP ratios exhibit prolonged and sustained activity compared to native trypsin in N-α-p-benzoyl-p-nitroanilide (BAPNA) assay as monitored by UV-Visible spectroscopy. The activity was monitored as a function of decreasing rate of linear release of p-nitro aniline (resulting from the cleavage of BAPNA by trypsin) with time during the assay, whose absorbance was measured at 410 nm (λ{sub max} p-nitro aniline). We have done extensive studies to understand structural basis of this trypsin GNP interaction by using atomic force microscopy (AFM), transmission electron microscopy (TEM) and circular dichroism (CD) techniques. Our findings suggest that on interaction, the gold nanoparticles probably form an adherent layer on trypsin that effectively changes the morphology and dimensions of the nanoconstructs. However, trypsin-to-GNP ratio is extremely important, as higher concentration of GNP might damage the conformation of protein. Stability studies related to denaturation show that 1:1 Trp–GNP constructs exhibit maximum stability and high efficiency in all assays performed.

  18. Structural and functional aspects of trypsin–gold nanoparticle interactions: An experimental investigation

    International Nuclear Information System (INIS)

    Nidhin, Marimuthu; Ghosh, Debasree; Yadav, Himanshu; Yadav, Nitu; Majumder, Sudip

    2015-01-01

    Highlights: • Trypsin undergoes activation on incubation with gold nanoparticles. • Enhanced activity depends on the stoichiometry of the mixture. • Higher concentration of nanoparticles damage stability and conformation of trypsin. • Gold nanoparticles undergo morphological change on incubation with trypsin. - Abstract: Trypsin (Trp) is arguably the most important member of the serine proteases. Constructs made up of gold nanoparticles (GNP) with trypsin have been known to exhibit increased efficiency and stability in various experiments. Here we report simple Trp–GNP constructs mixed in different trypsin-to-GNP ratios which exhibit higher efficiencies in biochemical assay, varying resistance to autolysis and higher ability in cell trypsinization. Trp–GNP constructs in different trypsin-to-GNP ratios exhibit prolonged and sustained activity compared to native trypsin in N-α-p-benzoyl-p-nitroanilide (BAPNA) assay as monitored by UV-Visible spectroscopy. The activity was monitored as a function of decreasing rate of linear release of p-nitro aniline (resulting from the cleavage of BAPNA by trypsin) with time during the assay, whose absorbance was measured at 410 nm (λ_m_a_x p-nitro aniline). We have done extensive studies to understand structural basis of this trypsin GNP interaction by using atomic force microscopy (AFM), transmission electron microscopy (TEM) and circular dichroism (CD) techniques. Our findings suggest that on interaction, the gold nanoparticles probably form an adherent layer on trypsin that effectively changes the morphology and dimensions of the nanoconstructs. However, trypsin-to-GNP ratio is extremely important, as higher concentration of GNP might damage the conformation of protein. Stability studies related to denaturation show that 1:1 Trp–GNP constructs exhibit maximum stability and high efficiency in all assays performed.

  19. A defining aspect of human resilience in the workplace: a structural modeling approach.

    Science.gov (United States)

    Everly, George S; Davy, Jeanettte A; Smith, Kenneth J; Lating, Jeffrey M; Nucifora, Frederick C

    2011-06-01

    It has been estimated that up to 90% of the US population is exposed to at least 1 traumatic event during their lifetime. Although there is growing evidence that most people are resilient, meaning that they have the ability to adapt to or rebound from adversity, between 5% and 10% of individuals exposed to traumatic events meet criteria for posttraumatic stress disorder. Therefore, identifying the elements of resilience could lead to interventions or training programs designed to enhance resilience. In this article, we test the hypothesis that the effects of stressor conditions on outcomes such as job-related variables may be mediated through the cognitive and affective registrations of those events, conceptualized as subjective stress arousal. The subjects were 491 individuals employed in public accounting, who were sampled from a mailing list provided by the American Institute of Certified Public Accountants. The stressors used in this study were role ambiguity, role conflict, and role overload and the outcome measures were performance, turnover intentions, job satisfaction, and burnout. Stress arousal was measured using a previously developed stress arousal scale. We conducted a series of 2 EQS structural modeling analyses to assess the impact of stress arousal. The first model examined only the direct effects from the role stressors to the outcome constructs. The second model inserted stress arousal as a mediator in the relations between the role stressors and the outcomes. The results of our investigation supported the notion that subjective stress arousal provides greater explanatory clarity by mediating the effects of stressors upon job-related outcome. Including stress arousal in the model provided a much more comprehensive understanding of the relation between stressor and outcomes, and the contribution of role ambiguity and role conflict were better explained. By understanding these relations, anticipatory guidance and crisis intervention programs can be

  20. Structural dynamics and quantum mechanical aspects of shikonin derivatives as CREBBP bromodomain inhibitors.

    Science.gov (United States)

    Mitra, Sarmistha; Dash, Raju

    2018-05-04

    The Proteins involved in the chemical modification of lysine residues in histone, is currently being excessively focused as the therapeutic target for the treatment of cell related diseases like cancer. Among these proteins, the epigenetic reader, CREB-binding protein (CREBBP) bromodomain is one of the most prominent targets for effective anticancer drug design, which is responsible for the reorganization of acetylated histone lysine residues. Therefore, this study employed an integrative approach of structure based drug design, in combination with Molecular Dynamics (MD) and QM/MM study to identify as well as to describe the binding mechanism of two shikonin derivatives, acetylshikonin and propionylshikonin as inhibitors of CREBBP bromodomain. Here induced fit docking strategy was employed to explore the important intrinsic interactions of ligands with CREBBP bromodomain, consistently molecular dynamics simulation with two different methods and binding energy calculations by MM-GBSA and MM-PBSA were adopted to determine the stability of intermolecular interactions between protein and ligands. The results showed that both these derivatives made direct contacts with the important conserved residues of the active site, where propionylshikonin demonstrated stronger binding and stability than acetylshikonin, according to molecular dynamics simulation and binding free energy calculations. Further, QM/MM energy calculation was employed to study the chemical reactivity of the propionylshikonin and also to describe the mechanism of non bonded interactions between the propionylshikonin and CREBBP bromodomain. Though this study demands in vitro and in vivo experiments to evaluate the efficiency of the compound, these insights would assist to design more potent CREBBP bromodomain inhibitor, guiding the site of modification of propionylshikonin moiety for designing selective inhibitors. Copyright © 2018 Elsevier Inc. All rights reserved.

  1. The structure of KPN03535 (gi|152972051), a novel putative lipoprotein from Klebsiella pneumoniae, reveals an OB-fold

    International Nuclear Information System (INIS)

    Das, Debanu; Kozbial, Piotr; Han, Gye Won; Carlton, Dennis; Jaroszewski, Lukasz; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L.; Bakolitsa, Constantina; Chen, Connie; Chiu, Hsiu-Ju; Chiu, Michelle; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Ellrott, Kyle; Elsliger, Marc-André; Ernst, Dustin; Farr, Carol L.; Feuerhelm, Julie; Grzechnik, Anna; Grant, Joanna C.; Jin, Kevin K.; Johnson, Hope A.; Klock, Heath E.; Knuth, Mark W.; Krishna, S. Sri; Kumar, Abhinav; Marciano, David; McMullan, Daniel; Miller, Mitchell D.; Morse, Andrew T.; Nigoghossian, Edward; Nopakun, Amanda; Okach, Linda; Oommachen, Silvya; Paulsen, Jessica; Puckett, Christina; Reyes, Ron; Rife, Christopher L.; Sefcovic, Natasha; Tien, Henry J.; Trame, Christine B.; Bedem, Henry van den; Weekes, Dana; Wooten, Tiffany; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

    2009-01-01

    KPN03535 is a protein unique to K. pneumoniae. The crystal structure reveals that KPN03535 represents a novel variant of the OB-fold and is likely to be a DNA-binding lipoprotein. KPN03535 (gi|152972051) is a putative lipoprotein of unknown function that is secreted by Klebsiella pneumoniae MGH 78578. The crystal structure reveals that despite a lack of any detectable sequence similarity to known structures, it is a novel variant of the OB-fold and structurally similar to the bacterial Cpx-pathway protein NlpE, single-stranded DNA-binding (SSB) proteins and toxins. K. pneumoniae MGH 78578 forms part of the normal human skin, mouth and gut flora and is an opportunistic pathogen that is linked to about 8% of all hospital-acquired infections in the USA. This structure provides the foundation for further investigations into this divergent member of the OB-fold family

  2. Impulsivity and Concussion in Juvenile Rats: Examining Molecular and Structural Aspects of the Frontostriatal Pathway.

    Directory of Open Access Journals (Sweden)

    Harleen Hehar

    Full Text Available Impulsivity and poor executive control have been implicated in the pathogenesis of many developmental and neuropsychiatric disorders. Similarly, concussions/mild traumatic brain injuries (mTBI have been associated with increased risk for neuropsychiatric disorders and the development of impulsivity and inattention. Researchers and epidemiologists have therefore considered whether or not concussions induce symptoms of attention-deficit/hyperactivity disorder (ADHD, or merely unmask impulsive tendencies that were already present. The purpose of this study was to determine if a single concussion in adolescence could induce ADHD-like impulsivity and impaired response inhibition, and subsequently determine if inherent impulsivity prior to a pediatric mTBI would exacerbate post-concussion symptomology with a specific emphasis on impulsive and inattentive behaviours. As these behaviours are believed to be associated with the frontostriatal circuit involving the nucleus accumbens (NAc and the prefrontal cortex (PFC, the expression patterns of 8 genes (Comt, Drd2, Drd3, Drd4, Maoa, Sert, Tph1, and Tph2 from these two regions were examined. In addition, Golgi-Cox staining of medium spiny neurons in the NAc provided a neuroanatomical examination of mTBI-induced structural changes. The study found that a single early brain injury could induce impulsivity and impairments in response inhibition that were more pronounced in males. Interestingly, when animals with inherent impulsivity experienced mTBI, injury-related deficits were exacerbated in female animals. The single concussion increased dendritic branching, but reduced synaptic density in the NAc, and these changes were likely associated with the increase in impulsivity. Finally, mTBI-induced impulsivity was associated with modifications to gene expression that differed dramatically from the gene expression pattern associated with inherent impulsivity, despite very similar behavioural phenotypes. Our

  3. Aspectos estruturais da membrana eritrocitária Structural aspects of the erythrocyte membrane

    Directory of Open Access Journals (Sweden)

    Priscila Murador

    2007-06-01

    ócito e é ainda responsável pela estabilidade sob mecanismos de estresse. Essa revisão da membrana eritrocitária é importante para um melhor entendimento das reações transfusionais, onde a formação de anticorpos contra antígenos de alta freqüência dificulta a transfusão compatível. O estudo da diversidade antigênica, a caracterização bioquímica de diferentes proteínas trará uma contribuição para o estabelecimento da saúde, assim como para o diagnóstico, desenvolvimento de tecnologias, como a produção de anticorpos monoclonais e conduta terapêutica para muitas enfermidades.This article describes the structures and functions of the erythrocyte membrane and its importance in transfusional medicine. The erythrocyte membrane is one of the best known membranes in terms of structure, function and genetic disorders. As any other plasma membrane, it mediates transport functions. It also provides the erythrocytes with their resilience and deformability. According to the International Society of Blood Transfusion (ISBT, more than 500 antigens are expressed in the erythrocyte membrane, and around 270 are involved in transfusion reaction cases and hemolytic diseases of the fetus and newborn. In the ISBT classification, the high frequency series is represented by antigens in more than 99% of population (high prevalence antigen. In transfusion, the absence of these antigens determines severe problems as for example, one woman without the P antigen suffered 6 repetitive miscarriages due to placental insufficiency, which was caused by an antibody formed against the absent P antigen. Some important erythrocyte membrane proteins are described here including Band 3, Glycophorins and spectrin. The most abundant integral membrane protein is Band 3 and its main function is to mediate exchange of chloride and bicarbonate anions across the plasma membrane. The second most abundant integral membrane protein in the human erythrocyte is sialoglycoprotein glycophorin A (GPA

  4. Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction

    International Nuclear Information System (INIS)

    Han, Gye Won; Bakolitsa, Constantina; Miller, Mitchell D.; Kumar, Abhinav; Carlton, Dennis; Najmanovich, Rafael J.; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L.; Chen, Connie; Chiu, Hsiu-Ju; Clayton, Thomas; Das, Debanu; Deller, Marc C.; Duan, Lian; Ernst, Dustin; Feuerhelm, Julie; Grant, Joanna C.; Grzechnik, Anna; Jaroszewski, Lukasz; Jin, Kevin K.; Johnson, Hope A.; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Krishna, S. Sri; Marciano, David; McMullan, Daniel; Morse, Andrew T.; Nigoghossian, Edward; Okach, Linda; Reyes, Ron; Rife, Christopher L.; Sefcovic, Natasha; Tien, Henry J.; Trame, Christine B.; Bedem, Henry van den; Weekes, Dana; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

    2010-01-01

    The crystal structures of SPO0140 and Sbal-2486 revealed a two-domain structure that adopts a novel fold. Analysis of the interdomain cleft suggests a nucleotide-based ligand with a genome context indicating signaling as a possible role for this family. The crystal structures of SPO0140 and Sbal-2486 were determined using the semiautomated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). The structures revealed a conserved core with domain duplication and a superficial similarity of the C-terminal domain to pleckstrin homology-like folds. The conservation of the domain interface indicates a potential binding site that is likely to involve a nucleotide-based ligand, with genome-context and gene-fusion analyses additionally supporting a role for this family in signal transduction, possibly during oxidative stress

  5. Whole-brain analytic measures of network communication reveal increased structure-function correlation in right temporal lobe epilepsy

    Directory of Open Access Journals (Sweden)

    Jonathan Wirsich

    2016-01-01

    In rTLE patients, we found a widespread hypercorrelated functional network. Network communication analysis revealed greater unspecific branching of the shortest path (search information in the structural connectome and a higher global correlation between the structural and functional connectivity for the patient group. We also found evidence for a preserved structural rich-club in the patient group. In sum, global augmentation of structure-function correlation might be linked to a smaller functional repertoire in rTLE patients, while sparing the central core of the brain which may represent a pathway that facilitates the spread of seizures.

  6. PREFACE: 10th International Conference on Clustering Aspects of Nuclear Structure and Dynamics (CLUSTER'12)

    Science.gov (United States)

    Lovas, R. G.; Dombrádi, Zs; Kiss, G. G.; Kruppa, A. T.; Lévai, G.

    2013-04-01

    As Editors of this Proceedings volume and organizers as well as participants of the Conference, let us sum up a few facts about the Conference and let us add some subjective notes. The conference was held at Köolcsey Centre, a prestigious site of scientific and business meetings and cultural events in the city of Debrecen, Hungary, 24-28 September 2012. The city was chosen as the home of the Institute of Nuclear Research of the Hungarian Academy of Sciences, the home institution of the organizers. The Institute was visited by some of the participants. The organizing team was complemented by some belonging to the University of Debrecen, which made it possible to hold the conference dinner in the marvellous covered 'ceremonial court' of the University. The participants were taken for an excursion and wine tasting to a wine cellar at Tokaj, centre of, historically, the most significant wine producing area in Hungary. By coincidence, the closing day coincided with the day of what is called the Researchers' Night in the European Union. That night, (or rather, that evening) every year there is a public lecture in the Institute of Nuclear Research for a general audience, mainly secondary-school pupils. The public lecture scheduled on this occasion was held by one of the participants of the conference who represented the world outside Hungary and yet was able to deliver a talk in Hungarian. He is Professor Kálmán Varga, Vanderbilt University. The title of his talk was Simulation of Nanosystems ( http://kutatokejszakaja.hu/2012/esemenynaptar/esemeny.php?id=112&menu_id=4). There were 115 registered participants, representing 22 countries of Europe, Africa, Asia, Central, South and North America. We had 44 plenary talks and 47 talks presented in parallel sessions. In the Programme list the talks are arranged following the session structure of the Conference. In this list the invited speakers are marked by asterisks. All the talks in the plenary sessions were invited talks

  7. Internal structure of a barrier beach as revealed by ground penetrating radar (GPR): Chesil beach, UK

    Science.gov (United States)

    Bennett, Matthew R.; Cassidy, Nigel J.; Pile, Jeremy

    2009-03-01

    Chesil Beach (Dorset) is one of the most famous coastal landforms on the British coast. The gravel beach is over 18 km long and is separated for much of its length from land by a tidal lagoon known as The Fleet. The beach links the Isle of Portland in the east to the mainland in the west. Despite its iconic status there is little available information on its internal geometry and evolutionary history. Here we present a three-fold model for the evolution of Chesil Beach based on a series of nine ground penetrating radar (GPR) traverses located at three sites along its length at Abbotsbury, Langton Herring and at Ferry Bridge. The GPR traverses reveal a remarkably consistent picture of the internal structure of this barrier beach. The first phase of evolution involves the landward transgression of a small sand and gravel beach which closed upon the coast leading to deposition of freshwater peat between 5 and 7 k yr BP. The second evolutionary phase involves the 'bulking-out' of the beach during continued sea level rise, but in the presence of abundant gravel supplied by down-drift erosion of periglacial slope deposits. This episode of growth was associated with a series of washover fans which accumulated on the landward flank of the barrier increasing its breadth and height but without significant landward transgression of the barrier as a whole. The final phase in the evolution of Chesil Beach involves the seaward progradation of the beach crest and upper beach face associated with continued sediment abundance, but during a still-stand or slight fall in relative sea level. This phase may provide further evidence of a slight fall in relative sea level noted elsewhere along the South Coast of Britain and dated to between 1.2 and 2.4 k yr BP. Subsequently the barrier appears to have become largely inactive, except for the reworking of sediment on the beach face during storm events. The case study not only refines the evolutionary picture of Chesil Beach, but

  8. Cloud top structure of Venus revealed by Subaru/COMICS mid-infrared images

    Science.gov (United States)

    Sato, T. M.; Sagawa, H.; Kouyama, T.; Mitsuyama, K.; Satoh, T.; Ohtsuki, S.; Ueno, M.; Kasaba, Y.; Nakamura, M.; Imamura, T.

    2014-11-01

    We have investigated the cloud top structure of Venus by analyzing ground-based images taken at the mid-infrared wavelengths of 8.66 μm and 11.34 μm. Venus at a solar phase angle of ∼90°, with the morning terminator in view, was observed by the Cooled Mid-Infrared Camera and Spectrometer (COMICS), mounted on the 8.2-m Subaru Telescope, during the period October 25-29, 2007. The disk-averaged brightness temperatures for the observation period are ∼230 K and ∼238 K at 8.66 μm and 11.34 μm, respectively. The obtained images with good signal-to-noise ratio and with high spatial resolution (∼200 km at the sub-observer point) provide several important findings. First, we present observational evidence, for the first time, of the possibility that the westward rotation of the polar features (the hot polar spots and the surrounding cold collars) is synchronized between the northern and southern hemispheres. Second, after high-pass filtering, the images reveal that streaks and mottled and patchy patterns are distributed over the entire disk, with typical amplitudes of ∼0.5 K, and vary from day to day. The detected features, some of which are similar to those seen in past UV images, result from inhomogeneities of both the temperature and the cloud top altitude. Third, the equatorial center-to-limb variations of brightness temperatures have a systematic day-night asymmetry, except those on October 25, that the dayside brightness temperatures are higher than the nightside brightness temperatures by 0-4 K under the same viewing geometry. Such asymmetry would be caused by the propagation of the migrating semidiurnal tide. Finally, by applying the lapse rates deduced from previous studies, we demonstrate that the equatorial center-to-limb curves in the two spectral channels give access to two parameters: the cloud scale height H and the cloud top altitude zc. The acceptable models for data on October 25 are obtained at H = 2.4-4.3 km and zc = 66-69 km; this supports

  9. Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain

    DEFF Research Database (Denmark)

    Sükösd, Zsuzsanna; Andersen, Ebbe Sloth; Seemann, Ernst Stefan

    2015-01-01

    of the HIV-1 genome is highly variable in most regions, with a limited number of stable and conserved RNA secondary structures. Most interesting, a set of long distance interactions form a core organizing structure (COS) that organize the genome into three major structural domains. Despite overlapping...

  10. Associations between the structural and functional aspects of social relations and poor mental health: a cross-sectional register study

    Directory of Open Access Journals (Sweden)

    Lise Røntved Hansen

    2017-11-01

    Full Text Available Abstract Background Social relations influence mental health through different pathways. To capture the complexity of social relations, it is beneficial to consider both the structural (e.g., reachability of social network and social integration and functional (e.g., instrumental and emotional support aspects of the concept. Both aspects are rarely investigated simultaneously. This study aimed to examine the association between the structural and functional aspects of social relations and poor mental health. Methods The study was designed as a cross-sectional register study. We used data on mental health and social relations from 15,839 individuals aged 16–92 years with a mean age of 49.0 years (SD 17.9 who responded to The North Denmark Region Health Survey 2013 among residents in Northern Jutland, Denmark. The 12-Item Short-Form Health Survey measured mental health; a cut-off point of 44.5 was used to dichotomize participants into poor and good mental health. The categorization of social relations was inspired by Berkman et al.’s conceptual model of social relations and health. The analyses were performed with survey logistic regression. Results We found that 21.6% (n = 3422 of participants reported poor mental health, and 59% (n = 2020 of these were women. Being in contact with family and friends less than once a month statistically significantly increased the risk for poor mental health (Family OR = 1.78, 95% CI = 1.51–2.10 and Friends OR = 2.65, 95% CI = 2.30–3.06. The individuals who were not in contact with their network as often as they liked had a significantly higher risk for poor mental health (OR = 2.40, 95% CI = 2.20–2.62. Lack of instrumental support was associated with a higher risk for poor mental health (OR = 2.81, 95% CI = 2.26–3.48. We found an interaction between age and emotional support; the youngest population had the highest risk for poor mental health when they did not have access to

  11. Associations between the structural and functional aspects of social relations and poor mental health: a cross-sectional register study.

    Science.gov (United States)

    Hansen, Lise Røntved; Pedersen, Stinna Bibi; Overgaard, Charlotte; Torp-Pedersen, Christian; Ullits, Line Rosenkilde

    2017-11-03

    Social relations influence mental health through different pathways. To capture the complexity of social relations, it is beneficial to consider both the structural (e.g., reachability of social network and social integration) and functional (e.g., instrumental and emotional support) aspects of the concept. Both aspects are rarely investigated simultaneously. This study aimed to examine the association between the structural and functional aspects of social relations and poor mental health. The study was designed as a cross-sectional register study. We used data on mental health and social relations from 15,839 individuals aged 16-92 years with a mean age of 49.0 years (SD 17.9) who responded to The North Denmark Region Health Survey 2013 among residents in Northern Jutland, Denmark. The 12-Item Short-Form Health Survey measured mental health; a cut-off point of 44.5 was used to dichotomize participants into poor and good mental health. The categorization of social relations was inspired by Berkman et al.'s conceptual model of social relations and health. The analyses were performed with survey logistic regression. We found that 21.6% (n = 3422) of participants reported poor mental health, and 59% (n = 2020) of these were women. Being in contact with family and friends less than once a month statistically significantly increased the risk for poor mental health (Family OR = 1.78, 95% CI = 1.51-2.10 and Friends OR = 2.65, 95% CI = 2.30-3.06). The individuals who were not in contact with their network as often as they liked had a significantly higher risk for poor mental health (OR = 2.40, 95% CI = 2.20-2.62). Lack of instrumental support was associated with a higher risk for poor mental health (OR = 2.81, 95% CI = 2.26-3.48). We found an interaction between age and emotional support; the youngest population had the highest risk for poor mental health when they did not have access to emotional support (Young OR = 5.26, 95% CI = 3

  12. Two crystal structures of dihydrofolate reductase-thymidylate synthase from Cryptosporidium hominis reveal protein–ligand interactions including a structural basis for observed antifolate resistance

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Amy C., E-mail: aca@dartmouth.edu [Dartmouth College, Department of Chemistry, Burke Laboratories, Hanover, NH 03755 (United States)

    2005-03-01

    An analysis of the protein–ligand interactions in two crystal structures of DHFR-TS from C. hominis reveals a possible structural basis for observed antifolate resistance in C. hominis DHFR. A comparison with the structure of human DHFR reveals residue substitutions that may be exploited for the design of species-selective inhibitors. Cryptosporidium hominis is a protozoan parasite that causes acute gastrointestinal illness. There are no effective therapies for cryptosporidiosis, highlighting the need for new drug-lead discovery. An analysis of the protein–ligand interactions in two crystal structures of dihydrofolate reductase-thymidylate synthase (DHFR-TS) from C. hominis, determined at 2.8 and 2.87 Å resolution, reveals that the interactions of residues Ile29, Thr58 and Cys113 in the active site of C. hominis DHFR provide a possible structural basis for the observed antifolate resistance. A comparison with the structure of human DHFR reveals active-site differences that may be exploited for the design of species-selective inhibitors.

  13. FRAMEWORK FOR STRUCTURAL ONLINE HEALTH MONITORING OF AGING AND DEGRADATION OF SECONDARY PIPING SYSTEMS DUE TO SOME ASPECTS OF EROSION

    Energy Technology Data Exchange (ETDEWEB)

    Gribok, Andrei V.; Agarwal, Vivek

    2017-06-01

    This paper describes the current state of research related to critical aspects of erosion and selected aspects of degradation of secondary components in nuclear power plants (NPPs). The paper also proposes a framework for online health monitoring of aging and degradation of secondary components. The framework consists of an integrated multi-sensor modality system, which can be used to monitor different piping configurations under different degradation conditions. The report analyses the currently known degradation mechanisms and available predictive models. Based on this analysis, the structural health monitoring framework is proposed. The Light Water Reactor Sustainability Program began to evaluate technologies that could be used to perform online monitoring of piping and other secondary system structural components in commercial NPPs. These online monitoring systems have the potential to identify when a more detailed inspection is needed using real time measurements, rather than at a pre-determined inspection interval. This transition to condition-based, risk-informed automated maintenance will contribute to a significant reduction of operations and maintenance costs that account for the majority of nuclear power generation costs. Furthermore, of the operations and maintenance costs in U.S. plants, approximately 80% are labor costs. To address the issue of rising operating costs and economic viability, in 2017, companies that operate the national nuclear energy fleet started the Delivering the Nuclear Promise Initiative, which is a 3 year program aimed at maintaining operational focus, increasing value, and improving efficiency. There is unanimous agreement between industry experts and academic researchers that identifying and prioritizing inspection locations in secondary piping systems (for example, in raw water piping or diesel piping) would eliminate many excessive in-service inspections. The proposed structural health monitoring framework takes aim at

  14. Two aspects of one loop structure: Unitarity delay in the Standard Model and modular invariance in string theory

    Energy Technology Data Exchange (ETDEWEB)

    Ahn, C.

    1989-08-01

    We study two aspects of one loop structures in quantum field theories which describe two different areas of particle physics: the one loop unitarity behavior of the Standard Model of electroweak interactions and modular invariance of string model theory. Loop expansion has its importance in that it contains quantum fluctuations due to all physical states in the theory. Therefore, by studying the various models to one loop, we can understand how the contents of the theory can contribute to physically measurable quantities and how the consistency at quantum level restricts the physical states of the theory, as well. In the first half of the thesis, we study one loop corrections to the process {ital e}{sup +}{ital e}{sup {minus}} {yields} {ital W}{sup +}{ital W}{sup {minus}}. In this process, there is a delicate unitarity-saving cancellation between s-channel and t-channel tree level Feynman diagrams. If the one loop contribution due to heavy particles corrects the channels asymmetrically, the cancellation, hence unitarity, will be delayed up to the mass scale of these heavy particles. We refer to this phenomena as the unitarity delay effect. Due to this effect, cross section below these mass scales can have significant radiative corrections which may provide an appropriate window through which we can see the high energy structure of the Standard Model from relatively low energy experiments. In the second half, we will show how quantum consistency can restrict the physical states in string theory. 53 refs., 13 figs.

  15. Single cell Hi-C reveals cell-to-cell variability in chromosome structure

    Science.gov (United States)

    Schoenfelder, Stefan; Yaffe, Eitan; Dean, Wendy; Laue, Ernest D.; Tanay, Amos; Fraser, Peter

    2013-01-01

    Large-scale chromosome structure and spatial nuclear arrangement have been linked to control of gene expression and DNA replication and repair. Genomic techniques based on chromosome conformation capture assess contacts for millions of loci simultaneously, but do so by averaging chromosome conformations from millions of nuclei. Here we introduce single cell Hi-C, combined with genome-wide statistical analysis and structural modeling of single copy X chromosomes, to show that individual chromosomes maintain domain organisation at the megabase scale, but show variable cell-to-cell chromosome territory structures at larger scales. Despite this structural stochasticity, localisation of active gene domains to boundaries of territories is a hallmark of chromosomal conformation. Single cell Hi-C data bridge current gaps between genomics and microscopy studies of chromosomes, demonstrating how modular organisation underlies dynamic chromosome structure, and how this structure is probabilistically linked with genome activity patterns. PMID:24067610

  16. Complex nuclear-structure phenomena revealed from the nuclide production in fragmentation reactions

    International Nuclear Information System (INIS)

    Ricciardi, M.V.; Kelic, A.; Napolitani, P.; Schmidt, K.H.; Yordanov, O.; Ignatyuk, A.V.; Rejmund, F.

    2003-12-01

    Complex structural effects in the nuclide production from the projectile fragmentation of 1 A GeV 238 U nuclei in a titanium target are reported. The structure seems to be insensitive to the excitation energy induced in the reaction. This is in contrast to the prominent structural features found in nuclear fission and in transfer reactions, which gradually disappear with increasing excitation energy. Using the statistical model of nuclear reactions, relations to structural effects in nuclear binding and in the nuclear level density are demonstrated. (orig.)

  17. MODIS-Aqua Reveals Evolving Phytoplankton Community Structure During the Arabian Sea Northeast Monsoon

    Science.gov (United States)

    Werdell, P. Jeremy; Roesler, Collin S.; Goes, Joaquim I.

    2016-01-01

    Applying a bio-optical model designed to identify the mixotrophic dinoflagellate Noctiluca miliaris to MODIS-Aqua revealed (1) patterns in its spatial distribution not previously seen (including its appearance in places not previously sampled), and (2) the surprising disassociation of total chlorophyll biomass with the presence of N. miliaris.

  18. Advances in Alkenone Paleotemperature Proxies: Analytical Methods, Novel Structures and Haptophyte Species, Biosynthesis, New indices and Ecological Aspects

    Science.gov (United States)

    Huang, Y.; Longo, W. M.; Zheng, Y.; Richter, N.; Dillon, J. T.; Theroux, S.; D'Andrea, W. J.; Toney, J. L.; Wang, L.; Amaral-Zettler, L. A.

    2017-12-01

    Alkenones are mature, well-established paleo-sea surface temperature proxies that have been widely applied for more than three decades. However, recent advances across a broad range of alkenone-related topics at Brown University are inviting new paleoclimate and paleo-environmental applications for these classic biomarkers. In this presentation, I will summarize our progress in the following areas: (1) Discovery of a freshwater alkenone-producing haptophyte species and structural elucidation of novel alkenone structures unique to the species, performing in-situ temperature calibrations, and classifying alkenone-producing haptophytes into three groups based on molecular ecological approaches (with the new species belonging to Group I Isochrysidales); (2) A global survey of Group I haptophyte distributions and environmental conditions favoring the presence of this alga, as well as examples of using Group I alkenones for paleotemperature reconstructions; (3) New gas chromatographic columns that allow unprecedented resolution of alkenones and alkenoates and associated structural isomers, and development of a new suite of paleotemperature and paleoenvironmental proxies; (4) A new liquid chromatographic separation technique that allows efficient cleanup of alkenones and alkenoates (without the need for saponification) for subsequent coelution-free gas chromatographic analysis; (5) Novel structural features revealed by new analytical methods that now allow a comprehensive re-assessment of taxonomic features of various haptophyte species, with principal component analysis capable of fully resolving species biomarker distributions; (6) Development of UK37 double prime (UK37'') for Group II haptophytes (e.g., those occurring in saline lakes and estuaries), that differs from the traditional unsaturation indices used for SST reconstructions; (7) New assessment of how mixed inputs from different alkenone groups may affect SST reconstructions in marginal ocean environments and

  19. Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase

    Directory of Open Access Journals (Sweden)

    Katja Venko

    Full Text Available The structural and functional details of transmembrane proteins are vastly underexplored, mostly due to experimental difficulties regarding their solubility and stability. Currently, the majority of transmembrane protein structures are still unknown and this present a huge experimental and computational challenge. Nowadays, thanks to X-ray crystallography or NMR spectroscopy over 3000 structures of membrane proteins have been solved, among them only a few hundred unique ones. Due to the vast biological and pharmaceutical interest in the elucidation of the structure and the functional mechanisms of transmembrane proteins, several computational methods have been developed to overcome the experimental gap. If combined with experimental data the computational information enables rapid, low cost and successful predictions of the molecular structure of unsolved proteins. The reliability of the predictions depends on the availability and accuracy of experimental data associated with structural information. In this review, the following methods are proposed for in silico structure elucidation: sequence-dependent predictions of transmembrane regions, predictions of transmembrane helix–helix interactions, helix arrangements in membrane models, and testing their stability with molecular dynamics simulations. We also demonstrate the usage of the computational methods listed above by proposing a model for the molecular structure of the transmembrane protein bilitranslocase. Bilitranslocase is bilirubin membrane transporter, which shares similar tissue distribution and functional properties with some of the members of the Organic Anion Transporter family and is the only member classified in the Bilirubin Transporter Family. Regarding its unique properties, bilitranslocase is a potentially interesting drug target. Keywords: Membrane proteins, Bilitranslocase, 3D protein structure, Transmembrane region predictors, Helix–helix interactions

  20. Molecular Dynamic Simulation of Space and Earth-Grown Crystal Structures of Thermostable T1 Lipase Geobacillus zalihae Revealed a Better Structure.

    Science.gov (United States)

    Ishak, Siti Nor Hasmah; Aris, Sayangku Nor Ariati Mohamad; Halim, Khairul Bariyyah Abd; Ali, Mohd Shukuri Mohamad; Leow, Thean Chor; Kamarudin, Nor Hafizah Ahmad; Masomian, Malihe; Rahman, Raja Noor Zaliha Raja Abd

    2017-09-25

    Less sedimentation and convection in a microgravity environment has become a well-suited condition for growing high quality protein crystals. Thermostable T1 lipase derived from bacterium Geobacillus zalihae has been crystallized using the counter diffusion method under space and earth conditions. Preliminary study using YASARA molecular modeling structure program for both structures showed differences in number of hydrogen bond, ionic interaction, and conformation. The space-grown crystal structure contains more hydrogen bonds as compared with the earth-grown crystal structure. A molecular dynamics simulation study was used to provide insight on the fluctuations and conformational changes of both T1 lipase structures. The analysis of root mean square deviation (RMSD), radius of gyration, and root mean square fluctuation (RMSF) showed that space-grown structure is more stable than the earth-grown structure. Space-structure also showed more hydrogen bonds and ion interactions compared to the earth-grown structure. Further analysis also revealed that the space-grown structure has long-lived interactions, hence it is considered as the more stable structure. This study provides the conformational dynamics of T1 lipase crystal structure grown in space and earth condition.

  1. Atomic-scale structure of dislocations revealed by scanning tunneling microscopy and molecular dynamics

    DEFF Research Database (Denmark)

    Christiansen, Jesper; Morgenstern, K.; Schiøtz, Jakob

    2002-01-01

    The intersection between dislocations and a Ag(111) surface has been studied using an interplay of scanning tunneling microscopy (STM) and molecular dynamics. Whereas the STM provides atomically resolved information about the surface structure and Burgers vectors of the dislocations, the simulati......The intersection between dislocations and a Ag(111) surface has been studied using an interplay of scanning tunneling microscopy (STM) and molecular dynamics. Whereas the STM provides atomically resolved information about the surface structure and Burgers vectors of the dislocations......, the simulations can be used to determine dislocation structure and orientation in the near-surface region. In a similar way, the subsurface structure of other extended defects can be studied. The simulations show dislocations to reorient the partials in the surface region leading to an increased splitting width...

  2. Integration of community structure data reveals observable effects below sediment guideline thresholds in a large estuary

    KAUST Repository

    Tremblay, Louis A.; Clark, Dana; Sinner, Jim; Ellis, Joanne

    2017-01-01

    The sustainable management of estuarine and coastal ecosystems requires robust frameworks due to the presence of multiple physical and chemical stressors. In this study, we assessed whether ecological health decline, based on community structure

  3. Multilayer networks reveal the spatial structure of seed-dispersal interactions across the Great Rift landscapes.

    Science.gov (United States)

    Timóteo, Sérgio; Correia, Marta; Rodríguez-Echeverría, Susana; Freitas, Helena; Heleno, Ruben

    2018-01-10

    Species interaction networks are traditionally explored as discrete entities with well-defined spatial borders, an oversimplification likely impairing their applicability. Using a multilayer network approach, explicitly accounting for inter-habitat connectivity, we investigate the spatial structure of seed-dispersal networks across the Gorongosa National Park, Mozambique. We show that the overall seed-dispersal network is composed by spatially explicit communities of dispersers spanning across habitats, functionally linking the landscape mosaic. Inter-habitat connectivity determines spatial structure, which cannot be accurately described with standard monolayer approaches either splitting or merging habitats. Multilayer modularity cannot be predicted by null models randomizing either interactions within each habitat or those linking habitats; however, as habitat connectivity increases, random processes become more important for overall structure. The importance of dispersers for the overall network structure is captured by multilayer versatility but not by standard metrics. Highly versatile species disperse many plant species across multiple habitats, being critical to landscape functional cohesion.

  4. The structure of a conserved Piezo channel domain reveals a novel beta sandwich fold

    Science.gov (United States)

    Kamajaya, Aron; Kaiser, Jens; Lee, Jonas; Reid, Michelle; Rees, Douglas C.

    2014-01-01

    Summary Piezo has recently been identified as a family of eukaryotic mechanosensitive channels composed of subunits containing over 2000 amino acids, without recognizable sequence similarity to other channels. Here, we present the crystal structure of a large, conserved extramembrane domain located just before the last predicted transmembrane helix of C. elegans PIEZO, which adopts a novel beta sandwich fold. The structure was also determined of a point mutation located on a conserved surface at the position equivalent to the human PIEZO1 mutation found in Dehydrated Hereditary Stomatocytosis (DHS) patients (M2225R). While the point mutation does not change the overall domain structure, it does alter the surface electrostatic potential that may perturb interactions with a yet-to-be identified ligand or protein. The lack of structural similarity between this domain and any previously characterized fold, including those of eukaryotic and bacterial channels, highlights the distinctive nature of the Piezo family of eukaryotic mechanosensitive channels. PMID:25242456

  5. Water's Interfacial Hydrogen Bonding Structure Reveals the Effective Strength of Surface-Water Interactions.

    Science.gov (United States)

    Shin, Sucheol; Willard, Adam P

    2018-06-05

    We combine all-atom molecular dynamics simulations with a mean field model of interfacial hydrogen bonding to analyze the effect of surface-water interactions on the structural and energetic properties of the liquid water interface. We show that the molecular structure of water at a weakly interacting ( i.e., hydrophobic) surface is resistant to change unless the strength of surface-water interactions are above a certain threshold. We find that below this threshold water's interfacial structure is homogeneous and insensitive to the details of the disordered surface, however, above this threshold water's interfacial structure is heterogeneous. Despite this heterogeneity, we demonstrate that the equilibrium distribution of molecular orientations can be used to quantify the energetic component of the surface-water interactions that contribute specifically to modifying the interfacial hydrogen bonding network. We identify this specific energetic component as a new measure of hydrophilicity, which we refer to as the intrinsic hydropathy.

  6. Developmental aspects of English argument structure constructions for Korean-speaking second language learners: Usage-based constructional approaches to language development

    Directory of Open Access Journals (Sweden)

    Gyu-Ho Shin

    2017-01-01

    Full Text Available This study investigates developmental aspects of English Argument Structure Constructions (ASCs for Korean-speaking second language (L2 learners, providing evidence of how they manifest human domain-general cognitive systems during language acquisition via usage-based constructional approaches to language development. Participants were instructed on six English ASC types with their representative verbs for three months. The data from grammaticality preference tasks, writing tests, and free-writing tasks were analysed. Comprehension data from the grammaticality preference tasks showed significant improvement in understanding ASCs after instruction, supporting sentence-level generalisations for language comprehension independent of individual verbs. The production data from the writing tests demonstrated more frequent use of two-argument constructions than three-argument ones, which indicates the internal complexity between ASC types. The results of the writing tests also displayed skewed exploitation of verbs representative of the target ASCs, implying a frequency-sensitive nature of language acquisition. All production data further revealed active use of prefabricated chunks and incorporation of new and old language items. Taken all together, these observations suggest language learners’ merging narrowly stabilised L2 routines with other (non-linguistic resources as necessary, sustaining efficiency in a sentence-building process, under the superintendence of cognitive factors when satisfying communicative intents.

  7. Aspects of the structure of film expression and anthropological paradigm of films reception in Croatian cinema and TV distribution.

    Science.gov (United States)

    Svilicić, Niksa

    2012-09-01

    This research paper deals with one part of a comprehensive study called "Causality of narratological-semiotic aspects of the structure of film expression and paradigms of reception of Croatian feature film". It is conceived as a response to the hypothesis that the expression of narrative-semiotic terms correlate with the reception of the Croatian feature film audience and all them leads into a broader holistic i.e. anthropological context.The basic idea of scientific research is to analyze the complete feature productions since Croatian independence 1991 to date, presented at the National Film Festival (film festival in Pula), identify, define and isolate positive social narrative-semiotic stereotypes, which can then serve as a paradigm of better ratings and increase of the currently very low rating of domestic films in Croatian cinemas, as well as TV distribution. In other words, the paper will be analyzed and processed by a range of different effects based on narrative-semiotic, set design and mise-en-scène motives, used in the Croatian feature films since independence to date, that we assume to positively influence the mood of the viewer, and thus increase the rating of the film.

  8. Evolutionary aspects of non-cell-autonomous regulation in vascular plants: structural background and models to study

    Directory of Open Access Journals (Sweden)

    Anastasiia I. Evkaikina

    2014-02-01

    Full Text Available Plasmodesmata (PD serve for the exchange of information in form of miRNA, proteins and mRNA between adjacent cells in the course of plant development. This fundamental role of PD is well established in angiosperms but has not yet been traced back to the evolutionary ancient plant taxa where functional studies lag behind studies of PD structure and ontogenetic origin. There is convincing evidence that the ability to form secondary (post-cytokinesis PD, which can connect any adjacent cells, contrary to primary PD which form during cytokinesis and link only cells of the same lineage, appeared in the evolution of higher plants at least twice: in seed plants and in some representatives of the Lycopodiophyta. The (inability to form secondary PD is manifested in the symplastic organization of the shoot apical meristem (SAM which in most taxa of seedless vascular plants differs dramatically from that in seed plants. Lycopodiophyta appear to be suitable models to analyze the transport of developmental regulators via PD in SAMs with symplastic organization both different from, as well as analogous to, that in angiosperms, and to understand the evolutionary aspects of the role of this transport in the morphogenesis of vascular plant taxa.

  9. Power plant design study of a high aspect ratio Tokamak using a SiC composite structure

    International Nuclear Information System (INIS)

    Murakami, Y.; Takase, H.; Shinya, K.

    1998-01-01

    The DREAM (drastically easy maintenance) tokamak is a fusion power plant which is designed from the viewpoint of maintenance feasibility. For this purpose, the DREAM reactor uses a plasma with a very high aspect ratio (A) and adopts SiC as a structural material. The choice of SiC affects the design of the core plasma, i.e. large inboard shield thickness, low synchrotron radiation reflectivity, and small plasma elongation for positional stability. The objectives of this study are to explore the feasibility of a high-A device, such as a power plant, and to clarify the technological impact of SiC material on the plasma design. Plasma size is optimized by the physics guidelines similar to ITER. The plasma major and minor radii of DREAM are 16 m and 2 m, respectively, and the average neutron wall load is 2.5 MW m -2 , the maximum toroidal field is 20 T, and the fusion power is 5.5 GW. Steady-state operation is obtained with 50 MW of external current-drive power and 90% bootstrap current. The divertor heat load is estimated to be about 10 MW m -2 . A radiative divertor concept is adopted to achieve a low divertor plasma temperature. The DREAM tokamak concept is found to be a possible candidate for a future power plant with more than 5 GW of fusion power and an acceptable divertor condition. (orig.)

  10. Studies of extractant molecules in solution and at liquid-liquid interfaces: structural and mechanistic aspects of synergy effects

    International Nuclear Information System (INIS)

    Baaden, Marc

    2000-01-01

    Molecular dynamics simulations reported herein provide new important insights into cation recognition and complexation in solution as well as liquid-liquid extraction, with a particular focus on the microscopic events taking place at the interface between two immiscible liquids. Preliminary studies concerned the representation of the trivalent rare earth cations La 3+ , Eu 3+ and Yb 3+ in force field simulations, probing structural and energetic features on an experimentally characterized model system based on substituted pyridine dicarboxamide ligands. Complexation of such cations by a novel calixarene derivative was investigated showing unexpected features, such as the position of the cation in the complex. Independent experimental studies published subsequently support these findings. Another part of the work is related to industrial liquid-liquid extraction systems using tri-n-butyl phosphate (TBP) as co-solvent, extractant, surfactant and synergist. We investigate 1) concentration effects simulating up to 60 TBP at a water/chloroform interface, 2) acidity using a neutral and ionic model of HNO 3 and 3) synergistic aspects of mixed TBP/calixarene extraction systems. These simulations provide the first microscopic insights into such issues. We finally addressed the topic of solute transfer across the water/chloroform interface. The potential of mean force for such a process has been calculated by both standard methods and novel approaches [fr

  11. The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection.

    Directory of Open Access Journals (Sweden)

    Leila do Nascimento Vieira

    Full Text Available BACKGROUND: Podocarpus lambertii (Podocarpaceae is a native conifer from the Brazilian Atlantic Forest Biome, which is considered one of the 25 biodiversity hotspots in the world. The advancement of next-generation sequencing technologies has enabled the rapid acquisition of whole chloroplast (cp genome sequences at low cost. Several studies have proven the potential of cp genomes as tools to understand enigmatic and basal phylogenetic relationships at different taxonomic levels, as well as further probe the structural and functional evolution of plants. In this work, we present the complete cp genome sequence of P. lambertii. METHODOLOGY/PRINCIPAL FINDINGS: The P. lambertii cp genome is 133,734 bp in length, and similar to other sequenced cupressophytes, it lacks one of the large inverted repeat regions (IR. It contains 118 unique genes and one duplicated tRNA (trnN-GUU, which occurs as an inverted repeat sequence. The rps16 gene was not found, which was previously reported for the plastid genome of another Podocarpaceae (Nageia nagi and Araucariaceae (Agathis dammara. Structurally, P. lambertii shows 4 inversions of a large DNA fragment ∼20,000 bp compared to the Podocarpus totara cp genome. These unexpected characteristics may be attributed to geographical distance and different adaptive needs. The P. lambertii cp genome presents a total of 28 tandem repeats and 156 SSRs, with homo- and dipolymers being the most common and tri-, tetra-, penta-, and hexapolymers occurring with less frequency. CONCLUSION: The complete cp genome sequence of P. lambertii revealed significant structural changes, even in species from the same genus. These results reinforce the apparently loss of rps16 gene in Podocarpaceae cp genome. In addition, several SSRs in the P. lambertii cp genome are likely intraspecific polymorphism sites, which may allow highly sensitive phylogeographic and population structure studies, as well as phylogenetic studies of species of

  12. ITS2 sequence-structure phylogeny reveals diverse endophytic Pseudocercospora fungi on poplars.

    Science.gov (United States)

    Yan, Dong-Hui; Gao, Qian; Sun, Xiaoming; Song, Xiaoyu; Li, Hongchang

    2018-04-01

    For matching the new fungal nomenclature to abolish pleomorphic names for a fungus, a genus Pseudocercospora s. str. was suggested to host holomorphic Pseudocercosproa fungi. But the Pseudocercosproa fungi need extra phylogenetic loci to clarify their taxonomy and diversity for their existing and coming species. Internal transcribed spacer 2 (ITS2) secondary structures have been promising in charactering species phylogeny in plants, animals and fungi. In present study, a conserved model of ITS2 secondary structures was confirmed on fungi in Pseudocercospora s. str. genus using RNAshape program. The model has a typical eukaryotic four-helix ITS2 secondary structure. But a single U base occurred in conserved motif of U-U mismatch in Helix 2, and a UG emerged in UGGU motif in Helix 3 to Pseudocercospora fungi. The phylogeny analyses based on the ITS2 sequence-secondary structures with compensatory base change characterizations are able to delimit more species for Pseudocercospora s. str. than phylogenic inferences of traditional multi-loci alignments do. The model was employed to explore the diversity of endophytic Pseudocercospora fungi in poplar trees. The analysis results also showed that endophytic Pseudocercospora fungi were diverse in species and evolved a specific lineage in poplar trees. This work suggested that ITS2 sequence-structures could become as additionally significant loci for species phylogenetic and taxonomic studies on Pseudocerospora fungi, and that Pseudocercospora endophytes could be important roles to Pseudocercospora fungi's evolution and function in ecology.

  13. Revealing the Link between Structural Relaxation and Dynamic Heterogeneity in Glass-Forming Liquids.

    Science.gov (United States)

    Wang, Lijin; Xu, Ning; Wang, W H; Guan, Pengfei

    2018-03-23

    Despite the use of glasses for thousands of years, the nature of the glass transition is still mysterious. On approaching the glass transition, the growth of dynamic heterogeneity has long been thought to play a key role in explaining the abrupt slowdown of structural relaxation. However, it still remains elusive whether there is an underlying link between structural relaxation and dynamic heterogeneity. Here, we unravel the link by introducing a characteristic time scale hiding behind an identical dynamic heterogeneity for various model glass-forming liquids. We find that the time scale corresponds to the kinetic fragility of liquids. Moreover, it leads to scaling collapse of both the structural relaxation time and dynamic heterogeneity for all liquids studied, together with a characteristic temperature associated with the same dynamic heterogeneity. Our findings imply that studying the glass transition from the viewpoint of dynamic heterogeneity is more informative than expected.

  14. Crystal structures of a GABAA-receptor chimera reveal new endogenous neurosteroid-binding sites.

    Science.gov (United States)

    Laverty, Duncan; Thomas, Philip; Field, Martin; Andersen, Ole J; Gold, Matthew G; Biggin, Philip C; Gielen, Marc; Smart, Trevor G

    2017-11-01

    γ-Aminobutyric acid receptors (GABA A Rs) are vital for controlling excitability in the brain. This is emphasized by the numerous neuropsychiatric disorders that result from receptor dysfunction. A critical component of most native GABA A Rs is the α subunit. Its transmembrane domain is the target for many modulators, including endogenous brain neurosteroids that impact anxiety, stress and depression, and for therapeutic drugs, such as general anesthetics. Understanding the basis for the modulation of GABA A R function requires high-resolution structures. Here we present the first atomic structures of a GABA A R chimera at 2.8-Å resolution, including those bound with potentiating and inhibitory neurosteroids. These structures define new allosteric binding sites for these modulators that are associated with the α-subunit transmembrane domain. Our findings will enable the exploitation of neurosteroids for therapeutic drug design to regulate GABA A Rs in neurological disorders.

  15. High-resolution structure of TBP with TAF1 reveals anchoring patterns in transcriptional regulation.

    Science.gov (United States)

    Anandapadamanaban, Madhanagopal; Andresen, Cecilia; Helander, Sara; Ohyama, Yoshifumi; Siponen, Marina I; Lundström, Patrik; Kokubo, Tetsuro; Ikura, Mitsuhiko; Moche, Martin; Sunnerhagen, Maria

    2013-08-01

    The general transcription factor TFIID provides a regulatory platform for transcription initiation. Here we present the crystal structure (1.97 Å) and NMR analysis of yeast TAF1 N-terminal domains TAND1 and TAND2 bound to yeast TBP, together with mutational data. We find that yeast TAF1-TAND1, which in itself acts as a transcriptional activator, binds TBP's concave DNA-binding surface by presenting similar anchor residues to TBP as does Mot1 but from a distinct structural scaffold. Furthermore, we show how TAF1-TAND2 uses an aromatic and acidic anchoring pattern to bind a conserved TBP surface groove traversing the basic helix region, and we find highly similar TBP-binding motifs also presented by the structurally distinct TFIIA, Mot1 and Brf1 proteins. Our identification of these anchoring patterns, which can be easily disrupted or enhanced, provides insight into the competitive multiprotein TBP interplay critical to transcriptional regulation.

  16. Revealing the Link between Structural Relaxation and Dynamic Heterogeneity in Glass-Forming Liquids

    Science.gov (United States)

    Wang, Lijin; Xu, Ning; Wang, W. H.; Guan, Pengfei

    2018-03-01

    Despite the use of glasses for thousands of years, the nature of the glass transition is still mysterious. On approaching the glass transition, the growth of dynamic heterogeneity has long been thought to play a key role in explaining the abrupt slowdown of structural relaxation. However, it still remains elusive whether there is an underlying link between structural relaxation and dynamic heterogeneity. Here, we unravel the link by introducing a characteristic time scale hiding behind an identical dynamic heterogeneity for various model glass-forming liquids. We find that the time scale corresponds to the kinetic fragility of liquids. Moreover, it leads to scaling collapse of both the structural relaxation time and dynamic heterogeneity for all liquids studied, together with a characteristic temperature associated with the same dynamic heterogeneity. Our findings imply that studying the glass transition from the viewpoint of dynamic heterogeneity is more informative than expected.

  17. Revised Mimivirus major capsid protein sequence reveals intron-containing gene structure and extra domain

    Directory of Open Access Journals (Sweden)

    Suzan-Monti Marie

    2009-05-01

    Full Text Available Abstract Background Acanthamoebae polyphaga Mimivirus (APM is the largest known dsDNA virus. The viral particle has a nearly icosahedral structure with an internal capsid shell surrounded with a dense layer of fibrils. A Capsid protein sequence, D13L, was deduced from the APM L425 coding gene and was shown to be the most abundant protein found within the viral particle. However this protein remained poorly characterised until now. A revised protein sequence deposited in a database suggested an additional N-terminal stretch of 142 amino acids missing from the original deduced sequence. This result led us to investigate the L425 gene structure and the biochemical properties of the complete APM major Capsid protein. Results This study describes the full length 3430 bp Capsid coding gene and characterises the 593 amino acids long corresponding Capsid protein 1. The recombinant full length protein allowed the production of a specific monoclonal antibody able to detect the Capsid protein 1 within the viral particle. This protein appeared to be post-translationnally modified by glycosylation and phosphorylation. We proposed a secondary structure prediction of APM Capsid protein 1 compared to the Capsid protein structure of Paramecium Bursaria Chlorella Virus 1, another member of the Nucleo-Cytoplasmic Large DNA virus family. Conclusion The characterisation of the full length L425 Capsid coding gene of Acanthamoebae polyphaga Mimivirus provides new insights into the structure of the main Capsid protein. The production of a full length recombinant protein will be useful for further structural studies.

  18. Tandem Mass Spectrometry and Ion Mobility Reveals Structural Insight into Eicosanoid Product Ion Formation.

    Science.gov (United States)

    Di Giovanni, James P; Barkley, Robert M; Jones, David N M; Hankin, Joseph A; Murphy, Robert C

    2018-04-23

    Ion mobility measurements of product ions were used to characterize the collisional cross section (CCS) of various complex lipid [M-H] - ions using traveling wave ion mobility mass spectrometry (TWIMS). TWIMS analysis of various product ions derived after collisional activation of mono- and dihydroxy arachidonate metabolites was found to be more complex than the analysis of intact molecular ions and provided some insight into molecular mechanisms involved in product ion formation. The CCS observed for the molecular ion [M-H] - and certain product ions were consistent with a folded ion structure, the latter predicted by the proposed mechanisms of product ion formation. Unexpectedly, product ions from [M-H-H 2 O-CO 2 ] - and [M-H-H 2 O] - displayed complex ion mobility profiles suggesting multiple mechanisms of ion formation. The [M-H-H 2 O] - ion from LTB 4 was studied in more detail using both nitrogen and helium as the drift gas in the ion mobility cell. One population of [M-H-H 2 O] - product ions from LTB 4 was consistent with formation of covalent ring structures, while the ions displaying a higher CCS were consistent with a more open-chain structure. Using molecular dynamics and theoretical CCS calculations, energy minimized structures of those product ions with the open-chain structures were found to have a higher CCS than a folded molecular ion structure. The measurement of product ion mobility can be an additional and unique signature of eicosanoids measured by LC-MS/MS techniques. Graphical Abstract ᅟ.

  19. Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis.

    Directory of Open Access Journals (Sweden)

    Pablo Cordero

    2015-11-01

    Full Text Available Landscapes exhibiting multiple secondary structures arise in natural RNA molecules that modulate gene expression, protein synthesis, and viral infection [corrected]. We report herein that high-throughput chemical experiments can isolate an RNA's multiple alternative secondary structures as they are stabilized by systematic mutagenesis (mutate-and-map, M2 and that a computational algorithm, REEFFIT, enables unbiased reconstruction of these states' structures and populations. In an in silico benchmark on non-coding RNAs with complex landscapes, M2-REEFFIT recovers 95% of RNA helices present with at least 25% population while maintaining a low false discovery rate (10% and conservative error estimates. In experimental benchmarks, M2-REEFFIT recovers the structure landscapes of a 35-nt MedLoop hairpin, a 110-nt 16S rRNA four-way junction with an excited state, a 25-nt bistable hairpin, and a 112-nt three-state adenine riboswitch with its expression platform, molecules whose characterization previously required expert mutational analysis and specialized NMR or chemical mapping experiments. With this validation, M2-REEFFIT enabled tests of whether artificial RNA sequences might exhibit complex landscapes in the absence of explicit design. An artificial flavin mononucleotide riboswitch and a randomly generated RNA sequence are found to interconvert between three or more states, including structures for which there was no design, but that could be stabilized through mutations. These results highlight the likely pervasiveness of rich landscapes with multiple secondary structures in both natural and artificial RNAs and demonstrate an automated chemical/computational route for their empirical characterization.

  20. Tandem Mass Spectrometry and Ion Mobility Reveals Structural Insight into Eicosanoid Product Ion Formation

    Science.gov (United States)

    Di Giovanni, James P.; Barkley, Robert M.; Jones, David N. M.; Hankin, Joseph A.; Murphy, Robert C.

    2018-04-01

    Ion mobility measurements of product ions were used to characterize the collisional cross section (CCS) of various complex lipid [M-H]- ions using traveling wave ion mobility mass spectrometry (TWIMS). TWIMS analysis of various product ions derived after collisional activation of mono- and dihydroxy arachidonate metabolites was found to be more complex than the analysis of intact molecular ions and provided some insight into molecular mechanisms involved in product ion formation. The CCS observed for the molecular ion [M-H]- and certain product ions were consistent with a folded ion structure, the latter predicted by the proposed mechanisms of product ion formation. Unexpectedly, product ions from [M-H-H2O-CO2]- and [M-H-H2O]- displayed complex ion mobility profiles suggesting multiple mechanisms of ion formation. The [M-H-H2O]- ion from LTB4 was studied in more detail using both nitrogen and helium as the drift gas in the ion mobility cell. One population of [M-H-H2O]- product ions from LTB4 was consistent with formation of covalent ring structures, while the ions displaying a higher CCS were consistent with a more open-chain structure. Using molecular dynamics and theoretical CCS calculations, energy minimized structures of those product ions with the open-chain structures were found to have a higher CCS than a folded molecular ion structure. The measurement of product ion mobility can be an additional and unique signature of eicosanoids measured by LC-MS/MS techniques. [Figure not available: see fulltext.

  1. Conductivity anisotropy helps to reveal the microscopic structure of a density wave at imperfect nesting

    International Nuclear Information System (INIS)

    Grigoriev, P.D.; Kostenko, S.S.

    2015-01-01

    Superconductivity or metallic state may coexist with density wave ordering at imperfect nesting of the Fermi surface. In addition to the macroscopic spatial phase separation, there are, at least, two possible microscopic structures of such coexistence: (i) the soliton-wall phase and (ii) the ungapped Fermi-surface pockets. We show that the conductivity anisotropy allows us to distinguish these two microscopic density-wave structures. The results obtained may help to analyze the experimental observations in layered organic metals (TMTSF) 2 PF 6 , (TMTSF) 2 ClO 4 , α-(BEDT-TTF) 2 KHg(SCN) 4 and in other compounds

  2. Mitochondrial and nuclear sequence polymorphisms reveal geographic structuring in Amazonian populations of Echinococcus vogeli (Cestoda: Taeniidae).

    Science.gov (United States)

    Santos, Guilherme B; Soares, Manoel do C P; de F Brito, Elisabete M; Rodrigues, André L; Siqueira, Nilton G; Gomes-Gouvêa, Michele S; Alves, Max M; Carneiro, Liliane A; Malheiros, Andreza P; Póvoa, Marinete M; Zaha, Arnaldo; Haag, Karen L

    2012-12-01

    To date, nothing is known about the genetic diversity of the Echinococcus neotropical species, Echinococcus vogeli and Echinococcus oligarthrus. Here we used mitochondrial and nuclear DNA sequence polymorphisms to uncover the genetic structure, transmission and history of E. vogeli in the Brazilian Amazon, based on a sample of 38 isolates obtained from human and wild animal hosts. We confirm that the parasite is partially synanthropic and show that its populations are diverse. Furthermore, significant geographical structuring is found, with western and eastern populations being genetically divergent. Copyright © 2012 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

  3. Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance

    DEFF Research Database (Denmark)

    Martin, Michael David; Zimmer, Elizabeth A.; Olsen, Morten Tange

    2014-01-01

    Invasive plants provide ample opportunity to study evolutionary shifts that occur after introduction to novel environments. However, although genetic characters pre-dating introduction can be important determinants of later success, large-scale investigations of historical genetic structure have......'s spatial genetic structure mirrors both the palaeo-record of Ambrosia pollen deposition and the historical pattern of agricultural density across the landscape. Furthermore, for unknown reasons, this spatial genetic pattern has changed substantially in the intervening years. Following on previous work...

  4. Hydrogen-induced structural changes in polycrystalline silicon as revealed by positron lifetime spectroscopy

    International Nuclear Information System (INIS)

    Arole, V.M.; Takwale, M.G.; Bhide, V.G.

    1989-01-01

    Hydrogen passivation of polycrystalline silicon wafer is carried out in order to reduce the deleterious effects of grain boundaries. A systematic variation is made in the process parameters implemented during hydrogen passivation and the results of room temperature resistivity measurements are reported. As an efficient tool to study the structure change, positron lifetime spectroscopic measurements are performed on original and hydrogenated polycrystalline silicon wafers and a systematic correlation is sought between the changes that take place in the electrical and structural properties of polycrystalline silicon wafer, brought about by hydrogen passivation. (author)

  5. Conductivity anisotropy helps to reveal the microscopic structure of a density wave at imperfect nesting

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, P.D., E-mail: grigorev@itp.ac.ru [L.D. Landau Institute for Theoretical Physics, Chernogolovka 142432 (Russian Federation); Institut Laue-Langevin, Grenoble (France); Kostenko, S.S. [Institute of Problems of Chemical Physics, 142432 Chernogolovka (Russian Federation)

    2015-03-01

    Superconductivity or metallic state may coexist with density wave ordering at imperfect nesting of the Fermi surface. In addition to the macroscopic spatial phase separation, there are, at least, two possible microscopic structures of such coexistence: (i) the soliton-wall phase and (ii) the ungapped Fermi-surface pockets. We show that the conductivity anisotropy allows us to distinguish these two microscopic density-wave structures. The results obtained may help to analyze the experimental observations in layered organic metals (TMTSF){sub 2}PF{sub 6}, (TMTSF){sub 2}ClO{sub 4}, α-(BEDT-TTF){sub 2}KHg(SCN){sub 4} and in other compounds.

  6. Limited tryptic proteolysis of the benzodiazepine binding proteins in different species reveals structural homologies.

    Science.gov (United States)

    Friedl, W; Lentes, K U; Schmitz, E; Propping, P; Hebebrand, J

    1988-12-01

    Peptide mapping can be used to elucidate further the structural similarities of the benzodiazepine binding proteins in different vertebrate species. Crude synaptic membrane preparations were photoaffinity-labeled with [3H]flunitrazepam and subsequently degraded with various concentrations of trypsin. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis followed by fluorography allowed a comparison of the molecular weights of photolabeled peptides in different species. Tryptic degradation led to a common peptide of 40K in all species investigated, a finding indicating that the benzodiazepine binding proteins are structurally homologous in higher bony fishes and tetrapods.

  7. Kinematic structures of the solar neighbourhood revealed by Gaia DR1/TGAS and RAVE

    Science.gov (United States)

    Kushniruk, I.; Schirmer, T.; Bensby, T.

    2017-12-01

    Context. The velocity distribution of stars in the solar neighbourhood is inhomogeneous and rich with stellar streams and kinematic structures. These may retain important clues regarding the formation and dynamical history of the Milky Way. However, the nature and origin of many of the streams and structures is unclear, hindering our understanding of how the Milky Way formed and evolved. Aims: We aim to study the velocity distribution of stars of the solar neighbourhood and investigate the properties of individual kinematic structures in order to improve our understanding of their origins. Methods: Using the astrometric data provided by Gaia DR1/TGAS and radial velocities from RAVE DR5 we perform a wavelet analysis with the à trous algorithm of 55 831 stars that have U and V velocity uncertainties less than 4 km s-1. An auto-convolution histogram method is used to filter the output data, and we then run Monte Carlo simulations to verify that the detected structures are real and are not caused by noise due to velocity uncertainties. Additionally we analysed our stellar sample by splitting all stars into a nearby sample (300 pc), and two chemically defined samples that to a first degree represent the thin and the thick disks. Results: We detect 19 kinematic structures in the solar neighbourhood in the range of scales 3-16 km s-1 at the 3σ confidence level. Among them we identified well-known groups (such as Hercules, Sirius, Coma Berenices, Pleiades, and Wolf 630), confirmed recently detected groups (such as Antoja12 and Bobylev16), and detected a new structure at (U,V) ≈ (37,8) km s-1. Another three new groups are tentatively detected, but require further confirmation. Some of the detected groups show clear dependence on distance in the sense that they are only present in the nearby sample (<300 pc), and others appear to be correlated with chemistry as they are only present in one of the chemically defined thin and thick disk samples. Conclusions: With the much

  8. Natural and Semisynthetic Analogues of Manadoperoxide B Reveal New Structural Requirements for Trypanocidal Activity

    Science.gov (United States)

    Chianese, Giuseppina; Scala, Fernando; Calcinai, Barbara; Cerrano, Carlo; Dien, Henny A.; Kaiser, Marcel; Tasdemir, Deniz; Taglialatela-Scafati, Orazio

    2013-01-01

    Chemical analysis of the Indonesian sponge Plakortis cfr. lita afforded two new analogues of the potent trypanocidal agent manadoperoxide B (1), namely 12-isomanadoperoxide B (2) and manadoperoxidic acid B (3). These compounds were isolated along with a new short chain dicarboxylate monoester (4), bearing some interesting relationships with the polyketide endoperoxides found in this sponge. Some semi-synthetic analogues of manadoperoxide B (6–8) were prepared and evaluated for antitrypanosomal activity and cytotoxicity. These studies revealed crucial structure–activity relationships that should be taken into account in the design of optimized and simplified endoperoxyketal trypanocidal agents. PMID:23989650

  9. Natural and Semisynthetic Analogues of Manadoperoxide B Reveal New Structural Requirements for Trypanocidal Activity

    Directory of Open Access Journals (Sweden)

    Orazio Taglialatela-Scafati

    2013-08-01

    Full Text Available Chemical analysis of the Indonesian sponge Plakortis cfr. lita afforded two new analogues of the potent trypanocidal agent manadoperoxide B (1, namely 12-isomanadoperoxide B (2 and manadoperoxidic acid B (3. These compounds were isolated along with a new short chain dicarboxylate monoester (4, bearing some interesting relationships with the polyketide endoperoxides found in this sponge. Some semi-synthetic analogues of manadoperoxide B (6–8 were prepared and evaluated for antitrypanosomal activity and cytotoxicity. These studies revealed crucial structure–activity relationships that should be taken into account in the design of optimized and simplified endoperoxyketal trypanocidal agents.

  10. A proton wire and water channel revealed in the crystal structure of isatin hydrolase

    DEFF Research Database (Denmark)

    Bjerregaard-Andersen, Kaare; Sommer, Theis; Jensen, Jan Kristian

    2014-01-01

    to a novel family of metalloenzymes that include the bacterial kynurenine formamidase. The product state, mimicked by bound thioisatinate, reveals a water molecule that bridges the thioisatinate to a proton wire in an adjacent water channel and thus allows the proton released by the reaction to escape only...... when the product is formed. The functional proton wire present in IH-b represents a unique catalytic feature common to all hydrolases is here trapped and visualized for the first time. The local molecular environment required to coordinate thioisatinate allows stronger and more confident identification...

  11. Cryo-EM structure of human adenovirus D26 reveals the conservation of structural organization among human adenoviruses.

    Science.gov (United States)

    Yu, Xiaodi; Veesler, David; Campbell, Melody G; Barry, Mary E; Asturias, Francisco J; Barry, Michael A; Reddy, Vijay S

    2017-05-01

    Human adenoviruses (HAdVs) cause acute respiratory, ocular, and gastroenteric diseases and are also frequently used as gene and vaccine delivery vectors. Unlike the archetype human adenovirus C5 (HAdV-C5), human adenovirus D26 (HAdV-D26) belongs to species-D HAdVs, which target different cellular receptors, and is differentially recognized by immune surveillance mechanisms. HAdV-D26 is being championed as a lower seroprevalent vaccine and oncolytic vector in preclinical and human clinical studies. To understand the molecular basis for their distinct biological properties and independently validate the structures of minor proteins, we determined the first structure of species-D HAdV at 3.7 Å resolution by cryo-electron microscopy. All the hexon hypervariable regions (HVRs), including HVR1, have been identified and exhibit a distinct organization compared to those of HAdV-C5. Despite the differences in the arrangement of helices in the coiled-coil structures, protein IX molecules form a continuous hexagonal network on the capsid exterior. In addition to the structurally conserved region (3 to 300) of IIIa, we identified an extra helical domain comprising residues 314 to 390 that further stabilizes the vertex region. Multiple (two to three) copies of the cleaved amino-terminal fragment of protein VI (pVIn) are observed in each hexon cavity, suggesting that there could be ≥480 copies of VI present in HAdV-D26. In addition, a localized asymmetric reconstruction of the vertex region provides new details of the three-pronged "claw hold" of the trimeric fiber and its interactions with the penton base. These observations resolve the previous conflicting assignments of the minor proteins and suggest the likely conservation of their organization across different HAdVs.

  12. Survey of structures revealed in nucleon-nucleon scattering experiments and dibaryon resonances

    International Nuclear Information System (INIS)

    Hidaka, K.; Yokosawa, A.

    1979-01-01

    Structures appearing in various experimental data (particularly those with polarized beams) in nucleon-nucleon systems are reviewed. Evidence is presented for the existence of dibaryon resonances with an emphasis on a diproton resonance in 3 F 3 (J/sup P/ = 3 - ) state. 38 references

  13. Non-Linear Behaviour Of Gelatin Networks Reveals A Hierarchical Structure

    KAUST Repository

    Yang, Zhi; Hemar, Yacine; Hilliou, loic; Gilbert, Elliot P.; McGillivray, Duncan James; Williams, Martin A. K.; Chaieb, Saharoui

    2015-01-01

    We investigate the strain hardening behaviour of various gelatin networks - namely physically-crosslinked gelatin gel, chemically-crosslinked gelatin gels, and a hybrid gels made of a combination of the former two - under large shear deformations using the pre-stress, strain ramp, and large amplitude oscillation shear protocols. Further, the internal structures of physically-crosslinked gelatin gel and chemically-crosslinked gelatin gels were characterized by small angle neutron scattering (SANS) to enable their internal structures to be correlated with their nonlinear rheology. The Kratky plots of SANS data demonstrate the presence of small cross-linked aggregates within the chemically-crosslinked network, whereas in the physically-crosslinked gels a relatively homogeneous structure is observed. Through model fitting to the scattering data, we were able to obtain structural parameters, such as correlation length (ξ), cross-sectional polymer chain radius (Rc), and the fractal dimension (df) of the gel networks. The fractal dimension df obtained from the SANS data of the physically-crosslinked and chemically crosslinked gels is 1.31 and 1.53, respectively. These values are in excellent agreement with the ones obtained from a generalized non-linear elastic theory we used to fit our stress-strain curves. The chemical crosslinking that generates coils and aggregates hinders the free stretching of the triple helices bundles in the physically-crosslinked gels.

  14. Survey of large protein complexes D. vulgaris reveals great structural diversity

    Energy Technology Data Exchange (ETDEWEB)

    Han, B.-G.; Dong, M.; Liu, H.; Camp, L.; Geller, J.; Singer, M.; Hazen, T. C.; Choi, M.; Witkowska, H. E.; Ball, D. A.; Typke, D.; Downing, K. H.; Shatsky, M.; Brenner, S. E.; Chandonia, J.-M.; Biggin, M. D.; Glaeser, R. M.

    2009-08-15

    An unbiased survey has been made of the stable, most abundant multi-protein complexes in Desulfovibrio vulgaris Hildenborough (DvH) that are larger than Mr {approx} 400 k. The quaternary structures for 8 of the 16 complexes purified during this work were determined by single-particle reconstruction of negatively stained specimens, a success rate {approx}10 times greater than that of previous 'proteomic' screens. In addition, the subunit compositions and stoichiometries of the remaining complexes were determined by biochemical methods. Our data show that the structures of only two of these large complexes, out of the 13 in this set that have recognizable functions, can be modeled with confidence based on the structures of known homologs. These results indicate that there is significantly greater variability in the way that homologous prokaryotic macromolecular complexes are assembled than has generally been appreciated. As a consequence, we suggest that relying solely on previously determined quaternary structures for homologous proteins may not be sufficient to properly understand their role in another cell of interest.

  15. A genome wide survey of SNP variation reveals the genetic structure of sheep breeds.

    Directory of Open Access Journals (Sweden)

    James W Kijas

    Full Text Available The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identifying the first genome-wide set of SNP for sheep, we report on levels of genetic variability both within and between a diverse sample of ovine populations. Then, using cluster analysis and the partitioning of genetic variation, we demonstrate sheep are characterised by weak phylogeographic structure, overlapping genetic similarity and generally low differentiation which is consistent with their short evolutionary history. The degree of population substructure was, however, sufficient to cluster individuals based on geographic origin and known breed history. Specifically, African and Asian populations clustered separately from breeds of European origin sampled from Australia, New Zealand, Europe and North America. Furthermore, we demonstrate the presence of stratification within some, but not all, ovine breeds. The results emphasize that careful documentation of genetic structure will be an essential prerequisite when mapping the genetic basis of complex traits. Furthermore, the identification of a subset of SNP able to assign individuals into broad groupings demonstrates even a small panel of markers may be suitable for applications such as traceability.

  16. Genetic structure of Polytrichum formosum in relation to the breeding system as revealed by microsatellites

    NARCIS (Netherlands)

    Van der Velde, M; Van de Zande, L; Bijlsma, R

    Microsatellite variation was determined for three Danish and three Dutch populations of the haploid moss species Polytrichum formosum to gain insight into the relative importance of sexual vs. asexual reproduction for the amount and structure of genetic variation. In general, low levels of

  17. Ichthyoplankton assemblage structure of springs in the Yangtze Estuary revealed by biological and environmental visions.

    Science.gov (United States)

    Zhang, Hui; Xian, Weiwei; Liu, Shude

    2015-01-01

    The ichthyoplankton assemblage structure in the Yangtze Estuary was analyzed based on four springs in 1999, 2001, 2004 and 2007 in order to provide detailed characterizations of the ichthyoplankton assemblage in springs, examine the long-term dynamics of spring ichthyoplankton assemblages, and evaluate the influence of environmental factors on the spatial distribution and inter-annual variations of ichthyoplankton assemblages associated with the Yangtze Estuary. Forty-two ichthyoplankton species belonging to 23 families were collected. Engraulidae was the most abundant family, including six species and comprising 67.91% of the total catch. Only four species (Coilia mystus, Engraulis japonicus, Trachidermis fasciatus and Allanetta bleekeri) could be considered dominant, accounting for 88.70% of total abundance. The structure of the ichthyoplankton spring assemblage persisted on an annual basis, with the dominant species reappearing consistently even though their abundance fluctuated from year to year. This inter-annual variation probably reflects variable environmental conditions influenced by jellyfish blooms, declining river flow, and overfishing. Canonical correspondence analysis indicated aspatial structure of the ichthyoplankton assemblage in three areas: (1) an inner assemblage dominated by C. mystus; (2) a central assemblage dominated by A. bleekeri and T. fasciatus; and (3) a shelf assemblage featuring E. japonicus. The observed ichthyoplankton assemblage structure appears to be strongly influenced by depth, salinity and suspended particulate matter gradients.

  18. Non-Linear Behaviour Of Gelatin Networks Reveals A Hierarchical Structure

    KAUST Repository

    Yang, Zhi

    2015-12-14

    We investigate the strain hardening behaviour of various gelatin networks - namely physically-crosslinked gelatin gel, chemically-crosslinked gelatin gels, and a hybrid gels made of a combination of the former two - under large shear deformations using the pre-stress, strain ramp, and large amplitude oscillation shear protocols. Further, the internal structures of physically-crosslinked gelatin gel and chemically-crosslinked gelatin gels were characterized by small angle neutron scattering (SANS) to enable their internal structures to be correlated with their nonlinear rheology. The Kratky plots of SANS data demonstrate the presence of small cross-linked aggregates within the chemically-crosslinked network, whereas in the physically-crosslinked gels a relatively homogeneous structure is observed. Through model fitting to the scattering data, we were able to obtain structural parameters, such as correlation length (ξ), cross-sectional polymer chain radius (Rc), and the fractal dimension (df) of the gel networks. The fractal dimension df obtained from the SANS data of the physically-crosslinked and chemically crosslinked gels is 1.31 and 1.53, respectively. These values are in excellent agreement with the ones obtained from a generalized non-linear elastic theory we used to fit our stress-strain curves. The chemical crosslinking that generates coils and aggregates hinders the free stretching of the triple helices bundles in the physically-crosslinked gels.

  19. The Structure of a Conserved Domain of TamB Reveals a Hydrophobic β Taco Fold.

    Science.gov (United States)

    Josts, Inokentijs; Stubenrauch, Christopher James; Vadlamani, Grishma; Mosbahi, Khedidja; Walker, Daniel; Lithgow, Trevor; Grinter, Rhys

    2017-12-05

    The translocation and assembly module (TAM) plays a role in the transport and insertion of proteins into the bacterial outer membrane. TamB, a component of this system spans the periplasmic space to engage with its partner protein TamA. Despite efforts to characterize the TAM, the structure and mechanism of action of TamB remained enigmatic. Here we present the crystal structure of TamB amino acids 963-1,138. This region represents half of the conserved DUF490 domain, the defining feature of TamB. TamB 963-1138 consists of a concave, taco-shaped β sheet with a hydrophobic interior. This β taco structure is of dimensions capable of accommodating and shielding the hydrophobic side of an amphipathic β strand, potentially allowing TamB to chaperone nascent membrane proteins from the aqueous environment. In addition, sequence analysis suggests that the structure of TamB 963-1138 is shared by a large portion of TamB. This architecture could allow TamB to act as a conduit for membrane proteins. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  20. The structure of Lactococcus lactis thioredoxin reductase reveals molecular features of photo-oxidative damage

    DEFF Research Database (Denmark)

    Skjoldager, Nicklas; Bang, Maria Blanner; Rykær, Martin

    2017-01-01

    The NADPH-dependent homodimeric flavoenzyme thioredoxin reductase (TrxR) provides reducing equivalents to thioredoxin, a key regulator of various cellular redox processes. Crystal structures of photo-inactivated thioredoxin reductase (TrxR) from the Gram-positive bacterium Lactococcus lactis have...

  1. Complex structure of the fission yeast SREBP-SCAP binding domains reveals an oligomeric organization.

    Science.gov (United States)

    Gong, Xin; Qian, Hongwu; Shao, Wei; Li, Jingxian; Wu, Jianping; Liu, Jun-Jie; Li, Wenqi; Wang, Hong-Wei; Espenshade, Peter; Yan, Nieng

    2016-11-01

    Sterol regulatory element-binding protein (SREBP) transcription factors are master regulators of cellular lipid homeostasis in mammals and oxygen-responsive regulators of hypoxic adaptation in fungi. SREBP C-terminus binds to the WD40 domain of SREBP cleavage-activating protein (SCAP), which confers sterol regulation by controlling the ER-to-Golgi transport of the SREBP-SCAP complex and access to the activating proteases in the Golgi. Here, we biochemically and structurally show that the carboxyl terminal domains (CTD) of Sre1 and Scp1, the fission yeast SREBP and SCAP, form a functional 4:4 oligomer and Sre1-CTD forms a dimer of dimers. The crystal structure of Sre1-CTD at 3.5 Å and cryo-EM structure of the complex at 5.4 Å together with in vitro biochemical evidence elucidate three distinct regions in Sre1-CTD required for Scp1 binding, Sre1-CTD dimerization and tetrameric formation. Finally, these structurally identified domains are validated in a cellular context, demonstrating that the proper 4:4 oligomeric complex formation is required for Sre1 activation.

  2. The structure of a conserved piezo channel domain reveals a topologically distinct β sandwich fold.

    Science.gov (United States)

    Kamajaya, Aron; Kaiser, Jens T; Lee, Jonas; Reid, Michelle; Rees, Douglas C

    2014-10-07

    Piezo has recently been identified as a family of eukaryotic mechanosensitive channels composed of subunits containing over 2,000 amino acids, without recognizable sequence similarity to other channels. Here, we present the crystal structure of a large, conserved extramembrane domain located just before the last predicted transmembrane helix of C. elegans PIEZO, which adopts a topologically distinct β sandwich fold. The structure was also determined of a point mutation located on a conserved surface at the position equivalent to the human PIEZO1 mutation found in dehydrated hereditary stomatocytosis patients (M2225R). While the point mutation does not change the overall domain structure, it does alter the surface electrostatic potential that may perturb interactions with a yet-to-be-identified ligand or protein. The lack of structural similarity between this domain and any previously characterized fold, including those of eukaryotic and bacterial channels, highlights the distinctive nature of the Piezo family of eukaryotic mechanosensitive channels. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Structures of down syndrome kinases, DYRKs, reveal mechanisms of kinase activation and substrate recognition

    DEFF Research Database (Denmark)

    Soundararajan, M.; Roos, A.K.; Savitsky, P.

    2013-01-01

    Dual-specificity tyrosine-(Y)-phosphorylation-regulated kinases (DYRKs) play key roles in brain development, regulation of splicing, and apoptosis, and are potential drug targets for neurodegenerative diseases and cancer. We present crystal structures of one representative member of each DYRK sub...

  4. The structure and dynamics of chitin nanofibrils in an aqueous environment revealed by molecular dynamics simulations

    Czech Academy of Sciences Publication Activity Database

    Střelcová, Z.; Kulhánek, P.; Friák, Martin; Fabritius, H.; Petrov, M.; Neugebauer, J.; Koča, J.

    2016-01-01

    Roč. 6, č. 36 (2016), s. 30710-30721 ISSN 2046-2069 Institutional support: RVO:68081723 Keywords : FREE-ENERGY CALCULATIONS * PARTICLE MESH EWALD * ALPHA-CHITIN * CRYSTAL-STRUCTURE * INSECT CHITIN * SURFACE-AREA * AB-INITIO Subject RIV: BO - Biophysics Impact factor: 3.108, year: 2016

  5. A high-quality human reference panel reveals the complexity and distribution of genomic structural variants

    NARCIS (Netherlands)

    Hehir-Kwa, J.Y.; Marschall, T.; Kloosterman, W.P.; Francioli, L.C.; Baaijens, J.A.; Dijkstra, L.J.; Abdellaoui, A.; Koval, V.; Thung, D.T.; Wardenaar, R.; Renkens, I.; Coe, B.P.; Deelen, P.; de Ligt, J.; Lameijer, E.W.; Dijk, F.; Hormozdiari, F.; Uitterlinden, A.G.; van Duijn, C.M.; Eichler, E.E.; Bakker, P.I.W.; Swertz, M.A.; Wijmenga, C.; van Ommen, G.J.B; Slagboom, P.E.; Boomsma, D.I.; Schönhuth, A.; Ye, K.; Guryev, V.

    2016-01-01

    Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority of studies provide neither a global view of the full spectrum of these variants nor integrate them into reference panels of genetic

  6. Community structure of arbuscular mycorrhizal fungi in undisturbed vegetation revealed by analyses of LSU rdna sequences

    DEFF Research Database (Denmark)

    Rosendahl, Søren; Holtgrewe-Stukenbrock, Eva

    2004-01-01

    Arbuscular mycorrhizal fungi (AMF) form a mutualistic symbiosis with plant roots and are found in most ecosystems. In this study the community structure of AMF in a clade of the genus Glomus was examined in undisturbed costal grassland using LSU rDNA sequences amplified from roots of Hieracium...

  7. Nuclear Species-Diagnostic SNP Markers Mined from 454 Amplicon Sequencing Reveal Admixture Genomic Structure of Modern Citrus Varieties

    Science.gov (United States)

    Curk, Franck; Ancillo, Gema; Ollitrault, Frédérique; Perrier, Xavier; Jacquemoud-Collet, Jean-Pierre; Garcia-Lor, Andres; Navarro, Luis; Ollitrault, Patrick

    2015-01-01

    Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species-diagnostic SNP

  8. Revealing Hidden Structural Order Controlling Both Fast and Slow Glassy Dynamics in Supercooled Liquids

    Directory of Open Access Journals (Sweden)

    Hua Tong

    2018-03-01

    Full Text Available The dynamics of a supercooled liquid near the glass transition is characterized by two-step relaxation, fast β and slow α relaxations. Because of the apparently disordered nature of glassy structures, there have been long debates over whether the origin of drastic slowing-down of the α relaxation accompanied by heterogeneous dynamics is thermodynamic or dynamic. Furthermore, it has been elusive whether there is any deep connection between fast β and slow α modes. To settle these issues, here we introduce a set of new structural order parameters characterizing sterically favored structures with high local packing capability, and then access structure-dynamics correlation by a novel nonlocal approach. We find that the particle mobility is under control of the static order parameter field. The fast β process is controlled by the instantaneous order parameter field locally, resulting in short-time particle-scale dynamics. Then the mobility field progressively develops with time t, following the initial order parameter field from disorder to more ordered regions. As is well known, the heterogeneity in the mobility field (dynamic heterogeneity is maximized with a characteristic length ξ_{4}, when t reaches the relaxation time τ_{α}. We discover that this mobility pattern can be predicted solely by a spatial coarse graining of the initial order parameter field at t=0 over a length ξ without any dynamical information. Furthermore, we find a relation ξ∼ξ_{4}, indicating that the static length ξ grows coherently with the dynamic one ξ_{4} upon cooling. This further suggests an intrinsic link between τ_{α} and ξ: the growth of the static length ξ is the origin of dynamical slowing-down. These we confirm for the first time in binary glass formers both in two and three spatial dimensions. Thus, a static structure has two intrinsic characteristic lengths, particle size and ξ, which control dynamics in local and nonlocal manners, resulting

  9. Revealing Hidden Structural Order Controlling Both Fast and Slow Glassy Dynamics in Supercooled Liquids

    Science.gov (United States)

    Tong, Hua; Tanaka, Hajime

    2018-01-01

    The dynamics of a supercooled liquid near the glass transition is characterized by two-step relaxation, fast β and slow α relaxations. Because of the apparently disordered nature of glassy structures, there have been long debates over whether the origin of drastic slowing-down of the α relaxation accompanied by heterogeneous dynamics is thermodynamic or dynamic. Furthermore, it has been elusive whether there is any deep connection between fast β and slow α modes. To settle these issues, here we introduce a set of new structural order parameters characterizing sterically favored structures with high local packing capability, and then access structure-dynamics correlation by a novel nonlocal approach. We find that the particle mobility is under control of the static order parameter field. The fast β process is controlled by the instantaneous order parameter field locally, resulting in short-time particle-scale dynamics. Then the mobility field progressively develops with time t , following the initial order parameter field from disorder to more ordered regions. As is well known, the heterogeneity in the mobility field (dynamic heterogeneity) is maximized with a characteristic length ξ4, when t reaches the relaxation time τα. We discover that this mobility pattern can be predicted solely by a spatial coarse graining of the initial order parameter field at t =0 over a length ξ without any dynamical information. Furthermore, we find a relation ξ ˜ξ4, indicating that the static length ξ grows coherently with the dynamic one ξ4 upon cooling. This further suggests an intrinsic link between τα and ξ : the growth of the static length ξ is the origin of dynamical slowing-down. These we confirm for the first time in binary glass formers both in two and three spatial dimensions. Thus, a static structure has two intrinsic characteristic lengths, particle size and ξ , which control dynamics in local and nonlocal manners, resulting in the emergence of the two

  10. Structure-function analysis of Staphylococcus aureus amidase reveals the determinants of peptidoglycan recognition and cleavage.

    Science.gov (United States)

    Büttner, Felix Michael; Zoll, Sebastian; Nega, Mulugeta; Götz, Friedrich; Stehle, Thilo

    2014-04-18

    The bifunctional major autolysin AtlA of Staphylococcus aureus cleaves the bacterium's peptidoglycan network (PGN) at two distinct sites during cell division. Deletion of the enzyme results in large cell clusters with disordered division patterns, indicating that AtlA could be a promising target for the development of new antibiotics. One of the two functions of AtlA is performed by the N-acetylmuramyl-l-alanine amidase AmiA, which cleaves the bond between the carbohydrate and the peptide moieties of PGN. To establish the structural requirements of PGN recognition and the enzymatic mechanism of cleavage, we solved the crystal structure of the catalytic domain of AmiA (AmiA-cat) in complex with a peptidoglycan-derived ligand at 1.55 Å resolution. The peptide stem is clearly visible in the structure, forming extensive contacts with protein residues by docking into an elongated groove. Less well defined electron density and the analysis of surface features indicate likely positions of the carbohydrate backbone and the pentaglycine bridge. Substrate specificity analysis supports the importance of the pentaglycine bridge for fitting into the binding cleft of AmiA-cat. PGN of S. aureus with l-lysine tethered with d-alanine via a pentaglycine bridge is completely hydrolyzed, whereas PGN of Bacillus subtilis with meso-diaminopimelic acid directly tethered with d-alanine is not hydrolyzed. An active site mutant, H370A, of AmiA-cat was completely inactive, providing further support for the proposed catalytic mechanism of AmiA. The structure reported here is not only the first of any bacterial amidase in which both the PGN component and the water molecule that carries out the nucleophilic attack on the carbonyl carbon of the scissile bond are present; it is also the first peptidoglycan amidase complex structure of an important human pathogen.

  11. Structure-Function Analysis of Staphylococcus aureus Amidase Reveals the Determinants of Peptidoglycan Recognition and Cleavage*

    Science.gov (United States)

    Büttner, Felix Michael; Zoll, Sebastian; Nega, Mulugeta; Götz, Friedrich; Stehle, Thilo

    2014-01-01

    The bifunctional major autolysin AtlA of Staphylococcus aureus cleaves the bacterium's peptidoglycan network (PGN) at two distinct sites during cell division. Deletion of the enzyme results in large cell clusters with disordered division patterns, indicating that AtlA could be a promising target for the development of new antibiotics. One of the two functions of AtlA is performed by the N-acetylmuramyl-l-alanine amidase AmiA, which cleaves the bond between the carbohydrate and the peptide moieties of PGN. To establish the structural requirements of PGN recognition and the enzymatic mechanism of cleavage, we solved the crystal structure of the catalytic domain of AmiA (AmiA-cat) in complex with a peptidoglycan-derived ligand at 1.55 Å resolution. The peptide stem is clearly visible in the structure, forming extensive contacts with protein residues by docking into an elongated groove. Less well defined electron density and the analysis of surface features indicate likely positions of the carbohydrate backbone and the pentaglycine bridge. Substrate specificity analysis supports the importance of the pentaglycine bridge for fitting into the binding cleft of AmiA-cat. PGN of S. aureus with l-lysine tethered with d-alanine via a pentaglycine bridge is completely hydrolyzed, whereas PGN of Bacillus subtilis with meso-diaminopimelic acid directly tethered with d-alanine is not hydrolyzed. An active site mutant, H370A, of AmiA-cat was completely inactive, providing further support for the proposed catalytic mechanism of AmiA. The structure reported here is not only the first of any bacterial amidase in which both the PGN component and the water molecule that carries out the nucleophilic attack on the carbonyl carbon of the scissile bond are present; it is also the first peptidoglycan amidase complex structure of an important human pathogen. PMID:24599952

  12. Coupled cryoconite ecosystem structure-function relationships are revealed by comparing bacterial communities in alpine and Arctic glaciers

    DEFF Research Database (Denmark)

    Edwards, Arwyn; Mur, Luis A. J.; Girdwood, Susan E.

    2014-01-01

    Cryoconite holes are known as foci of microbial diversity and activity on polar glacier surfaces, but are virtually unexplored microbial habitats in alpine regions. In addition, whether cryoconite community structure reflects ecosystem functionality is poorly understood. Terminal restriction...... revealed Proteobacteria were particularly abundant, with Cyanobacteria likely acting as ecosystem engineers in both alpine and Arctic cryoconite communities. However, despite these generalities, significant differences in bacterial community structures, compositions and metabolomes are found between alpine...... fragment length polymorphism and Fourier transform infrared metabolite fingerprinting of cryoconite from glaciers in Austria, Greenland and Svalbard demonstrated cryoconite bacterial communities are closely correlated with cognate metabolite fingerprints. The influence of bacterial-associated fatty acids...

  13. Structural Analysis of Silicic Lavas Reveals the Importance of Endogenous Flow During Emplacement

    Science.gov (United States)

    Andrews, G. D.; Martens, A.; Isom, S.; Maxwell, A.; Brown, S. R.

    2017-12-01

    Recent observations of silicic lava flows in Chile strongly suggest sustained, endogeneous flow beneath an insulating carapace, where the flow advances through breakouts at the flow margin. New mapping of vertical exposures around the margin of Obsidian Dome, California, has identified discreet lobe structures in cross-section, suggesting that flow-front breakouts occured there during emplacement. The flow lobes are identified through structural measurements of flow-banding orientation and the stretching directions of vesicles. Newly acquired lidar of the Inyo Domes, including Obsidian Dome, is being analyzed to better understand the patterns of folding on the upper surface of the lavas, and to test for fold vergence patterns that may distinguish between endogenous and exogenous flow.

  14. Population structure of Aggarwals of north India as revealed by molecular markers.

    Science.gov (United States)

    Gupta, Vipin; Khadgawat, Rajesh; Ng, Hon Keung Tony; Kumar, Satish; Rao, Vadlamudi Raghavendra; Sachdeva, Mohinder Pal

    2010-12-01

    Using molecular genetic data on Aggarwals (Vaish/Vysya), an endogamous population group of north India, we provide evidence of its homogeneous unstratified population structure. We found the mean average heterozygosity value of 0.33 for 14 single nucleotide polymorphisms belonging to four genes (TCF7L2-, HHEX-, KCNJ11-, and ADIPOQ-) in the Aggarwal population (sample of 184 individuals) and tried to evaluate the genomic efficiency of endogamy in this population with the help of clan-based stratified analysis. We concluded that the sociocultural identity of the endogamous population groups could act as a robust proxy maker for inferring their homogeneity and population structure in India, which is ideal also for population selection for future genome-wide association studies in the country.

  15. 3D structure of eukaryotic flagella in a quiescent state revealed by cryo-electron tomography

    Science.gov (United States)

    Nicastro, Daniela; McIntosh, J. Richard; Baumeister, Wolfgang

    2005-01-01

    We have used cryo-electron tomography to investigate the 3D structure and macromolecular organization of intact, frozen-hydrated sea urchin sperm flagella in a quiescent state. The tomographic reconstructions provide information at a resolution better than 6 nm about the in situ arrangements of macromolecules that are key for flagellar motility. We have visualized the heptameric rings of the motor domains in the outer dynein arm complex and determined that they lie parallel to the plane that contains the axes of neighboring flagellar microtubules. Both the material associated with the central pair of microtubules and the radial spokes display a plane of symmetry that helps to explain the planar beat pattern of these flagella. Cryo-electron tomography has proven to be a powerful technique for helping us understand the relationships between flagellar structure and function and the design of macromolecular machines in situ. PMID:16246999

  16. Elements of the Chicxulub Impact Structure as Revealed in SRTM and Surface GPS Topographic Data

    Science.gov (United States)

    Kinsland, Gary L.; Sanchez, Gary; Kobrick, Michael; Cardador, Manuel Hurtado

    2003-01-01

    Pope et al. [1] utilized the elevations from the Petroleos Mexicanos (PEMEX) gravity data files to show that the main component of the surface expression of the Chicxulub Impact Structure is a roughly semi-circular, lowrelief depression about 90 km in diameter. They also identified other topographic features and the elements of the buried impact, which possibly led to the development of these features. These are summarized in Table 1. Kinsland et al. [2] presented a connection between these topographic anomalies, small gravity anomalies and buried structure of the impact. Very recently we have acquired digital topography data from NASA s Shuttle Radar Topography Mission (SRTM). Our subset covers 6 square degrees from 20deg N 91degW to 22deg N 88degW (corner to corner) with a pixel size of about 90m. This area includes all of the identified portion of the crater on land.

  17. Crystal Structure of Ripk4 Reveals Dimerization-Dependent Kinase Activity.

    Science.gov (United States)

    Huang, Christine S; Oberbeck, Nina; Hsiao, Yi-Chun; Liu, Peter; Johnson, Adam R; Dixit, Vishva M; Hymowitz, Sarah G

    2018-05-01

    Receptor-interacting protein kinase 4 (RIPK4) is a highly conserved regulator of epidermal differentiation. Members of the RIPK family possess a common kinase domain as well as unique accessory domains that likely dictate subcellular localization and substrate preferences. Mutations in human RIPK4 manifest as Bartsocas-Papas syndrome (BPS), a genetic disorder characterized by severe craniofacial and limb abnormalities. We describe the structure of the murine Ripk4 (MmRipk4) kinase domain, in ATP- and inhibitor-bound forms. The crystallographic dimer of MmRipk4 is similar to those of RIPK2 and BRAF, and we show that the intact dimeric entity is required for MmRipk4 catalytic activity through a series of engineered mutations and cell-based assays. We also assess the impact of BPS mutations on protein structure and activity to elucidate the molecular origins of the disease. Copyright © 2018 Elsevier Ltd. All rights reserved.

  18. Agarose gel shift assay reveals that calreticulin favors substrates with a quaternary structure in solution

    DEFF Research Database (Denmark)

    Boelt, Sanne Grundvad; Houen, Gunnar; Højrup, Peter

    2015-01-01

    Here we present an agarose gel shift assay that, in contrast to other electrophoresis approaches, is loaded in the center of the gel. This allows proteins to migrate in either direction according to their isoelectric points. Therefore, the presented assay enables a direct visualization, separation...... structure. It is also demonstrated that the agarose gel shift assay is useful in the study of other protein interactions and can be used as an alternative method to native polyacrylamide gel electrophoresis....... measure of interactions. Therefore, no interaction studies between calreticulin and substrates in solution have been investigated previously. The results presented here indicate that calreticulin has a preference for substrates with a quaternary structure and primarily β-sheets in their secondary...

  19. Diverse Brain Myeloid Expression Profiles Reveal Distinct Microglial Activation States and Aspects of Alzheimer’s Disease Not Evident in Mouse Models

    Directory of Open Access Journals (Sweden)

    Brad A. Friedman

    2018-01-01

    Full Text Available Microglia, the CNS-resident immune cells, play important roles in disease, but the spectrum of their possible activation states is not well understood. We derived co-regulated gene modules from transcriptional profiles of CNS myeloid cells of diverse mouse models, including new tauopathy model datasets. Using these modules to interpret single-cell data from an Alzheimer’s disease (AD model, we identified microglial subsets—distinct from previously reported “disease-associated microglia”—expressing interferon-related or proliferation modules. We then analyzed whole-tissue RNA profiles from human neurodegenerative diseases, including a new AD dataset. Correcting for altered cellular composition of AD tissue, we observed elevated expression of the neurodegeneration-related modules, but also modules not implicated using expression profiles from mouse models alone. We provide a searchable, interactive database for exploring gene expression in all these datasets (http://research-pub.gene.com/BrainMyeloidLandscape. Understanding the dimensions of CNS myeloid cell activation in human disease may reveal opportunities for therapeutic intervention.

  20. Factor analysis of regional brain activation in bipolar and healthy individuals reveals a consistent modular structure.

    Science.gov (United States)

    Fleck, David E; Welge, Jeffrey A; Eliassen, James C; Adler, Caleb M; DelBello, Melissa P; Strakowski, Stephen M

    2018-07-01

    The neurophysiological substrates of cognition and emotion, as seen with fMRI, are generally explained using modular structures. The present study was designed to probe the modular structure of cognitive-emotional processing in bipolar and healthy individuals using factor analysis and compare the results with current conceptions of the neurophysiology of bipolar disorder. Exploratory factor analysis was used to assess patterns of covariation among brain regions-of-interest activated during the Continuous Performance Task with Emotional and Neutral Distractors in healthy and bipolar individuals without a priori constraints on the number or composition of latent factors. Results indicated a common cognitive-emotional network consisting of prefrontal, medial temporal, limbic, parietal, anterior cingulate and posterior cingulate modules. However, reduced brain activation to emotional stimuli in the frontal, medial temporal and limbic modules was apparent in the bipolar relative to the healthy group, potentially accounting for emotional dysregulation in bipolar disorder. This study is limited by a relatively small sample size recruited at a single site. The results have yet to be validated on a larger independent sample. Although the modular structure of cognitive-emotional processing is similar in bipolar and healthy individuals, activation in response to emotional/neutral cues varies. These findings are not only consistent with recent conceptions of mood regulation in bipolar disorder, but also suggest that regional activation can be considered within tighter modular structures without compromising data interpretation. This demonstration may serve as a template for data reduction in future region-of-interest analyses to increase statistical power. Copyright © 2018 Elsevier B.V. All rights reserved.

  1. A personal view of nucleon structure as revealed by electron scattering

    International Nuclear Information System (INIS)

    Hofstadter, R.

    1989-01-01

    In this article the author charts his scientific career from graduation in 1935. His work on the No I (T1) scintillator detector developed a widely used tool for particle physicists. He later used these detectors in experiments to study nucleon structure via inelastic electron scattering, working mainly with deuterium, alpha particles and beryllium. Proton and neutron ''size'' were early successes of the fifties, with nucleon form factors following after several years' more work. (UK)

  2. Chromatin organization at the nuclear periphery as revealed by image analysis of structured illumination microscopy data

    Czech Academy of Sciences Publication Activity Database

    Fišerová, Jindřiška; Efenberková, Michaela; Sieger, T.; Maninová, Miloslava; Uhlířová, Jana; Hozák, Pavel

    2017-01-01

    Roč. 130, č. 12 (2017), s. 2066-2077 ISSN 0021-9533 R&D Projects: GA ČR GJ15-08835Y; GA MŠk(CZ) LM2015062 Institutional support: RVO:68378050 Keywords : Structured illumination * Image analysis * Chromation * Nucleus * Histone modification * Nuclear pore complexes Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Cell biology Impact factor: 4.431, year: 2016

  3. Lithosphere structure in Madagascar as revealed from receiver functions and surface waves analysis.

    Science.gov (United States)

    Rindraharisaona, E. J.; Tilmann, F. J.; Yuan, X.; Dreiling, J.; Priestley, K. F.; Barruol, G.; Wysession, M. E.

    2017-12-01

    The geological history of Madagascar makes it an ideal place to study the lithospheric structure and its evolution. It comprises Archean to Proterozoic units on the central eastern part, which is surrounded by a Triassic to Jurassic basin formation in the west and Cretaceous volcanics along the coasts. Quaternary volcanic rocks have been embedded in crystalline and sedimentary rocks. The aim of the present work is to characterize the crustal structure and determine the imprint of the dominant geodynamic events that have affected Madagascar: the Pan-African orogeny, the breakup of Gondwanaland and Neogene tectonic activity. From 2011 to 2014 different temporary seismic arrays were deployed in Madagascar. We based the current study mostly on SELASOMA project, which is composed of 50 seismic stations that were installed traversing southern Madagascar from the west to the east, sampling the different geological units. To measured seismic dispersion curves, one a wide period ranges using ambient noise, Rayleigh and Love surface waves. To compute the average crustal Vp/Vs ratio internal crustal structure and discontinuities in the mantle, we use both P- and S-waves receiver functions. To better resolve of the crustal structure, we jointly inverted P-wave receiver functions and Rayleigh wave group velocity.The crustal extension during the Carboniferous to Cenozoic has thinned the igneous crust down to 15 km in the western Morondava basin by removing much of the lower crust, while the thickness of the upper crust is nearly identical in the sedimentary basin and under Proterozoic and Archaean rocks of the eastern two thirds of Southern Madagascar. In general, the Archean crust is thicker than the Proterozoic, because mafic component is missing in the Proterozoic domain while it forms the bottom of the Archean crust. The lithosphere thickness in the southern part of Madagascar is estimated to be between 90 and 125 km.

  4. Crystal structure of an orthomyxovirus matrix protein reveals mechanisms for self-polymerization and membrane association.

    Science.gov (United States)

    Zhang, Wenting; Zheng, Wenjie; Toh, Yukimatsu; Betancourt-Solis, Miguel A; Tu, Jiagang; Fan, Yanlin; Vakharia, Vikram N; Liu, Jun; McNew, James A; Jin, Meilin; Tao, Yizhi J

    2017-08-08

    Many enveloped viruses encode a matrix protein. In the influenza A virus, the matrix protein M1 polymerizes into a rigid protein layer underneath the viral envelope to help enforce the shape and structural integrity of intact viruses. The influenza virus M1 is also known to mediate virus budding as well as the nuclear export of the viral nucleocapsids and their subsequent packaging into nascent viral particles. Despite extensive studies on the influenza A virus M1 (FLUA-M1), only crystal structures of its N-terminal domain are available. Here we report the crystal structure of the full-length M1 from another orthomyxovirus that infects fish, the infectious salmon anemia virus (ISAV). The structure of ISAV-M1 assumes the shape of an elbow, with its N domain closely resembling that of the FLUA-M1. The C domain, which is connected to the N domain through a flexible linker, is made of four α-helices packed as a tight bundle. In the crystal, ISAV-M1 monomers form infinite 2D arrays with a network of interactions involving both the N and C domains. Results from liposome flotation assays indicated that ISAV-M1 binds membrane via electrostatic interactions that are primarily mediated by a positively charged surface loop from the N domain. Cryoelectron tomography reconstruction of intact ISA virions identified a matrix protein layer adjacent to the inner leaflet of the viral membrane. The physical dimensions of the virion-associated matrix layer are consistent with the 2D ISAV-M1 crystal lattice, suggesting that the crystal lattice is a valid model for studying M1-M1, M1-membrane, and M1-RNP interactions in the virion.

  5. Unique C. elegans telomeric overhang structures reveal the evolutionarily conserved properties of telomeric DNA

    Czech Academy of Sciences Publication Activity Database

    Školáková, Petra; Foldynová-Trantírková, Silvie; Bednářová, Klára; Fiala, R.; Vorlíčková, Michaela; Trantírek, L.

    2015-01-01

    Roč. 43, č. 9 (2015), s. 4733-4745 ISSN 0305-1048 R&D Projects: GA ČR(CZ) GA13-28310S; GA ČR(CZ) GAP205/12/0466 Institutional support: RVO:68081707 ; RVO:60077344 Keywords : NUCLEASE HYPERSENSITIVE ELEMENT * G-QUADRUPLEX STRUCTURES * I-MOTIF Subject RIV: BO - Biophysics Impact factor: 9.202, year: 2015

  6. Structural-Functional Analysis Reveals a Specific Domain Organization in Family GH20 Hexosaminidases.

    Science.gov (United States)

    Val-Cid, Cristina; Biarnés, Xevi; Faijes, Magda; Planas, Antoni

    2015-01-01

    Hexosaminidases are involved in important biological processes catalyzing the hydrolysis of N-acetyl-hexosaminyl residues in glycosaminoglycans and glycoconjugates. The GH20 enzymes present diverse domain organizations for which we propose two minimal model architectures: Model A containing at least a non-catalytic GH20b domain and the catalytic one (GH20) always accompanied with an extra α-helix (GH20b-GH20-α), and Model B with only the catalytic GH20 domain. The large Bifidobacterium bifidum lacto-N-biosidase was used as a model protein to evaluate the minimal functional unit due to its interest and structural complexity. By expressing different truncated forms of this enzyme, we show that Model A architectures cannot be reduced to Model B. In particular, there are two structural requirements general to GH20 enzymes with Model A architecture. First, the non-catalytic domain GH20b at the N-terminus of the catalytic GH20 domain is required for expression and seems to stabilize it. Second, the substrate-binding cavity at the GH20 domain always involves a remote element provided by a long loop from the catalytic domain itself or, when this loop is short, by an element from another domain of the multidomain structure or from the dimeric partner. Particularly, the lacto-N-biosidase requires GH20b and the lectin-like domain at the N- and C-termini of the catalytic GH20 domain to be fully soluble and functional. The lectin domain provides this remote element to the active site. We demonstrate restoration of activity of the inactive GH20b-GH20-α construct (model A architecture) by a complementation assay with the lectin-like domain. The engineering of minimal functional units of multidomain GH20 enzymes must consider these structural requirements.

  7. The Crystal Structure of Streptococcus pyogenes Uridine Phosphorylase Reveals a Distinct Subfamily of Nucleoside Phosphorylases

    Energy Technology Data Exchange (ETDEWEB)

    Tran, Timothy H.; Christoffersen, S.; Allan, Paula W.; Parker, William B.; Piskur, Jure; Serra, I.; Terreni, M.; Ealick, Steven E. (Cornell); (Pavia); (Lund); (Southern Research)

    2011-09-20

    Uridine phosphorylase (UP), a key enzyme in the pyrimidine salvage pathway, catalyzes the reversible phosphorolysis of uridine or 2'-deoxyuridine to uracil and ribose 1-phosphate or 2'-deoxyribose 1-phosphate. This enzyme belongs to the nucleoside phosphorylase I superfamily whose members show diverse specificity for nucleoside substrates. Phylogenetic analysis shows Streptococcus pyogenes uridine phosphorylase (SpUP) is found in a distinct branch of the pyrimidine subfamily of nucleoside phosphorylases. To further characterize SpUP, we determined the crystal structure in complex with the products, ribose 1-phosphate and uracil, at 1.8 {angstrom} resolution. Like Escherichia coli UP (EcUP), the biological unit of SpUP is a hexamer with an ?/? monomeric fold. A novel feature of the active site is the presence of His169, which structurally aligns with Arg168 of the EcUP structure. A second active site residue, Lys162, is not present in previously determined UP structures and interacts with O2 of uracil. Biochemical studies of wild-type SpUP showed that its substrate specificity is similar to that of EcUP, while EcUP is {approx}7-fold more efficient than SpUP. Biochemical studies of SpUP mutants showed that mutations of His169 reduced activity, while mutation of Lys162 abolished all activity, suggesting that the negative charge in the transition state resides mostly on uracil O2. This is in contrast to EcUP for which transition state stabilization occurs mostly at O4.

  8. Substrate binding and specificity of rhomboid intramembrane protease revealed by substrate-peptide complex structures

    Czech Academy of Sciences Publication Activity Database

    Zoll, Sebastian; Stanchev, Stancho; Began, Jakub; Škerle, Jan; Lepšík, Martin; Peclinovská, Lucie; Majer, Pavel; Stříšovský, Kvido

    2014-01-01

    Roč. 33, č. 20 (2014), s. 2408-2421 ISSN 0261-4189 R&D Projects: GA ČR GAP305/11/1886; GA MŠk(CZ) LK11206; GA MŠk LO1302; GA ČR GBP208/12/G016 Institutional support: RVO:61388963 Keywords : intramembrane protease * rhomboid family * rhomboid protease * structure * substrate recognition Subject RIV: CE - Biochemistry Impact factor: 10.434, year: 2014

  9. High-Pressure-Driven Reversible Dissociation of α-Synuclein Fibrils Reveals Structural Hierarchy.

    Science.gov (United States)

    Piccirilli, Federica; Plotegher, Nicoletta; Ortore, Maria Grazia; Tessari, Isabella; Brucale, Marco; Spinozzi, Francesco; Beltramini, Mariano; Mariani, Paolo; Militello, Valeria; Lupi, Stefano; Perucchi, Andrea; Bubacco, Luigi

    2017-10-17

    The analysis of the α-synuclein (aS) aggregation process, which is involved in Parkinson's disease etiopathogenesis, and of the structural feature of the resulting amyloid fibrils may shed light on the relationship between the structure of aS aggregates and their toxicity. This may be considered a paradigm of the ground work needed to tackle the molecular basis of all the protein-aggregation-related diseases. With this aim, we used chemical and physical dissociation methods to explore the structural organization of wild-type aS fibrils. High pressure (in the kbar range) and alkaline pH were used to disassemble fibrils to collect information on the hierarchic pathway by which distinct β-sheets sequentially unfold using the unique possibility offered by high-pressure Fourier transform infrared spectroscopy. The results point toward the formation of kinetic traps in the energy landscape of aS fibril disassembly and the presence of transient partially folded species during the process. Since we found that the dissociation of wild-type aS fibrils by high pressure is reversible upon pressure release, the disassembled molecules likely retain structural information that favors fibril reformation. To deconstruct the role of the different regions of aS sequence in this process, we measured the high-pressure dissociation of amyloids formed by covalent chimeric dimers of aS (syn-syn) and by the aS deletion mutant that lacks the C-terminus, i.e., aS (1-99). The results allowed us to single out the role of dimerization and that of the C-terminus in the complete maturation of fibrillar aS. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  10. Assembly of Collagen Matrices as a Phase Transition Revealed by Structural and Rheologic Studies

    OpenAIRE

    Forgacs, Gabor; Newman, Stuart A.; Hinner, Bernhard; Maier, Christian W.; Sackmann, Erich

    2003-01-01

    We have studied the structural and viscoelastic properties of assembling networks of the extracellular matrix protein type-I collagen by means of phase contrast microscopy and rotating disk rheometry. The initial stage of the assembly is a nucleation process of collagen monomers associating to randomly distributed branched clusters with extensions of several microns. Eventually a sol-gel transition takes place, which is due to the interconnection of these clusters. We analyzed this transition...

  11. Traveling salesman problems with PageRank Distance on complex networks reveal community structure

    Science.gov (United States)

    Jiang, Zhongzhou; Liu, Jing; Wang, Shuai

    2016-12-01

    In this paper, we propose a new algorithm for community detection problems (CDPs) based on traveling salesman problems (TSPs), labeled as TSP-CDA. Since TSPs need to find a tour with minimum cost, cities close to each other are usually clustered in the tour. This inspired us to model CDPs as TSPs by taking each vertex as a city. Then, in the final tour, the vertices in the same community tend to cluster together, and the community structure can be obtained by cutting the tour into a couple of paths. There are two challenges. The first is to define a suitable distance between each pair of vertices which can reflect the probability that they belong to the same community. The second is to design a suitable strategy to cut the final tour into paths which can form communities. In TSP-CDA, we deal with these two challenges by defining a PageRank Distance and an automatic threshold-based cutting strategy. The PageRank Distance is designed with the intrinsic properties of CDPs in mind, and can be calculated efficiently. In the experiments, benchmark networks with 1000-10,000 nodes and varying structures are used to test the performance of TSP-CDA. A comparison is also made between TSP-CDA and two well-established community detection algorithms. The results show that TSP-CDA can find accurate community structure efficiently and outperforms the two existing algorithms.

  12. Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity.

    Science.gov (United States)

    Nicoludis, John M; Lau, Sze-Yi; Schärfe, Charlotta P I; Marks, Debora S; Weihofen, Wilhelm A; Gaudet, Rachelle

    2015-11-03

    Clustered protocadherin (Pcdh) proteins mediate dendritic self-avoidance in neurons via specific homophilic interactions in their extracellular cadherin (EC) domains. We determined crystal structures of EC1-EC3, containing the homophilic specificity-determining region, of two mouse clustered Pcdh isoforms (PcdhγA1 and PcdhγC3) to investigate the nature of the homophilic interaction. Within the crystal lattices, we observe antiparallel interfaces consistent with a role in trans cell-cell contact. Antiparallel dimerization is supported by evolutionary correlations. Two interfaces, located primarily on EC2-EC3, involve distinctive clustered Pcdh structure and sequence motifs, lack predicted glycosylation sites, and contain residues highly conserved in orthologs but not paralogs, pointing toward their biological significance as homophilic interaction interfaces. These two interfaces are similar yet distinct, reflecting a possible difference in interaction architecture between clustered Pcdh subfamilies. These structures initiate a molecular understanding of clustered Pcdh assemblies that are required to produce functional neuronal networks. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Superresolution imaging reveals structurally distinct periodic patterns of chromatin along pachytene chromosomes

    Science.gov (United States)

    Fournier, David; Redl, Stefan; Best, Gerrit; Borsos, Máté; Tiwari, Vijay K.; Tachibana-Konwalski, Kikuë; Ketting, René F.; Parekh, Sapun H.; Cremer, Christoph; Birk, Udo J.

    2015-01-01

    During meiosis, homologous chromosomes associate to form the synaptonemal complex (SC), a structure essential for fertility. Information about the epigenetic features of chromatin within this structure at the level of superresolution microscopy is largely lacking. We combined single-molecule localization microscopy (SMLM) with quantitative analytical methods to describe the epigenetic landscape of meiotic chromosomes at the pachytene stage in mouse oocytes. DNA is found to be nonrandomly distributed along the length of the SC in condensed clusters. Periodic clusters of repressive chromatin [trimethylation of histone H3 at lysine (Lys) 27 (H3K27me3)] are found at 500-nm intervals along the SC, whereas one of the ends of the SC displays a large and dense cluster of centromeric histone mark [trimethylation of histone H3 at Lys 9 (H3K9me3)]. Chromatin associated with active transcription [trimethylation of histone H3 at Lys 4 (H3K4me3)] is arranged in a radial hair-like loop pattern emerging laterally from the SC. These loops seem to be punctuated with small clusters of H3K4me3 with an average spread larger than their periodicity. Our findings indicate that the nanoscale structure of the pachytene chromosomes is constrained by periodic patterns of chromatin marks, whose function in recombination and higher order genome organization is yet to be elucidated. PMID:26561583

  14. Structures of human folate receptors reveal biological trafficking states and diversity in folate and antifolate recognition.

    Science.gov (United States)

    Wibowo, Ardian S; Singh, Mirage; Reeder, Kristen M; Carter, Joshua J; Kovach, Alexander R; Meng, Wuyi; Ratnam, Manohar; Zhang, Faming; Dann, Charles E

    2013-09-17

    Antifolates, folate analogs that inhibit vitamin B9 (folic acid)-using cellular enzymes, have been used over several decades for the treatment of cancer and inflammatory diseases. Cellular uptake of the antifolates in clinical use occurs primarily via widely expressed facilitative membrane transporters. More recently, human folate receptors (FRs), high affinity receptors that transport folate via endocytosis, have been proposed as targets for the specific delivery of new classes of antifolates or folate conjugates to tumors or sites of inflammation. The development of specific, FR-targeted antifolates would be accelerated if additional biophysical data, particularly structural models of the receptors, were available. Here we describe six distinct crystallographic models that provide insight into biological trafficking of FRs and distinct binding modes of folate and antifolates to these receptors. From comparison of the structures, we delineate discrete structural conformations representative of key stages in the endocytic trafficking of FRs and propose models for pH-dependent conformational changes. Additionally, we describe the molecular details of human FR in complex with three clinically prevalent antifolates, pemetrexed (also Alimta), aminopterin, and methotrexate. On the whole, our data form the basis for rapid design and implementation of unique, FR-targeted, folate-based drugs for the treatment of cancer and inflammatory diseases.

  15. Revealing New Structural Insights from Surfactant Micelles through DLS, Microrheology and Raman Spectroscopy

    Directory of Open Access Journals (Sweden)

    Samiul Amin

    2015-06-01

    Full Text Available The correlation between molecular changes and microstructural evolution of rheological properties has been demonstrated for the first time in a mixed anionic/zwitterionic surfactant-based wormlike micellar system. Utilizing a novel combination of DLS-microrheology and Raman Spectroscopy, the effect of electrostatic screening on these properties of anionic (SLES and zwitterionic (CapB surfactant mixtures was studied by modulating the NaCl concentration. As Raman Spectroscopy delivers information about the molecular structure and DLS-microrheology characterizes viscoelastic properties, the combination of data delivered allows for a deeper understanding of the molecular changes underlying the viscoelastic ones. The high frequency viscoelastic response obtained through DLS-microrheology has shown the persistence of the Maxwell fluid response for low viscosity solutions at high NaCl concentrations. The intensity of the Raman band at 170 cm−1 exhibits very strong correlation with the viscosity variation. As this Raman band is assigned to hydrogen bonding, its variation with NaCl concentration additionally indicates differences in water structuring due to potential microstructural differences at low and high NaCl concentrations. The microstructural differences at low and high NaCl concentrations are further corroborated by persistence of a slow mode at the higher NaCl concentrations as seen through DLS measurements. The study illustrates the utility of the combined DLS, DLS-optical microrheology and Raman Spectroscopy in providing new molecular structural insights into the self-assembly process in complex fluids.

  16. Thermal annealing of carbon nanotubes reveals a toxicological impact of the structural defects

    Energy Technology Data Exchange (ETDEWEB)

    Figarol, Agathe, E-mail: figarol@emse.fr [Ecole Nationale Supérieure des Mines, SPIN-EMSE, CNRS: UMR 5307, LGF (France); Pourchez, Jérémie, E-mail: pourchez@emse.fr [Ecole Nationale Supérieure des Mines, CIS-EMSE, EA 4624, SFR IFRESIS, LINA (France); Boudard, Delphine [Université Jean Monnet Saint-Etienne, EA 4624, SFR IFRESIS, LINA (France); Forest, Valérie [Ecole Nationale Supérieure des Mines, CIS-EMSE, EA 4624, SFR IFRESIS, LINA (France); Berhanu, Sarah [Armines - Mines ParisTech, Centre des Matériaux, CNRS UMR 7633 (France); Tulliani, Jean-Marc [Politecnico di Torino, Department of Applied Science and Technology (Italy); Lecompte, Jean-Pierre [Centre Européen de la céramique CNRS: UMR 7315, SPCTS (France); Cottier, Michèle [Université Jean Monnet Saint-Etienne, EA 4624, SFR IFRESIS, LINA (France); Bernache-Assollant, Didier [Ecole Nationale Supérieure des Mines, CIS-EMSE, EA 4624, SFR IFRESIS, LINA (France); Grosseau, Philippe [Ecole Nationale Supérieure des Mines, SPIN-EMSE, CNRS: UMR 5307, LGF (France)

    2015-04-15

    The biological response to pristine and annealed multi-walled carbon nanotubes (MWCNT) was assessed on murine macrophages (RAW 264.7). First, the physicochemical features of the as-produced MWCNT and annealed at 2125 °C for 1 h were fully characterized. A decrease in structural defects, hydrophobicity and catalytic impurities was detected after annealing. Thereafter, their impact on cytotoxicity, oxidative stress, and pro-inflammatory response was investigated at concentrations ranging from 15 to 120 µg mL{sup −1}. No effect of the 2125 °C treatment was detected on the cytotoxicity. In contrast, the annealed carbon nanotubes showed a significant increase of the pro-inflammatory response. We assumed that this behavior was due to the reduction in structural defects that may modify the layer of adsorbed biomolecules. Surprisingly, the purification of metallic catalysts did not have any significant impact on the oxidative stress. We suggested that the structural improvements from the 2125 °C treatment can decrease the carbon nanotube scavenging capacity and thus allow a higher free radical release which may counterbalance the decrease of oxidative stress due to a lower content of metallic impurities.

  17. Microsatellites loci reveal heterozygosis and population structure in vampire bats (Desmodus rotundus) (Chiroptera: Phyllostomidae) of Mexico.

    Science.gov (United States)

    Romero-Nava, Claudia; León-Paniagua, Livia; Ortega, Jorge

    2014-06-01

    A limited number of studies have focused on the population genetic structure of vampire bats (Desmous rotundus) in America. This medium-sized bat is distributed in tropical areas of the continent with high prevalence in forested livestock areas. The aim of this work was to characterize the vampire population structure and their genetic differentiation. For this, we followed standard methods by which live vampires (caught by mist-netting) and preserved material from scientific collections, were obtained for a total of 15 different locations, ranging from Chihuahua (North) to Quintana Roo (Southeast). Tissue samples were obtained from both live and collected animals, and the genetic differentiation, within and among localities, was assessed by the use of seven microsatellite loci. Our results showed that all loci were polymorphic and no private alleles were detected. High levels of heterozygosis were detected when the proportion of alleles in each locus were compared. Pairwise (ST) and R(ST) detected significant genetic differentiation among individuals from different localities. Our population structure results indicate the presence of eleven clusters, with a high percentage of assigned individuals to some specific collecting site.

  18. Mass spectrometry footprinting reveals the structural rearrangements of cyanobacterial orange carotenoid protein upon light activation

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Haijun [Washington University; Zhang, Hao [Washington University; King, Jeremy D. [Washington University; Wolf, Nathan R. [Washington University; Prado, Mindy [Washington University; Gross, Michael L. [Washington University; Blankenship, Robert E. [Washington University

    2014-12-01

    The orange carotenoid protein (OCP), a member of the family of blue light photoactive proteins, is required for efficient photoprotection in many cyanobacteria. Photoexcitation of the carotenoid in the OCP results in structural changes within the chromophore and the protein to give an active red form of OCP that is required for phycobilisome binding and consequent fluorescence quenching. We characterized the light-dependent structural changes by mass spectrometry-based carboxyl footprinting and found that an α helix in the N-terminal extension of OCP plays a key role in this photoactivation process. Although this helix is located on and associates with the outside of the β-sheet core in the C-terminal domain of OCP in the dark, photoinduced changes in the domain structure disrupt this interaction. We propose that this mechanism couples light-dependent carotenoid conformational changes to global protein conformational dynamics in favor of functional phycobilisome binding, and is an essential part of the OCP photocycle.

  19. Light-harvesting features revealed by the structure of plant Photosystem I

    CERN Document Server

    Ben-Shem, A; Nelson, N; 10.1023/B:PRES.0000036881.23512.42

    2004-01-01

    Oxygenic photosynthesis is driven by two multi-subunit membrane protein complexes, Photosystem I and Photosystem II. In plants and green algae, both complexes are composed of two moieties: a reaction center (RC), where light-induced charge translocation occurs, and a peripheral antenna that absorbs light and funnels its energy to the reaction center. The peripheral antenna of PS I (LHC I) is composed of four gene products (Lhca 1-4) that are unique among the chlorophyll a/b binding proteins in their pronounced long-wavelength absorbance and in their assembly into dimers. The recently determined structure of plant Photosystem I provides the first relatively high- resolution structural model of a super-complex containing a reaction center and its peripheral antenna. We describe some of the structural features responsible for the unique properties of LHC I and discuss the advantages of the particular LHC I dimerization mode over monomeric or trimeric forms. In addition, we delineate some of the interactions betw...

  20. Microsatellites loci reveal heterozygosis and population structure in vampire bats (Desmodus rotundus (Chiroptera: Phyllostomidae of Mexico

    Directory of Open Access Journals (Sweden)

    Claudia Romero-Nava

    2014-08-01

    Full Text Available A limited number of studies have focused on the population genetic structure of vampire bats (Desmodus rotundus in America. This medium-sized bat is distributed in tropical areas of the continent with high prevalence in forested livestock areas. The aim of this work was to characterize the vampire population structure and their genetic differentiation. For this, we followed standard methods by which live vampires (caught by mist-netting and preserved material from scientific collections, were obtained for a total of 15 different locations, ranging from Chihuahua (North to Quintana Roo (Southeast. Tissue samples were obtained from both live and collected animals, and the genetic differentiation, within and among localities, was assessed by the use of seven microsatellite loci. Our results showed that all loci were polymorphic and no private alleles were detected. High levels of heterozygosis were detected when the proportion of alleles in each locus were compared. Pairwise F ST and R ST detected significant genetic differentiation among individuals from different localities. Our population structure results indicate the presence of eleven clusters, with a high percentage of assigned individuals to some specific collecting site. Rev. Biol. Trop. 62 (2: 659-669. Epub 2014 June 01.

  1. Structure of a Reptilian Adenovirus Reveals a Phage Tailspike Fold Stabilizing a Vertebrate Virus Capsid.

    Science.gov (United States)

    Menéndez-Conejero, Rosa; Nguyen, Thanh H; Singh, Abhimanyu K; Condezo, Gabriela N; Marschang, Rachel E; van Raaij, Mark J; San Martín, Carmen

    2017-10-03

    Although non-human adenoviruses (AdVs) might offer solutions to problems posed by human AdVs as therapeutic vectors, little is known about their basic biology. In particular, there are no structural studies on the complete virion of any AdV with a non-mammalian host. We combine mass spectrometry, cryo-electron microscopy, and protein crystallography to characterize the composition and structure of a snake AdV (SnAdV-1, Atadenovirus genus). SnAdV-1 particles contain the genus-specific proteins LH3, p32k, and LH2, a previously unrecognized structural component. Remarkably, the cementing protein LH3 has a trimeric β helix fold typical of bacteriophage host attachment proteins. The organization of minor coat proteins differs from that in human AdVs, correlating with higher thermostability in SnAdV-1. These findings add a new piece to the intriguing puzzle of virus evolution, hint at the use of cell entry pathways different from those in human AdVs, and will help development of new, thermostable SnAdV-1-based vectors. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Structure of the Cyanuric Acid Hydrolase TrzD Reveals Product Exit Channel.

    Science.gov (United States)

    Bera, Asim K; Aukema, Kelly G; Elias, Mikael; Wackett, Lawrence P

    2017-03-27

    Cyanuric acid hydrolases are of industrial importance because of their use in aquatic recreational facilities to remove cyanuric acid, a stabilizer for the chlorine. Degradation of excess cyanuric acid is necessary to maintain chlorine disinfection in the waters. Cyanuric acid hydrolase opens the cyanuric acid ring hydrolytically and subsequent decarboxylation produces carbon dioxide and biuret. In the present study, we report the X-ray structure of TrzD, a cyanuric acid hydrolase from Acidovorax citrulli. The crystal structure at 2.19 Å resolution shows a large displacement of the catalytic lysine (Lys163) in domain 2 away from the active site core, whereas the two other active site lysines from the two other domains are not able to move. The lysine displacement is proposed here to open up a channel for product release. Consistent with that, the structure also showed two molecules of the co-product, carbon dioxide, one in the active site and another trapped in the proposed exit channel. Previous data indicated that the domain 2 lysine residue plays a role in activating an adjacent serine residue carrying out nucleophilic attack, opening the cyanuric acid ring, and the mobile lysine guides products through the exit channel.

  3. Revealing strong bias in common measures of galaxy properties using new inclination-independent structures

    Science.gov (United States)

    Devour, Brian M.; Bell, Eric F.

    2017-06-01

    Accurate measurement of galaxy structures is a prerequisite for quantitative investigation of galaxy properties or evolution. Yet, the impact of galaxy inclination and dust on commonly used metrics of galaxy structure is poorly quantified. We use infrared data sets to select inclination-independent samples of disc and flattened elliptical galaxies. These samples show strong variation in Sérsic index, concentration and half-light radii with inclination. We develop novel inclination-independent galaxy structures by collapsing the light distribution in the near-infrared on to the major axis, yielding inclination-independent 'linear' measures of size and concentration. With these new metrics we select a sample of Milky Way analogue galaxies with similar stellar masses, star formation rates, sizes and concentrations. Optical luminosities, light distributions and spectral properties are all found to vary strongly with inclination: When inclining to edge-on, r-band luminosities dim by >1 magnitude, sizes decrease by a factor of 2, 'dust-corrected' estimates of star formation rate drop threefold, metallicities decrease by 0.1 dex and edge-on galaxies are half as likely to be classified as star forming. These systematic effects should be accounted for in analyses of galaxy properties.

  4. AFLP analysis reveals a lack of phylogenetic structure within Solanum section Petota

    Directory of Open Access Journals (Sweden)

    Vleeshouwers Vivianne GAA

    2008-05-01

    Full Text Available Abstract Background The secondary genepool of our modern cultivated potato (Solanum tuberosum L. consists of a large number of tuber-bearing wild Solanum species under Solanum section Petota. One of the major taxonomic problems in section Petota is that the series classification (as put forward by Hawkes is problematic and the boundaries of some series are unclear. In addition, the classification has received only partial cladistic support in all molecular studies carried out to date. The aim of the present study is to describe the structure present in section Petota. When possible, at least 5 accessions from each available species and 5 individual plants per accession (totally approx. 5000 plants were genotyped using over 200 AFLP markers. This resulted in the largest dataset ever constructed for Solanum section Petota. The data obtained are used to evaluate the 21 series hypothesis put forward by Hawkes and the 4 clade hypothesis of Spooner and co-workers. Results We constructed a NJ tree for 4929 genotypes. For the other analyses, due to practical reasons, a condensed dataset was created consisting of one representative genotype from each available accession. We show a NJ jackknife and a MP jackknife tree. A large part of both trees consists of a polytomy. Some structure is still visible in both trees, supported by jackknife values above 69. We use these branches with >69 jackknife support in the NJ jackknife tree as a basis for informal species groups. The informal species groups recognized are: Mexican diploids, Acaulia, Iopetala, Longipedicellata, polyploid Conicibaccata, diploid Conicibaccata, Circaeifolia, diploid Piurana and tetraploid Piurana. Conclusion Most of the series that Hawkes and his predecessors designated can not be accepted as natural groups, based on our study. Neither do we find proof for the 4 clades proposed by Spooner and co-workers. A few species groups have high support and their inner structure displays also

  5. Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY

    International Nuclear Information System (INIS)

    Shi, Jade; Schwantes, Christian; Bilsel, Osman

    2017-01-01

    The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. We report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble. The resulting prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. We then predict incisive single molecule FRET experiments, using these results, as a means of model validation. Our study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments.

  6. Two-photon imaging during prolonged middle cerebral artery occlusion in mice reveals recovery of dendritic structure after reperfusion.

    Science.gov (United States)

    Li, Ping; Murphy, Timothy H

    2008-11-12

    Filament occlusion of the middle cerebral artery (MCA) is a well accepted animal model of focal ischemia. Advantages of the model are relatively long occlusion times and a large penumbra region that simulates aspects of human stroke. Here, we use two-photon and confocal microscopy in combination with regional measurement of blood flow using laser speckle to assess the spatial relationship between the borders of the MCA ischemic territory and loss of dendrite structure, as well as the effect of reperfusion on dendritic damage in adult YFP (yellow fluorescent protein) and GFP (green fluorescent protein) C57BL/6 transgenic mice with fluorescent (predominantly layer 5) neurons. By examining the spatial extent of dendritic damage, we determined that 60 min of MCA occlusion produced a core with severe structural damage that did not recover after reperfusion (begins approximately 3.8 mm lateral to midline), a reversibly damaged area up to 0.6 mm medial to the core that recovered after reperfusion (penumbra), and a relatively structurally intact area ( approximately 1 mm wide; medial penumbra) with hypoperfusion. Loss of structure was preceded by a single ischemic depolarization 122.1 +/- 10.2 s after occlusion onset. Reperfusion of animals after 60 min of ischemia was not associated with exacerbation of damage (reperfusion injury) and resulted in a significant restoration of blebbed dendritic structure, but only within approximately 0.6 mm lateral of the dendritic damage structural border. In summary, we find that recovery of dendritic structure can occur after reperfusion after even 60 min of ischemia, but is likely restricted to a relatively small penumbra region with partial blood flow or oxygenation.

  7. The structure of bradyzoite-specific enolase from Toxoplasma gondii reveals insights into its dual cytoplasmic and nuclear functions

    Energy Technology Data Exchange (ETDEWEB)

    Ruan, Jiapeng [Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611 (United States); Mouveaux, Thomas [Université Lille Nord de France, (France); Light, Samuel H.; Minasov, George; Anderson, Wayne F. [Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611 (United States); Tomavo, Stanislas [Université Lille Nord de France, (France); Ngô, Huân M., E-mail: h-ngo@northwestern.edu [Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611 (United States); BrainMicro LLC, 21 Pendleton Street, New Haven, CT 06511 (United States)

    2015-03-01

    The second crystal structure of a parasite protein preferentially enriched in the brain cyst of T. gondii has been solved at 2.75 Å resolution. Bradyzoite enolase 1 is reported to have differential functions as a glycolytic enzyme and a transcriptional regulator in bradyzoites. In addition to catalyzing a central step in glycolysis, enolase assumes a remarkably diverse set of secondary functions in different organisms, including transcription regulation as documented for the oncogene c-Myc promoter-binding protein 1. The apicomplexan parasite Toxoplasma gondii differentially expresses two nuclear-localized, plant-like enolases: enolase 1 (TgENO1) in the latent bradyzoite cyst stage and enolase 2 (TgENO2) in the rapidly replicative tachyzoite stage. A 2.75 Å resolution crystal structure of bradyzoite enolase 1, the second structure to be reported of a bradyzoite-specific protein in Toxoplasma, captures an open conformational state and reveals that distinctive plant-like insertions are located on surface loops. The enolase 1 structure reveals that a unique residue, Glu164, in catalytic loop 2 may account for the lower activity of this cyst-stage isozyme. Recombinant TgENO1 specifically binds to a TTTTCT DNA motif present in the cyst matrix antigen 1 (TgMAG1) gene promoter as demonstrated by gel retardation. Furthermore, direct physical interactions of both nuclear TgENO1 and TgENO2 with the TgMAG1 gene promoter are demonstrated in vivo using chromatin immunoprecipitation (ChIP) assays. Structural and biochemical studies reveal that T. gondii enolase functions are multifaceted, including the coordination of gene regulation in parasitic stage development. Enolase 1 provides a potential lead in the design of drugs against Toxoplasma brain cysts.

  8. J. Piaget's theory of intelligence: operational aspect

    Directory of Open Access Journals (Sweden)

    Xenia Naidenova

    2001-08-01

    Full Text Available The Piaget's theory of intelligence is considered from the point of view of genesis and gradual development of human thinking operations. Attention is given to operational aspects of cognitive structures and knowledge. The significance of the Piaget's theory of intelligence is revealed for modeling conceptual reasoning in the framework of artificial intelligence.

  9. Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors

    Directory of Open Access Journals (Sweden)

    Raymond Kiu

    2017-12-01

    Full Text Available Clostridium perfringens is an important cause of animal and human infections, however information about the genetic makeup of this pathogenic bacterium is currently limited. In this study, we sought to understand and characterise the genomic variation, pangenomic diversity, and key virulence traits of 56 C. perfringens strains which included 51 public, and 5 newly sequenced and annotated genomes using Whole Genome Sequencing. Our investigation revealed that C. perfringens has an “open” pangenome comprising 11667 genes and 12.6% of core genes, identified as the most divergent single-species Gram-positive bacterial pangenome currently reported. Our computational analyses also defined C. perfringens phylogeny (16S rRNA gene in relation to some 25 Clostridium species, with C. baratii and C. sardiniense determined to be the closest relatives. Profiling virulence-associated factors confirmed presence of well-characterised C. perfringens-associated exotoxins genes including α-toxin (plc, enterotoxin (cpe, and Perfringolysin O (pfo or pfoA, although interestingly there did not appear to be a close correlation with encoded toxin type and disease phenotype. Furthermore, genomic analysis indicated significant horizontal gene transfer events as defined by presence of prophage genomes, and notably absence of CRISPR defence systems in >70% (40/56 of the strains. In relation to antimicrobial resistance mechanisms, tetracycline resistance genes (tet and anti-defensins genes (mprF were consistently detected in silico (tet: 75%; mprF: 100%. However, pre-antibiotic era strain genomes did not encode for tet, thus implying antimicrobial selective pressures in C. perfringens evolutionary history over the past 80 years. This study provides new genomic understanding of this genetically divergent multi-host bacterium, and further expands our knowledge on this medically and veterinary important pathogen.

  10. Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors.

    Science.gov (United States)

    Kiu, Raymond; Caim, Shabhonam; Alexander, Sarah; Pachori, Purnima; Hall, Lindsay J

    2017-01-01

    Clostridium perfringens is an important cause of animal and human infections, however information about the genetic makeup of this pathogenic bacterium is currently limited. In this study, we sought to understand and characterise the genomic variation, pangenomic diversity, and key virulence traits of 56 C. perfringens strains which included 51 public, and 5 newly sequenced and annotated genomes using Whole Genome Sequencing. Our investigation revealed that C. perfringens has an "open" pangenome comprising 11667 genes and 12.6% of core genes, identified as the most divergent single-species Gram-positive bacterial pangenome currently reported. Our computational analyses also defined C. perfringens phylogeny (16S rRNA gene) in relation to some 25 Clostridium species, with C. baratii and C. sardiniense determined to be the closest relatives. Profiling virulence-associated factors confirmed presence of well-characterised C. perfringens -associated exotoxins genes including α-toxin ( plc ), enterotoxin ( cpe ), and Perfringolysin O ( pfo or pfoA ), although interestingly there did not appear to be a close correlation with encoded toxin type and disease phenotype. Furthermore, genomic analysis indicated significant horizontal gene transfer events as defined by presence of prophage genomes, and notably absence of CRISPR defence systems in >70% (40/56) of the strains. In relation to antimicrobial resistance mechanisms, tetracycline resistance genes ( tet ) and anti-defensins genes ( mprF ) were consistently detected in silico ( tet : 75%; mprF : 100%). However, pre-antibiotic era strain genomes did not encode for tet , thus implying antimicrobial selective pressures in C. perfringens evolutionary history over the past 80 years. This study provides new genomic understanding of this genetically divergent multi-host bacterium, and further expands our knowledge on this medically and veterinary important pathogen.

  11. Comparative analyses of reproductive structures in harvestmen (opiliones reveal multiple transitions from courtship to precopulatory antagonism.

    Directory of Open Access Journals (Sweden)

    Mercedes M Burns

    Full Text Available Explaining the rapid, species-specific diversification of reproductive structures and behaviors is a long-standing goal of evolutionary biology, with recent research tending to attribute reproductive phenotypes to the evolutionary mechanisms of female mate choice or intersexual conflict. Progress in understanding these and other possible mechanisms depends, in part, on reconstructing the direction, frequency and relative timing of phenotypic evolution of male and female structures in species-rich clades. Here we examine evolution of reproductive structures in the leiobunine harvestmen or "daddy long-legs" of eastern North America, a monophyletic group that includes species in which males court females using nuptial gifts and other species that are equipped for apparent precopulatory antagonism (i.e., males with long, hardened penes and females with sclerotized pregenital barriers. We used parsimony- and Bayesian likelihood-based analyses to reconstruct character evolution in categorical reproductive traits and found that losses of ancestral gift-bearing penile sacs are strongly associated with gains of female pregenital barriers. In most cases, both events occur on the same internal branch of the phylogeny. These coevolutionary changes occurred at least four times, resulting in clade-specific designs in the penis and pregenital barrier. The discovery of convergent origins and/or enhancements of apparent precopulatory antagonism among closely related species offers an unusual opportunity to investigate how major changes in reproductive morphology have occurred. We propose new hypotheses that attribute these enhancements to changes in ecology or life history that reduce the duration of breeding seasons, an association that is consistent with female choice, sexual conflict, and/or an alternative evolutionary mechanism.

  12. The genetic structure of fermentative vineyard-associated Saccharomyces cerevisiae populations revealed by microsatellite analysis.

    Science.gov (United States)

    Schuller, Dorit; Casal, Margarida

    2007-02-01

    From the analysis of six polymorphic microsatellite loci performed in 361 Saccharomyces cerevisiae isolates, 93 alleles were identified, 52 of them being described for the first time. All these isolates have a distinct mtDNA RFLP pattern. They are derived from a pool of 1620 isolates obtained from spontaneous fermentations of grapes collected in three vineyards of the Vinho Verde Region in Portugal, during the 2001-2003 harvest seasons. For all loci analyzed, observed heterozygosity was 3-4 times lower than the expected value supposing a Hardy-Weinberg equilibrium (random mating and no evolutionary mechanisms acting), indicating a clonal structure and strong populational substructuring. Genetic differences among S. cerevisiae populations were apparent mainly from gradations in allele frequencies rather than from distinctive "diagnostic" genotypes, and the accumulation of small allele-frequency differences across six loci allowed the identification of population structures. Genetic differentiation in the same vineyard in consecutive years was of the same order of magnitude as the differences verified among the different vineyards. Correlation of genetic differentiation with the distance between sampling points within a vineyard suggested a pattern of isolation-by-distance, where genetic divergence in a vineyard increased with size. The continuous use of commercial yeasts has a limited influence on the autochthonous fermentative yeast population collected from grapes and may just slightly change populational structures of strains isolated from sites very close to the winery where they have been used. The present work is the first large-scale approach using microsatellite typing allowing a very fine resolution of indigenous S. cerevisiae populations isolated from vineyards.

  13. Molecular structure of self-assembled chiral nanoribbons and nanotubules revealed in the hydrated state.

    Science.gov (United States)

    Oda, Reiko; Artzner, Franck; Laguerre, Michel; Huc, Ivan

    2008-11-05

    A detailed molecular organization of racemic 16-2-16 tartrate self-assembled multi-bilayer ribbons in the hydrated state is proposed where 16-2-16 amphiphiles, tartrate ions, and water molecules are all accurately positioned by comparing experimental X-ray powder diffraction and diffraction patterns derived from modeling studies. X-ray diffuse scattering studies show that molecular organization is not fundamentally altered when comparing the flat ribbons of the racemate to chirally twisted or helical ribbons of the pure tartrate enantiomer. Essential features of the three-dimensional molecular organizations of these structures include interdigitation of alkyl chains within each bilayer and well-defined networks of ionic and hydrogen bonds between cations, anions, and water molecules between bilayers. The detailed study of diffraction patterns also indicated that the gemini headgroups are oriented parallel to the long edge of the ribbons. The structure thus possesses a high cohesion and good crystallinity, and for the first time, we could relate the packing of the chiral molecules to the expression of the chirality at a mesoscopic scale. The organization of the ribbons at the molecular level sheds light on a number of their macroscopic features. Among these are the reason why enantiomerically pure 16-2-16 tartrate forms ribbons that consist of exactly two bilayers, and a plausible mechanism by which a chirally twisted or helical shape may emerge from the packing of chiral tartrate ions. Importantly, the distinction between commonly observed helical and twisted morphologies could be related to a subtle symmetry breaking. These results demonstrate that accurately solving the molecular structure of self-assembled soft materials--a process rarely achieved--is within reach, that it is a valid approach to correlate molecular parameters to macroscopic properties, and thus that it offers opportunities to modulate properties through molecular design.

  14. Lens-Aided Multi-Angle Spectroscopy (LAMAS) Reveals Small-Scale Outflow Structure in Quasars

    Science.gov (United States)

    Green, Paul J.

    2006-06-01

    Spectral differences between lensed quasar image components are common. Since lensing is intrinsically achromatic, these differences are typically explained as the effect of either microlensing, or as light path time delays sampling intrinsic quasar spectral variability. Here we advance a novel third hypothesis: some spectral differences are due to small line-of-sight differences through quasar disk wind outflows. In particular, we propose that variable spectral differences seen only in component A of the widest separation lens SDSS J1004+4112 are due to differential absorption along the sight lines. The absorber properties required by this hypothesis are akin to known broad absorption line (BAL) outflows but must have a broader, smoother velocity profile. We interpret the observed C IV emission-line variability as further evidence for spatial fine structure transverse to the line of sight. Since outflows are likely to be rotating, such absorber fine structure can consistently explain some of the UV and X-ray variability seen in AGNs. The implications are many: (1) Spectroscopic differences in other lensed objects may be due to this ``lens-aided multi-angle spectroscopy'' (LAMAS). (2) Outflows have fine structure on size scales of arcseconds, as seen from the nucleus. (3) Assuming either broad absorption line region sizes proposed in recent wind models, or typically assumed continuum emission region sizes, LAMAS and/or variability provide broadly consistent absorber size scale estimates of ~1015 cm. (4) Very broad smooth absorption may be ubiquitous in quasar spectra, even when no obvious troughs are seen.

  15. Heart structure-specific transcriptomic atlas reveals conserved microRNA-mRNA interactions.

    Science.gov (United States)

    Vacchi-Suzzi, Caterina; Hahne, Florian; Scheubel, Philippe; Marcellin, Magali; Dubost, Valerie; Westphal, Magdalena; Boeglen, Catherine; Büchmann-Møller, Stine; Cheung, Ming Sin; Cordier, André; De Benedetto, Christopher; Deurinck, Mark; Frei, Moritz; Moulin, Pierre; Oakeley, Edward; Grenet, Olivier; Grevot, Armelle; Stull, Robert; Theil, Diethilde; Moggs, Jonathan G; Marrer, Estelle; Couttet, Philippe

    2013-01-01

    MicroRNAs are short non-coding RNAs that regulate gene expression at the post-transcriptional level and play key roles in heart development and cardiovascular diseases. Here, we have characterized the expression and distribution of microRNAs across eight cardiac structures (left and right ventricles, apex, papillary muscle, septum, left and right atrium and valves) in rat, Beagle dog and cynomolgus monkey using microRNA sequencing. Conserved microRNA signatures enriched in specific heart structures across these species were identified for cardiac valve (miR-let-7c, miR-125b, miR-127, miR-199a-3p, miR-204, miR-320, miR-99b, miR-328 and miR-744) and myocardium (miR-1, miR-133b, miR-133a, miR-208b, miR-30e, miR-499-5p, miR-30e*). The relative abundance of myocardium-enriched (miR-1) and valve-enriched (miR-125b-5p and miR-204) microRNAs was confirmed using in situ hybridization. MicroRNA-mRNA interactions potentially relevant for cardiac functions were explored using anti-correlation expression analysis and microRNA target prediction algorithms. Interactions between miR-1/Timp3, miR-125b/Rbm24, miR-204/Tgfbr2 and miR-208b/Csnk2a2 were identified and experimentally investigated in human pulmonary smooth muscle cells and luciferase reporter assays. In conclusion, we have generated a high-resolution heart structure-specific mRNA/microRNA expression atlas for three mammalian species that provides a novel resource for investigating novel microRNA regulatory circuits involved in cardiac molecular physiopathology.

  16. Heart structure-specific transcriptomic atlas reveals conserved microRNA-mRNA interactions.

    Directory of Open Access Journals (Sweden)

    Caterina Vacchi-Suzzi

    Full Text Available MicroRNAs are short non-coding RNAs that regulate gene expression at the post-transcriptional level and play key roles in heart development and cardiovascular diseases. Here, we have characterized the expression and distribution of microRNAs across eight cardiac structures (left and right ventricles, apex, papillary muscle, septum, left and right atrium and valves in rat, Beagle dog and cynomolgus monkey using microRNA sequencing. Conserved microRNA signatures enriched in specific heart structures across these species were identified for cardiac valve (miR-let-7c, miR-125b, miR-127, miR-199a-3p, miR-204, miR-320, miR-99b, miR-328 and miR-744 and myocardium (miR-1, miR-133b, miR-133a, miR-208b, miR-30e, miR-499-5p, miR-30e*. The relative abundance of myocardium-enriched (miR-1 and valve-enriched (miR-125b-5p and miR-204 microRNAs was confirmed using in situ hybridization. MicroRNA-mRNA interactions potentially relevant for cardiac functions were explored using anti-correlation expression analysis and microRNA target prediction algorithms. Interactions between miR-1/Timp3, miR-125b/Rbm24, miR-204/Tgfbr2 and miR-208b/Csnk2a2 were identified and experimentally investigated in human pulmonary smooth muscle cells and luciferase reporter assays. In conclusion, we have generated a high-resolution heart structure-specific mRNA/microRNA expression atlas for three mammalian species that provides a novel resource for investigating novel microRNA regulatory circuits involved in cardiac molecular physiopathology.

  17. Structured pathway across the transition state for peptide folding revealed by molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Lipi Thukral

    2011-09-01

    Full Text Available Small globular proteins and peptides commonly exhibit two-state folding kinetics in which the rate limiting step of folding is the surmounting of a single free energy barrier at the transition state (TS separating the folded and the unfolded states. An intriguing question is whether the polypeptide chain reaches, and leaves, the TS by completely random fluctuations, or whether there is a directed, stepwise process. Here, the folding TS of a 15-residue β-hairpin peptide, Peptide 1, is characterized using independent 2.5 μs-long unbiased atomistic molecular dynamics (MD simulations (a total of 15 μs. The trajectories were started from fully unfolded structures. Multiple (spontaneous folding events to the NMR-derived conformation are observed, allowing both structural and dynamical characterization of the folding TS. A common loop-like topology is observed in all the TS structures with native end-to-end and turn contacts, while the central segments of the strands are not in contact. Non-native sidechain contacts are present in the TS between the only tryptophan (W11 and the turn region (P7-G9. Prior to the TS the turn is found to be already locked by the W11 sidechain, while the ends are apart. Once the ends have also come into contact, the TS is reached. Finally, along the reactive folding paths the cooperative loss of the W11 non-native contacts and the formation of the central inter-strand native contacts lead to the peptide rapidly proceeding from the TS to the native state. The present results indicate a directed stepwise process to folding the peptide.

  18. Whole-brain analytic measures of network communication reveal increased structure-function correlation in right temporal lobe epilepsy.

    Science.gov (United States)

    Wirsich, Jonathan; Perry, Alistair; Ridley, Ben; Proix, Timothée; Golos, Mathieu; Bénar, Christian; Ranjeva, Jean-Philippe; Bartolomei, Fabrice; Breakspear, Michael; Jirsa, Viktor; Guye, Maxime

    2016-01-01

    The in vivo structure-function relationship is key to understanding brain network reorganization due to pathologies. This relationship is likely to be particularly complex in brain network diseases such as temporal lobe epilepsy, in which disturbed large-scale systems are involved in both transient electrical events and long-lasting functional and structural impairments. Herein, we estimated this relationship by analyzing the correlation between structural connectivity and functional connectivity in terms of analytical network communication parameters. As such, we targeted the gradual topological structure-function reorganization caused by the pathology not only at the whole brain scale but also both in core and peripheral regions of the brain. We acquired diffusion (dMRI) and resting-state fMRI (rsfMRI) data in seven right-lateralized TLE (rTLE) patients and fourteen healthy controls and analyzed the structure-function relationship by using analytical network communication metrics derived from the structural connectome. In rTLE patients, we found a widespread hypercorrelated functional network. Network communication analysis revealed greater unspecific branching of the shortest path (search information) in the structural connectome and a higher global correlation between the structural and functional connectivity for the patient group. We also found evidence for a preserved structural rich-club in the patient group. In sum, global augmentation of structure-function correlation might be linked to a smaller functional repertoire in rTLE patients, while sparing the central core of the brain which may represent a pathway that facilitates the spread of seizures.

  19. Crustal Structure and Deformation of the Sichuan-Yunnan Region Revealed by receiver Function Data

    Science.gov (United States)

    Zeng, S.; Zheng, Y.

    2017-12-01

    Sichuan-Yunnan and its surrounding areas locates in the southeast side to the Tibetan Plateau, due to the intrusion of the Indian Plate under the Tibetan Plateau, materials escape from the Tibetan Plateau and flow southward to southeastward. Because of such tectonic environment, the Sichuan-Yunnan region is experiencing high tectonic movement, and is capable of highly diffused seismicity. Based on dynamic simulation and field survey investigations, tectonic and geological studies proposed a decoupling model in this region and lower crustal flow may inflate in the crust. However, this idea needs more evidences, especially anisotropic structures to support it, since the anisotropic structures are usually directly related to the movement of materials, or to the tectonic distributions. In the past several years, a number of works have been done on the anisotropic structures in the Tibetan Plateau and its surroundings. In usually, previous studies were mainly carried out by two kinds of methods. First, the shear wave splitting of SKS, which mainly reflects the accumulation effect of the anisotropy of the crust to the mantle; the other way is use surface wave to investigate the anisotropic features at different azimuths and depths. In the recent years, receiver function is used to determine the inclination and anisotropy of the subsurface structure, comparing with the other two methods, receiver functions can provide higher resolution and reliable anisotropic features in the crust. Following the method of Liu and Niu(2012), we collected teleseismic data from the Himalayan first term network, and picked out high quality data based on the waveform SNR ratio, as well as the azimuthal distributions. Comparing with previous work (e.g., Sun et al.,2012), our work can provide more receiver functions results with higher reliability. We find that the crust beneath the Sichuan-Yunnan region has a thickness of 30-60 km and Vp/Vs ratio of 1.70-1.80. The Moho depth from northwest to

  20. Key Players in I-DmoI Endonuclease Catalysis Revealed from Structure and Dynamics

    DEFF Research Database (Denmark)

    Molina, Rafael; Besker, Neva; Marcaida, Maria Jose

    2016-01-01

    . The cleavage mechanism was related both to key structural effects, such as the position of water molecules and ions participating in the cleavage reaction, and to dynamical effects related to protein behavior. In particular, we found that the protein perturbation pattern significantly changes between cleaved......Homing endonucleases, such as I-DmoI, specifically recognize and cleave long DNA target sequences (∼20 bp) and are potentially powerful tools for genome manipulation. However, inefficient and off-target DNA cleavage seriously limits specific editing in complex genomes. One approach to overcome...

  1. Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius)

    DEFF Research Database (Denmark)

    Milano, I.; Babbucci, M.; Cariani, A.

    2014-01-01

    fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (FCT = 0.016) and weak differentiation within basins...... even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess largeand fine-scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European...

  2. Mutational and structural analyses of Caldanaerobius polysaccharolyticus Man5B reveal novel active site residues for family 5 glycoside hydrolases.

    Science.gov (United States)

    Oyama, Takuji; Schmitz, George E; Dodd, Dylan; Han, Yejun; Burnett, Alanna; Nagasawa, Naoko; Mackie, Roderick I; Nakamura, Haruki; Morikawa, Kosuke; Cann, Isaac

    2013-01-01

    CpMan5B is a glycoside hydrolase (GH) family 5 enzyme exhibiting both β-1,4-mannosidic and β-1,4-glucosidic cleavage activities. To provide insight into the amino acid residues that contribute to catalysis and substrate specificity, we solved the structure of CpMan5B at 1.6 Å resolution. The structure revealed several active site residues (Y12, N92 and R196) in CpMan5B that are not present in the active sites of other structurally resolved GH5 enzymes. Residue R196 in GH5 enzymes is thought to be strictly conserved as a histidine that participates in an electron relay network with the catalytic glutamates, but we show that an arginine fulfills a functionally equivalent role and is found at this position in every enzyme in subfamily GH5_36, which includes CpMan5B. Residue N92 is required for full enzymatic activity and forms a novel bridge over the active site that is absent in other family 5 structures. Our data also reveal a role of Y12 in establishing the substrate preference for CpMan5B. Using these molecular determinants as a probe allowed us to identify Man5D from Caldicellulosiruptor bescii as a mannanase with minor endo-glucanase activity.

  3. Molecular cloning and construction of the coding region for human acetylcholinesterase reveals a G + C-rich attenuating structure

    International Nuclear Information System (INIS)

    Soreq, H.; Ben-Aziz, R.; Prody, C.A.; Seidman, S.; Gnatt, A.; Neville, L.; Lieman-Hurwitz, J.; Lev-Lehman, E.; Ginzberg, D.; Lapidot-Lifson, Y.; Zakut, H.

    1990-01-01

    To study the primary structure of human acetylcholinesterase and its gene expression and amplification, cDNA libraries from human tissues expressing oocyte-translatable AcChoEase mRNA were constructed and screened with labeled oligodeoxynucleotide probes. Several cDNA clones were isolated that encoded a polypeptide with ≥50% identically aligned amino acids to Torpedo AcChoEase and human butyrylcholinesterase. However, these cDNA clones were all truncated within a 300-nucleotide-long G + C-rich region with a predicted pattern of secondary structure having a high Gibbs free energy downstream from the expected 5' end of the coding region. Screening of a genomic DNA library revealed the missing 5' domain. When ligated to the cDNA and constructed into a transcription vector, this sequence encoded a synthetic mRNA translated in microinjected oocytes into catalytically active AcChoEase with marked preference for acetylthiocholine over butyrylthiocholine as a substrate, susceptibility to inhibition by the AcChoEase inhibitor BW284C51, and resistance to the AcChoEase inhibitor tetraisopropylpyrophosphoramide. Blot hybridization of genomic DNA from different individuals carrying amplified AcChoEase genes revealed variable intensities and restriction patterns with probes from the regions upstream and downstream from the predicted G + C-rich structure. Thus, the human AcChoEase gene includes a putative G + C-rich attenuator domain and is subject to structural alterations in cases of AcChoEase gene amplification

  4. Mutational and structural analyses of Caldanaerobius polysaccharolyticus Man5B reveal novel active site residues for family 5 glycoside hydrolases.

    Directory of Open Access Journals (Sweden)

    Takuji Oyama

    Full Text Available CpMan5B is a glycoside hydrolase (GH family 5 enzyme exhibiting both β-1,4-mannosidic and β-1,4-glucosidic cleavage activities. To provide insight into the amino acid residues that contribute to catalysis and substrate specificity, we solved the structure of CpMan5B at 1.6 Å resolution. The structure revealed several active site residues (Y12, N92 and R196 in CpMan5B that are not present in the active sites of other structurally resolved GH5 enzymes. Residue R196 in GH5 enzymes is thought to be strictly conserved as a histidine that participates in an electron relay network with the catalytic glutamates, but we show that an arginine fulfills a functionally equivalent role and is found at this position in every enzyme in subfamily GH5_36, which includes CpMan5B. Residue N92 is required for full enzymatic activity and forms a novel bridge over the active site that is absent in other family 5 structures. Our data also reveal a role of Y12 in establishing the substrate preference for CpMan5B. Using these molecular determinants as a probe allowed us to identify Man5D from Caldicellulosiruptor bescii as a mannanase with minor endo-glucanase activity.

  5. Crystal Structure of the FGFR4/LY2874455 Complex Reveals Insights into the Pan-FGFR Selectivity of LY2874455.

    Science.gov (United States)

    Wu, Daichao; Guo, Ming; Philips, Michael A; Qu, Lingzhi; Jiang, Longying; Li, Jun; Chen, Xiaojuan; Chen, Zhuchu; Chen, Lin; Chen, Yongheng

    2016-01-01

    Aberrant FGFR4 signaling has been documented abundantly in various human cancers. The majority of FGFR inhibitors display significantly reduced potency toward FGFR4 compared to FGFR1-3. However, LY2874455 has similar inhibition potency for FGFR1-4 with IC50 less than 6.4 nM. To date, there is no published crystal structure of LY2874455 in complex with any kinase. To better understand the pan-FGFR selectivity of LY2874455, we have determined the crystal structure of the FGFR4 kinase domain bound to LY2874455 at a resolution of 2.35 Å. LY2874455, a type I inhibitor for FGFR4, binds to the ATP-binding pocket of FGFR4 in a DFG-in active conformation with three hydrogen bonds and a number of van der Waals contacts. After alignment of the kinase domain sequence of 4 FGFRs, and superposition of the ATP binding pocket of 4 FGFRs, our structural analyses reveal that the interactions of LY2874455 to FGFR4 are largely conserved in 4 FGFRs, explaining at least partly, the broad inhibitory activity of LY2874455 toward 4 FGFRs. Consequently, our studies reveal new insights into the pan-FGFR selectivity of LY2874455 and provide a structural basis for developing novel FGFR inhibitors that target FGFR1-4 broadly.

  6. Pathway-based outlier method reveals heterogeneous genomic structure of autism in blood transcriptome.

    Science.gov (United States)

    Campbell, Malcolm G; Kohane, Isaac S; Kong, Sek Won

    2013-09-24

    Decades of research strongly suggest that the genetic etiology of autism spectrum disorders (ASDs) is heterogeneous. However, most published studies focus on group differences between cases and controls. In contrast, we hypothesized that the heterogeneity of the disorder could be characterized by identifying pathways for which individuals are outliers rather than pathways representative of shared group differences of the ASD diagnosis. Two previously published blood gene expression data sets--the Translational Genetics Research Institute (TGen) dataset (70 cases and 60 unrelated controls) and the Simons Simplex Consortium (Simons) dataset (221 probands and 191 unaffected family members)--were analyzed. All individuals of each dataset were projected to biological pathways, and each sample's Mahalanobis distance from a pooled centroid was calculated to compare the number of case and control outliers for each pathway. Analysis of a set of blood gene expression profiles from 70 ASD and 60 unrelated controls revealed three pathways whose outliers were significantly overrepresented in the ASD cases: neuron development including axonogenesis and neurite development (29% of ASD, 3% of control), nitric oxide signaling (29%, 3%), and skeletal development (27%, 3%). Overall, 50% of cases and 8% of controls were outliers in one of these three pathways, which could not be identified using group comparison or gene-level outlier methods. In an independently collected data set consisting of 221 ASD and 191 unaffected family members, outliers in the neurogenesis pathway were heavily biased towards cases (20.8% of ASD, 12.0% of control). Interestingly, neurogenesis outliers were more common among unaffected family members (Simons) than unrelated controls (TGen), but the statistical significance of this effect was marginal (Chi squared P < 0.09). Unlike group difference approaches, our analysis identified the samples within the case and control groups that manifested each expression

  7. Genetic diversity and structure of Brazilian ginger germplasm (Zingiber officinale) revealed by AFLP markers.

    Science.gov (United States)

    Blanco, Eleonora Zambrano; Bajay, Miklos Maximiliano; Siqueira, Marcos Vinícius Bohrer Monteiro; Zucchi, Maria Imaculada; Pinheiro, José Baldin

    2016-12-01

    Ginger is a vegetable with medicinal and culinary properties widely cultivated in the Southern and Southeastern Brazil. The knowledge of ginger species' genetic variability is essential to direct correctly future studies of conservation and genetic improvement, but in Brazil, little is known about this species' genetic variability. In this study, we analyzed the genetic diversity and structure of 55 Brazilian accessions and 6 Colombian accessions of ginger, using AFLP (Amplified Fragment Length Polymorphism) molecular markers. The molecular characterization was based on 13 primers combinations, which generated an average of 113.5 polymorphic loci. The genetic diversity estimates of Nei (Hj), Shannon-Weiner index (I) and an effective number of alleles (n e ) were greater in the Colombian accessions in relation to the Brazilian accessions. The analysis of molecular variance showed that most of the genetic variation occurred between the two countries while in the Brazilian populations there is no genetic structure and probably each region harbors 100 % of genetic variation found in the samples. The bayesian model-based clustering and the dendrogram using the dissimilarity's coefficient of Jaccard were congruent with each other and showed that the Brazilian accessions are highly similar between themselves, regardless of the geographic region of origin. We suggested that the exploration of the interspecific variability and the introduction of new varieties of Z.officinale are viable alternatives for generating diversity in breeding programs in Brazil. The introduction of new genetic materials will certainly contribute to a higher genetic basis of such crop.

  8. Confirmatory factor analysis reveals a latent cognitive structure common to bipolar disorder, schizophrenia, and normal controls.

    Science.gov (United States)

    Schretlen, David J; Peña, Javier; Aretouli, Eleni; Orue, Izaskun; Cascella, Nicola G; Pearlson, Godfrey D; Ojeda, Natalia

    2013-06-01

    We sought to determine whether a single hypothesized latent factor structure would characterize cognitive functioning in three distinct groups. We assessed 576 adults (340 community controls, 126 adults with bipolar disorder, and 110 adults with schizophrenia) using 15 measures derived from nine cognitive tests. Confirmatory factor analysis (CFA) was conducted to examine the fit of a hypothesized six-factor model. The hypothesized factors included attention, psychomotor speed, verbal memory, visual memory, ideational fluency, and executive functioning. The six-factor model provided an excellent fit for all three groups [for community controls, root mean square error of approximation (RMSEA) schizophrenia, RMSEA = 0.06 and CFI = 0.98]. Alternate models that combined fluency with processing speed or verbal and visual memory reduced the goodness of fit. Multi-group CFA results supported factor invariance across the three groups. Confirmatory factor analysis supported a single six-factor structure of cognitive functioning among patients with schizophrenia or bipolar disorder and community controls. While the three groups clearly differ in level of performance, they share a common underlying architecture of information processing abilities. These cognitive factors could provide useful targets for clinical trials of treatments that aim to enhance information processing in persons with neurological and neuropsychiatric disorders. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  9. Crystal structure of equine serum albumin in complex with cetirizine reveals a novel drug binding site.

    Science.gov (United States)

    Handing, Katarzyna B; Shabalin, Ivan G; Szlachta, Karol; Majorek, Karolina A; Minor, Wladek

    2016-03-01

    Serum albumin (SA) is the main transporter of drugs in mammalian blood plasma. Here, we report the first crystal structure of equine serum albumin (ESA) in complex with antihistamine drug cetirizine at a resolution of 2.1Å. Cetirizine is bound in two sites--a novel drug binding site (CBS1) and the fatty acid binding site 6 (CBS2). Both sites differ from those that have been proposed in multiple reports based on equilibrium dialysis and fluorescence studies for mammalian albumins as cetirizine binding sites. We show that the residues forming the binding pockets in ESA are highly conserved in human serum albumin (HSA), and suggest that binding of cetirizine to HSA will be similar. In support of that hypothesis, we show that the dissociation constants for cetirizine binding to CBS2 in ESA and HSA are identical using tryptophan fluorescence quenching. Presence of lysine and arginine residues that have been previously reported to undergo nonenzymatic glycosylation in CBS1 and CBS2 suggests that cetirizine transport in patients with diabetes could be altered. A review of all available SA structures from the PDB shows that in addition to the novel drug binding site we present here (CBS1), there are two pockets on SA capable of binding drugs that do not overlap with fatty acid binding sites and have not been discussed in published reviews. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation

    Science.gov (United States)

    Pandey, R. B.; Jacobs, D. J.; Farmer, B. L.

    2017-05-01

    The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (Rg) of the protein exhibits a non-monotonic dependence on solvent interaction over a wide range of f within an effective medium, an abrupt collapse in Rg occurs in a narrow range of f when solute molecules rapidly bind to a preferential set of sites on the protein. The structure factor S(q) of the protein with wave vector (q) becomes oscillatory in the collapsed state, which reflects segmental correlations caused by spatial fluctuations in solute-protein binding. Spatial fluctuations in solute binding also modify the effective dimension (D) of the protein in fibrous (D ˜ 1.3), random-coil (D ˜ 1.75), and globular (D ˜ 3) conformational ensembles as the interaction strength increases, which differ from an effective medium with respect to the magnitude of D and the length scale.

  11. The shallow structure of Solfatara Volcano, Italy, revealed by dense, wide-aperture seismic profiling.

    Science.gov (United States)

    Bruno, Pier Paolo G; Maraio, Stefano; Festa, Gaetano

    2017-12-12

    Two active-source, high-resolution seismic profiles were acquired in the Solfatara tuff cone in May and November 2014, with dense, wide-aperture arrays. Common Receiver Surface processing was crucial in improving signal-to-noise ratio and reflector continuity. These surveys provide, for the first time, high-resolution seismic images of the Solfatara crater, depicting a ~400 m deep asymmetrical crater filled by volcanoclastic sediments and rocks and carved within an overall non-reflective pre-eruptive basement showing features consistent with the emplacement of shallow intrusive bodies. Seismic reflection data were interpreted using the trace complex attributes and clearly display several steep and segmented collapse faults, generally having normal kinematics and dipping toward the crater centre. Fault/fracture planes are imaged as sudden amplitude drops that generate narrow low-similarity and high-dip attributes. Uprising fluids degassed by a magmatic source are the most probable cause of the small-scale amplitude reduction. Seismic data also support the interpretation of the shallow structure of the Solfatara crater as a maar. Our results provides a solid framework to constrain the near-surface geological interpretation of such a complex area, which improves our understanding of the temporal changes of the structure in relation with other geophysical and geochemical measurements.

  12. The structure of the human ABC transporter ABCG2 reveals a novel mechanism for drug extrusion.

    Science.gov (United States)

    Khunweeraphong, Narakorn; Stockner, Thomas; Kuchler, Karl

    2017-10-23

    The human ABC transporter ABCG2 (Breast Cancer Resistance Protein, BCRP) is implicated in anticancer resistance, in detoxification across barriers and linked to gout. Here, we generate a novel atomic model of ABCG2 using the crystal structure of ABCG5/G8. Extensive mutagenesis verifies the structure, disclosing hitherto unrecognized essential residues and domains in the homodimeric ABCG2 transporter. The elbow helix, the first intracellular loop (ICL1) and the nucleotide-binding domain (NBD) constitute pivotal elements of the architecture building the transmission interface that borders a central cavity which acts as a drug trap. The transmission interface is stabilized by salt-bridge interactions between the elbow helix and ICL1, as well as within ICL1, which is essential to control the conformational switch of ABCG2 to the outward-open drug-releasing conformation. Importantly, we propose that ICL1 operates like a molecular spring that holds the NBD dimer close to the membrane, thereby enabling efficient coupling of ATP hydrolysis during the catalytic cycle. These novel mechanistic data open new opportunities to therapeutically target ABCG2 in the context of related diseases.

  13. Mesoscopic Community Structure of Financial Markets Revealed by Price and Sign Fluctuations.

    Science.gov (United States)

    Almog, Assaf; Besamusca, Ferry; MacMahon, Mel; Garlaschelli, Diego

    2015-01-01

    The mesoscopic organization of complex systems, from financial markets to the brain, is an intermediate between the microscopic dynamics of individual units (stocks or neurons, in the mentioned cases), and the macroscopic dynamics of the system as a whole. The organization is determined by "communities" of units whose dynamics, represented by time series of activity, is more strongly correlated internally than with the rest of the system. Recent studies have shown that the binary projections of various financial and neural time series exhibit nontrivial dynamical features that resemble those of the original data. This implies that a significant piece of information is encoded into the binary projection (i.e. the sign) of such increments. Here, we explore whether the binary signatures of multiple time series can replicate the same complex community organization of the financial market, as the original weighted time series. We adopt a method that has been specifically designed to detect communities from cross-correlation matrices of time series data. Our analysis shows that the simpler binary representation leads to a community structure that is almost identical with that obtained using the full weighted representation. These results confirm that binary projections of financial time series contain significant structural information.

  14. Two-Photon Autofluorescence Imaging Reveals Cellular Structures Throughout the Retina of the Living Primate Eye.

    Science.gov (United States)

    Sharma, Robin; Williams, David R; Palczewska, Grazyna; Palczewski, Krzysztof; Hunter, Jennifer J

    2016-02-01

    Although extrinsic fluorophores can be introduced to label specific cell types in the retina, endogenous fluorophores, such as NAD(P)H, FAD, collagen, and others, are present in all retinal layers. These molecules are a potential source of optical contrast and can enable noninvasive visualization of all cellular layers. We used a two-photon fluorescence adaptive optics scanning light ophthalmoscope (TPF-AOSLO) to explore the native autofluorescence of various cell classes spanning several layers in the unlabeled retina of a living primate eye. Three macaques were imaged on separate occasions using a custom TPF-AOSLO. Two-photon fluorescence was evoked by pulsed light at 730 and 920 nm excitation wavelengths, while fluorescence emission was collected in the visible range from several retinal layers and different locations. Backscattered light was recorded simultaneously in confocal modality and images were postprocessed to remove eye motion. All retinal layers yielded two-photon signals and the heterogeneous distribution of fluorophores provided optical contrast. Several structural features were observed, such as autofluorescence from vessel walls, Müller cell processes in the nerve fibers, mosaics of cells in the ganglion cell and other nuclear layers of the inner retina, as well as photoreceptor and RPE layers in the outer retina. This in vivo survey of two-photon autofluorescence throughout the primate retina demonstrates a wider variety of structural detail in the living eye than is available through conventional imaging methods, and broadens the use of two-photon imaging of normal and diseased eyes.

  15. Structural differences between yeast and mammalian microtubules revealed by cryo-EM

    Energy Technology Data Exchange (ETDEWEB)

    Howes, Stuart C. [Univ. of California, Berkeley, CA (United States). Biophysics Graduate Group; Geyer, Elisabeth A. [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Biophysics; Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Biochemistry; LaFrance, Benjamin [Univ. of California, Berkeley, CA (United States). Molecular and Cell Biology Graduate Program; Zhang, Rui [Univ. of California, Berkeley, CA (United States). Howard Hughes Medical Inst.; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division; Kellogg, Elizabeth H. [Univ. of California, Berkeley, CA (United States). Howard Hughes Medical Inst.; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division; Westermann, Stefan [Univ. of Duisburg-Essen, Essen (Germany). Dept. of Molecular Genetics, Center for Medical Biotechnology; Rice, Luke M. [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Biophysics; Univ. of Texas Southwestern Medical Center, Dallas, TX (United States). Dept. of Biochemistry; Nogales, Eva [Univ. of California, Berkeley, CA (United States). Howard Hughes Medical Inst.; Univ. of California, Berkeley, CA (United States). Dept. of Molecular Biology and California Inst. for Quantitative Biosciences; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Molecular Biophysics and Integrated Bioimaging Division

    2017-06-26

    Microtubules are polymers of αβ-tubulin heterodimers essential for all eukaryotes. Despite sequence conservation, there are significant structural differences between microtubules assembled in vitro from mammalian or budding yeast tubulin. Yeast MTs were not observed to undergo compaction at the interdimer interface as seen for mammalian microtubules upon GTP hydrolysis. Lack of compaction might reflect slower GTP hydrolysis or a different degree of allosteric coupling in the lattice. The microtubule plus end–tracking protein Bim1 binds yeast microtubules both between αβ-tubulin heterodimers, as seen for other organisms, and within tubulin dimers, but binds mammalian tubulin only at interdimer contacts. At the concentrations used in cryo-electron microscopy, Bim1 causes the compaction of yeast microtubules and induces their rapid disassembly. In conclusion, our studies demonstrate structural differences between yeast and mammalian microtubules that likely underlie their differing polymerization dynamics. These differences may reflect adaptations to the demands of different cell size or range of physiological growth temperatures.

  16. Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation.

    Science.gov (United States)

    Glyde, Robert; Ye, Fuzhou; Darbari, Vidya Chandran; Zhang, Nan; Buck, Martin; Zhang, Xiaodong

    2017-07-06

    Gene transcription is carried out by RNA polymerases (RNAPs). For transcription to occur, the closed promoter complex (RPc), where DNA is double stranded, must isomerize into an open promoter complex (RPo), where the DNA is melted out into a transcription bubble and the single-stranded template DNA is delivered to the RNAP active site. Using a bacterial RNAP containing the alternative σ 54 factor and cryoelectron microscopy, we determined structures of RPc and the activator-bound intermediate complex en route to RPo at 3.8 and 5.8 Å. Our structures show how RNAP-σ 54 interacts with promoter DNA to initiate the DNA distortions required for transcription bubble formation, and how the activator interacts with RPc, leading to significant conformational changes in RNAP and σ 54 that promote RPo formation. We propose that DNA melting is an active process initiated in RPc and that the RNAP conformations of intermediates are significantly different from that of RPc and RPo. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  17. Structural and functional properties of hemoglobins from unicellular organisms as revealed by resonance Raman spectroscopy.

    Science.gov (United States)

    Egawa, Tsuyoshi; Yeh, Syun-Ru

    2005-01-01

    Hemoglobins have been discovered in organisms from virtually all kingdoms. Their presence in unicellular organisms suggests that the gene for hemoglobin is very ancient and that the hemoglobins must have functions other than oxygen transport, in view of the fact that O2 delivery is a diffusion-controlled process in these organisms. Based on sequence alignment, three groups of hemoglobins have been characterized in unicellular organisms. The group-one hemoglobins, termed truncated hemoglobins, consist of proteins with 110-140 amino acid residues and a novel two-over-two alpha-helical sandwich motif. The group-two hemoglobins, termed flavohemoglobins, consist of a hemoglobin domain, with a classical three-over-three alpha-helical sandwich motif, and a flavin-containing reductase domain that is covalently attached to it. The group-three hemoglobins consist of myoglobin-like proteins that have high sequence homology and structural similarity to the hemoglobin domain of flavohemoglobins. In this review, recent resonance Raman studies of each group of these proteins are presented. Their implications are discussed in the context of the structural and functional properties of these novel hemoglobins.

  18. Mesoscopic Community Structure of Financial Markets Revealed by Price and Sign Fluctuations.

    Directory of Open Access Journals (Sweden)

    Assaf Almog

    Full Text Available The mesoscopic organization of complex systems, from financial markets to the brain, is an intermediate between the microscopic dynamics of individual units (stocks or neurons, in the mentioned cases, and the macroscopic dynamics of the system as a whole. The organization is determined by "communities" of units whose dynamics, represented by time series of activity, is more strongly correlated internally than with the rest of the system. Recent studies have shown that the binary projections of various financial and neural time series exhibit nontrivial dynamical features that resemble those of the original data. This implies that a significant piece of information is encoded into the binary projection (i.e. the sign of such increments. Here, we explore whether the binary signatures of multiple time series can replicate the same complex community organization of the financial market, as the original weighted time series. We adopt a method that has been specifically designed to detect communities from cross-correlation matrices of time series data. Our analysis shows that the simpler binary representation leads to a community structure that is almost identical with that obtained using the full weighted representation. These results confirm that binary projections of financial time series contain significant structural information.

  19. Effect of iron oxide loading on magnetoferritin structure in solution as revealed by SAXS and SANS.

    Science.gov (United States)

    Melníková, L; Petrenko, V I; Avdeev, M V; Garamus, V M; Almásy, L; Ivankov, O I; Bulavin, L A; Mitróová, Z; Kopčanský, P

    2014-11-01

    Synthetic biological macromolecule of magnetoferritin containing an iron oxide core inside a protein shell (apoferritin) is prepared with different content of iron. Its structure in aqueous solution is analysed by small-angle synchrotron X-ray (SAXS) and neutron (SANS) scattering. The loading factor (LF) defined as the average number of iron atoms per protein is varied up to LF=800. With an increase of the LF, the scattering curves exhibit a relative increase in the total scattered intensity, a partial smearing and a shift of the match point in the SANS contrast variation data. The analysis shows an increase in the polydispersity of the proteins and a corresponding effective increase in the relative content of magnetic material against the protein moiety of the shell with the LF growth. At LFs above ∼150, the apoferritin shell undergoes structural changes, which is strongly indicative of the fact that the shell stability is affected by iron oxide presence. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Structural, Bioinformatic, and In Vivo Analyses of Two Treponema pallidum Lipoproteins Reveal a Unique TRAP Transporter

    Energy Technology Data Exchange (ETDEWEB)

    Deka, Ranjit K.; Brautigam, Chad A.; Goldberg, Martin; Schuck, Peter; Tomchick, Diana R.; Norgard, Michael V. (NIH); (UTSMC)

    2012-05-25

    Treponema pallidum, the bacterial agent of syphilis, is predicted to encode one tripartite ATP-independent periplasmic transporter (TRAP-T). TRAP-Ts typically employ a periplasmic substrate-binding protein (SBP) to deliver the cognate ligand to the transmembrane symporter. Herein, we demonstrate that the genes encoding the putative TRAP-T components from T. pallidum, tp0957 (the SBP), and tp0958 (the symporter), are in an operon with an uncharacterized third gene, tp0956. We determined the crystal structure of recombinant Tp0956; the protein is trimeric and perforated by a pore. Part of Tp0956 forms an assembly similar to those of 'tetratricopeptide repeat' (TPR) motifs. The crystal structure of recombinant Tp0957 was also determined; like the SBPs of other TRAP-Ts, there are two lobes separated by a cleft. In these other SBPs, the cleft binds a negatively charged ligand. However, the cleft of Tp0957 has a strikingly hydrophobic chemical composition, indicating that its ligand may be substantially different and likely hydrophobic. Analytical ultracentrifugation of the recombinant versions of Tp0956 and Tp0957 established that these proteins associate avidly. This unprecedented interaction was confirmed for the native molecules using in vivo cross-linking experiments. Finally, bioinformatic analyses suggested that this transporter exemplifies a new subfamily of TPATs (TPR-protein-associated TRAP-Ts) that require the action of a TPR-containing accessory protein for the periplasmic transport of a potentially hydrophobic ligand(s).