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Sample records for biophys biomol struct

  1. Multi-language Struct Support in Babel

    Energy Technology Data Exchange (ETDEWEB)

    Ebner, D; Prantl, A; Epperly, T W

    2011-03-22

    Babel is an open-source language interoperability framework tailored to the needs of high-performance scientific computing. As an integral element of the Common Component Architecture (CCA) it is used in a wide range of research projects. In this paper we describe how we extended Babel to support interoperable tuple data types (structs). Structs are a common idiom in scientific APIs; they are an efficient way to pass tuples of nonuniform data between functions, and are supported natively by most programming languages. Using our extended version of Babel, developers of scientific code can now pass structs as arguments between functions implemented in any of the supported languages. In C, C++ and Fortran 2003, structs can be passed without the overhead of data marshaling or copying, providing language interoperability at minimal cost. Other supported languages are Fortran 77, Fortran 90, Java and Python. We will show how we designed a struct implementation that is interoperable with all of the supported languages and present benchmark data compare the performance of all language bindings, highlighting the differences between languages that offer native struct support and an object-oriented interface with getter/setter methods.

  2. UTILIZATION OF BIOMOL AND TEA COMPOST SOLUTION FERMENTED BY THE FUNGUS Trichoderma spp. ON THE GROWTH OF SOYBEAN (Glycine Max (L. Merr. IN DRY LAND

    Directory of Open Access Journals (Sweden)

    Zurriyatun Solihah

    2017-02-01

    Full Text Available ABSTRACT The purpose of this research is to know whether the use of Biomol and Tea Compost solution fermented by Trichoderma spp. can increase the growth and development of soybean plants in dry land. The experiment was conducted in the field and was arranged according to a Split Plot Design with the main plot is Tea Compost Solution with 4 levels of treatment, i.e. at the rate of 0, 5, 10, or 15 liters/plot and the subplot is Biomol solution with 4 levels of treatment, i.e. 0, 5, 10, or 15 liters/plot. The treatments were repeated three times. The results showed that the use of the Biomol at the rate of 15 liters/plot and Tea Compost at the of 15 liters/plot can increase the growth and development of soybean plants mainly on plant height. In addition, Biomol and Tea Compost solution applied to soybean can  increase the weight of the wet and the dry berangkasan Keywords: Biomol, Tea Compost, Soybean, Trichoderma spp.

  3. Applications of the BIOPHYS Algorithm for Physically-Based Retrieval of Biophysical, Structural and Forest Disturbance Information

    Science.gov (United States)

    Peddle, Derek R.; Huemmrich, K. Fred; Hall, Forrest G.; Masek, Jeffrey G.; Soenen, Scott A.; Jackson, Chris D.

    2011-01-01

    Canopy reflectance model inversion using look-up table approaches provides powerful and flexible options for deriving improved forest biophysical structural information (BSI) compared with traditional statistical empirical methods. The BIOPHYS algorithm is an improved, physically-based inversion approach for deriving BSI for independent use and validation and for monitoring, inventory and quantifying forest disturbance as well as input to ecosystem, climate and carbon models. Based on the multiple-forward mode (MFM) inversion approach, BIOPHYS results were summarized from different studies (Minnesota/NASA COVER; Virginia/LEDAPS; Saskatchewan/BOREAS), sensors (airborne MMR; Landsat; MODIS) and models (GeoSail; GOMS). Applications output included forest density, height, crown dimension, branch and green leaf area, canopy cover, disturbance estimates based on multi-temporal chronosequences, and structural change following recovery from forest fires over the last century. Good correspondences with validation field data were obtained. Integrated analyses of multiple solar and view angle imagery further improved retrievals compared with single pass data. Quantifying ecosystem dynamics such as the area and percent of forest disturbance, early regrowth and succession provide essential inputs to process-driven models of carbon flux. BIOPHYS is well suited for large-area, multi-temporal applications involving multiple image sets and mosaics for assessing vegetation disturbance and quantifying biophysical structural dynamics and change. It is also suitable for integration with forest inventory, monitoring, updating, and other programs.

  4. StructRNAfinder: an automated pipeline and web server for RNA families prediction.

    Science.gov (United States)

    Arias-Carrasco, Raúl; Vásquez-Morán, Yessenia; Nakaya, Helder I; Maracaja-Coutinho, Vinicius

    2018-02-17

    The function of many noncoding RNAs (ncRNAs) depend upon their secondary structures. Over the last decades, several methodologies have been developed to predict such structures or to use them to functionally annotate RNAs into RNA families. However, to fully perform this analysis, researchers should utilize multiple tools, which require the constant parsing and processing of several intermediate files. This makes the large-scale prediction and annotation of RNAs a daunting task even to researchers with good computational or bioinformatics skills. We present an automated pipeline named StructRNAfinder that predicts and annotates RNA families in transcript or genome sequences. This single tool not only displays the sequence/structural consensus alignments for each RNA family, according to Rfam database but also provides a taxonomic overview for each assigned functional RNA. Moreover, we implemented a user-friendly web service that allows researchers to upload their own nucleotide sequences in order to perform the whole analysis. Finally, we provided a stand-alone version of StructRNAfinder to be used in large-scale projects. The tool was developed under GNU General Public License (GPLv3) and is freely available at http://structrnafinder.integrativebioinformatics.me . The main advantage of StructRNAfinder relies on the large-scale processing and integrating the data obtained by each tool and database employed along the workflow, of which several files are generated and displayed in user-friendly reports, useful for downstream analyses and data exploration.

  5. ObStruct: a method to objectively analyse factors driving population structure using Bayesian ancestry profiles.

    Directory of Open Access Journals (Sweden)

    Velimir Gayevskiy

    Full Text Available Bayesian inference methods are extensively used to detect the presence of population structure given genetic data. The primary output of software implementing these methods are ancestry profiles of sampled individuals. While these profiles robustly partition the data into subgroups, currently there is no objective method to determine whether the fixed factor of interest (e.g. geographic origin correlates with inferred subgroups or not, and if so, which populations are driving this correlation. We present ObStruct, a novel tool to objectively analyse the nature of structure revealed in Bayesian ancestry profiles using established statistical methods. ObStruct evaluates the extent of structural similarity between sampled and inferred populations, tests the significance of population differentiation, provides information on the contribution of sampled and inferred populations to the observed structure and crucially determines whether the predetermined factor of interest correlates with inferred population structure. Analyses of simulated and experimental data highlight ObStruct's ability to objectively assess the nature of structure in populations. We show the method is capable of capturing an increase in the level of structure with increasing time since divergence between simulated populations. Further, we applied the method to a highly structured dataset of 1,484 humans from seven continents and a less structured dataset of 179 Saccharomyces cerevisiae from three regions in New Zealand. Our results show that ObStruct provides an objective metric to classify the degree, drivers and significance of inferred structure, as well as providing novel insights into the relationships between sampled populations, and adds a final step to the pipeline for population structure analyses.

  6. Addendum: Compliant electrostatic chuck based on hairy microstructure (2013 Smart Mater. Struct. 22 015019) and Electrostatic chuck consisting of polymeric electrostatic inductive fibers for handling of objects with rough surfaces (2013 Smart Mater. Struct. 22 095010)

    International Nuclear Information System (INIS)

    Saito, Shigeki; Soda, Fumiaki; Sawai, Kenji; Dhelika, Radon; Kikutani, Takeshi; Takarada, Wataru; Takahashi, Kunio

    2014-01-01

    The recent papers Saito et al 2013 Smart Mater. Struct. 22 015019 and Dhelika et al 2013 Smart Mater. Struct. 22 095010 described studies of an electrostatic chuck that mimics the structure of gecko-like toes. Earlier work published by the authors and other researchers is cited to further illustrate the origin and motivation of the research. (paper)

  7. Physically-based Canopy Reflectance Model Inversion of Vegetation Biophysical-Structural Information from Terra-MODIS Imagery in Boreal and Mountainous Terrain for Ecosystem, Climate and Carbon Models using the BIOPHYS-MFM Algorithm

    Science.gov (United States)

    Peddle, D. R.; Hall, F.

    2009-12-01

    The BIOPHYS algorithm provides innovative and flexible methods for the inversion of canopy reflectance models (CRM) to derive essential biophysical structural information (BSI) for quantifying vegetation state and disturbance, and for input to ecosystem, climate and carbon models. Based on spectral, angular, temporal and scene geometry inputs that can be provided or automatically derived, the BIOPHYS Multiple-Forward Mode (MFM) approach generates look-up tables (LUTs) that comprise reflectance data, structural inputs over specified or computed ranges, and the associated CRM output from forward mode runs. Image pixel and model LUT spectral values are then matched. The corresponding BSI retrieved from the LUT matches is output as the BSI results. BIOPHYS-MFM has been extensively used with agencies in Canada and the USA over the past decade (Peddle et al 2000-09; Soenen et al 2005-09; Gamon et al 2004; Cihlar et al 2003), such as CCRS, CFS, AICWR, NASA LEDAPS, BOREAS and MODIS Science Teams, and for the North American Carbon Program. The algorithm generates BSI products such as land cover, biomass, stand volume, stem density, height, crown closure, leaf area index (LAI) and branch area, crown dimension, productivity, topographic correction, structural change from harvest, forest fires and mountain pine beetle damage, and water / hydrology applications. BIOPHYS-MFM has been applied in different locations in Canada (six provinces from Newfoundland to British Columbia) and USA (NASA COVER, MODIS and LEDAPS sites) using 7 different CRM models and a variety of imagery (e.g. MODIS, Landsat, SPOT, IKONOS, airborne MSV, MMR, casi, Probe-1, AISA). In this paper we summarise the BIOPHYS-MFM algorithm and results from Terra-MODIS imagery from MODIS validation sites at Kananaskis Alberta in the Canadian Rocky Mountains, and from the Boreal Ecosystem Atmosphere Study (BOREAS) in Saskatchewan Canada. At the montane Rocky Mountain site, BIOPHYS-MFM density estimates were within

  8. Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data.

    Science.gov (United States)

    Greenfeld, Max; van de Meent, Jan-Willem; Pavlichin, Dmitri S; Mabuchi, Hideo; Wiggins, Chris H; Gonzalez, Ruben L; Herschlag, Daniel

    2015-01-16

    Single-molecule techniques have emerged as incisive approaches for addressing a wide range of questions arising in contemporary biological research [Trends Biochem Sci 38:30-37, 2013; Nat Rev Genet 14:9-22, 2013; Curr Opin Struct Biol 2014, 28C:112-121; Annu Rev Biophys 43:19-39, 2014]. The analysis and interpretation of raw single-molecule data benefits greatly from the ongoing development of sophisticated statistical analysis tools that enable accurate inference at the low signal-to-noise ratios frequently associated with these measurements. While a number of groups have released analysis toolkits as open source software [J Phys Chem B 114:5386-5403, 2010; Biophys J 79:1915-1927, 2000; Biophys J 91:1941-1951, 2006; Biophys J 79:1928-1944, 2000; Biophys J 86:4015-4029, 2004; Biophys J 97:3196-3205, 2009; PLoS One 7:e30024, 2012; BMC Bioinformatics 288 11(8):S2, 2010; Biophys J 106:1327-1337, 2014; Proc Int Conf Mach Learn 28:361-369, 2013], it remains difficult to compare analysis for experiments performed in different labs due to a lack of standardization. Here we propose a standardized single-molecule dataset (SMD) file format. SMD is designed to accommodate a wide variety of computer programming languages, single-molecule techniques, and analysis strategies. To facilitate adoption of this format we have made two existing data analysis packages that are used for single-molecule analysis compatible with this format. Adoption of a common, standard data file format for sharing raw single-molecule data and analysis outcomes is a critical step for the emerging and powerful single-molecule field, which will benefit both sophisticated users and non-specialists by allowing standardized, transparent, and reproducible analysis practices.

  9. SucStruct: Prediction of succinylated lysine residues by using structural properties of amino acids.

    Science.gov (United States)

    López, Yosvany; Dehzangi, Abdollah; Lal, Sunil Pranit; Taherzadeh, Ghazaleh; Michaelson, Jacob; Sattar, Abdul; Tsunoda, Tatsuhiko; Sharma, Alok

    2017-06-15

    Post-Translational Modification (PTM) is a biological reaction which contributes to diversify the proteome. Despite many modifications with important roles in cellular activity, lysine succinylation has recently emerged as an important PTM mark. It alters the chemical structure of lysines, leading to remarkable changes in the structure and function of proteins. In contrast to the huge amount of proteins being sequenced in the post-genome era, the experimental detection of succinylated residues remains expensive, inefficient and time-consuming. Therefore, the development of computational tools for accurately predicting succinylated lysines is an urgent necessity. To date, several approaches have been proposed but their sensitivity has been reportedly poor. In this paper, we propose an approach that utilizes structural features of amino acids to improve lysine succinylation prediction. Succinylated and non-succinylated lysines were first retrieved from 670 proteins and characteristics such as accessible surface area, backbone torsion angles and local structure conformations were incorporated. We used the k-nearest neighbors cleaning treatment for dealing with class imbalance and designed a pruned decision tree for classification. Our predictor, referred to as SucStruct (Succinylation using Structural features), proved to significantly improve performance when compared to previous predictors, with sensitivity, accuracy and Mathew's correlation coefficient equal to 0.7334-0.7946, 0.7444-0.7608 and 0.4884-0.5240, respectively. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Membranes suited for immobilizing biomolecules

    NARCIS (Netherlands)

    2009-01-01

    The present invention relates to flow-through membranes suitable for the immobilization of biomols., methods for the prepn. of such membranes and the use of such membranes for the immobilization of biomols. and subsequent detection of immobilized biomols. The invention concerns a flow-through

  11. La combinación de los azúcares con las biomoléculas: Desde la cocina al organismo The combination of sugars with biomolecules: From the kitchen to the organism

    Directory of Open Access Journals (Sweden)

    Juan Pablo Rossi

    2007-04-01

    Full Text Available A pesar de nuestra profesión, cuando cocinamos no reflexionamos demasiado acerca de lo complejas que resultan las operaciones culinarias desde el punto de vista químico. Nuestra condición humana requiere alimentarnos con productos que además de nutrirnos, sorprendan nuestros sentidos y nos satisfagan espiritualmente. Para introducirnos en la complejidad de los alimentos es necesario comprender la diferencia entre gusto y sabor y relacionarlos con los alimentos resultantes de la combinación de diversas biomoléculas. Debemos a ciertas reacciones químicas la generación de una enorme variedad de compuestos aromáticos, que combinados en forma adecuada, producen alimentos de los cuales disfrutamos diariamente. Mucho de este tema gira alrededor de Louis Camille Maillard, un médico que a principios del siglo XX estudió la combinación de los azúcares con las proteínas. Su principal aporte fue relacionar los procesos culinarios con los que ocurren en el organismo. Las reacciones de Maillard -la llamada glucosilación no enzimática- modifican profundamente las biomoléculas, como se ha comprobado en muchos trabajos científicos. En el organismo las reacciones de Maillard son similares a las que ocurren en la cocina, pero transcurren más lentamente y se relacionan con la enfermedad y el envejecimiento.In spite of our profession, when we cook we do not think too much about the complex processes that take place in culinary operations from the chemical point of view. Our human nature makes us desire not only a meal that nourishes us, but also surprises our senses and satisfies us spiritually. In order to introduce ourselves in the complexity of food, it is necessary to understand the difference between taste and flavor, and to relate them to food as an outcome of a diverse combination of biomolecules. We owe to certain chemical reactions the generation of an enormous variety of aromatic compounds that combined in a suitable way, produce the

  12. Perspective: revisiting the field dependence of TROSY sensitivity

    Energy Technology Data Exchange (ETDEWEB)

    Takeuchi, Koh [National Institute of Advanced Industrial Science and Technology, Molecular Profiling Research Center for Drug Discovery (Japan); Arthanari, Haribabu [Dana Farber Cancer Institute, Department of Cancer Biology (United States); Wagner, Gerhard, E-mail: gerhard-wagner@hms.harvard.edu [Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology (United States)

    2016-12-15

    The discovery of the TROSY effect (Pervushin et al. in Proc Natl Acad Sci USA 94:12366–12371, 1997) for reducing transverse relaxation and line sharpening through selecting pathways in which dipole–dipole and CSA Hamiltonians partially cancel each other had a tremendous impact on solution NMR studies of macromolecules. Together with the methyl TROSY (Tugarinov and Kay in J Biomol NMR 28:165–172, 2004) it enabled structural and functional studies of significantly larger systems. The optimal field strengths for TROSY have been estimated to be on spectrometers operating around 900 MHz (21.14 T) for the {sup 1}H{sub N} TROSY (Pervushin et al. in Proc Natl Acad Sci USA 94:12366–12371, 1997) while the aromatic {sup 13}C ({sup 13}C{sub aro}) TROSY is posited to be optimal at around 600 MHz (14.09 T) (Pervushin et al. in J Am Chem Soc 120:6394–6400, 1998b; Pervushin in Q Rev Biophys 33:161–197, 2000). The initial rational was based on the consideration of where the quadratic B{sub 0} field dependences of the TROSY relaxation rates reach a minimum. For sensitivity consideration, however, it is interesting to estimate which field strengths yield the tallest peaks. Recent studies of {sup 15}N-detected TROSYs suggested that maximal peak heights are expected at 1.15 GHz (27.01 T) although the slowest relaxation rates or longest transverse relaxation times T{sub 2} are indeed expected around 900 MHz (21.14 T) (Takeuchi in J Biomol NMR 63:323–331, 2015; Takeuchi et al. in J Biomol NMR 64:143–151, 2016). This was based on the fact that the heights of Lorentzian lines are proportional to B{sub o}{sup 3/2} * T{sub 2} (B{sub o}). Thus, multiplying the parabolic T{sub 2}(B{sub o}) dependence with the increasing function of B{sub o}{sup 3/2} shifts the maxima of peak-height field dependence from the T{sub 2} maximum at 900 MHz to higher fields. Moreover, besides shifting the peak height maximum for {sup 15}N TROSY, this analysis yields estimates for optimal peak

  13. An extended sampling of the configurational space of HPr from E-coli

    NARCIS (Netherlands)

    de Groot, B.L.; Amadei, A; Scheek, R.M.; van Nuland, N.A.J.; Berendsen, H.J.C.

    1996-01-01

    Recently, we developed a method (Amadei et al., J. Biomol, Str. Dyn, 13: 815-626; de Groot et al., J. Biomol. Str. Dyn. 13: 741-751, 1996) to obtain an extended sampling of the configurational space of proteins, casing an adapted form of molecular dynamics (MD) simulations, based on the essential

  14. An extended sampling of the configurational space of HPr from E-coli

    NARCIS (Netherlands)

    de Groot, B.L.; Amadei, A; Scheek, R.M.; van Nuland, N.A.J.; Berendsen, H.J.C.

    Recently, we developed a method (Amadei et al., J. Biomol, Str. Dyn, 13: 815-626; de Groot et al., J. Biomol. Str. Dyn. 13: 741-751, 1996) to obtain an extended sampling of the configurational space of proteins, casing an adapted form of molecular dynamics (MD) simulations, based on the essential

  15. Study of ethanol-lysozyme interactions using neutron diffraction

    International Nuclear Information System (INIS)

    Lehmann, M.S.; Mason, S.A.; McIntyre, G.J.

    1985-01-01

    Single-crystal neutron diffraction has been used to observe the interactions between deuterated ethanol (CD3CD2OH) and lysozyme in triclinic crystals of hen egg white lysozyme soaked in 25% (v/v) ethanol solutions. A total of 6047 observed reflections to a resolution of 2 A were used, and 13 possible ethanol sites were identified. The three highest occupied sites are close to locations for bromoethanol found in an earlier study by Yonath et al. [Yonath, A., Podjarny, A., Honig, B., Traub, W., Sielecki, A., Herzberg, O., and Moult, J. (1978) Biophys. Struct. Mech. 4, 27-36]. Structure refinements including a model for the flat solvent lead to a final crystallographic agreement factor of 0.097. Comparison with earlier neutron studies on triclinic lysozyme showed that neither the molecular structure nor the thermal motions were affected significantly by the ethanol. A detailed analysis of the ethanol-lysozyme contacts showed 61% of these to be with hydrophobic sites, in agreement with the dominant hydrophobic nature of ethanol. This, together with the fact that the molecular structure of lysozyme is not perturbed, suggests a model for denaturation of lysozyme by alcohol, which proceeds via a dehydration of the protein at high alcohol concentration

  16. Cross-language Babel structs—making scientific interfaces more efficient

    International Nuclear Information System (INIS)

    Prantl, Adrian; Epperly, Thomas G W; Ebner, Dietmar

    2013-01-01

    Babel is an open-source language interoperability framework tailored to the needs of high-performance scientific computing. As an integral element of the Common Component Architecture, it is employed in a wide range of scientific applications where it is used to connect components written in different programming languages. In this paper we describe how we extended Babel to support interoperable tuple data types (structs). Structs are a common idiom in (mono-lingual) scientific application programming interfaces (APIs); they are an efficient way to pass tuples of nonuniform data between functions, and are supported natively by most programming languages. Using our extended version of Babel, developers of scientific codes can now pass structs as arguments between functions implemented in any of the supported languages. In C, C++, Fortran 2003/2008 and Chapel, structs can be passed without the overhead of data marshaling or copying, providing language interoperability at minimal cost. Other supported languages are Fortran 77, Fortran 90/95, Java and Python. We will show how we designed a struct implementation that is interoperable with all of the supported languages and present benchmark data to compare the performance of all language bindings, highlighting the differences between languages that offer native struct support and an object-oriented interface with getter/setter methods. A case study shows how structs can help simplify the interfaces of scientific codes significantly. (paper)

  17. UNC Pembroke Laser Scanning Confocal Microscopy Facility

    Science.gov (United States)

    2016-04-29

    an aggregation-dependent manner. Biochim Biophys Acta (Mol. Basis of Disease) 1812:1664-1674. Technology Transfer 1    Scientific progress and...receptors and presynaptic markers in an aggregation-dependent manner. Biochim Biophys Acta (Mol. Basis of Disease) 1812:1664-1674.

  18. Composite materials with arbitrary geometry - computer analysis with MATMEC

    DEFF Research Database (Denmark)

    Nielsen, Lauge Fuglsang

    1999-01-01

    Text note for the Summer school on "Hydration and Microstructure of High Performance Concrete, held at Dept. Struct. Eng. and Materials, DTU.......Text note for the Summer school on "Hydration and Microstructure of High Performance Concrete, held at Dept. Struct. Eng. and Materials, DTU....

  19. Effects of Polymer Hydrophobicity on Protein Structure and Aggregation Kinetics in Crowded Milieu.

    Science.gov (United States)

    Breydo, Leonid; Sales, Amanda E; Frege, Telma; Howell, Mark C; Zaslavsky, Boris Y; Uversky, Vladimir N

    2015-05-19

    We examined the effects of water-soluble polymers of various degrees of hydrophobicity on the folding and aggregation of proteins. The polymers we chose were polyethylene glycol (PEG) and UCON (1:1 copolymer of ethylene glycol and propylene glycol). The presence of additional methyl groups in UCON makes it more hydrophobic than PEG. Our earlier analysis revealed that similarly sized PEG and UCON produced different changes in the solvent properties of water in their solutions and induced morphologically different α-synuclein aggregates [Ferreira, L. A., et al. (2015) Role of solvent properties of aqueous media in macromolecular crowding effects. J. Biomol. Struct. Dyn., in press]. To improve our understanding of molecular mechanisms defining behavior of proteins in a crowded environment, we tested the effects of these polymers on secondary and tertiary structure and aromatic residue solvent accessibility of 10 proteins [five folded proteins, two hybrid proteins; i.e., protein containing ordered and disordered domains, and three intrinsically disordered proteins (IDPs)] and on the aggregation kinetics of insulin and α-synuclein. We found that effects of both polymers on secondary and tertiary structures of folded and hybrid proteins were rather limited with slight unfolding observed in some cases. Solvent accessibility of aromatic residues was significantly increased for the majority of the studied proteins in the presence of UCON but not PEG. PEG also accelerated the aggregation of protein into amyloid fibrils, whereas UCON promoted aggregation to amyloid oligomers instead. These results indicate that even a relatively small change in polymer structure leads to a significant change in the effect of this polymer on protein folding and aggregation. This is an indication that protein folding and especially aggregation are highly sensitive to the presence of other macromolecules, and an excluded volume effect is insufficient to describe their effect.

  20. Prediction of proton chemical shifts in RNA - Their use in structure refinement and validation

    International Nuclear Information System (INIS)

    Cromsigt, Jenny A.M.T.C.; Hilbers, Cees W.; Wijmenga, Sybren S.

    2001-01-01

    An analysis is presented of experimental versus calculated chemical shifts of the non-exchangeable protons for 28 RNA structures deposited in the Protein Data Bank, covering a wide range of structural building blocks. We have used existing models for ring-current and magnetic-anisotropy contributions to calculate the proton chemical shifts from the structures. Two different parameter sets were tried: (i) parameters derived by Ribas-Prado and Giessner-Prettre (GP set) [(1981) J. Mol. Struct.,76, 81-92.]; (ii) parameters derived by Case [(1995) J. Biomol. NMR, 6, 341-346]. Both sets lead to similar results. The detailed analysis was carried using the GP set. The root-mean-square-deviation between the predicted and observed chemical shifts of the complete database is 0.16 ppm with a Pearson correlation coefficient of 0.79. For protons in the usually well-defined A-helix environment these numbers are, 0.08 ppm and 0.96, respectively. As a result of this good correspondence, a reliable analysis could be made of the structural dependencies of the 1 H chemical shifts revealing their physical origin. For example, a down-field shift of either H2' or H3' or both indicates a high-syn/syn χ-angle. In an A-helix it is essentially the 5'-neighbor that affects the chemical shifts of H5, H6 and H8 protons. The H5, H6 and H8 resonances can therefore be assigned in an A-helix on the basis of their observed chemical shifts. In general, the chemical shifts were found to be quite sensitive to structural changes. We therefore propose that a comparison between calculated and observed 1 H chemical shifts is a good tool for validation and refinement of structures derived from NOEs and J-couplings

  1. Correction: Synthesis of pyrrolidine-3-carboxylic acid derivatives via asymmetric Michael addition reactions of carboxylate-substituted enones.

    Science.gov (United States)

    Yin, Feng; Garifullina, Ainash; Tanaka, Fujie

    2018-04-25

    Correction for 'Synthesis of pyrrolidine-3-carboxylic acid derivatives via asymmetric Michael addition reactions of carboxylate-substituted enones' by Feng Yin et al., Org. Biomol. Chem., 2017, 15, 6089-6092.

  2. Pore size distribution, moisture distribution, and shrinkage of porous materials - as determined by computer analysis (MATSORP) of measured sorption data

    DEFF Research Database (Denmark)

    Nielsen, Lauge Fuglsang

    1999-01-01

    Text note for the Summer school on 'Hydration and Microstructure of High Performance Concrete', held at Dept. Struct. Eng. and Materials, DTU, august 16-25, 1999......Text note for the Summer school on 'Hydration and Microstructure of High Performance Concrete', held at Dept. Struct. Eng. and Materials, DTU, august 16-25, 1999...

  3. A crystal chemical approach to superconductivity. I. A bond-valence sum analysis of inorganic compounds

    International Nuclear Information System (INIS)

    Liebau, Friedrich; Klein, Hans-Joachim; Wang, Xiqu

    2011-01-01

    A crystal-chemical approach to superconductivity is described that is intended to complement the corresponding physical approach. The former approach takes into account the distinction between the stoichiometric valence ( stoich V) and the structural valence ( struct V) which is represented by the bond-valence sums (BVS). Through calculations of BVS values from crystal-structure data determined at ambient temperature and pressure it has been found that in chalcogenides und pnictides of the transition metals Fe, Co, Ni, Mn, Hf, and Zr the atoms of the potential superconducting units yield values of vertical stroke BVS vertical stroke = vertical stroke struct V vertical stroke ≥ 1.11 x vertical stroke stoich V vertical stroke, whereas the atoms of the charge reservoirs have in general values of vertical stroke struct V vertical stroke stoich V vertical stroke. In corresponding compounds which contain the same elements but are not becoming superconducting, nearly all atoms are found to have vertical stroke struct V vertical stroke stoich V vertical stroke. For atoms of oxocuprates that are not becoming superconducting and for atoms of the charge reservoirs of oxocuprates that become superconducting, the relation vertical stroke struct V vertical stroke stoich V vertical stroke seems also to be fulfilled, with the exception of Ba. However, in several oxocuprates the relation vertical stroke struct V vertical stroke = 1.11 x vertical stroke stoich V vertical stroke for the atoms that become superconducting units is violated. These violations seem to indicate that in oxocuprates it is the local bond-valence distribution rather than the bond-valence sums that is essential for superconductivity. The present analysis can possibly be used to predict, by a simple consideration of ambient-T, P structures, whether a compound can become an unconventional superconductor at low T, under high P and/or by doping, or not. (orig.)

  4. Biomoléculas interactivas a escala humana

    Directory of Open Access Journals (Sweden)

    José C. Diez

    2013-11-01

    Full Text Available En el proyecto “MolecularPlayground @ UAH.es” se ha instalado una exposición que muestra modelos de diferentes estructuras moleculares de forma programada, en un espacio de acceso común dentro de una facultad. Los estudiantes –y visitantes– pueden controlar la rotación del modelo proyectado moviéndose frente a la pantalla o moviendo sus manos, lo que proporciona interactividad y permite, en cierta medida, la manipulación de la imagen para el análisis e investigación de la estructura. Por ejemplo, el control de la molécula permite analizar los sitios de interacción con receptores u otras dianas, o considerar las fuerzas que definen las interacciones intermoleculares. Cada modelo se presenta de acuerdo a un guión, con diferentes vistas y estilos de representación de la molécula, combinados con breves textos explicativos de su relevancia y enfocando los aspectos notables de la estructura. Los objetivos pueden resumirse en: - Atraer la atención de los alumnos, la comunidad universitaria y el público en general hacia la estructura de las moléculas y su aplicación en campos de interés general: salud, industria, materiales... - Promover, especialmente en los alumnos, el interés por la investigación y la exploración personales. - Promover el análisis de las estructuras de interés bioquímico y farmacológico en la interacción con sus dianas. - Complementar la docencia y el estudio de las ciencias moleculares con materiales multimedia, de comprensión más rápida y eficaz. Proporcionar a los profesores un formato y un medio de difusión de material relacionado con sus asignaturas. Proporcionar a los alumnos material y actividades para el trabajo no presencial.   El proyecto se ha instalado con financiación de la Universidad de Alcalá, proyecto de innovación docente UAH/EV493.

  5. Synonymous codon usage in different protein secondary structural ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    2007-06-21

    Jun 21, 2007 ... in the DSSP file, beta-sheets by E and B and coils by the rest. 3. Results ...... Authors are thankful to the Department of Biotechnology,. New Delhi for ... thermophilic Aquifex aeolicus and mesophilic Bacillus subtilis;. J. Biomol.

  6. Temperature dependent heterogeneous rotational correlation in lipids.

    Science.gov (United States)

    Dadashvand, Neda; Othon, Christina M

    2016-11-15

    Lipid structures exhibit complex and highly dynamic lateral structure; and changes in lipid density and fluidity are believed to play an essential role in membrane targeting and function. The dynamic structure of liquids on the molecular scale can exhibit complex transient density fluctuations. Here the lateral heterogeneity of lipid dynamics is explored in free standing lipid monolayers. As the temperature is lowered the probes exhibit increasingly broad and heterogeneous rotational correlation. This increase in heterogeneity appears to exhibit a critical onset, similar to those observed for glass forming fluids. We explore heterogeneous relaxation in in a single constituent lipid monolayer of 1, 2-dimyristoyl-sn-glycero-3-phosphocholine  by measuring the rotational diffusion of a fluorescent probe (1-palmitoyl-2-[1]-sn-glycero-3-phosphocholine), which is embedded in the lipid monolayer at low labeling density. Dynamic distributions are measured using wide-field time-resolved fluorescence anisotropy. The observed relaxation exhibits a narrow, liquid-like distribution at high temperatures (τ ∼ 2.4 ns), consistent with previous experimental measures (Dadashvand et al 2014 Struct. Dyn. 1 054701, Loura and Ramalho 2007 Biochim. Biophys. Acta 1768 467-478). However, as the temperature is quenched, the distribution broadens, and we observe the appearance of a long relaxation population (τ ∼ 16.5 ns). This supports the heterogeneity observed for lipids at high packing densities, and demonstrates that the nanoscale diffusion and reorganization in lipid structures can be significantly complex, even in the simplest amorphous architectures. Dynamical heterogeneity of this form can have a significant impact on the organization, permeability and energetics of lipid membrane structures.

  7. Proceedings of NEUROTOX󈨜, Molecular Basis of Drug & Pesticide Action (3rd) Held in Bath, England on 10-15 April 1988: Abstracts

    Science.gov (United States)

    1988-04-15

    cxy e n/ and i nve s iati r. t-’-e cs si~ mechanisms cf :.’.e cx~nac;:4on. RP 60- 2P~ 3- 40 5 /*I on fn A min in mh andr menrmm ma 1.1Lceda,K., Kaplan ,V...Biophys. Acca . 1988, (submitted for publica- tion). 5. Coronado.R. and Latore.R. Biophys. 1. 1983, 43 231-236. 144 POTASSIUM CHANNELS IN CULTURED

  8. Metabolismo

    OpenAIRE

    Battaner Arias, Enrique

    2013-01-01

    Una introducción al metabolismo de biomoléculas, con una introducción sobre ciclos geoquímicos. Trata también de metabolismo de xenobióticos, iones inorgánicos, metabolismo basal y aspectos metabólicos de la dieta

  9. Prevention of the Post traumatic Fibrotic Response in Joints

    Science.gov (United States)

    2016-12-01

    hydroxylation and mutations cause recessive osteogenesis imperfecta. Cell 127:291–304. 13. Engel J, Prockop DJ. 1991. The zipper-like folding of...collagen triple helices and the effects of mutations that disrupt the zipper. Annu Rev Biophys Biophys Chem 20:137–152. 14. Lamande SR, Bateman JF. 1999...prolyl 4-hydroxylase and type III collagen in the yeast pichia pastoris: formation of a stable enzyme tetramer requires coexpression with collagen and

  10. WebStruct and VisualStruct: web interfaces and visualization for Structure software implemented in a cluster environment

    Directory of Open Access Journals (Sweden)

    Jayashree B.

    2008-03-01

    Full Text Available Structure, is a widely used software tool to investigate population genetic structure with multi-locus genotyping data. The software uses an iterative algorithm to group individuals into “K” clusters, representing possibly K genetically distinct subpopulations. The serial implementation of this programme is processor-intensive even with small datasets. We describe an implementation of the program within a parallel framework. Speedup was achieved by running different replicates and values of K on each node of the cluster. A web-based user-oriented GUI has been implemented in PHP, through which the user can specify input parameters for the programme. The number of processors to be used can be specified in the background command. A web-based visualization tool “Visualstruct”, written in PHP (HTML and Java script embedded, allows for the graphical display of population clusters output from Structure, where each individual may be visualized as a line segment with K colors defining its possible genomic composition with respect to the K genetic sub-populations. The advantage over available programs is in the increased number of individuals that can be visualized. The analyses of real datasets indicate a speedup of up to four, when comparing the speed of execution on clusters of eight processors with the speed of execution on one desktop. The software package is freely available to interested users upon request.

  11. WebStruct and VisualStruct: Web interfaces and visualization for Structure software implemented in a cluster environment.

    Science.gov (United States)

    Jayashree, B; Rajgopal, S; Hoisington, D; Prasanth, V P; Chandra, S

    2008-09-24

    Structure, is a widely used software tool to investigate population genetic structure with multi-locus genotyping data. The software uses an iterative algorithm to group individuals into "K" clusters, representing possibly K genetically distinct subpopulations. The serial implementation of this programme is processor-intensive even with small datasets. We describe an implementation of the program within a parallel framework. Speedup was achieved by running different replicates and values of K on each node of the cluster. A web-based user-oriented GUI has been implemented in PHP, through which the user can specify input parameters for the programme. The number of processors to be used can be specified in the background command. A web-based visualization tool "Visualstruct", written in PHP (HTML and Java script embedded), allows for the graphical display of population clusters output from Structure, where each individual may be visualized as a line segment with K colors defining its possible genomic composition with respect to the K genetic sub-populations. The advantage over available programs is in the increased number of individuals that can be visualized. The analyses of real datasets indicate a speedup of up to four, when comparing the speed of execution on clusters of eight processors with the speed of execution on one desktop. The software package is freely available to interested users upon request.

  12. Interfacial stresses in damaged RC beams strengthened with externally bonded CFRP plate

    International Nuclear Information System (INIS)

    Benrahou, K.H.; Adda bedia, E.A.; Benyoucef, S.; Tounsi, A.; Benguediab, M.

    2006-01-01

    A theoretical method to predict the interfacial stresses in the adhesive layer of damaged reinforced concrete beams strengthened with externally bonded carbon fiber-reinforced polymer (CFRP) plate is presented. The adopted model is developed including the adherend shear deformations by assuming a linear shear stress through the depth of the RC beam [A. Tounsi, Int. J. Solids Struct., in press], while all existing solutions neglect this effect [e.g. S. Benyoucef, A. Tounsi, S.A. Meftah, E.A. Adda Bedia, Compos. Interfaces, in press; S.T. Smith, J.G. Teng, Eng. Struct. 23 (7) (2001) 857-871; T.M. Roberts, Struct. Eng. 67 (12) (1989) 229-233; A. Tounsi, S. Benyoucef, Int. J. Adhes. Adhes., in press; T. Stratford, J. Cadei, Construct. Building Mater. 20 (2006) 34-35]. In addition, in the present study the anisotropic damage model is adopted to describe the damage of the RC beams. It is shown that the damage has a significant effect on the interfacial stresses in FRP-damaged RC beam

  13. Application of a PEG precipitation method for solubility screening: A tool for developing high protein concentration formulations

    OpenAIRE

    Li, Li; Kantor, Angela; Warne, Nicholas

    2013-01-01

    Previous publications demonstrated that the extrapolated solubility by polyethylene glycol (PEG) precipitation method (Middaugh et al., J Biol Chem 1979; 254:367–370; Juckes, Biochim Biophys Acta 1971; 229:535–546; Foster et al., Biochim Biophys Acta 1973; 317:505; Mahadevan and Hall, AIChE J 1990; 36:1517–1528; Stevenson and Hageman, Pharm Res 1995; 12:1671–1676) has a strong correlation to experimentally measured solubility of proteins. Here, we explored the utility of extrapolated solubili...

  14. Charged Slurry Droplet Research

    Science.gov (United States)

    1989-02-20

    short i; struct mice f short deltax, deltay; char sec[3]; char sixtyths, -66- buttons, stype; Imouse; while (read(tfd,&ch,l) 1) if (ch ==E SC) ( if...read~tfd,&ch,1) ==1) && (ch IT) if ((read(tfd,&ch,l) == 1) && (ch y== ’Y for (i =0; i < sizeof(struct mice ); i++) if (read(tfd,((ohar *) &mouse) + i,1...Spectrometer. J. of Physics E. Scientific Instruments 1972, Vol 5. 40. R.F.Lever, Computation of Ion Trajectories in the Monopole Mass Spectrometer

  15. Incorporation of fluorophosphate into zinc–aluminium–nitrate ...

    Indian Academy of Sciences (India)

    Laboratoire de Chimie Biomoléculaire, Substances Naturelles et Réactivités, Unité des Matériaux, Faculté des Sciences Semlalia, Université Cadi Ayyad, BP 2390, Marrakech 40000, Morocco; Centre des Classes Préparatoires Ibnou Taimya, Route d'Essaouira, Marrakech 40000, Morocco; School of Science and ...

  16. Research

    African Journals Online (AJOL)

    ebutamanya

    29 mai 2015 ... Diagnostic moléculaire du complexe Mycobacterium tuberculosis résistant à ... 1Centre de Recherche Biomoléculaire Pietro Annigoni, CERBA/LABIOGENE, Université de ... Les résistances à la Rifampicine et à l'Isoniazide ont été étudiées par la technique de la PCR en .... leur statut sérologique au VIH-1.

  17. Correction: β-Amyrin synthase from Euphorbia tirucalli L. functional analyses of the highly conserved aromatic residues Phe413, Tyr259 and Trp257 disclose the importance of the appropriate steric bulk, and cation-π and CH-π interactions for the efficient catalytic action of the polyolefin cyclization cascade.

    Science.gov (United States)

    Ito, Ryousuke; Nakada, Chika; Hoshino, Tsutomu

    2017-01-18

    Correction for 'β-Amyrin synthase from Euphorbia tirucalli L. functional analyses of the highly conserved aromatic residues Phe413, Tyr259 and Trp257 disclose the importance of the appropriate steric bulk, and cation-π and CH-π interactions for the efficient catalytic action of the polyolefin cyclization cascade' by Ryousuke Ito et al., Org. Biomol. Chem., 2017, 15, 177-188.

  18. Molecular Characterization of Squamous Cell Carcinomas From Recessive Dystrophic Epidermolysis Bullosa

    Science.gov (United States)

    2006-09-01

    8 A ppendices ...................................................................................... 8 3 Mahoney...activation after acute injury to stratified epithelia. Biochem. Biophys. Res. Commun. 236, 231-238. Cowin, P. (1994). Unraveling the cytoplasmic

  19. The Role of the Caspase-8 Inhibitor FLIP in Androgen-Withdrawal Induced Death of Prostate Epithelium

    Science.gov (United States)

    2007-01-01

    cells. Cancer Res 2000;60:2384-9. 20. Voelkel-Johnson C, King DL, Norris JS. Resistance of prostate cancer cells to soluble TNF-related apoptosis...Mukhopadhyay A, Bueso-Ramos C, Chatterjee D, Pantazis P, Aggarwal BB. Curcumin downregulates cell survival mechanisms in human prostate cancer cell...ethanol. LY294002 (Cayman) was dissolved in Androgens and FOXO3a regulate FLIP page 7 dimethylsulfoxide (DMSO). Soluble recombinant human TRAIL (Biomol

  20. ConStruct: Improved construction of RNA consensus structures

    Directory of Open Access Journals (Sweden)

    Steger Gerhard

    2008-04-01

    Full Text Available Abstract Background Aligning homologous non-coding RNAs (ncRNAs correctly in terms of sequence and structure is an unresolved problem, due to both mathematical complexity and imperfect scoring functions. High quality alignments, however, are a prerequisite for most consensus structure prediction approaches, homology searches, and tools for phylogeny inference. Automatically created ncRNA alignments often need manual corrections, yet this manual refinement is tedious and error-prone. Results We present an extended version of CONSTRUCT, a semi-automatic, graphical tool suitable for creating RNA alignments correct in terms of both consensus sequence and consensus structure. To this purpose CONSTRUCT combines sequence alignment, thermodynamic data and various measures of covariation. One important feature is that the user is guided during the alignment correction step by a consensus dotplot, which displays all thermodynamically optimal base pairs and the corresponding covariation. Once the initial alignment is corrected, optimal and suboptimal secondary structures as well as tertiary interaction can be predicted. We demonstrate CONSTRUCT's ability to guide the user in correcting an initial alignment, and show an example for optimal secondary consensus structure prediction on very hard to align SECIS elements. Moreover we use CONSTRUCT to predict tertiary interactions from sequences of the internal ribosome entry site of CrP-like viruses. In addition we show that alignments specifically designed for benchmarking can be easily be optimized using CONSTRUCT, although they share very little sequence identity. Conclusion CONSTRUCT's graphical interface allows for an easy alignment correction based on and guided by predicted and known structural constraints. It combines several algorithms for prediction of secondary consensus structure and even tertiary interactions. The CONSTRUCT package can be downloaded from the URL listed in the Availability and requirements section of this article.

  1. Biochemistry: from supermarket to laboratory

    OpenAIRE

    F. R. Freitas-Rego; M. G. Pereira; S. O. Loureiro; M. T. de Santana; R.G. Garrido; F. de S.R.G Garrido

    2007-01-01

    After new campi as Instituto Multidisciplinar em Saúde (IMS/UFBA) startedworking, it was necessary to develop practical classes using domestic reagents atBiochemistry to Pharmacy (IMS078). Firstly, students visited a supermarket to readnutritional information at label and select possible products to be used in class. Moreover,chemical processes and fermentation were discussed as different foods and drinks wereanalysed. Some food were token to laboratories so that biomole cules qualitative ana...

  2. Disease: H00419 [KEGG MEDICUS

    Lifescience Database Archive (English)

    Full Text Available ... Garg A, Agarwal AK ... TITLE ... Lipodystrophies: disorders of adipose tissue biology. ... JOURNAL ... Biochim Biophys Acta 1791:507-13 (2009) DOI:10.1016/j.bbalip.2008.12.014 ...

  3. From Calculus to Wavelets: ANew Mathematical Technique

    Indian Academy of Sciences (India)

    expansions have many theoretical and practical ..... them into a rigorous mathematical theory. Meyer con- structed an ... engineers for signal processing, Ingrid Daubechies con- ..... and its applications on a somewhat higher mathematical level.

  4. Synthesis, Characterization and DNA Cleavage of Copper(II ...

    African Journals Online (AJOL)

    Keywords: DNA shearing, Copper(II) complex, Dithiothreitol, Attenuated total reflectance-Fourier transform .... confirm the fragmentation of DNA by the newly .... sperm. Biochem Biophys Acta 1986; 884: 124-134. 7. Cornell NW, Crivaro KE.

  5. The Development and Study of Molecular Electronic Switches and their Field-Effect Transistor (FET) Device Properties

    Science.gov (United States)

    2015-02-27

    Grand Rapids, MI) meetings and conferences. References 1. L.N Lucas, J.J.D. de Jong, J.H. van Esch, R.M. Kellogg , B.L. Berringa. Eur. J. Org...R.M. Kellogg , H.L. Feringa, H.L. Eur. J. Org. Chem., 2003, 155-166. 6. B. Qin, R. Yao, X. Zhao, H. Tian. Org. Biomol. Chem., 1, 2003, 2187-2191...7. L.N. Lucas, J.H. van Euch, R.M. Kellogg , B. Feringa. Chem. Comm., 1998, 2313-2314.

  6. Large-scale laboratory observations of wave forces on a highway bridge superstructure.

    Science.gov (United States)

    2011-10-01

    The experimental setup and data are presented for a laboratory experiment conducted to examine realistic wave forcing on a highway bridge : superstructure. The experiments measure wave conditions along with the resulting forces, pressures, and struct...

  7. Three-dimensional hybrid networks based on aspartic acid

    Indian Academy of Sciences (India)

    WINTEC

    Keywords. Aspartic acid; hybrid compounds; nickel aspartate; lead aspartate; achiral frameworks. ..... and coordinated to water molecules as well as car- .... (b) Dan M 2004 J. Mol. Struct. ... Sheldrick G M 1994 SADABS: Siemens area detector.

  8. Genetics Home Reference: aspartylglucosaminuria

    Science.gov (United States)

    ... Sources for This Page Aronson NN Jr. Aspartylglycosaminuria: biochemistry and molecular biology. Biochim Biophys Acta. 1999 Oct ... not be used as a substitute for professional medical care or advice. Users with questions about a ...

  9. Genetics Home Reference: CLN10 disease

    Science.gov (United States)

    ... Foundation CLIMB: Children Living with Inherited Metabolic Diseases March of Dimes: Neonatal Death The ... Sources for This Page Anderson GW, Goebel HH, Simonati A. Human pathology in NCL. Biochim Biophys Acta. 2013 Nov;1832( ...

  10. FAA computer security : concerns remain due to personnel and other continuing weaknesses

    Science.gov (United States)

    2000-08-01

    FAA has a history of computer security weaknesses in a number of areas, including its physical security management at facilities that house air traffic control (ATC) systems, systems security for both operational and future systems, management struct...

  11. Learning connective-based word representations for implicit discourse relation identification

    DEFF Research Database (Denmark)

    Braud, Chloé Elodie; Denis, Pascal

    2016-01-01

    We introduce a simple semi-supervised ap-proach to improve implicit discourse relation identification. This approach harnesses large amounts of automatically extracted discourse connectives along with their arguments to con-struct new distributional word representations. Specifically, we represen...... their simplicity, these connective-based rep-resentations outperform various off-the-shelf word embeddings, and achieve state-of-the-art performance on this problem.......We introduce a simple semi-supervised ap-proach to improve implicit discourse relation identification. This approach harnesses large amounts of automatically extracted discourse connectives along with their arguments to con-struct new distributional word representations. Specifically, we represent...... words in the space of discourse connectives as a way to directly encode their rhetorical function. Experiments on the Penn Discourse Treebank demonstrate the effectiveness of these task-tailored repre-sentations in predicting implicit discourse re-lations. Our results indeed show that, despite...

  12. Modulation of Ionic Channel Function by Protein Phosphorylation

    Science.gov (United States)

    1992-11-12

    were prepared from the cloned cDNAs using the SP6 RNA promoter/polymerase system (32) with capping accomplished by priming with cap analogues (33...triphosphate (ATP), cytidine triphosphate (CTP) and uridine triphosphate (UTP) [ct-32p]UTP at 80 Cilmmol; 0.1 mM GTP; 0.5 mM diguanosinetriphosphate; 200 g.g/ml...state NMR spectroscopy . J. Biomol. NMR 1:167-173. (1991). Tomich, J.M., A. Grove, T. Iwamoto, S. Marrer, M.S. Montal and M. Montal. Design principles

  13. Scalable data structure detection and classification for C/C++ binaries

    NARCIS (Netherlands)

    Haller, I.; Slowinska, J.M.; Bos, H.J.

    2015-01-01

    Many existing techniques for reversing data structures in C/C ++ binaries are limited to low-level programming constructs, such as individual variables or structs. Unfortunately, without detailed information about a program's pointer structures, forensics and reverse engineering are exceedingly

  14. Combined effect of vanadium and nickel on lipid peroxidation and ...

    African Journals Online (AJOL)

    use

    2011-12-12

    Dec 12, 2011 ... to nickel led to a significant decrease (p < 0.001) in SOD, GST activities in liver and GSH content in ..... administration and GSH is oxidized to disulfide form .... Chasteen N (1983). The biochemistry of vanadium. Struct. Bond.

  15. Transcription of gD and gI genes in BHV1-infected cells

    Indian Academy of Sciences (India)

    2012-09-28

    Sep 28, 2012 ... 2000) it was reported that from the bicistronic gD–gI con- struct, both gD ... The following protocol was adopted for studying pro- moter activity. ..... live infectious bovine rhinotracheitis parainfluenza-3 vaccine ad- ministered to ...

  16. Data of evolutionary structure change: 2UXML-2UXLM [Confc[Archive

    Lifescience Database Archive (English)

    Full Text Available 2UXML-2UXLM 2UXM 2UXL L M -----ALLSFE--------------RKYRVPGG--TLVG... 2UXML RVPGG--TLVGG ...dex> 2UXM L 2UXML YG...dbID>2UXM L 2UXML AANPEKGKEMRTPDHL 2UXML TIWFDQWVDWWQWWV struct

  17. Effects of electron–phonon interaction and impurity on optical ...

    Indian Academy of Sciences (India)

    2017-02-10

    Feb 10, 2017 ... struct a grid in real space using a discrete number of points. The eigenenergies and ... In order to perform simulation numerically, one needs to discretize ... without the electro- magnetic field E(t), and q is the electronic charge.

  18. MemPick : High-level data structure detection in C/C++ binaries

    NARCIS (Netherlands)

    Haller, Istvan; Slowinska, Asia; Bos, Herbert

    2013-01-01

    Many existing techniques for reversing data structures in C/C++ binaries are limited to low-level programming constructs, such as individual variables or structs. Unfortunately, without detailed information about a program's pointer structures, forensics and reverse engineering are exceedingly hard.

  19. Estimation in the partially observed stochastic Morris-Lecar neuronal model with particle filter and stochastic approximation methods

    DEFF Research Database (Denmark)

    Ditlevsen, Susanne; Samson, Adeline

    2014-01-01

    Parameter estimation in multidimensional diffusion models with only one coordinate observed is highly relevant in many biological applications, but a statistically difficult problem. In neuroscience, the membrane potential evolution in single neurons can be measured at high frequency, but biophys...

  20. Potencial de los quito-oligosacáridos generados de quitina y quitosana Potencial de los quito-oligosacáridos generados de quitina y quitosana

    OpenAIRE

    José Eleazar Barboza Corona; Rubén Darío Pacheco Cano; Tomás Ortiz-Rodríguez; Norma M. de la Fuente Salcido; Cristóbal Castañeda Ramírez

    2012-01-01

    Las quitinasas sintetizadas por plantas, hongos, insectos y bacterias tienen un gran poten­cial debido a su amplio espectro de aplicaciones. En este trabajo revisamos generalidades sobre las quitinasas y quitosanasas bacterianas y su uso en la producción de quito-oligo­sacáridos. Este tipo de biomoléculas han creado un mercado biotecnológico diversificado e ilimitado que incluye aplicaciones en alimentos como aditivos y bioconservadores, asi­mismo en múltiples aplicaciones biomédicas enfocada...

  1. Understanding the Relative Contributions of and Critical Enzymes for the Three Pathways for Intracrine Metabolism of Testicular Androgens in Advanced Prostate Cancer

    Science.gov (United States)

    2017-10-01

    Peroxisomal Enzymes: Cytisine-linked Isoflavonoids as Inhibitors of Hydroxysteroid 17-beta-dehydrogenase-4 (HSD17B4) Journal: Org Biomol Chem Volume...J. Chem. 2010, 88, 1233–1239; c) R. A. Valiulin, T. M. Arisco, A. G. Kutateladze, J. Org . Chem. 2011, 76, 1319–1332; d) P. J. Cremins, S. T...Saengchantara, T. W. Wallace, Tetrahedron 1987, 43, 3075–3082; e) R. P. Hsung, J. Org . Chem. 1997, 62, 7904–7905. [11] a) M. Von Strandtmann, M. P. Cohen, J

  2. Producción y caracterización de biocatalizadores implicados en la obtención de ácido siálico y compuestos relacionados = Production and characterization of biocatalysts involved in obtaining sialic acid and related compounds.

    OpenAIRE

    García García, María Inmaculada

    2012-01-01

    Palabras claves: Enzymes Biocatalysts N-acetyl neuraminte lyase N-acetyl neuraminate synthase Sialic acid Kinetic parameters CLEAs GRAS microorganism Aldolase Protein Cloning N-acetyl-D-mannosamine Pyruvate Resumen El ácido siálico y sus derivados son un grupo importante de biomoléculas implicadas en muchos fenómenos biológicos. Su síntesis y aplicación es de gran interés en la industria farmacéutica para la obtención de fármacos co...

  3. Electrochemically controlled patterning for biosensor arrays.

    OpenAIRE

    Dondapati, Srujan Kumar

    2006-01-01

    Existe una demanda creciente de dispositivos de análisis multianalito, con aplicaciones potenciales en los campos de la biomedicina y biotecnología, así como en el ámbito industrial y ambiental. Para el desarrollo de estos dispositivos resulta esencial un buen control espacial durante la etapa de inmovilización de las biomoléculas de interés; cada una de ellas debe ser depositada de forma precisa sobre la superficie del sensor (por ejemplo, un transductor amperométrico), evitan...

  4. Aplicación y nuevos desarrollos de la espectroscopía por RMN para el estudio de procesos de reconocimiento molecular entre carbohidratos y sus receptores

    OpenAIRE

    Berbís Moreno, Manuel Álvaro

    2014-01-01

    Los carbohidratos constituyen uno de los tipos de biomoléculas más complejos y ubicuos, cuyo reconocimiento por parte de receptores proteicos pertenecientes a diversas familias (lectinas, anticuerpos, enzimas y virus) determina una variedad de respuestas relacionadas con procesos fisiológicos y patológicos. El conocimiento, a nivel atómico, de la estructura de los carbohidratos y de sus interacciones con proteínas es esencial para una completa comprensión de muchos procesos vitales, así como ...

  5. Assessing diversity and phytoremediation potential of seagrass in tropical region

    Science.gov (United States)

    Seagrass ecosystem is one of the most important resources in the coastal areas. Seagrasses support and provide habitats for many coastal organisms in tropical region. Seagrasses are specialized marine flowering plants that have adapted to the nearshore environment with heterogeneous landscape struct...

  6. Locomotor circuits in the mammalian spinal cord

    DEFF Research Database (Denmark)

    Kiehn, Ole

    2006-01-01

    Intrinsic spinal networks, known as central pattern generators (CPGs), control the timing and pattern of the muscle activity underlying locomotion in mammals. This review discusses new advances in understanding the mammalian CPGs with a focus on experiments that address the overall network struct...

  7. Models for Aircrew Safety Assessment: Uses, Limitations and Requirements

    Science.gov (United States)

    1999-08-01

    altitude, the preoxygenation time, and the calorimetric or other thermometric methods. Accurate SAR level of exercise undertaken. Taking these...air- structed with an approximately 13 mm thick aluminium craft that meet the objectives of the Federal Aviation plate supported by a steel triangular

  8. Novel non-autonomous transposable elements on W chromosome ...

    Indian Academy of Sciences (India)

    2010-09-06

    Sep 6, 2010 ... Development as a female is determined by the ... element is believed to be analogous to the human Alu ele- ment. Numerous SINEs have ... designated as p50-library and C108-library, were also con- structed using genomic ...

  9. Role of Tumor Collagenase Stimulating Factor in Breast Cancer Invasion and Metastasis.

    Science.gov (United States)

    1997-12-01

    involving hazardous organisms, theZinvestigator(s) adhered to the CDC-NIH Guide for Biosafety in Microbiological and Biomedical Laboratories. ’Z...sequencing and characterization of the tumor cell-derived collagenase stimulatory factor. Arch. Biochem. Biophys., 285: 90-96, 1991. 15. Prescott , J

  10. Soyasaponin Bh, a Triterpene Saponin Containing a Unique Hemiacetal-Functional Five-Membered Ring from Glycine max (Soybeans)

    Science.gov (United States)

    Soybeans (Glycine max L. Merill) and soy-based food products are major dietary sources of saponins. An oleanane triterpenoid saponin, soyasaponin Bh (1) containing a unique five-membered ring with a hemiacetal functionality together with seven known saponins were isolated from soybeans. Their struct...

  11. Isolation, Characterization and X-ray Structure Determination of the ...

    African Journals Online (AJOL)

    NICO

    2014-12-20

    Dec 20, 2014 ... applications in diverse areas.1 They can be used in laser materials, as 1H NMR shift reagents, ... spectra were measured at 400.22 and 100.63 MHz, respectively, ..... tions in solutions and in the gas phase, J. Mol. Struct., 2001 ...

  12. Cloning and molecular characterization of TaAGO1, a member of ...

    African Journals Online (AJOL)

    Jane

    2011-10-12

    Oct 12, 2011 ... shares high similarities to AtAGO1 in Arabidopsis and OsAGO1 in rice, was characterized. As a cDNA .... Phylogenetic analysis of TaAGO1 and its plant homologous. For generation of a ..... human RISC. Nat. Struct. Mol. Biol.

  13. Estrés oxidativo, nitrosativo y daño cardiovascular en pacientes pediátricos obesos.

    OpenAIRE

    Tavárez Alonso, Sandra

    2015-01-01

    La obesidad predispone fuertemente al riesgo cardiovascular y se relaciona con alteraciones en diferentes marcadores de funcionalidad del tejido adiposo, inflamación y daño a biomoléculas. Establecer la presencia de alteraciones precoces en la obesidad infantil es el objetivo de este estudio realizado en pacientes pediátricos (7-14 años) obesos (N=60) y controles (N=42). En él hemos evaluado como marcadores de estrés oxidativo y nitrosativo los niveles de malondialdehído, 8-isoprostanos, pro...

  14. Caracterización de propiedades electrónicas de sensores nanoestructurados en base a carbono para la detección de tuberculosis

    OpenAIRE

    Rojas Valle, Merlyn

    2016-01-01

    La Tuberculosis constituye uno de los principales factores de mortalidad en el mundo; en particular, en el Perú representa un problema de salud pública cada vez mayor. Por otro lado, el constante interés y avance en los estudios sobre la detección de biomoléculas con el uso de nanoestructuras constituye una alternativa de diagnóstico eficiente en sensibilidad y especificidad, con potencial para generar dispositivos económicos y de fácil fabricación. El presente trabajo de te...

  15. Caracterización de Propiedades Electrónicas de Sensores Nanoestructurados en Base a Carbón para la Detección de Tuberculosis

    OpenAIRE

    Rojas Valle, Merlyn

    2016-01-01

    La Tuberculosis constituye uno de los principales factores de mortalidad en el mundo; en particular, en el Perú representa un problema de salud pública cada vez mayor. Por otro lado, el constante interés y avance en los estudios sobre la detección de biomoléculas con el uso de nanoestructuras constituye una alternativa de diagnóstico eficiente en sensibilidad y especificidad, con potencial para generar dispositivos económicos y de fácil fabricación. El presente trabajo de te...

  16. Caracterización y fotoestabilidad de compuestos fluorescentes y pardos generados en reacciones enzimáticas y no enzimáticas. Implicancias en la conservación de materiales orgánicos

    OpenAIRE

    Matiacevich, Silvia Beatriz

    2008-01-01

    Las reacciones de pardeamiento no enzimático (reacción de Maillard) y enzimático (polimerización de polifenoles oxidados) generan productos fluorescentes y pigmentos pardos que contribuyen a las características físico-químicas de materiales orgánicos (biomoléculas, alimentos, fármacos). El objetivo de esta tesis fue analizar las características cromáticas y de fluorescencia y la fotoestabilidad de los compuestos generados por la reacción de Maillard y de pigmentos polifenólicos, para dilucida...

  17. Sintesis y evaluación biológica de nuevos derivados de tipo imidazolina y etanolamina fluorados

    OpenAIRE

    Flores Penalba, Sonia

    2011-01-01

    Una de las principales áreas de interés de la química orgánica es la búsqueda de nuevos compuestos con actividad biológica. En este sentido cabe destacar el especial interés que despiertan los compuestos nitrogenados debido a que constituyen una de las familias más numerosas entre las biomoléculas y que están implicados en múltiples procesos a nivel metabólico y estructural. Un ejemplo representativo los constituyen los compuestos de tipo etanolamina, ampliamente estudiados por sus variad...

  18. Adaptive Redox Response of Mesenchymal Stromal Cells to Stimulation with Lipopolysaccharide Inflammagen: Mechanisms of Remodeling of Tissue Barriers in Sepsis

    Science.gov (United States)

    2013-03-08

    conditions. It is well accepted that numerous vitagenes are evolutionarily adapted by cells to manage oxidative stress; they include but are not...hormetic phytochemicals and vitagenes in aging and longevity. Biochim Biophys Acta. 2012; 1822(5):753-83. [36] Martin LJ. Biology of mitochondria

  19. Amazon forest dynamics under changing abiotic conditions in the early Miocene (Colombian Amazonia)

    NARCIS (Netherlands)

    Salamanca Villegas, S.; van Soelen, E.; Teunissen van Manen, M.L.; Flantua, S.G.A.; Santos, R.V.; Roddaz, M.; Dantas, E.L.; van Loon, E.; Sinninghe Damsté, J.S.; Kim, J.-H.; Hoorn, C.

    2016-01-01

    Aim We analysed in detail a past marine incursion event in north-westernAmazonia and measured its effect on the forest composition. We also deter-mined the sediment provenance in the ?uvio-estuarine system and recon-structed the overall ?oral composition of the Amazon lowland forest duringthe

  20. To bee or not to bee—comments on “Discrete optimum design of truss structures using artificial bee colony algorithm”

    DEFF Research Database (Denmark)

    Stolpe, Mathias

    2011-01-01

    to three alternative heuristics on the same benchmark examples. The most advanced heuristics presented herein find equally good, or better, designs compared to those presented in Sonmez (Struct Multidisc Optim 43:85–97, 2011). However, for the largest benchmark example, we use four orders of magnitude...

  1. High-spatial-multiplicity multi-core fibres for future dense space-division-multiplexing system

    DEFF Research Database (Denmark)

    Matsuo, Shoichiro; Takenaga, Katsuhiro; Saitoh, Kunimasa

    2015-01-01

    Design and fabrication results of high-spatial-multiplicity multi-core fibres are presented. A 30-core single-mode multi-core fibre and a 36-spatial-channels multi-core fibre with low differential mode delay have been realized with low-crosstalk characteristics through optimisation of core struct...

  2. In Vitro and In Vivo Phlebovirus Inhibition by Ribavirin

    Science.gov (United States)

    1988-03-01

    as x%%eliais oin the encephalutic disease in viaj rechnassociates. Inc. I Rockx ille. Md. i in dry- poxvder mice Indtuced by a neurotropic strain oft...1980. Ribavirin treatment of its capping of messenger RNA. Biochem. Biophys. Res. Com- toga. arena - and bunvavirus infections in subhuman prittiates

  3. Treatment of Synthetic Urinous Wastewater Using Combined Reverse Osmosis, Immobilized Urease, and Ion Exchange Systems

    Science.gov (United States)

    1974-09-01

    invertase on DEAE-Cellulose while glucoamylase bound to the same carrier has been studied (Bachler et al., 1970; Gruesbeck and Rase, 1972). Adsorption of...Arch. Biochem. Biophys. 130, 384. Katchalski, E., Silman, I., and Goldstein, R. (1971) Adv. Enzymology 34., 445. Katz, S. A., and Cowans, J

  4. Basic to industrial research on neutron platform in Japan

    Indian Academy of Sciences (India)

    Building on these successes, a new spallation neutron source (KENS) was con- structed at KEK (the present High Energy Accelerator Research Organization) in. 618. Pramana – J. Phys., Vol. 71, No. ... Ministry of Education, Science and Culture (MONBUSHO) planned the Hadron. Project consisting of four major facilities ...

  5. Development of a non invasion real-time PCR assay for the quantitation of chicken parvovirus in fecal swabs

    Science.gov (United States)

    The present study describes the development of a real time Taqman polymerase chain reaction (PCR) assay using a fluorescent labeled probe for the detection and quantitation of chicken parvovirus (ChPV) in feces. The primers and probes were designed based on the nucleotide sequence of the non struct...

  6. GIS and SBF for estimating groundwater recharge of a mountainous ...

    Indian Academy of Sciences (India)

    face water for human consumption. The problem became worse in ... has been increasingly employed to replace on-site exploration or .... GIS technology was used to digitize the hydrologic and geographic information, and a fundamental database was con- structed. Appropriate scores were set for differ- ent factors. Finally ...

  7. The construction of periodic unfolding operators on some compact Riemannian manifolds

    DEFF Research Database (Denmark)

    Dobberschütz, Sören; Böhm, Michael

    2014-01-01

    The notion of periodic unfolding has become a standard tool in the theory of periodic homogenization. However, all the results obtained so far are only applicable to the "flat" Euclidean space R n. In this paper, we present a generalization of the method of periodic unfolding applicable to struct...

  8. Optimal Infinite Runs in One-Clock Priced Timed Automata

    DEFF Research Database (Denmark)

    David, Alexandre; Ejsing-Duun, Daniel; Fontani, Lisa

    We address the problem of finding an infinite run with the optimal cost-time ratio in a one-clock priced timed automaton and pro- vide an algorithmic solution. Through refinements of the quotient graph obtained by strong time-abstracting bisimulation partitioning, we con- struct a graph with time...

  9. Dollar Summary of Federal Supply Classification and Service Category by Company, FY83, Part 6 (W061-Z299).

    Science.gov (United States)

    1983-01-01

    RENT OF FAC /FUEL SUPPLY 29 X299 AUTO TECHNIQUE BELGIQUE S A BELGIUM ARMY LEASE-RENT OF FAC /OTHER NON-BLDG STRUCT 31 HOFFMAN CO VIRGINIA ARMY LEASE...HARRISON & PALMI RIDGE ELECTRICAL E INC MISSOURI ARMY CONSTR: CONSTRUCTION/PARFING FACILITIES $ 123 SUSSEX ELECTRICO C MARYLAND ARMY CONSTR: CONSTRUCTION

  10. Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain

    NARCIS (Netherlands)

    Periole, Xavier; Vendruscolo, Michele; Mark, Alan E.

    2007-01-01

    A series of molecular dynamics simulations in explicit solvent were started from nine structural models of the transition state of the SH3 domain of alpha-spectrin, which were generated by Lindorff Larsen et al. (Nat Struct Mol Biol 2004;11:443-449) using molecular dynamics simulations in which

  11. Isolation and characterization of Arabidopsis mutants with enhanced tolerance to oxidative stress

    NARCIS (Netherlands)

    Qureshi, Muhammad K.; Radeva, Vesela; Genkov, Todor; Minkov, Ivan; Hille, Jacques; Gechev, Tsanko S.; Liu, J.-H.

    We have previously reported a method for isolation of mutants with enhanced tolerance to the fungal AAL toxin and given a detailed characterization of atr1 (AAL toxin resistant, Gechev et al. in Biochem Biophys Res Commun 375:639-644, 2008). Herewith, we report eight more mutants with enhanced

  12. Genetics Home Reference: palmoplantar keratoderma with deafness

    Science.gov (United States)

    ... Melegh B. Phenotypic variants of the deafness-associated mitochondrial DNA A7445G mutation. Curr Med Chem. 2008;15(13):1257-62. Review. Citation on PubMed Xu J, Nicholson BJ. The role of connexins in ear and skin physiology - functional insights from disease-associated mutations. Biochim Biophys ...

  13. Generation of specific deoxynojirimycin-type inhibitors of the non-lysosomal glucosylceramidase

    NARCIS (Netherlands)

    Overkleeft, H. S.; Renkema, G. H.; Neele, J.; Vianello, P.; Hung, I. O.; Strijland, A.; van der Burg, A. M.; Koomen, G. J.; Pandit, U. K.; Aerts, J. M.

    1998-01-01

    The existence of a non-lysosomal glucosylceramidase in human cells has been documented (van Weely, S., Brandsma, M., Strijland, A., Tager, J. M., and Aerts, J. M. F. G. (1993) Biochim. Biophys. Acta 1181, 55-62). Hypothetically, the activity of this enzyme, which is localized near the cell surface,

  14. Gaussian curvature elasticity determined from global shape transformations and local stress distributions : a comparative study using the MARTINI model

    NARCIS (Netherlands)

    Hu, Mingyang; de Jong, Djurre H.; Marrink, Siewert J.; Deserno, Markus

    2013-01-01

    We calculate the Gaussian curvature modulus (k) over bar of a systematically coarse-grained (CG) one-component lipid membrane by applying the method recently proposed by Hu et al. [Biophys. J., 2012, 102, 1403] to the MARTINI representation of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). We

  15. The Opposing Roles of Nucleophosmin and the ARF Tumor Suppressor in Breast Cancer

    Science.gov (United States)

    2007-04-01

    3809.2006 Copyright © 2006, American Society for Microbiology . All Rights Reserved. Nucleophosmin Is Essential for Ribosomal Protein L5 Nuclear Export Yue...Gotanda, T.; Kubo, H.; Nishiyama, K.; Kawahara, M.; Nakagawa, M. Biochem. Biophys. Res. Commun., 2006, 339, 790. [71] Woods, Y.L.; Xirodimas, D.P.; Prescott

  16. Prostate Cancer Progression and Serum Sibling (Small Integrin Binding N-Linked Glycoprotein) Levels

    Science.gov (United States)

    2008-10-01

    4302. Respondents should be aware that notwithstanding any other provision of law , no person shall be subject to any penalty for failing to comply...SIBLING proteins, bone sialoprotein, and osteopontin. Biochem Biophys Res Commun 2001;280:460–465. [PubMed: 11162539] 27. Tompa P, Szasz C, Buday L

  17. Scaling Factor Estimation Using Optimized Mass Change Strategy, Part 2: Experimental Results

    DEFF Research Database (Denmark)

    Fernández, Pelayo Fernández; Aenlle, Manuel López; Garcia, Luis M. Villa

    2007-01-01

    The mass change method is used to estimate the scaling factors, the uncertainty is reduced when, for each mode, the frequency shift is maximized and the changes in the mode shapes are minimized, which in turn, depends on the mass change strategy chosen to modify the dynamic behavior of the struct...

  18. Phonon dispersions in graphene sheet and single-walled carbon ...

    Indian Academy of Sciences (India)

    Abstract. In the present research paper, phonons in graphene sheet have been calculated by con- structing a dynamical matrix using the force constants derived from the second-generation reactive empirical bond order potential by Brenner and co-workers. Our results are comparable to inelastic. X-ray scattering as well as ...

  19. Rhipicephalus (Boophilus) microplus strain Deutsch, 5 BAC clone sequencing, including two encoding Cytochrome P450s and one encoding CzEst9 carboxylesterase

    Science.gov (United States)

    The cattle tick, Rhipicephalus (Boophilus) microplus, has a genome over 2.4 times the size of the human genome, and with over 70% of repetitive DNA, this genome would prove very costly to sequence at today's prices and difficult to assemble and analyze. BAC clones give insight into the genome struct...

  20. Caractérisation biomoléculaire et structure de la population des ...

    African Journals Online (AJOL)

    En vue de caractériser la diversité génétique des populations de cobayes domestiques (Cavia porcellus) dans la région agro-écologique du Cameroun, un panel de16 marqueurs microsatellites ont été utilisés. L'ADN génomique provenait de 110 prélèvements sanguins obtenus chez des animaux non apparentés des ...

  1. Packaging of single DNA molecules by the yeast mitochondrial protein Abf2p: reinterpretation of recent single molecule experiments.

    Science.gov (United States)

    Stigter, Dirk

    2004-07-01

    Brewer et al. (Biophys. J. 85 (2003) 2519-2524) have studied the compaction of dsDNA in a double flow cell by observing the extension of stained DNA tethered in buffer solutions with or without Abf2p. They use a Langmuir adsorption model in which one Abf2p molecule adsorbs on one site on the DNA, and the binding constant, K, is given as the ratio of the experimental rates of adsorption and desorption. This paper presents an improved interpretation. Instead of Langmuir adsorption we use the more appropriate McGhee-von Hippel (J. Mol. Biol. 86 (1974) 469-489) theory for the adsorption of large ligands to a one-dimensional lattice. We assume that each adsorbed molecule shortens the effective contour length of DNA by the foot print of Abf2p of 27 base pairs. When Abf2p adsorbs to DNA stretched in the flowing buffer solution, we account for a tension effect that decreases the adsorption rate and the binding constant by a factor of 2 to 4. The data suggest that the accessibility to Abf2p decreases significantly with increasing compaction of DNA, resulting in a lower adsorption rate and a lower binding constant. The kinetics reported by Brewer et al. (Biophys. J. 85 (2003) 2519-2524) lead to a binding constant K=3.6 x 10(6) M(-1) at the beginning, and to K=5 x 10(5) M(-1) near the end of a compaction run, more than an order of magnitude lower than the value K=2.57 x 10(7) M(-1) calculated by Brewer et al. (Biophys. J. 85 (2003) 2519-2524).

  2. Marine Bioinorganic Chemistry Workshop Held in Heron Island on 28 June - 2nd July 1989

    Science.gov (United States)

    1990-02-09

    Vilter, H. Phytochemistry, 1984, 23, 1387-1390. 2. Vilter, H. Botanica Marina, 1983, 26, 451-455. 3. Wever, R., Plat, H. and De Boer, E., Biochim. Biophys...and DSc (1977) Vf degrees from the University of Melbourne, where he held teaching and research positions. His major research interests involve the

  3. Apical Membrane Potassium Conductance in Guinea Pig Gallbladder Epithelial Cells

    Science.gov (United States)

    1988-12-01

    did block the accompanying der short-circuit conditions except for brief periods (300 change in fR.. TEA was ineffective when added to the ms) during...toad skin. Biochim. 29. RICHARDS, N. W., AND D. C. DAWSON. Single potassium channelsBiophys. Acta 728: 455-459, 1983. blocked by lidocaine and quinidine

  4. The Efflux of a Fluorescent Probe Is Catalyzed by an ATP-Driven Extrusion System in Lactococcus lactis

    NARCIS (Netherlands)

    MOLENAAR, D; BOLHUIS, H; ABEE, T; POOLMAN, B; KONINGS, WN

    Many bacteria, both gram positive and negative, extrude in an energy-dependent manner the fluorescent pH indicator 2',7'-bis-(2-carboxyethyl)-5[and -6]-carboxyfluorescein (BCECF) (D. Molenaar, T. Abee, and W. N. Konings, Biochim. Biophys. Acta 1115:75-83, 1991). This efflux was studied in detail in

  5. Comparative Biochemistry and Metabolism

    Science.gov (United States)

    1978-12-01

    Junod (1972). Animals were infused with 32 vimoles of 5-hydroxytryptamine in 3 minutes. The uptake of the amine varied considerably between animals in...M., McNaught, A. D., and Schell, P. (1966). The chemical basis of hydrazine mutagenesis. Biochem. Biophys. Res. Comm. 24:967-971. Junod , A. F. (1972

  6. Fulltext PDF

    Indian Academy of Sciences (India)

    But, since there is no general method to find equations of a given surface analytically, we found it. in- teresting to consider some well known surfaces to find their parametric equations analytically. Here, in fact. , we model those surfaces by exploiting their struct.ural synl- metry. We also provide their plots using Mathelnatica.

  7. Validation of the visitor and resident framework in an e-book setting

    DEFF Research Database (Denmark)

    Engelsmann, Hazel C.; Greifeneder, Elke Susanne; Lauridsen, Nikoline D.

    2014-01-01

    Introduction. By applying the visitor and resident framework on e-book usage, the article explores whether the concepts of a resident and a visitor can help to explain e-book use, and can help to gain a better insight into users' motivations for e-book use. Method. A questionnaire and semi-struct...

  8. Deformations and strain energy in fragments of tempered glass: experimental and numerical investigation

    DEFF Research Database (Denmark)

    Nielsen, Jens Henrik; Bjarrum, Marie

    2017-01-01

    energy and thereby the stress in a fragment post failure. The FE-model have been established in previous work Nielsen (Glass Struct Eng, 2016. doi: 10.1007/s40940-016-0036-z) and is applied here on the specific geometry and initial state of the investigated fragments. This is done by measuring...

  9. Modeling the Role of Bulk and Surface Characteristics of Carbon Fiber on Thermal Conductance across the Carbon Fiber/Matrix Interface (Postprint)

    Science.gov (United States)

    2015-11-09

    heat flow from carbon fiber to the matrix (most of the laser energy is absorbed by the carbon fiber), subsequently determining the temperature rise and...Reductase- Trimethoprim , a Drug-Receptor System. Proteins: Struct., Funct., Genet. 1988, 4, 31−47. (37) Sun, H.; Mumby, S. J.; Maple, J. R.; Hagler, A. T

  10. Receptores para hormonas sexuales en pituitaria y sistema nervioso central

    OpenAIRE

    Weisenberg, Liliana Sara

    1985-01-01

    Las Biomoléculas pueden clasificarse en informacionales y no informacionales. En este último grupo se encuentran los azúcares y las grasas mientras que las moléculas informacionales son: las proteínas, los ácidos nucléicos y las hormonas esteroideas implica que un cambio tan sutil como la introducción o carencia de un oxígeno o un hidrógeno modifique sustancialmente su actividad biológica. En el caso de los estrógenos su elaboración por los ovarios es compleja y su carácter fenólico los disti...

  11. biomoleculas extraídas por sbas: ejemplos prácticos

    OpenAIRE

    Dutra Molino, João; Feitosa, V. Araujo; Lencastre Novaes, L. C. de; Santos Ebinuma, V. de Carvalho; Lópes, A. Moreni; Jozala, A. Faustino; Marquez, D. de Araujo Viana; Pellegrini Malpiedi, Luciana; Pessoa Junior, Adalberto

    2017-01-01

    La industria biotecnologica actual exige procesos rápidos y económicos para la producción y la purificación de biomoléculas. En este contexto, diferentes técnicas separativas que ofrezcan un alto rendimiento y una alta pureza del producto final han sido evaluadas por diferentes grupos de investigación. La extracción líquido-líquido con sistemas bifasicos acuosos (SBAs) es una de las metodologías más estudiadas para bio-separación. Esta técnica presenta varias ventajas, tales como condiciones ...

  12. The application of mercury-containing labels in protein analysis using complementary mass spectrometric techniques

    OpenAIRE

    Kutscher, Daniel Jurgen

    2014-01-01

    En la presente tesis doctoral se desarrollaron nuevas metodologías para el análisis cuantitativo de proteínas basadas en la introducción química de un compuesto de mercurio capaz de unirse a las cisteínas libres de estas biomoléculas. El ácido hidroximercuribenzoico tiene un alto potencial como agente derivatizante, ya que es capaz de actuar de forma selectiva y completa sobre los residuos de cisteína presentes en las proteínas. El objetivo fundamental del proyecto ha sido la utilización d...

  13. Astrocitos y zinc: alteraciones inducidas en modelos in vitro de los síndromes alcohólico fetal y de Down

    OpenAIRE

    Ballestín Hinojosa, Raúl

    2015-01-01

    El zinc es un elemento traza esencial; crítico para un gran número de proteínas estructurales, procesos enzimáticos y factores de transcripción. Esta variada ubicación en las biomoléculas hace que participe en multitud de funciones celulares y tisulares. En el caso particular del cerebro, los iones zinc están implicados, además, en la transmisión sináptica. Por todo ello, la homeostasis del zinc es crucial para la función y supervivencia de las células, y estas han desarrollado una amplia var...

  14. Efeito do resveratrol e do ácido ascórbico na criopreservação de sêmen humano

    OpenAIRE

    Garcez, Márcia Esteves Silva

    2011-01-01

    A criopreservação de sêmen humano é de grande importância para a medicina reprodutiva, porém esse processo pode causar danos ao espermatozóide devido, entre outros aspectos, à produção de espécies reativas de oxigênio, as quais podem lesar as biomoléculas. Tanto o resveratrol quanto o ácido ascórbico são compostos com reconhecida capacidade antioxidante, porém ainda pouco estudados em relação à prevenção de criodanos em espermatozóides humanos. Desta forma, o objetivo deste est...

  15. Sustancias bioactivas obtenidas de extractos de aislados fúngicos nativos

    OpenAIRE

    Pelaéz Gutiérrez, Enelia Cristina

    2015-01-01

    Resumen: en el presente trabajo se evaluó el potencial antimicrobiano, antifúngico, antioxidante y la producción de ácidos orgánicos a partir de los extractos obtenidos mediante fermentación con medio líquido extracto de malta en 25 aislados fúngicos nativos (LVN100 – LVN124) que hacen parte de la colección de cepas microbianas del grupo de investigación Producción, Estructura y Aplicación de Biomoléculas (PROBIOM). Se seleccionaron los dos aislados fúngicos más promisorios para cada activida...

  16. Diabetes mellitus, estrés oxidativo y embarazo

    OpenAIRE

    Clapés Hernández, Sonia

    2000-01-01

    El estrés oxidativo es un estado que se caracteriza por un desequilibrio entre la producción de especies reactivas del oxígeno y la capacidad antioxidante de las células. La implicación del estrés oxidativo en diversas patologías, ha sido demostrada; entre ellas se encuentran la diabetes mellitus y el embarazo, aunque este último no es un estado patológico sino de adaptación metabólica. En el embarazo se producen modificaciones en el metabolismo de las biomoléculas celulares, en particular en...

  17. Evaluating the Anti-Seizure Efficacy of Novel Adenosine Treatment Regimens in a Soman Rat Model

    Science.gov (United States)

    2015-06-01

    rubric : 0= No lesion; 1= Minimal (1-10%); 2= Mild (11-25%); 3= Moderate (26-45%); 4= Severe (>45%). To further stratify the data and obtain a more...the central nervous system revealed by genetic knockout studies. Biochim Biophys Acta 1808(5): 1358-1379. Youssef, A. F. and B. W. Santi (1997

  18. Biosynthesis of acid phosphatase of baker's yeast . Characterization of a protoplast-bound fraction containing precursors of the exo-enzyme

    NARCIS (Netherlands)

    Boer, Pieter; Rijn, Herman J.M. van; Reinking, A.; Steyn-Parvé, Elizabeth P.

    1975-01-01

    1. 1.|Yest protoplasts, secreting acid phosphatase (orthophosphoric-monoester phosphohydrolase (acid optimum) EC 3.1.3.2) contain a small amount of firmly bound enzyme, even after lysis (Van Rijn, H.J.M.; Boer, P. and Steyn-Parvé, E.P. (1972) Biochim. Biophys. Acta 268, 431–441). The major part

  19. The Role of Cumulative Genetic Defeats in NF1 Tumorigenesis

    Science.gov (United States)

    2000-10-01

    without LOH of the NF1 tumors’ slow and limited growth, and lack of gene. Biochem Biophys Res Comm 234:346-350. Decker H-JH, Cannizzaro LA, Mendez MJ, Leong... Caro - lina; and the 4 Department of Pediatrics, Division of Genetics, University of Florida, Gaines- Center, Durham. ville, Florida L. Messiaen

  20. Breast Cancer-Targeted Nuclear Drug Delivery Overcoming Drug Resistance for Breast Cancer Chemotherapy

    Science.gov (United States)

    2010-09-01

    Sakamaki T, Pestell RG: Cyclin D1: normal and abnormal functions. Endocrinology 145, 5439–5447 (2004). 43 Hengstschlager M, Braun K, Soucek T...culture system. Cell Biochem Biophys 2008;52(1):37e46. [44] Fu M, Wang C, Li Z, Sakamaki T, Pestell RG. Cyclin D1: normal and abnormal functions

  1. Seasonal prediction of precipitation over Nigeria | Adeniyi | Journal ...

    African Journals Online (AJOL)

    While for the training and verification periods of 1986-2012, correlations are not gener-ally significant although some were found to be above the significant level of 5%. For the recon-structed seasonal precipitation, correlations of ten stations were found to be significant at 5 %, but at 10 % level, their number increased to 13.

  2. The Run 2 ATLAS Analysis Event Data Model

    CERN Document Server

    SNYDER, S; The ATLAS collaboration; NOWAK, M; EIFERT, T; BUCKLEY, A; ELSING, M; GILLBERG, D; MOYSE, E; KOENEKE, K; KRASZNAHORKAY, A

    2014-01-01

    During the LHC's first Long Shutdown (LS1) ATLAS set out to establish a new analysis model, based on the experience gained during Run 1. A key component of this is a new Event Data Model (EDM), called the xAOD. This format, which is now in production, provides the following features: A separation of the EDM into interface classes that the user code directly interacts with, and data storage classes that hold the payload data. The user sees an Array of Structs (AoS) interface, while the data is stored in a Struct of Arrays (SoA) format in memory, thus making it possible to efficiently auto-vectorise reconstruction code. A simple way of augmenting and reducing the information saved for different data objects. This makes it possible to easily decorate objects with new properties during data analysis, and to remove properties that the analysis does not need. A persistent file format that can be explored directly with ROOT, either with or without loading any additional libraries. This allows fast interactive naviga...

  3. Molecular cloning and genomic organization of a second probable allatostatin receptor from Drosophila melanogaster

    DEFF Research Database (Denmark)

    Lenz, C; Williamson, M; Grimmelikhuijzen, C J

    2000-01-01

    We (C. Lenz et al. (2000) Biochem. Biophys. Res. Commun. 269, 91-96) and others (N. Birgül et al. (1999) EMBO J. 18, 5892-5900) have recently cloned a Drosophila receptor that was structurally related to the mammalian galanin receptors, but turned out to be a receptor for a Drosophila peptide bel...

  4. Molecular Effects of 13C/DIM in Prostate Cancer

    Science.gov (United States)

    2007-04-01

    expression, Arch. Biochem. Biophys. 352 (1998) 59–70. [36] M.G. Busby, A.R. Jeffcoat, L.T. Bloedon, M.A. Koch, T. Black, K.J. Dix, W.D. Heizer , B.F. Thomas...the extracellular environment is implicated in the angiogenic switch. They found that MMP-9 could render normal islets angiogenic releasing VEGF

  5. Transient Delivery of Adenosine as a Novel Therapy to Prevent Epileptogenesis

    Science.gov (United States)

    2015-10-01

    Chemother 6:98–101. Bukoski RD, Sparks HV, and Mela -Riker LM (1986) A role for mitochondria in myocardial adenosine production. Adv Exp Med Biol 194:157–167...Bukoski RD, Sparks HV, and Mela LM (1983) Rat heart mitochondria release adenosine. Biochem Biophys Res Commun 113:990–995. Burnstock G, Fredholm BB

  6. Structural behaviour of AgNO3 at low temperatures by neutron ...

    Indian Academy of Sciences (India)

    [4] F El-Kabbany, Y Badr, G Said and S Taha, Appl. Phys. A43, 65 (1987). [5] Z Shen, W F Sherman and G R Wilkinson, J. Mol. Struct. 175, 395 (1988). [6] R Rodriguez-Carvajal, FULLPROF: A Program for Rietveld Refinement, profile matching and integrated intensity, version 3.1 (LLB, France) (1995). [7] R Feyerherm, M F ...

  7. Clean Energy for the Commonwealth Powered by UMass

    Science.gov (United States)

    2009-04-15

    Nanomagnetics Zeolite membranes Polymer-inorganic nanocomposites MEMS Nanostructured catalysts Plant Biotechnology Biochem., Cell wall struct., Agronomy Crambe...power management Low-power device networks Energy scavenging Flame Modeling Combustion chemistry Molecular-beam mass spectrometry Building Design...Thayumanavan, PhD. UMass Amherst Professor of Chemistry and Director, Fueling the Future Center for Chemical Innovation – Paul Osenar, PhD. Chief

  8. First Spectroscopic Identification of Pyrocarbonate for High CO2 Flux Membranes Containing Highly Interconnected Three Dimensional Ionic Channels

    Science.gov (United States)

    2013-01-01

    Koura, S. Kohara , K. Takeuchi, S. Takahashi, L. A. Curtiss, M. Grimsditch and M.-L. Saboungi, J. Mol. Struct., 1996, 382, 163–169. 49 L.-J. Chen, X...Cheng, C.-J. Lin and C.-M. Huang, Electrochim. Acta, 2002, 47, 1475–1480. 50 S. Kohara , N. Koura, Y. Idemoto, S. Takahashi, M.-L. Saboungi and L. A

  9. Photoinduced Partial Unfolding of Tubulin Bound to Meso-tetrakis(sulfonatophenyl) Porphyrin Leads to Inhibition of Microtubule Formation In Vitro

    Science.gov (United States)

    2013-07-30

    Bio- chemistry 44, 524–536 (2005). [4] M. Loweneck, A. G. Milbradt, C. Root , H. Satzger, W. Zinth, L. Moroder, and C. Renner, Biophys. J. 90, 2099–2108...H. Nettles , B. Cornett, K. H. Downing, and E. Nogales, Proc. Natl. Acad. Sci. 98, 5312–5316 (2001). B. McMicken et al.: Photoinduced unfolding of

  10. Biological Applications and Effects of Optical Masers

    Science.gov (United States)

    1987-04-01

    et a174 present data to demonstrate that melanin functions as an efficient electron-transfer agent in redox systems. Blois and associates 7 8...and Polis, B.D. Arch. Biochem. Biophys. 10, 171-177 (1963). 74. San, E.V., Haberman, H.F. and Menon, I.A. ibid. 󈨍f 666-672 (1972). 75. Blois , H.S

  11. Structural Organization and Strain Variation in the Genome of Varicella Zoster Virus

    Science.gov (United States)

    1984-10-23

    penetrated by the negative stain. By the time VZV reached the plasma membrane there were almost no 11 FIGURE 1 VZV-infected cell plaque. This is a...Denhardt, P.T. 1966. A menbrane - f i l te r technique for the detect ion of complementary PNA. Biochera. Biophys. Res. Commun. 23: 641-546. Des ros i e r

  12. Effect of Radiofrequency Radiation on DNA Duplex Stability and Replication.

    Science.gov (United States)

    1983-08-01

    Ando, T. A nuclease specific for heat-denatured DNA isolated from a product of Aspergillus oryzae . Biochim Biophys Acta 114:158-168 (1966). Blakeley...metabolic acti- vation. Mutation Res 64:315-328 (1979). Vogt,. V.M. Purification and further properties of single-strand-specific nuclease from Aspergillus oryzae . Eur J Biochem 33:192-200 (1973). 42

  13. EZ-ASSIGN, a program for exhaustive NMR chemical shift assignments of large proteins from complete or incomplete triple-resonance data

    Energy Technology Data Exchange (ETDEWEB)

    Zuiderweg, Erik R. P., E-mail: zuiderwe@umich.edu; Bagai, Ireena [The University of Michigan Medical School, Department of Biological Chemistry (United States); Rossi, Paolo [Rutgers University, Center for Integrative Proteomics Research (United States); Bertelsen, Eric B. [Arbor Communications, Inc. (United States)

    2013-10-15

    For several of the proteins in the BioMagResBank larger than 200 residues, 60 % or fewer of the backbone resonances were assigned. But how reliable are those assignments? In contrast to complete assignments, where it is possible to check whether every triple-resonance Generalized Spin System (GSS) is assigned once and only once, with incomplete data one should compare all possible assignments and pick the best one. But that is not feasible: For example, for 200 residues and an incomplete set of 100 GSS, there are 1.6 Multiplication-Sign 10{sup 260} possible assignments. In 'EZ-ASSIGN', the protein sequence is divided in smaller unique fragments. Combined with intelligent search approaches, an exhaustive comparison of all possible assignments is now feasible using a laptop computer. The program was tested with experimental data of a 388-residue domain of the Hsp70 chaperone protein DnaK and for a 351-residue domain of a type III secretion ATPase. EZ-ASSIGN reproduced the hand assignments. It did slightly better than the computer program PINE (Bahrami et al. in PLoS Comput Biol 5(3):e1000307, 2009) and significantly outperformed SAGA (Crippen et al. in J Biomol NMR 46:281-298, 2010), AUTOASSIGN (Zimmerman et al. in J Mol Biol 269:592-610, 1997), and IBIS (Hyberts and Wagner in J Biomol NMR 26:335-344, 2003). Next, EZ-ASSIGN was used to investigate how well NMR data of decreasing completeness can be assigned. We found that the program could confidently assign fragments in very incomplete data. Here, EZ-ASSIGN dramatically outperformed all the other assignment programs tested.

  14. EZ-ASSIGN, a program for exhaustive NMR chemical shift assignments of large proteins from complete or incomplete triple-resonance data

    International Nuclear Information System (INIS)

    Zuiderweg, Erik R. P.; Bagai, Ireena; Rossi, Paolo; Bertelsen, Eric B.

    2013-01-01

    For several of the proteins in the BioMagResBank larger than 200 residues, 60 % or fewer of the backbone resonances were assigned. But how reliable are those assignments? In contrast to complete assignments, where it is possible to check whether every triple-resonance Generalized Spin System (GSS) is assigned once and only once, with incomplete data one should compare all possible assignments and pick the best one. But that is not feasible: For example, for 200 residues and an incomplete set of 100 GSS, there are 1.6 × 10 260 possible assignments. In “EZ-ASSIGN”, the protein sequence is divided in smaller unique fragments. Combined with intelligent search approaches, an exhaustive comparison of all possible assignments is now feasible using a laptop computer. The program was tested with experimental data of a 388-residue domain of the Hsp70 chaperone protein DnaK and for a 351-residue domain of a type III secretion ATPase. EZ-ASSIGN reproduced the hand assignments. It did slightly better than the computer program PINE (Bahrami et al. in PLoS Comput Biol 5(3):e1000307, 2009) and significantly outperformed SAGA (Crippen et al. in J Biomol NMR 46:281–298, 2010), AUTOASSIGN (Zimmerman et al. in J Mol Biol 269:592–610, 1997), and IBIS (Hyberts and Wagner in J Biomol NMR 26:335–344, 2003). Next, EZ-ASSIGN was used to investigate how well NMR data of decreasing completeness can be assigned. We found that the program could confidently assign fragments in very incomplete data. Here, EZ-ASSIGN dramatically outperformed all the other assignment programs tested

  15. Intermetallic Matrix Composites 3 Symposium Held in San Francisco, California on April 4 - 6, 1994. Materials Research Society Symposium Proceedings. Volume 350

    Science.gov (United States)

    1994-04-06

    1992). 17 M.G. Mendiratta, J.J. Lewandowski and D.M. Dimiduk, Metal. Trans., f2A. 1573 (1991). 18. F. Dave , A.G. Evans, G.R. Odette, R. Mehrabian, M.L...S. C. Ur and M. Dollar, in (Proc. 2nd Int. Conf. Struct. Appl. Mech. Alloying. Vancouver. Canada, 1993) pp. 291-296. 6. P. A. Zielinski . R. Schulz, S

  16. Conference on the Physics and Chemistry of Semiconductor Interfaces (26th) Held in the Catamaran Resort Hotel in Pacific Beach, San Diego, California on 17 January 1999 to 21 January 1999. Microelectronics and Nanometer Structures: Processing, Measurement, and Phenomena

    Science.gov (United States)

    2000-01-27

    II-IV)1/2_ Type I m-OV- VDi /2 Type IT" One possibility which is denoted as type I materials is con- structed by replacing two group-Ill...71, 2048 (1992). I4A. L. Wachs, T. Miller, A. P. Shapiro, and T.-C. Chiang, Phys. Rev. B 35, 5514 (1987). 15T. Miller, T.-C. Hsieh, and T.-C

  17. Final Treatability Study in Support of Remediation by Natural Attenuation Site FT-1 at Fairchild Air Force Base, Spokane, Washington

    Science.gov (United States)

    1997-10-01

    aquifer: Ground Water Monitoring Review, Winter, 1987, p. 64-71. Bartha , R., 1986, Biotechnology of petroleum pollutant biodegradation: Microbial Ecology ...trichloroethylene by the ammonia-oxidizing bacterium Nitrosomonas europaea: Biochem. Biophys. Res. Commun., vol. 159, p. 640-643. Atlas , R.M., 1981, Microbial ...role of electron donor for microbial metabolism and are completely degraded or detoxified (Bouwer, 1992). Electron acceptors are elements or

  18. Self-Assessment of the Use of Plagiarism Avoiding Techniques to Create Ethical Scholarship Among Research Students

    OpenAIRE

    Saeed Ahmad; Ahsan Ullah

    2015-01-01

    The use of plagiarism avoiding techniques can be helpful to maintain academic integrity, a better learning environment and intellectual honesty. This explored the use of plagiarism avoiding techniques for creating ethical scholarship among research students. It also measured the association between the frequency of using plagiarism avoiding techniques and the satisfaction about knowledge of plagiarism. Data were collected from seven universities through an online self-struct...

  19. Triethylammonium salt of dimethyl diphenyldithiophosphates: Single ...

    Indian Academy of Sciences (India)

    Moreno-Esparza R 2010 Struct. Chem. 21 191. 24. Bajia S C 2011 Synth. React. Inorg. Met.-Org. Nano. Met. Chem. 41 746. 25. Khajuria R, Kumar S, Kour G, Anthal S, Gupta V K,. Kant R and Pandey S K 2014 J. Coord. Chem. 67 2925. 26. Kumar S, Khajuria R, Gupta V K, Kant R and Pandey S. K 2014 Polyhedron 72 140.

  20. Hydrogen-1 NMR relaxation time studies in membrane: anesthetic systems

    International Nuclear Information System (INIS)

    Pinto, L.M.A.; Fraceto, L.; Paula, E. de; Franzoni, L.; Spisni, A.

    1997-01-01

    The study of local anesthetics'(LA) interaction with model phospholipid membranes is justified by the direct correlation between anesthetic's hydrophobicity and its potency/toxicity. By the same reason, uncharged LA species seems to play a crucial role in anesthesia. Most clinically used LA are small amphiphilics with a protonated amine group (pKa around 8). Although both charged (protonated) and uncharged forms can coexist at physiological pH, it has been shown (Lee, Biochim. Biophys. Acta 514:95, 1978; Screier et al. Biochim. Biophys. Acta 769:231, 1984) that the real anesthetic pka can be down-shifted, due to differential partition into membranes, increasing the ratio of uncharged species at pH 7.4. We have measured 1 H-NMR longitudinal relaxation times (T 1 ) for phospholipid and three local anesthetics (tetracaine, lidocaine, benzocaine), in sonicated vesicles at a 3:1 molar ratio. All the LA protons have shown smaller T 1 in this system than in isotropic phases, reflecting LA immobilization caused by insertion in the membrane. T 1 values for the lipid protons in the presence of LA were analyzed, in an attempt to identify specific LA:lipid contact regions. (author)

  1. An Integrated Procedure for the Structural Design of a Composite Rotor-Hydrofoil of a Water Current Turbine (WCT)

    Science.gov (United States)

    Oller Aramayo, S. A.; Nallim, L. G.; Oller, S.

    2013-12-01

    This paper shows an integrated structural design optimization of a composite rotor-hydrofoil of a water current turbine by means the finite elements method (FEM), using a Serial/Parallel mixing theory (Rastellini et al. Comput. Struct. 86:879-896, 2008, Martinez et al., 2007, Martinez and Oller Arch. Comput. Methods. 16(4):357-397, 2009, Martinez et al. Compos. Part B Eng. 42(2011):134-144, 2010) coupled with a fluid-dynamic formulation and multi-objective optimization algorithm (Gen and Cheng 1997, Lee et al. Compos. Struct. 99:181-192, 2013, Lee et al. Compos. Struct. 94(3):1087-1096, 2012). The composite hydrofoil of the turbine rotor has been design using a reinforced laminate composites, taking into account the optimization of the carbon fiber orientation to obtain the maximum strength and lower rotational-inertia. Also, these results have been compared with a steel hydrofoil remarking the different performance on both structures. The mechanical and geometrical parameters involved in the design of this fiber-reinforced composite material are the fiber orientation, number of layers, stacking sequence and laminate thickness. Water pressure in the rotor of the turbine is obtained from a coupled fluid-dynamic simulation (CFD), whose detail can be found in the reference Oller et al. (2012). The main purpose of this paper is to achieve a very low inertia rotor minimizing the start-stop effect, because it is applied in axial water flow turbine currently in design by the authors, in which is important to take the maximum advantage of the kinetic energy. The FEM simulation codes are engineered by CIMNE (International Center for Numerical Method in Engineering, Barcelona, Spain), COMPack for the solids problem application, KRATOS for fluid dynamic application and RMOP for the structural optimization. To validate the procedure here presented, many turbine rotors made of composite materials are analyzed and three of them are compared with the steel one.

  2. Distribution and Characterization of Antigens Found in Subcellular Fractions of African Trypanosomes.

    Science.gov (United States)

    1979-08-01

    34 • . . .. . -. 11. (i.e., Trypanosoma cruzi, Pereira et al 1978; Entamoeba histolytica, McLaughlin and Muller in preparation...Partial purification and some properties of a neutral sulfhydryl and an acid proteinase from Entamoeba histolytica. Can. J. Microbiol. 23 420-425...in membrane fragments isolated from Acanthamoeba sp . Biochem. Biophys. Acta 193 203-211. Voorheis, H.P. Gale, J.S., Owen, M.J. and Edwards W. (1979

  3. Targeting PRMT5 as a Novel Radiosensitization Approach for Primary and Recurrent Prostate Cancer Treatment

    Science.gov (United States)

    2016-10-01

    pressor programmed cell death 4, Cancer Res. 71 (2011) 5579–5587. [8] C. Nicholas , J. Yang, S.B. Peters, M.A. Bill, R.A. Baiocchi, F. Yan, S. Sif, S...Biochim. Biophys. Acta 1839 (2014) 1330–1340. [13] C.M. Koh, M. Bezzi, D.H. Low, W.X. Ang, S.X. Teo, F.P. Gay, M. Al-Haddawi, S.Y. Tan , M. Osato, A. Sabo

  4. Floating Ocean Platform

    Science.gov (United States)

    2003-08-15

    Proc ICOSSAR 89 5th Int Conf Struct Saf Reliab, 1989, p 183-190 Fukusumi, Tadahiro (Kobe Univ); Kusakabe, Kaoru , Dynamic response 162 characteristics...Harbor Research Institute, Ministry of Transport, Japan, October, 348--359, 1994 Maeda, N. and Morikawa, M. and Ishikawa , K. and Kakuta, Y., Fatigue...Harbor Research Institute, Ministry of Transport, Japan, October, 383--394, 1994 Morikawa, M. and Suzuki, H. and Ishikawa , K. and Komiya, H. and Yoshida

  5. FACTORS INFLUENCING MOBILE-LEARNING ADOPTION INTENTION: AN EMPIRICAL INVESTIGATION IN HIGH EDUCATION

    OpenAIRE

    Ngo Tan Vu Khanh; Gwangyong Gim

    2014-01-01

    This study investigates the use of mobile phones and tablets for learning purposes among university students in Vietnam. For this purpose, the research is based on relevant technology acceptance literature and the Technology Acceptance Model (TAM) is proposed to analyze the adoption of mobile devices and smart phones by Vietnam students for accessing course materials, searching the web for information related to their discipline, sharing knowledge, conducting assignments etc. Employing struct...

  6. Unexpected and novel putative viruses in the sediments of a deep-dark permanently anoxic freshwater habitat

    OpenAIRE

    Borrel, Guillaume; Colombet, Jonathan; Robin, Agnès; Lehours, Anne-Catherine; Prangishvili, David; Sime-Ngando, Télesphore

    2012-01-01

    Morphological diversity, abundance and community structure of viruses were examined in the deep and anoxic sediments of the volcanic Lake Pavin (France). The sediment core, encompassing 130 years of sedimentation, was subsampled every centimeter. High viral abundances were recorded and correlated to prokaryotic densities. Abundances of viruses and prokaryotes decreased with the depth, contrasting the pattern of virus-to-prokaryote ratio. According to fingerprint analyses, the community struct...

  7. A review of visual memory capacity: Beyond individual items and towards structured representations

    OpenAIRE

    Brady, Timothy F.; Konkle, Talia; Alvarez, George A.

    2011-01-01

    Traditional memory research has focused on identifying separate memory systems and exploring different stages of memory processing. This approach has been valuable for establishing a taxonomy of memory systems and characterizing their function, but has been less informative about the nature of stored memory representations. Recent research on visual memory has shifted towards a representation-based emphasis, focusing on the contents of memory, and attempting to determine the format and struct...

  8. After the War: Nation-Building from FDR to George W. Bush

    Science.gov (United States)

    2008-01-01

    how a president will structure deci- sionmaking. The first is cognitive style, which includes mental con- structs about how the world works, how the...characterized as having a very open, free- flowing cognitive style, a strong and well-justified sense of his own effi- cacy in management, a mastery of...the administration of President Harry Truman to actually execute nation-building in Germany and Japan. Stylistically , Truman was almost the

  9. Architectures à clusters dans les phases intermétalliques du gallium. Élaboration, caractérisation structurale, analyse de la liaison et propriétés.

    OpenAIRE

    Tillard , Monique

    1993-01-01

    Gallium phases with electropositive elements are at interface between semiconductors and metals, the Ga-richest are characterised by macroanionic tridimensional frameworks built with clusters. The originality of these phases is due to the presence of locally delocalised electrons at clusters. Nevertheless these clusters display well defined electron numbers in adequacy with their geometries. This work reports the new phase diagrams of binary systems of gallium and alkali metals.Crystal struct...

  10. Isolation of biologically active peptides from the venom of Japanese carpenter bee, Xylocopa appendiculata

    OpenAIRE

    Kawakami, Hiroko; Goto, Shin G.; Murata, Kazuya; Matsuda, Hideaki; Shigeri, Yasushi; Imura, Tomohiro; Inagaki, Hidetoshi; Shinada, Tetsuro

    2017-01-01

    Background Mass spectrometry-guided venom peptide profiling is a powerful tool to explore novel substances from venomous animals in a highly sensitive manner. In this study, this peptide profiling approach is successfully applied to explore the venom peptides of a Japanese solitary carpenter bee, Xylocopa appendiculata (Hymenoptera: Apoidea: Apidae: Anthophila: Xylocopinae: Xylocopini). Although interesting biological effects of the crude venom of carpenter bees have been reported, the struct...

  11. Attachment, emotion regulation and coping in portuguese emerging adults: a test of a mediation hypothesis

    OpenAIRE

    Joana Cabral; Paula Mena Matos; Wim Beyers; Bart Soenens

    2012-01-01

    Although the quality of parent-adolescent emotional bonds has consistently been proposed as a major influence on young adult's psycho-emotional functioning, the precise means by which these bonds either facilitate or impede adaptive coping are not well-understood. In an effort to advance this inquiry, the present study examined interrelationships among measures of parental attachment, emotion regulation processes, and preferred coping strategies within a sample of 942 college freshmen. Struct...

  12. Disease: H01184 [KEGG MEDICUS

    Lifescience Database Archive (English)

    Full Text Available H01184 Familial dementia, including: Familial British dementia (FBD); Familial Danish dementia... (FDD) Familial British dementia (FBD) and familial Danish dementia (FDD) are two autosomal domi...nant neurodegenerative diseases caused by mutations in the BRI/ ITM2B gene. Familial dementia is characteriz... ... TITLE ... Modeling familial British and Danish dementia. ... JOURNAL ... Brain Struct Funct 214:235-44 (2010) DOI:10.1007/s00429-009-0221-9

  13. Comment on 'Modeling and analysis of a bimorph piezoelectric cantilever beam for voltage generation'

    International Nuclear Information System (INIS)

    Erturk, A; Inman, D J

    2008-01-01

    In a recent paper, Ajitsaria et al (2007 Smart Mater. Struct. 16 447–54) presented a mathematical formulation for the modeling and analysis of a bimorph piezoelectric cantilever beam for voltage generation. Their motivation was the recent increasing trend in using the piezoelectric effect to harvest electrical energy from ambient vibrations. This comment addresses the modeling errors and numerous undefined and missing terms in the mentioned work. (comment)

  14. Evaluación de la actividad inmunomoduladora de biomoléculas de origen vegetal

    OpenAIRE

    Pérez Rosés, Renato

    2015-01-01

    [spa] OBJETIVO. El estudio busca la valoración de la actividad antioxidante e inmunomoduladora in vitro de quince aceites esenciales, cuatro fracciones de aceites esenciales y tres compuestos (timol, carvacrol y eugenol). MÉTODOS. Las muestras fueron caracterizadas por GC y GC-MS. El ensayo del DPPH y la cuantificación de la producción de ROS por oxidación de la 2´,7´-diclorofluorescina diacetato (DCFH-DA) en los leucocitos humanos estimulados (PMA o H2O2) permitieron estudiar la activ...

  15. Polarization-Difference Imaging: Biophysical Mechanisms and Engineering Applications to Visibility Enhancement in Scattering Media

    Science.gov (United States)

    1993-07-01

    to neglect the variation in refractive Average refractive index. Using refractometry and dif. index along they axis, so that the assumed index...output. photoreceptor calls studied by refractometry and interference microscopy," J. Biophys. Biochem. Cytolol. 3, 15-33 (1957). curves) indicate...of rhodopsin in the visual Science 300, 540-52 (1978). receptor membrane," Nature (London) 386, 39-43 (1972) 26. R. Borer and S. Joseph, " Refractometry

  16. StructUre and test results of the Tokamak-7 device cryogenic system

    International Nuclear Information System (INIS)

    Babaev, I.V.; VolobUev, A.N.; Zhul'kin, V.F.

    1982-01-01

    A cryogenic system (CS) of the Tokamak-7 (T-7) installation with the longitudinal field superconducting magnetic system (SMS) is described. The CS is designed for cool-down, cryostatic cooling and heating of the T-7 cryogenic objects and consists of a helium system (HS) and a nitrogen cryogenic system (NCS). The HS consists of:a a heliUm delivery system intended for distributing and controlling the helium flows in the SMS; cryogenic helium units; a 1.25 m 3 volume for storing liquid helium; a compressor compartment using piston compressors at the 3 MPa operating pressure and 140 g/s total capacity; gaseous helium storages (3600 m 3 under normal conditions); helium cleaning and drying systems; a gas holder of 20 m 3 operating volume; cryogenic pipelines and pipe fittings. The NCS operates on delivered nitrogen and includes a 120 m 3 liquid nitrogen storage, evaporators and electric heaters producing up to 230 g/s of gaseous nitrogen at 300 K, a separator, cryogenic pipelines and fittings. It is found that the CS has the necessary cold production reserve, ensures reliable operation of the Tokamak-7 device and permits to carry out practically continuous plasma experiments

  17. Teacher autonomy in the era of New Public Management

    OpenAIRE

    Lundström, Ulf

    2015-01-01

    This article examines how upper secondary school teachers perceive and respond to the consequences for their professional autonomy of recent school reforms and restructurings. Based on empirical material from interviews of 119 teachers in three studies conducted between 2002 and 2014, the findings indicate that teacher autonomy has been reduced by school reforms and restructurings since the late 1980s. Regardless of their individual aims, these reforms have collectively created a power struct...

  18. Marking out the clinical expert/clinical leader/clinical scholar: perspectives from nurses in the clinical arena

    OpenAIRE

    Mannix, Judy; Wilkes, Lesley; Jackson, Debra

    2013-01-01

    Background Clinical scholarship has been conceptualised and theorised in the nursing literature for over 30?years but no research has captured nurses? clinicians? views on how it differs or is the same as clinical expertise and clinical leadership. The aim of this study was to determine clinical nurses? understanding of the differences and similarities between the clinical expert, clinical leader and clinical scholar. Methods A descriptive interpretative qualitative approach using semi-struct...

  19. La conservación del patrimonio arquitectónico maya. Primeras experiencias (1891-1969)

    OpenAIRE

    MATARREDONA DESANTES, NURIA

    2016-01-01

    [EN] The Mayan civilization is, undoubtedly, the most advanced of those that flourished in America during pre-Columbian times. During its heyday period, the ancient Maya built large cities and created large residential areas where they erected an impressive architecture in harmony with the ferocious nature that surrounded them. Today, the testimony of these settlements comes immersed in a wild environment, buried under abundant vegetation and even the collapse of the same architectural struct...

  20. Protein Receptor(s) of Botulinum Neurotoxin

    Science.gov (United States)

    2005-01-01

    therapeutic agent, which is a more effective drug in this form than the pure BoNT (12). Again, the molecular basis of the superior therapeutic efficacy of...neurotoxin B, Nat Struct Biol 7, 693-699 36. Hanson, M. A. and Stevens, R. C. (2000) Cocrystal structure of synaptobrevin-II bound to botulinum...designing novel drugs , Biochimie 82 (2000) 943-53. 21. L.A. Smith, Development of recombinant vaccines for botulinum neurotoxin, Toxicon 36 (1998) 539

  1. A Fusion-Inhibiting Peptide against Rift Valley Fever Virus Inhibits Multiple, Diverse Viruses

    Science.gov (United States)

    2013-09-12

    performance liquid chroma- tography to greater than 95% purity (Bio-synthesis, Inc., Lewisville, TX). Lyophilized peptides were initially resuspended in...lesser extent RVFV-6sc, were found to precipitate Gc (Figure 5); however, in the presence of the non- ionic detergent Triton-X, which will solubilize...Viral membrane fusion. Nat Struct Mol Biol 15: 690–698. 12. Allison SL, Schalich J, Stiasny K, Mandl CW, Kunz C, et al. (1995) Oligomeric rearrangement

  2. Architectural Survey of Pence Elementary School, Fort Leonard Wood, Missouri

    Science.gov (United States)

    2011-09-01

    younger students often learned what they needed to know from older students (Graves 1993, 22). During the first half of the 19th century , urban...of class- rooms with an applied Gothic, Greek Revival, or Victorian facade to create a cohesive building (Figure 5). ERDC/CERL TR-11-25 8...with Eliel and Eero Saarinen and con- structed in 1940, this school was the first to separate from the traditional Victorian style of school buildings

  3. Large eddy simulation of premixed and non-premixed combustion

    OpenAIRE

    Malalasekera, W; Ibrahim, SS; Masri, AR; Sadasivuni, SK; Gubba, SR

    2010-01-01

    This paper summarises the authors experience in using the Large Eddy Simulation (LES) technique for the modelling of premixed and non-premixed combustion. The paper describes the application of LES based combustion modelling technique to two well defined experimental configurations where high quality data is available for validation. The large eddy simulation technique for the modelling flow and turbulence is based on the solution of governing equations for continuity and momentum in a struct...

  4. The effects of a new financial supervisory system on consolidation in banking sector

    OpenAIRE

    Novickytė, L.

    2012-01-01

    The recent financial turmoil has prompted to review the current financial regulatory framework mechanism. The present financial system reform could be a cause of the integration and consolidation processes in banking, because banks play a very important role in the economy. This article examines the changes of European Union's financial system, regulatory rules, and extending the potential of the financial sector perspective. This paper attempts to evaluate the European Union financial struct...

  5. Prevalence of protein supplement use at gyms Estudio estadístico del consumo de suplementos proteícos en gimnasios

    OpenAIRE

    A. Sánchez Oliver; Mª T. Miranda León; E. Guerra-Hernández

    2011-01-01

    At the present time, the abuse of all class of sport nutritional supplements (NS) has extended the people who go regularly to gymnasiums. Between these substances there are the Protein Powder Supplements (PPS). The purpose of this study is to examine the consumption of PPS in 415 individuals from Seville fitness centers. All individuals were evaluated with anthropometric measurements and completed a questionnaire previously reviewed, evaluating the validity of the content, application, struct...

  6. Novel micellar systems for the formulation of poorly water soluble drugs : biocompatibility aspects and pharmaceutical applications

    OpenAIRE

    Dumontet Mondon, Karine

    2010-01-01

    Amongst the large number of novel drugs, 95% are lipophilic and poorly water soluble. Particularly, this renders their aqueous formulation very difficult. In this regard this thesis focused on polymeric micelles based on novel MPEG-hexPLA copolymers forming a hydrophilic shell and a very hydrophobic core that favors the incorporation of poorly water soluble drugs. Although the drug hydrophobicity and water solubility are the main parameters in respect to their incorporation efficiency, struct...

  7. Iron Intercalation in Covalent-Organic Frameworks: A Promising Approach for Semiconductors

    OpenAIRE

    Pakhira, Srimanta; Lucht, Kevin P.; Mendoza-Cortes, Jose L.

    2017-01-01

    Covalent-organic frameworks (COFs) are intriguing platforms for designing functional molecular materials. Here, we present a computational study based on van der Waals dispersion-corrected hybrid density functional theory (DFT-D) to design boroxine-linked and triazine-linked COFs intercalated with Fe. Keeping the original $P-6m2$ symmetry of the pristine COF (COF-Fe-0), we have computationally designed seven new COFs by intercalating Fe atoms between two organic layers. The equilibrium struct...

  8. Magnetic nanoparticles formed in glasses co-doped with iron and larger radius elements

    OpenAIRE

    Edelman , Irina; Ivanova , Oxana; Ivantsov , Ruslan; Velikanov , D.; Zabluda , V.; Zubavichus , Y.; Veligzhanin , A.; Zaikovskiy , V.; Stepanov , S.; Artemenko , Alla; Curély , Jacques; Kliava , Janis

    2012-01-01

    International audience; A new type of nanoparticle-containing glasses based on borate glasses co-doped with low contents of iron and larger radius elements, Dy, Tb, Gd, Ho, Er, Y, and Bi, is studied. Heat treatment of these glasses results in formation of magnetic nanoparticles, radically changing their physical properties. Transmission electron microscopy and synchrotron radiation-based techniques: x-ray diffraction, extended x-ray absorption fine structure, x-ray absorption near-edge struct...

  9. Dynamic Multiaxial Response of a Hot-Pressed Aluminum Nitride

    Science.gov (United States)

    2012-01-05

    Hutchinson, Adv. Appl . Mech. 29 (1992). [34] H. Ming-Yuan, J.W. Hutchinson, Int. J. Solids Struct. 25 (1989) 1053. [35] J. Salem , L. Ghosn, Int. J...Dynamic Multiaxial Response of a Hot- Pressed Aluminum Nitride by Guangli Hu, C. Q. Chen, K. T. Ramesh, and J. W. McCauley ARL-RP-0487...Laboratory Aberdeen Proving Ground, MD 21005-5066 ARL-RP-0487 June 2014 Dynamic Multiaxial Response of a Hot- Pressed Aluminum Nitride

  10. Simple Multi-Authority Attribute-Based Encryption for Short Messages

    OpenAIRE

    Viktoria I. Villanyi

    2016-01-01

    Central authority free multi-authority attribute based encryption scheme for short messages will be presented. Several multi-authority attribute based encryption schemes were recently proposed. We can divide these schemes into two groups, one of them are the ciphertext-policy attribute based encryption schemes (CP-ABE), the another one are the key-policy attribute based encryption schemes (KP-ABE). In our new multi-authority attribute based encryption scheme we combine them: the access struct...

  11. Annexes (tableaux, cartes; graphiques)

    OpenAIRE

    2013-01-01

    PREMIÈRE PARTIE. UN BILAN : L'ÉCONOMIE AGRICOLE ET LA SOCIÉTÉ PAYSANNE TRADITIONNELLES VERS 1860 CHAPITRE I. L'AGRICULTURE LE VAUCLUSE PHYSIQUE 1852 SUPERFICIES CULTIVÉES % ha SRU TABLEAU DES ÉLÉMENTS D'ANALYSE DES ASSOCIATIONS CULTURALES EN VAUCLUSE VERS 1860 (SOURCES : ENQUÊTE AGRICOLE DE 1852) ASSOCIATIONS CULTURALES 1961 CHAPITRE II. POPULATIONPAYSANNE 1861 POPULATION DENSITÉ ET DISPERSION POPULATION DENSITÉ 1861 POPULATION IMPORTANCE, CONCENTRATION, DISPERSION 1981 TYPES DE STRUCT...

  12. A Toolkit for Designing User Interfaces

    Science.gov (United States)

    1990-03-01

    as the NPS IB can provide prototyping capability. Interface generators are available commercially for nearly every computing machine on the market ...structure which holds attributes of the message buffer window is shown in Figure 4.2. The variables nlines and nchars hold the number of lines in the...window its appearance of scrolling 46 /* define a type and structure for the message buffer */ struct messbuf( long nlines ; /* number of lines in the

  13. Mineralogy and microstructure of hydrated phases during the pozzolanic reaction in the sanitary ware waste/Ca(OH)2 system

    OpenAIRE

    Medina, César; Sáez del Bosque, Isabel F.; Asensio, Eloy; Frías, Moisés; Sánchez de Rojas, M Isabel

    2016-01-01

    Despite technological improvements in its production process, the sanitary ware industry inevitably generates a certain volume of discards, products whose quality is not up to standard. The present paper is the first to scientifically explore claybased sanitary ware waste (SW) with a view to its valorization as an addition in the design of new, more environmentally friendly cements. The focus is on characterization of the waste and its pozzolanicity, as well as the struct...

  14. Robustness - theoretical framework

    DEFF Research Database (Denmark)

    Sørensen, John Dalsgaard; Rizzuto, Enrico; Faber, Michael H.

    2010-01-01

    More frequent use of advanced types of structures with limited redundancy and serious consequences in case of failure combined with increased requirements to efficiency in design and execution followed by increased risk of human errors has made the need of requirements to robustness of new struct...... of this fact sheet is to describe a theoretical and risk based framework to form the basis for quantification of robustness and for pre-normative guidelines....

  15. Functioning of the English tourism terminology in the guides to Ukraine

    OpenAIRE

    Прима, В. В.

    2015-01-01

    The article outlines main aspects of study of English tourism terminology, in particular, functional. General specific features of English guides and peculiarities of tourism terms functioning in them have been reviewed in the article.Attempted analysis of theoretical and practical aspects of investigating terminology in the works of contemporary scientists made it possible for us to identify a general tendency to consider terminological vocabulary from the points of view of semantics, struct...

  16. Characterization of a single 90-degrees 'UREAD' energy channel

    OpenAIRE

    LUPOI, ROCCO

    2006-01-01

    Most engineering products are designed to either deliver or withstand a specific maximum force or level of energy. It is important however that the design of a struct ure or a machine incorporates an external or internal mechanism to overcome excessive loading, so as to reduce human discomfort and unsafe operations. Most high-energy absorption devices are not re-usable and have rebound forces comparable to those that being absorbed. This paper examines t...

  17. A Tense Situation: Forcing Tumour Progression

    Science.gov (United States)

    2009-02-01

    Bailey AJ. The effects of the Maillard reaction on the physical properties and cell interactions of collagen. Pathol Biol (Paris) 2006;54:387–395... reaction and, following this law, cells in vivo will respond to alterations in the mechanical properties of their surrounding matrix by adjusting...cell marker for testing malignant transformation and metastatic competence. Biophys J 2005;88:3689–369. [PubMed: 15722433] 29. Cross SE, Jin YS, Rao J

  18. AFRRI Reports, First Quarter 1993

    Science.gov (United States)

    1993-05-01

    and 5-hvdroxvtrvptamine, as well as other circulatinlg factors, (abnormal) access to neurons that modulate hippocampal NA release 112). It has been...McCann SM. hamster monoclonal antibodies that neutralize tumor necrosis fac- Interleukin-1 alpha (IL-ler)-irnmunoreactive neurons in the hypo- tars. J...Biochem. Biophys. Res. Commun. 69. 446-454. 29. Espejo . R.T. and Lebowitz, J. (1976) Analyt. Biochem. 72, 95-103. 30. Lang. M.C.E., Freund, A.M., de

  19. Cross-Linking in Collagen by Nonenzymatic Glycation Increases the Matrix Stiffness in Rabbit Achilles Tendon

    OpenAIRE

    Reddy, G. Kesava

    2004-01-01

    Nonenzymatic glycation of connective tissue matrix proteins is a major contributor to the pathology of diabetes and aging. Previously the author and colleagues have shown that nonenzymatic glycation significantly enhances the matrix stability in the Achilles tendon (Reddy et al., 2002, Arch. Biochem. Biophys., 399, 174–180). The present study was designed to gain further insight into glycation-induced collagen cross-linking and its relationship to matrix stiffness in the rabbit Achilles tendo...

  20. Carnitine prevents the early mitochondrial damage induced by methylglyoxal bis(guanylhydrazone) in L1210 leukaemia cells.

    OpenAIRE

    Nikula, P; Ruohola, H; Alhonen-Hongisto, L; Jänne, J

    1985-01-01

    We previously found that the anti-cancer drug methylglyoxal bis(guanylhydrazone) (mitoguazone) depresses carnitine-dependent oxidation of long-chain fatty acids in cultured mouse leukaemia cells [Nikula, Alhonen-Hongisto, Seppänen & Jänne (1984) Biochem. Biophys. Res. Commun. 120, 9-14]. We have now investigated whether carnitine also influences the development of the well-known mitochondrial damage produced by the drug in L1210 leukaemia cells. Palmitate oxidation was distinctly inhibited in...

  1. Diversity, Replication, Pathogenicity and Cell Biology of Crimean Congo Hemorrhagic Fever Virus

    Science.gov (United States)

    2010-10-01

    1990. Hen egg white lysozyme expressed in, and secreted from, Aspergillus niger is correctly processed and folded. Biotechnology (New York) 8:741–745. 7...in bunyavirus-infected cells. J. Virol. 41:643–648. 18. Garry, C. E., and R. F. Garry. 2004. Proteomics computational analyses suggest that the...2005). Proteomic identification of proteins conjugated to ISG15 in mouse and human cells. Biochem. Biophys. Res. Commun. 336, 496–506. Haas, A.L

  2. Of maps and scripts

    DEFF Research Database (Denmark)

    Schmidt, Kjeld

    1999-01-01

    The received understanding of the status of formal organizational constructs in cooperative work is problematic. The paper shows that the empirical evidence is not as strong as we may have believed and that there is evidence from other studies that contradicts what we may have taken for granted...... for years. This indicates that the role of formal con-structs is more differentiated than generally taken for granted. They not only serve as ‘maps’ but also as ‘scripts’....

  3. Training Program in the Molecular Basis of Breast Cancer Research

    Science.gov (United States)

    1996-10-01

    the pathogenesis of these cancers. In concert decidua were immunostained with an anti-BrdU monoclonal with Knudson’s "two- hit " theory of...12618-12622ical homogeneity from bovine testes. The high level of DNA 32. Higashitani, A., Tabata , S., Endo, H., and Hotta, Y. (1990) Cell Struct. Funct...separate enzymes. J. Biol. Chem. 250:8438-8444. 21. Higashitani, A., S. Tabata , H. Endo, and Y. Hotta. 1990. Purification of DNA 51. Stubbs, L., and H

  4. Creative China? The University, Tolerance and Talent in Chinese Regional Development

    OpenAIRE

    Florida, Richard; Mellander, Charlotta; Qian, Haifeng

    2008-01-01

    The relationships between talent, technology and regional development have been widely examined in the advanced economies. While there is a general consensus as to the important role talent plays in regional development, debate has emerged on two key issues. The first involves the efficacy of educational (i.e. human capital) versus occupational (i.e. the creative class) measures of talent; the second involves the factors affecting the distribution of talent. In this study, we have used struct...

  5. Electric equipment technical regulation on a relay

    International Nuclear Information System (INIS)

    1995-01-01

    It is about a relay for power protection. It describes the definitions of structure, a point of contact protection of contact, reclosing, relay scheme and input circuit. It explains normal use condition, special use condition, rated frequency, rated voltage and rated current, fluctuation range of permission of incoming relay. It deals with general structing outer case, correction device, operation indicator and outer terminal condition sort and method of the test. It adds the marks and pictures about currents

  6. Ill Posedness Results for Generalized Water Wave Models

    OpenAIRE

    Teyekpiti, Vincent Tetteh

    2013-01-01

    In the first part of the study, the weak asymptotic method is used to find singular solutions of the shallow water system in both one and two space dimensions. The singular solutions so constructed are allowed to contain Dirac-delta; distributions (Espinosa & Omel'yanov, 2005). The idea is to con- struct complex-valued approximate solutions which become real-valued in the distributional limit. The approach, which extends the range f possible singular solutions, is used to construct solutions ...

  7. Budování značky Career Days na českém trhu

    OpenAIRE

    Boskovičová, Alexandra

    2009-01-01

    The paper is analyzing the strategy of the brand Career Days. Career Days, similar to job fairs, offer university students and graduates work opportunities. Annually, they are hold by the international non-profit student organization AIESEC. The aim of the bachelor thesis is to describe and evaluate the position of this brand on the Czech market and suggest changes which would help increasing its awareness. In the introduction, I am addressing to the organization AIESEC, describing its struct...

  8. CsPbBr3 Perovskites: Theoretical and Experimental Investigation on Water-Assisted Transition From Nanowire Formation to Degradation

    OpenAIRE

    Akbali, Baris; Topcu, Gokhan; Guner, Tugrul; Ozcan, Mehmet; Demir, Mustafa Muammer; Sahin, Hasan

    2018-01-01

    Recent advances in colloidal synthesis methods have led to increased research focus on halide perovskites. Due to highly ionic crystal structure of perovskite materials, stability issue pops up especially against polar solvents such as water. In this study, we investigate water-driven structural evolution of CsPbBr3 by performing experiments and state-of-the-art first-principles calculations. It is seen that while optical image shows the gradual degradation of yellowish-colored CsPbBr3 struct...

  9. The Use of Wetting Agents/Fume Suppressants for Minimizing the Atmospheric Emissions from Hard Chromium Electroplating Baths

    Science.gov (United States)

    2004-03-01

    PFOA), perfluorooctane sulphonic acid (PFOSA) and clofibric acid . Biochim Biophys Acta 1128: 65-72 Kannan K, Koistinen J, Beckmen K, Evans T...mg/dscm (6.6 x 10-6 gr/dscf) Decorative Chromium Plating Baths Using Chromic Acid All new and existing baths 0.01 mg/dscm (4.4 x 10-6 gr/dscf...surface of the baths, causing the production of chromic acid mist. “Surface active” fume suppressants (also called surfactants) are added directly

  10. Application of TensorFlow to recognition of visualized results of fragment molecular orbital (FMO) calculations

    OpenAIRE

    Saitou, Sona; Iijima, Jun; Fujimoto, Mayu; Mochizuki, Yuji; Okuwaki, Koji; Doi, Hideo; Komeiji, Yuto

    2018-01-01

    We have applied Google's TensorFlow deep learning toolkit to recognize the visualized results of the fragment molecular orbital (FMO) calculations. Typical protein structures of alpha-helix and beta-sheet provide some characteristic patterns in the two-dimensional map of inter-fragment interaction energy termed as IFIE-map (Kurisaki et al., Biophys. Chem. 130 (2007) 1). A thousand of IFIE-map images with labels depending on the existences of alpha-helix and beta-sheet were prepared by employi...

  11. Desenvolvimento de um sistema para irradiação por ultravioleta de biomoléculas

    OpenAIRE

    Mota, Carlos Daniel Silva

    2011-01-01

    Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do grau de Mestre em Engenharia Biomédica Foi desenvolvido um sistema destinado ao estudo do efeito da radiação Ultravioleta em amostras biológicas, nomeadamente em estruturas membranares constituídas por lípidos, proteínas, DNA e moléculas intercalantes de DNA potenciadoras do efeito da radiação. O sistema desenvolvido é constituído por uma fonte de luz Ultravioleta, uma lâmpada de...

  12. Yeast Interacting Proteins Database: YDR490C, YGR086C [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available bait as prey (0) YGR086C PIL1 Primary component of eisosomes, which are large immobile cell cortex struct...ctures associated with endocytosis; null mutants show activation of Pkc1p/Ypk1p str...y (0) Prey ORF YGR086C Prey gene name PIL1 Prey description Primary component of eisosomes, which are large immobile cell cortex stru...ures associated with endocytosis; null mutants show activation of Pkc1p/Ypk1p stres

  13. Impact of Corporate Governance on Diversification in Finance Companies: Evidence from Malaysia

    OpenAIRE

    KALLAMU, Basiru Salisu

    2016-01-01

    Abstract. The board of directors performs a very important role in formulating and monitoring the strategy of a company. Recent development in technology and the change in business environment as well as change in the nature of demand by customers has necessitated the change in the products and services offered by finance companies. Based on data from finance companies listed on Bursa Malaysia over the period 2007 to 2011 this paper examined the impact of board attributes and ownership struct...

  14. Potent Inhibition of HhaI DNA Methylase by the Aglycon of 2-(1H)-Pyrimidinone Riboside (Zebularine) at the GCGC Recognition Domain

    OpenAIRE

    Márquez, Víctor E.; Kelley, James A.; Eritja Casadellà, Ramón; Vanbemmel, Dana; Christman, Judith K.

    2003-01-01

    A short oligodeoxynucleotide (ODN) with 2-(1H)-pyrimidinone at the HhaI DNA methyltransferase target site (GCGC) is shown to induce a level of inhibition of methyl transfer and thermal stability of the complex with the enzyme identical to that achieved with a similar ODN substituted with 5-azacytosine. The drugs responsible for these effects - zebularine and 5-azacytidine/2′-deoxy-5-azacytidine - are contrasted in terms of chemical stability and possible metabolic activation by a brief struct...

  15. Molecular Mechanisms Underlying Genomic Instability in Brca-Deficient Cells

    Science.gov (United States)

    2014-03-01

    repair defects asso- ciated with downstream mediators of the HR reaction (e.g., XRCC2, BRCA2, or PALB2) (Bouwman et al., 2010; Bowman- Colin et al., 2013...and BRCA-mutated breast cancers. Nat. Struct. Mol. Biol. 17, 688–695. Bowman- Colin , C., Xia, B., Bunting, S., Klijn, C., Drost, R., Bouwman, P., Fine...chromosomes. It is thus surprising that cells use ‘quick and dirty ’ repair by NHEJ rather than the slower, more accurate repair by homologous recombination

  16. Lamb Wave Propagation in a Restricted Geometry Composite PI-Joint Specimen (Preprint)

    Science.gov (United States)

    2011-11-01

    adhesive, and were located along the length and height of the specimen as depicted in Figure 3. The sensors were 6.35 mm round disks of PZT , with a...in both cases for R1, R2, and R3. 3D Finite Element Model Geometry 200mm length 50mm width 140mm height x z y PZT Actuation Sensor...health monitoring using scanning laser vibrometry: III. Lamb waves for fatigue crack detection”, Smart Mater. Struct., Vol. 14, No. 6, 2005. 16

  17. New insights into the tectonic evolution of the Andaman basin, northeast Indian Ocean

    Digital Repository Service at National Institute of Oceanography (India)

    KameshRaju, K.A.; Ramprasad, T.; Rao, P.S.; Rao, B.R.; Varghese, J.

    rifts and transforms in the central basin of the Andaman Sea has been suggested to be the con- sequence of spreading with an opening rate of 3.72 cm/yr [2]. This spreading center is connected to the Sagaing fault system in the eastern Burma highlands... spreading center. The western part is dominated by volcanic con- structs that are related to arc volcanism and back- arc spreading activity, whereas the eastern part represents distinctly smooth topography probably resulting from the sediment ¢ll...

  18. Substrate Independence of THz Vibrational Modes of Polycrystalline Thin Films of Molecular Solids in Waveguide THz-TDS

    Science.gov (United States)

    2012-01-01

    2001). 2J. Zhang and D. Grischkowsky, Opt. Lett. 19, 1617 (2004). 3J. S. Melinger, N. Laman , S. Sree Harsha, and D. Grischkowsky, Appl. Phys. Lett...89, 251110 (2006). 4N. Laman , S. Sree Harsha, D. Grischkowsky, and J. S. Melinger, Biophys. J. 94, 1010 (2008). 5N. Laman , S. Sree Harsha, and D...Grischkowsky, Appl. Spect. 62, 319 (2008). 6J. S. Melinger, N. Laman , and D. Grischkowsky, Appl. Phys. Lett. 93, 011102 (2008). 7J. S. Melinger, S. Sree

  19. Factors determining the oxygen consumption rate (VO2) on-kinetics in skeletal muscles.

    OpenAIRE

    Korzeniewski, Bernard; Zoladz, Jerzy A

    2004-01-01

    Using a computer model of oxidative phosphorylation developed previously [Korzeniewski and Mazat (1996) Biochem. J. 319, 143-148; Korzeniewski and Zoladz (2001) Biophys. Chem. 92, 17-34], we analyse the effect of several factors on the oxygen-uptake kinetics, especially on the oxygen consumption rate (VO2) and half-transition time t(1/2), at the onset of exercise in skeletal muscles. Computer simulations demonstrate that an increase in the total creatine pool [PCr+/-Cr] (where Cr stands for c...

  20. Targeting Tryptophan Catabolism: A Novel Method to Block Triple-Negative Breast Cancer Metastasis

    Science.gov (United States)

    2017-04-01

    Negative Breast Cancer Nicholas C. D’Amato1, Thomas J. Rogers1, Michael A. Gordon1, Lisa I. Greene1, Dawn R. Cochrane1, Nicole S. Spoelstra1, Travis G...cancer progression. Biochim Biophys Acta 2013;1833:3481–98. 10. Kamarajugadda S, Stemboroski L, Cai Q, Simpson NE, Nayak S, Tan M, et al. Glucose...4664. Published OnlineFirst September 11, 2015.Cancer Res Nicholas C. D’Amato, Thomas J. Rogers, Michael A. Gordon, et al. Metastasis in Triple

  1. Host-Pathogen Coupled Networks: Model for Bacillus Anthracis Interaction with Host Macrophages

    Science.gov (United States)

    2015-09-01

    circles). Data points represent absorbance values at 570 nm following the MTT assay. Fitted values are KX2 = 10-6 nM-1s-1 and R = 0.21 nM s-1. (B...represent absorbance values at 570 nm following MTT assay. Here cell “death”, as indicated by the diminution of the signal (corrected for residual...cleaves the N-terminus of MAPKKs and induces tyrosine /threonine phosphorylation of MAPKs in cultured macrophages. Biochem Biophys Res Commun. 248(3):706

  2. The mobile phone - a resource in schoolwork?

    OpenAIRE

    Blomander, Karin; Hansson, Sofia; Påhlsson, Bodil

    2012-01-01

    The aim of this thesis was to investigate how students, teachers and special teachers use, or may want to use, mobile phones as a resource in everyday schoolwork. An analysis of the result was made base on two main theories. One i Säljös theory about the sociocultural perspective, where artefacts play an important part in the devolopment of human society. The other is Laurillardss thougts of social learning and the use of technology in teaching. The methods used were inquiries and semi-struct...

  3. Productive High Performance Parallel Programming with Auto-tuned Domain-Specific Embedded Languages

    Science.gov (United States)

    2013-01-02

    an array similar to that in the scalar case, but where each item in the array is a C struct instead of a built-in datatype ; this is called an array of...provide methods in our class that enable execution. In addition, we restrict the elemental datatypes to a subset of those supported by NumPy [88... datatypes and C++ datatypes when necessary, but in the case of the Scala backend, the DSEL uses Asp’s Scala support to translate datatypes using the Apache

  4. Development of knowledge tests for multi-disciplinary emergency training

    DEFF Research Database (Denmark)

    Sorensen, J. L.; Thellesen, L.; Strandbygaard, J.

    2015-01-01

    and evaluating a multiple-choice question(MCQ) test for use in a multi-disciplinary training program inobstetric-anesthesia emergencies. Methods: A multi-disciplinary working committee with 12members representing six professional healthcare groups andanother 28 participants were involved. Recurrent revisions......, 40 out of originally50 items were included in the final MCQ test. The MCQ test wasable to distinguish between levels of competence, and good con-struct validity was indicated by a significant difference in the meanscore between consultants and first-year trainees, as well as betweenfirst...

  5. A nano capacitor with graphene electrodes and Methane - (h-BN)insulator

    OpenAIRE

    Farrokh Roya Nikmaram

    2016-01-01

    Methan has a large potential to adsorb and diffuse among h-BN and graphene surfaces as the suitable dielectric. With this background the nanoscale dielectric capacitors have been widely studied due to their ability to store a high amount of energy. In this research, I have modeled one which is composed of two graphene layers including insulating medium of a h-BN layers which are filed out (Methane)n,m {n=m=7). It has been indicated thatthe Methane moleculeis the suitable gas for hetero-struct...

  6. Interannual variability of the South Pacific Convergence Zone and implications for tropical cyclone genesis

    Digital Repository Service at National Institute of Oceanography (India)

    Vincent, E.M.; Lengaigne, M.; Menkes, C.E.; Jourdain, N.C.; Marchesiello, P.; Madec, G.

    SPCZ con- trols the large scale environment favouring cyclonic activity have not yet been investigated. In addition, the characteristics of El Nin˜o events vary widely from one event to another, and the influence of this diversity on the SPCZ location... which the classification is performed) accu- rately summarizes the large-scale precipitation variability in the tropical South Pacific (on which the EOFs are con- structed). The same AHC applied to PC1–PC2 coordinates instead of latW–latE indices gives...

  7. Do Deregulated Cas Proteins Induce Genomic Instability In Early Stage Ovarian Cancer?

    Science.gov (United States)

    2007-12-01

    Tensional homeostasis and the malignant phenotype. Cancer Cell 2005;8:241–54. [PubMed: 16169468] 40. Zhang Z, Hernandez- Lagunas L, Horne WC, Baron R...disassembly. Nat Cell Biol 2004;6:154–61. [PubMed: 14743221] 58. Huang J, Hamasaki H, Nakamoto T, Honda H, Hirai H, Saito M, Takato T, Sakai R...Cell Struct Funct 2001;26:619–26. [PubMed: 11942617] 87. Yi J, Kloeker S, Jensen CC, Bockholt S, Honda H, Hirai H, Beckerle MC. Members of the zyxin

  8. DETERMINING COSTS-RETURNS PROFITABILITY IN HONEY MARKETING IN CROSS RIVER STATE, NIGERIA

    OpenAIRE

    Adinya, I.B; Ayuk, E.A; Akpet, S.O; Agiopu, B.F

    2017-01-01

    This study examined costs-returns profitability in honey marketing in Cross River State. Honey contains 29 percent of protein, 19 percent of amino acid, vitamins and minerals for bodybuilding. Honey mixed with aloe vera gel is use for cure of dandruff and rapid hair growth. This mixture could also help to prevent hair breakage. Honey pollen enhances vitality and brings about a longer life span. Data were obtained from a random sample of 120 honey marketers in the study area by means of struct...

  9. Measures for the characterisation of pattern-recognition data sets

    CSIR Research Space (South Africa)

    Van der Walt, Christiaan M

    2007-11-01

    Full Text Available artificial data sets to construct a meta-classifier. 4.1. Classifiers We will use model-based and discriminative classifiers to con- struct our meta-classifier; these classifiers are the Naı¨ve Bayes (NB), Gaussian (Gauss), Gaussian Mixture Model (GMM... of these classifiers for real-world data sets. 4.2. Artificial data We will make use of artificial data sets to construct a meta- classification training set; these artificial data sets are gener- ated with very specific data properties that influence classifi...

  10. Role of Stat3 and ErbB2 in Breast Cancer

    Science.gov (United States)

    2013-12-01

    Nemoto, K.E. Pestell , K. Cooley, E.C. Southwick, D.A. Mitchell, W. Furey, R. Gussio, D.W. Zaharevitz, B. Joo, P. Wipf, Identification of a potent...7). Inorg Chem 2008, 47:2798–2804. 26. Bromberg JF, Wrzeszczynska MH, Devgan G, Zhao Y, Pestell RG, Albanese C, et al: Stat3 as an oncogene. Cell...Biochem Biophys Res Commun 382: 440-444, 2009. 7 Bromberg JF, Wrzeszczynska MH, Devgan G, Zhao Y, Pestell RG, Albanese C and Darnell JE Jr.: Stat3 as an

  11. An Assay of RNA Synthesis in Hepatic Nuclei from Control and Streptococcus pneumoniae-Infected Rats

    Science.gov (United States)

    1982-02-22

    26) as modified by pended in 2.0 ml of 1.0 N KOH and incu- McNamara et al. (27). Nuclei (about 0.25 mg bated for 20 hr at 370 to hydrolyze RNA (28...containing hydrolyzed RNA was ml yeast RNA, 18 units pyruvate kinase, I counted in Scintisol. The pellet was solubi- mM cytidine triphosphate (CTP), I mM...WC. Lecithin biosynthesis in liver mi- 16. Blobel G, Potter VR. Nuclei from rat liver, isolation tochondrial fractions. Biochem Biophys Res Coin

  12. An adaptive left–right eigenvector evolution algorithm for vibration isolation control

    International Nuclear Information System (INIS)

    Wu, T Y

    2009-01-01

    The purpose of this research is to investigate the feasibility of utilizing an adaptive left and right eigenvector evolution (ALREE) algorithm for active vibration isolation. As depicted in the previous paper presented by Wu and Wang (2008 Smart Mater. Struct. 17 015048), the structural vibration behavior depends on both the disturbance rejection capability and mode shape distributions, which correspond to the left and right eigenvector distributions of the system, respectively. In this paper, a novel adaptive evolution algorithm is developed for finding the optimal combination of left–right eigenvectors of the vibration isolator, which is an improvement over the simultaneous left–right eigenvector assignment (SLREA) method proposed by Wu and Wang (2008 Smart Mater. Struct. 17 015048). The isolation performance index used in the proposed algorithm is defined by combining the orthogonality index of left eigenvectors and the modal energy ratio index of right eigenvectors. Through the proposed ALREE algorithm, both the left and right eigenvectors evolve such that the isolation performance index decreases, and therefore one can find the optimal combination of left–right eigenvectors of the closed-loop system for vibration isolation purposes. The optimal combination of left–right eigenvectors is then synthesized to determine the feedback gain matrix of the closed-loop system. The result of the active isolation control shows that the proposed method can be utilized to improve the vibration isolation performance compared with the previous approaches

  13. Topology Optimization in Electric Car Body Frame Based on Optistruct

    Directory of Open Access Journals (Sweden)

    Ge Dongdong

    2017-01-01

    Full Text Available In order to optimize the structure of the electric car body frame, the static analysis of the car frame were carried on. For the goal of the frame’s weight minimum, OptiStruct software was used to topology optimization design. And the optimal material distribution program of the frame structure was got. Static strength before and after optimization was comprehensive compared through the stress, deformation. The results showed that the weight of frame after optimization was reduced by 18.96%, and the requirements of the strength and stiffness were ensured.

  14. Redetermination of 3-methylisoquinoline at 150 K

    Directory of Open Access Journals (Sweden)

    Andrew D. Bond

    2010-11-01

    Full Text Available The structure of the title compound, C19H9O, has been redetermined at 150 K. The redetermination is of significantly higher precision than a previous room-temperature structure [Ribar et al. (1974. Cryst. Struct. Commun. 3, 323–325]. The C—N bond lengths for this redetermination are much closer to those observed in comparable structures, and the orientation of the methyl group with respect to the isoquinoline plane is clarified. Intermolecular weak C—H...N contacts are present in the crystal.

  15. Teaching English Grammar Through Communicative Language Teaching Approach

    Institute of Scientific and Technical Information of China (English)

    王玮

    2013-01-01

    Grammar is an important part of language learning. In order for students to have a functional knowledge of a language (in other words, that they can spontaneously produce language) they must have at least some knowledge about the grammatical con⁃structs of the language in question. How grammar can be taught? Considering various second language teaching methods, teaching grammar through Communicative Language Teaching Approach is the most talked. Emphasis in this article is put on the applica⁃tion of Communicative Language Teaching Approach in grammar teaching in college English classes.

  16. Interatomic bonding in solids fundamentals, simulation, applications

    CERN Document Server

    Levitin , Valim

    2013-01-01

    The connection between the quantum behavior of the structure elements of a substance and the parameters that determine the macroscopic behavior of materials has a major influence on the properties exhibited by different solids. Although quantum engineering and theory should complement each other, this is not always the case. This book aims to demonstrate how the properties of materials can be derived and predicted from the features of their structural elements, generally electrons. In a sense, electronic structure forms the glue holding solids together and it is central to determining struct

  17. A short numerical study on the optimization methods influence on topology optimization

    DEFF Research Database (Denmark)

    Rojas Labanda, Susana; Sigmund, Ole; Stolpe, Mathias

    2017-01-01

    Structural topology optimization problems are commonly defined using continuous design variables combined with material interpolation schemes. One of the challenges for density based topology optimization observed in the review article (Sigmund and Maute Struct Multidiscip Optim 48(6):1031–1055...... 2013) is the slow convergence that is often encountered in practice, when an almost solid-and-void design is found. The purpose of this forum article is to present some preliminary observations on how designs evolves during the optimization process for different choices of optimization methods...

  18. Development and Translation of Hybrid Optoacoustic/Ultrasonic Tomography for Early Breast Cancer Detection

    Science.gov (United States)

    2015-09-01

    second, more crude , data completion strategy was to simply fill the missing data with zeros, i.e., [ ]g gm mm L l m L l mm mcomb0 incpl rec good rec rec...correct speed of sound of 1.522 mm/ µs, corresponding to the speed of sound in the ambient distilled water at 36°C. Image shows sharp cross-sections...images of an agar/ oil phantom were recon- structed using straight-ray fan-beam CT and showed good quality of two 8 mm and 5 mm square inclusions

  19. Management of professionals in school practices

    DEFF Research Database (Denmark)

    Jacobsen, Alice Juel; Buch, Anders

    2016-01-01

    related to an under-standing of professionals are used to investigate the practices involved in the change processes. The article argues that the ambiguity of a primus inter pares management position among professionals leads to several paradoxes, deadlocks, and detours, all of which affect the work......This article investigates organizational reform changes as they are con-structed in the interaction between managers and teachers in a school context. The empirical basis is comprised of case studies carried out in Danish upper secondary schools. An ethnographic approach and a concept of paradox...

  20. Magnetic studies of basement off the coast of Bombay, West of India

    Digital Repository Service at National Institute of Oceanography (India)

    Rao, D.G.

    ) and present stud- ies. Geological setting Onshore geology The geology of the onshore area between lati- tudes 15 o N and 25” N and longitudes 69”30’E and 82”OO’E adjacent to the study area is con- cealed underneath basalts (Deccan traps) of un- known... resulted in the observed struct- ural configuration in the study area of the con- tinental margin, northwest of India. Acknowledgements The author is indebted to Dr. B.N. Desai, for encouragement while carrying out the studies. Part of the data...

  1. Analysis of myo-inositol hexakisphosphate hydrolysis by Bacillus phytase

    DEFF Research Database (Denmark)

    Kerovuo, J.; Rouvinen, J.; Hatzack, Frank-Andreas

    2000-01-01

    Phytic acid (myo-inositol hexakisphosphate, InsP(6)) hydrolysis by Bacillus phytase (PhyC) was studied. The enzyme hydrolyses only three phosphates from phytic acid. Moreover, the enzyme seems to prefer the hydrolysis of every second phosphate over that of adjacent ones. Furthermore, it is very...... a reaction mechanism different from that of other phytases. By combining the data presented in this study with (1) structural information obtained from the crystal structure of Bacillus amyloliquefaciens phytase [Ha, Oh, Shin, Kim, Oh, Kim, Choi and Oh (2000) Nat. Struct. Biol. 7, 147-153], and (2) computer...

  2. Efficient topology optimization in MATLAB using 88 lines of code

    DEFF Research Database (Denmark)

    Andreassen, Erik; Clausen, Anders; Schevenels, Mattias

    2011-01-01

    The paper presents an efficient 88 line MATLAB code for topology optimization. It has been developed using the 99 line code presented by Sigmund (Struct Multidisc Optim 21(2):120–127, 2001) as a starting point. The original code has been extended by a density filter, and a considerable improvemen...... of the basic code to include recent PDE-based and black-and-white projection filtering methods. The complete 88 line code is included as an appendix and can be downloaded from the web site www.topopt.dtu.dk....

  3. Cobinding of bilirubin and laurate to human serum albumin: spectroscopic characterization of stoichiometric complexes

    DEFF Research Database (Denmark)

    Honoré, B; Sato, H; Brodersen, R

    1988-01-01

    Light absorption and CD spectra of bound bilirubin and albumin fluorescence spectra have been recorded from mixtures containing albumin, A, bilirubin, B, and laurate, L, in Tris-NaCl buffer at pH 8.2, 25 degrees C. Concentrations of the corresponding stoichiometric complexes, ABiLj, for i = 0....../3 and j = 0/3, have been calculated from previously determined stoichiometric cobinding constants (H. Sato et al. (1988) Arch. Biochem. Biophys. 260, 811-821). Spectral data of the complexes have finally been found by iterative computer fitting using the principle of several acceptable solutions (R...

  4. Sequential assignment of proline-rich regions in proteins: Application to modular binding domain complexes

    International Nuclear Information System (INIS)

    Kanelis, Voula; Donaldson, Logan; Muhandiram, D.R.; Rotin, Daniela; Forman-Kay, Julie D.; Kay, Lewis E.

    2000-01-01

    Many protein-protein interactions involve amino acid sequences containing proline-rich motifs and even poly-proline stretches. The lack of amide protons in such regions complicates assignment, since 1 HN-based triple-resonance assignment strategies cannot be employed. Two such systems that we are currently studying include an SH2 domain from the protein Crk with a region containing 9 prolines in a 14 amino acid sequence, as well as a WW domain that interacts with a proline-rich target. A modified version of the HACAN pulse scheme, originally described by Bax and co-workers [Wang et al. (1995) J. Biomol. NMR, 5, 376-382], and an experiment which correlates the intra-residue 1 H α , 13 C α / 13 C β chemical shifts with the 15 N shift of the subsequent residue are presented and applied to the two systems listed above, allowing sequential assignment of the molecules

  5. Síntesis de nanoestructuras de ZnO en vidrio recubierto con In2O3/SnO2 Deposición química en fase gaseosa

    Directory of Open Access Journals (Sweden)

    Alberto Hernández-Valle

    2014-12-01

    Full Text Available En este proyecto se sintetizaron nano- y microestructuras de óxido de zinc en un sustrato transparente de vidrio cubierto con In2O3/ SnO2(ITO por el método de deposición química de vapor. El material depositado exhibe distintas morfologías, incluyendo capa homogénea, nanobarras rectas y curvilíneas, nanopartículas poliformes, nanotetrápodos, microbarras y micropartículas. Los resultados comprueban que el tipo de estructuras de óxido de zinc que se producenson altamente dependientes de la distancia entre el contenedor del polvo de zinc y el sustrato, de la relación molar O:Zn, y del tiempo de síntesis. El material compuesto fabricado tiene gran potencial para ser usado como fotoánodo en celdas solares sensibilizadas con tintes y biomoléculas.

  6. Identifying food-related life style segments by a cross-culturally valid scaling device

    DEFF Research Database (Denmark)

    Brunsø, Karen; Grunert, Klaus G.

    1994-01-01

    -related life style in a cross-culturally valid way. To this end, we have col-lected a pool of 202 items, collected data in three countries, and have con-structed scales based on cross-culturally stable patterns. These scales have then been subjected to a number of tests of reliability and vali-dity. We have...... then applied the set of scales to a fourth country, Germany, based on a representative sample of 1000 respondents. The scales had, with a fe exceptions, moderately good reliabilities. A cluster ana-ly-sis led to the identification of 5 segments, which differed on all 23 scales....

  7. 2 : 2 Fe(III): ligand and "adamantane core" 4 : 2 Fe(III): ligand (hydr)oxo complexes of an acyclic ditopic ligand

    DEFF Research Database (Denmark)

    Ghiladi, Morten; Larsen, Frank B.; McKenzie, Christine J.

    2005-01-01

    A bis-hydroxo-bridged diiron(III) complex and a bis-mu-oxo-bis-mu-hydroxo-bridged tetrairon( III) complex are isolated from the reaction of 2,6-bis((N, N'-bis-(2-picolyl) amino) methyl)-4-tert-butylphenol (Hbpbp) with iron perchlorate in acidic and neutral solutions respectively. The X-ray struct......A bis-hydroxo-bridged diiron(III) complex and a bis-mu-oxo-bis-mu-hydroxo-bridged tetrairon( III) complex are isolated from the reaction of 2,6-bis((N, N'-bis-(2-picolyl) amino) methyl)-4-tert-butylphenol (Hbpbp) with iron perchlorate in acidic and neutral solutions respectively. The X...

  8. The Fourier Transform Microwave (ftmw) Spectra of Cyclohexene Oxide and its Argon Complex

    Science.gov (United States)

    Frohman, Daniel J.; Novick, Stewart E.; Pringle, Wallace C.

    2012-06-01

    The microwave spectrum of cyclohexene oxide and its isotopologues have been observed and assigned, improving upon previous rotational studies of this molecule. Additionally, the 17O isotopomer of cyclohexene oxide and the Ar complex of the normal isotopologue of cyclohexene oxide have been fit for the first time. Fits for the 13C-cyclohexene oxide Ar complexes will also be presented. Tatsuya Ikeda, Roger Kewley, and R. F. Curl, Jr. J. Mol. Spectrosc., 4} (1972), 459-469. Raquel Sánchez, Susana Blanco, Juan C. López, and José L. Alonso. J. Mol. Struct., 780-781 (2006), 57-64.

  9. Microtermolides A and B from termite-associated Streptomyces sp. and structural revision of vinylamycin

    DEFF Research Database (Denmark)

    Carr, Gavin; Poulsen, Michael; Klassen, Jonathan L.

    2012-01-01

    Microtermolides A (1) and B (2) were isolated from a Streptomyces sp. strain associated with fungus-growing termites. The structures of 1 and 2 were determined by 1D- and 2D-NMR spectroscopy and high-resolution mass spectrometry. Structural elucidation of 1 led to the re-examination of the struct......Microtermolides A (1) and B (2) were isolated from a Streptomyces sp. strain associated with fungus-growing termites. The structures of 1 and 2 were determined by 1D- and 2D-NMR spectroscopy and high-resolution mass spectrometry. Structural elucidation of 1 led to the re...

  10. Desarrollo de nuevos sistemas separativos para la determinación de biomoléculas en matrices vegetales

    OpenAIRE

    Vergara Barberán, María

    2017-01-01

    La presente memoria se enmarca dentro de las líneas de investigación del grupo de investigación, entre las que se encuentran: i) el desarrollo de materiales poliméricos con fines separativos, y ii) la puesta a punto de metodologías analíticas rápidas y fiables para el control de calidad en la industria de aceites vegetales y otros productos de interés agroalimentario. En consecuencia, los objetivos principales de esta Tesis Doctoral son: i) el diseño y optimización de soportes poliméricos mod...

  11. Glycomic and sialoproteomic data of gastric carcinoma cells overexpressing ST3GAL4

    DEFF Research Database (Denmark)

    Mereiter, Stefan; Magalhães, Ana; Adamczyk, Barbara

    2016-01-01

    Gastric carcinoma MKN45 cells stably transfected with the full-length ST3GAL4 gene were characterised by glycomic and sialoproteomic analysis. Complementary strategies were applied to assess the glycomic alterations induced by ST3GAL4 overexpression. The N- and O-glycome data were generated in two......-MS/MS identification was performed. This analysis identified 47 proteins with significantly increased sialylation. The data in this article is associated with the research article published in Biochim Biophys Acta "Glycomic analysis of gastric carcinoma cells discloses glycans as modulators of RON receptor tyrosine...... kinase activation in cancer" [1]....

  12. 13CHD2–CEST NMR spectroscopy provides an avenue for studies of conformational exchange in high molecular weight proteins

    International Nuclear Information System (INIS)

    Rennella, Enrico; Huang, Rui; Velyvis, Algirdas; Kay, Lewis E.

    2015-01-01

    An NMR experiment for quantifying slow (millisecond) time-scale exchange processes involving the interconversion between visible ground state and invisible, conformationally excited state conformers is presented. The approach exploits chemical exchange saturation transfer (CEST) and makes use of 13 CHD 2 methyl group probes that can be readily incorporated into otherwise highly deuterated proteins. The methodology is validated with an application to a G48A Fyn SH3 domain that exchanges between a folded conformation and a sparsely populated and transiently formed unfolded ensemble. Experiments on a number of different protein systems, including a 360 kDa half-proteasome, establish that the sensitivity of this 13 CHD 2 13 C–CEST technique can be upwards of a factor of 5 times higher than for a previously published 13 CH 3 13 C–CEST approach (Bouvignies and Kay in J Biomol NMR 53:303–310, 2012), suggesting that the methodology will be powerful for studies of conformational exchange in high molecular weight proteins

  13. Innovative intelligent technology of distance learning for visually impaired people

    Science.gov (United States)

    Samigulina, Galina; Shayakhmetova, Assem; Nuysuppov, Adlet

    2017-12-01

    The aim of the study is to develop innovative intelligent technology and information systems of distance education for people with impaired vision (PIV). To solve this problem a comprehensive approach has been proposed, which consists in the aggregate of the application of artificial intelligence methods and statistical analysis. Creating an accessible learning environment, identifying the intellectual, physiological, psychophysiological characteristics of perception and information awareness by this category of people is based on cognitive approach. On the basis of fuzzy logic the individually-oriented learning path of PIV is con- structed with the aim of obtaining high-quality engineering education with modern equipment in the joint use laboratories.

  14. Wiki Web Collaboration

    CERN Document Server

    Ebersbach, Anja; Heigl, Richard

    2006-01-01

    A book about wikis! That's what people need. Because with wiki technology, lots of people can freely work - gether - they can even generate very large works in the intellectual realm. See for yourself: Today, we still marvel at our massive church buildings, each c- structed over a period of centuries, requiring an immense amount of labor and often bearing the cultural stamp of all of the epochs during which it was created. Someone just has to begin by placing stone upon stone and motivate the people nearby to help out a bit. In places where such enthusiastic fellow men and women lend a hand an

  15. Sense and Sensibility:The Erotic Triangle in Shakespearean Sonnets

    Institute of Scientific and Technical Information of China (English)

    舒畅

    2017-01-01

    The male-female-male relationship is a recurrent theme in William Shakespeare's sonnets. In Eve Sedgwick's influen-tial queer study book Between Men:English Literature and Male Homosocial Desire, she first interpreted the relationship within the model of erotic triangle. On the basis of Sedgwick's theory, the triangle relationship in the Sonnets is analyzed—Shakespeare con-structs an erotic triangle where males by identifying, cooperating, and competing with each other, maintain their homosocial bond upon heterosexual but misogynous desires towards a female. The contradictory relationship reflects Shakespeare 's struggle vis-à-vis a Renaissance literary theme:rationality versus passion, with the former mounting over the latter.

  16. Sense and Sensibility:The Erotic Triangle in Shakespearean Sonnets

    Institute of Scientific and Technical Information of China (English)

    舒畅

    2017-01-01

    The male-female-male relationship is a recurrent theme in William Shakespeare's sonnets. In Eve Sedgwick's influen-tial queer study book Between Men: English Literature and Male Homosocial Desire, she first interpreted the relationship within the model of erotic triangle. On the basis of Sedgwick's theory, the triangle relationship in the Sonnets is analyzed—Shakespeare con-structs an erotic triangle where males by identifying, cooperating, and competing with each other, maintain their homosocial bond upon heterosexual but misogynous desires towards a female. The contradictory relationship reflects Shakespeare's struggle vis-à-vis a Renaissance literary theme: rationality versus passion, with the former mounting over the latter.

  17. BWR stability using a reduced dynamical model

    International Nuclear Information System (INIS)

    Ballestrin Bolea, J.M.; Blazquez, J.B.

    1990-01-01

    BWR stability can be treated with reduced order dynamical models. When the parameters of the model came from experimental data, the predictions are accurate. In this work an alternative derivation for the void fraction equation is made, but remarking the physical struct-ure of the parameters. As the poles of power/reactivity transfer function are related with the parameters, the measurement of the poles by other techniques such as noise analysis will lead to the parameters, but the system of equations in non-linear. Simple parametric calculat-ion of decay ratio are performed, showing why BWRs become unstable when they are operated at low flow and high power. (Author). 7 refs

  18. 2-(4-Fluorobenzylidenepropanedinitrile: monoclinic polymorph

    Directory of Open Access Journals (Sweden)

    Ahmed M. El-Agrody

    2013-04-01

    Full Text Available The title compound, C10H5FN2, is a monoclinic (P21/c polymorph of the previously reported triclinic (P-1 form [Antipin et al. (2003. J. Mol. Struct. 650, 1–20]. The 13 non-H atoms in the title polymorph are almost coplanar (r.m.s. deviation = 0.020 Å; a small twist between the fluorobenzene and dinitrile groups [C—C—C—C torsion angle = 175.49 (16°] is evident in the triclinic polymorph. In the crystal, C—H...N interactions lead to supramolecular layers parallel to (-101; these are connected by C—F...π interactions.

  19. Perceptions of Caribbean type 2 diabetes patients on self-monitoring of blood glucose

    DEFF Research Database (Denmark)

    Ezenwaka, C. E.; Olukoga, A.; Onuoha, P.

    2012-01-01

    Context: The views of type 2 diabetes (T2DM) patients have not been considered in the debate on the role of self-monitoring of blood glucose (SMBG) in the management of T2DM. Objective: To assess the views of T2DM patients on SMBG. Methods: Two previously trained research assistants used a struct......Context: The views of type 2 diabetes (T2DM) patients have not been considered in the debate on the role of self-monitoring of blood glucose (SMBG) in the management of T2DM. Objective: To assess the views of T2DM patients on SMBG. Methods: Two previously trained research assistants used...

  20. Innovative intelligent technology of distance learning for visually impaired people

    Directory of Open Access Journals (Sweden)

    Samigulina Galina

    2017-12-01

    Full Text Available The aim of the study is to develop innovative intelligent technology and information systems of distance education for people with impaired vision (PIV. To solve this problem a comprehensive approach has been proposed, which consists in the aggregate of the application of artificial intelligence methods and statistical analysis. Creating an accessible learning environment, identifying the intellectual, physiological, psychophysiological characteristics of perception and information awareness by this category of people is based on cognitive approach. On the basis of fuzzy logic the individually-oriented learning path of PIV is con- structed with the aim of obtaining high-quality engineering education with modern equipment in the joint use laboratories.

  1. Accidental beam loss in superconducting accelerators: Simulations, consequences of accidents and protective measures

    International Nuclear Information System (INIS)

    Drozhdin, A.; Mokhov, N.; Parker, B.

    1994-02-01

    The consequences of an accidental beam loss in superconducting accelerators and colliders of the next generation range from the mundane to rather dramatic, i.e., from superconducting magnet quench, to overheating of critical components, to a total destruction of some units via explosion. Specific measures are required to minimize and eliminate such events as much as practical. In this paper we study such accidents taking the Superconducting Supercollider complex as an example. Particle tracking, beam loss and energy deposition calculations were done using the realistic machine simulation with the Monte-Carlo codes MARS 12 and STRUCT. Protective measures for minimizing the damaging effects of prefire and misfire of injection and extraction kicker magnets are proposed here

  2. Damage-based life prediction model for uniaxial low-cycle stress fatigue of super-elastic NiTi shape memory alloy microtubes

    Science.gov (United States)

    Song, Di; Kang, Guozheng; Kan, Qianhua; Yu, Chao; Zhang, Chuanzeng

    2015-08-01

    Based on the experimental observations for the uniaxial low-cycle stress fatigue failure of super-elastic NiTi shape memory alloy microtubes (Song et al 2015 Smart Mater. Struct. 24 075004) and a new definition of damage variable corresponding to the variation of accumulated dissipation energy, a phenomenological damage model is proposed to describe the damage evolution of the NiTi microtubes during cyclic loading. Then, with a failure criterion of Dc = 1, the fatigue lives of the NiTi microtubes are predicted by the damage-based model, the predicted lives are in good agreement with the experimental ones, and all of the points are located within an error band of 1.5 times.

  3. Damage-based life prediction model for uniaxial low-cycle stress fatigue of super-elastic NiTi shape memory alloy microtubes

    International Nuclear Information System (INIS)

    Song, Di; Kang, Guozheng; Kan, Qianhua; Yu, Chao; Zhang, Chuanzeng

    2015-01-01

    Based on the experimental observations for the uniaxial low-cycle stress fatigue failure of super-elastic NiTi shape memory alloy microtubes (Song et al 2015 Smart Mater. Struct. 24 075004) and a new definition of damage variable corresponding to the variation of accumulated dissipation energy, a phenomenological damage model is proposed to describe the damage evolution of the NiTi microtubes during cyclic loading. Then, with a failure criterion of D c = 1, the fatigue lives of the NiTi microtubes are predicted by the damage-based model, the predicted lives are in good agreement with the experimental ones, and all of the points are located within an error band of 1.5 times. (paper)

  4. Aeroelastic flutter energy harvesters self-polarized by triboelectric effects

    Science.gov (United States)

    Perez, M.; Boisseau, S.; Geisler, M.; Gasnier, P.; Willemin, J.; Despesse, G.; Reboud, J. L.

    2018-01-01

    This paper presents the performances of several electrostatic flutter energy harvesters tested in a wind tunnel between 0 and 20 m s-1. The main idea is to use the flutter capability of thin flexible films confined between lateral walls to induce simultaneously the capacitance variations and the electrostatic polarization required by the triboelectric/electrostatic conversion. This technology provides thin and flexible devices and solve the electret’s stability issue (Perez et al 2015 Smart Mater. Struct., Perez et al 2015 New Circuits and Systems). Our prototypes (management circuit has finally been used to supply an 868 MHz wireless sensor node with temperature and acceleration measurements, validating the complete energy harvesting chain.

  5. Stress Distribution, Friction and Listeria Propulsion

    Science.gov (United States)

    Prost, Jacques

    2003-03-01

    I will review our work on the physics of listeria propulsion based on an unavoidable elastic analysis of the stress distribution in the actin gel and dynamical boundary conditions (both normal and tangential). I will show in particular that it provides a natural explanation for the symmetry breaking transition occurring with beads (work with K. Sekimoto and F. Julicher), of the saltatory behavior of beads reported by A Bernheim et al (Nature 2002) and of the shape of soft beads (with O. Campas and J.F Joanny). This last analysis proves that, as announced in an earlier paper (F; Gerbal et al Biophys Journal 2000) the rear part of the gel contributes negatively to the motion.

  6. Método fisicoquímico para el control de Pediculus humanus capitis

    Directory of Open Access Journals (Sweden)

    C. Corredor

    1994-03-01

    Full Text Available La pediculosis humana causada por el ectoparásito Pediculus humanus capitis, ha sido exitosamente controlada utilizando como insecticida los alcoholes presentes en las bebidas etílicas (aguardiente. La acción ietal de los alcoholes de bebida sobre el parásito es atribuida al efecto neurotóxico, así como a su acción desnaturalizante de biomoléculas celulares. El tratamiento se hace cubriendo el cabello y todas las áreas del cuero cabelludo con una bolsa plástica desechable, fijada con cinta adhesiva, previo remojo con 15-50 ml de alcohol de bebida, de todo el cabello. La atmósfera circundante del parásito queda saturada de vapores etílicos, de agua y CO2, por un período de 30-60 minutos, lo cual es letal para huevos, larvas y adultos del insecto parásito. Se dan normas cautelosas para garantizar la acción insecticida de los alcoholes de bebida en el control de la pediculosis.

  7. Empleo de nanopartículas metálicas para la detección de tensioactivos y biomoléculas

    OpenAIRE

    Vergara O’Neale, Lourdes

    2016-01-01

    Actualmente, las nanopartículas juegan un papel muy importante en el campo de la investigación científica debido a la gran variedad de aplicaciones en distintas áreas tales como la farmacología, la medicina, la industria alimentaria, la tecnología, o la biología. Las nanopartículas más estudiadas con este fin son aquellas formadas por materiales metálicos. De entre todos los metales nobles, el oro destaca por sus interesantes propiedades ópticas, magnéticas, eléctricas, catalíticas, biocidas ...

  8. Compact and Wide Stopband Lowpass Filter Using Open Complementary Split Ring Resonator and Defected Ground Structure

    Directory of Open Access Journals (Sweden)

    S. S. Karthikeyan

    2015-09-01

    Full Text Available A compact (0.16 λg x 0.08 λg and wide stop¬band lowpass filter design using open complementary split ring resonator (OCSRR and defected ground structure (DGS is presented in this paper. Low pass filter is con-structed using two cascaded stages of OCSRR. Since the rejection bandwidth of the OCSRR is narrow, tapered dumbbell shaped DGS section is placed under the OCSRR to enhance the bandwidth. The cutoff frequency (fc of the proposed lowpass filter is 1.09 GHz. The rejection band¬width of the filter covers the entire ultra wideband spec¬trum. Hence the spurious passband suppression is achieved up to 10 fc. The designed filter has been fabri¬cated and validated by experimental results

  9. Trust and Satisfaction in Online Tourism Consumption

    Directory of Open Access Journals (Sweden)

    Ana Alice Domenech Oneto

    2015-08-01

    Full Text Available Despite its growing importance, there is still a gap in the literature about the motivations and barriers involved in the e-commerce of tourism-related services and products. The central purpose of this study is to evaluate trust and its anteced-ents role in the formation of the intention of purchasing travel products and services on the Internet. Structural equations modeling performed with data from a survey of 292 previous buyers of online tourism products and services was used to test the proposed model. The results point towards significant relationships between trust and the other addressed con-structs, particularly security and satisfaction, most of which were found to significantly influence the intention to purchase tourism-related services or products online.

  10. Calumenin interacts with serum amyloid P component

    DEFF Research Database (Denmark)

    Vorum, H; Jacobsen, Christian; Honoré, Bent

    2000-01-01

    We recently reported the identification of human calumenin, a novel Ca(2+) binding, transformation-sensitive and secreted protein [Vorum et al. (1998) Biochim. Biophys. Acta 1386, 121-131; Vorum et al. (1999) Exp. Cell Res. 248, 473-481] belonging to the family of multiple EF-hand proteins...... with calumenin in the presence of Ca(2+). Amino acid sequencing identified this protein as serum amyloid P component (SAP). Furthermore, we verified and characterized the calumenin-SAP interaction by the surface plasmon resonance technique. The findings indicate that calumenin may participate...... in the immunological defense system and could be involved in the pathological process of amyloidosis that leads to formation of amyloid deposits seen in different types of tissues. Udgivelsesdato: 2000-Jan-14...

  11. Probing hydrogen bonds in the antibody-bound HIV-1 gp120 V3 loop by solid state NMR REDOR measurements

    Energy Technology Data Exchange (ETDEWEB)

    Balbach, John J. [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Yang Jun; Weliky, David P. [Michigan State University, Department of Chemistry (United States); Steinbach, Peter J. [National Institutes of Health, Center for Molecular Modeling, Center for Information Technology (United States); Tugarinov, Vitali; Anglister, Jacob [Weizmann Institute of Science, Department of Structural Biology (Israel); Tycko, Robert [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2000-04-15

    We describe solid state NMR measurements on frozen solutions of the complex of the 24-residue HIV-1 gp120 V3 loop peptide RP135 with the Fab fragment of the anti-gp120 antibody 0.5{beta}, using rotational echo double resonance (REDOR). In order to probe possible hydrogen bonding between arginine side chains and glycine backbone carbonyls in the region of the conserved Gly-Pro-Gly-Arg (GPGR) motif of the V3 loop, RP135 samples were prepared with {sup 15}N labels at the {eta} nitrogen positions of arginine side chains and {sup 13}C labels at glycine carbonyl positions and {sup 13}C-detected {sup 13}C-{sup 15}N REDOR measurements were performed on peptide/antibody complexes of these labeled samples. Such hydrogen bonding was previously observed in a crystal structure of the V3 loop peptide/antibody complex RP142/59.1 [Ghiara et al. (1994) Science, 264, 82-85], but is shown by the REDOR measurements to be absent in the RP135/0.5{beta} complex. These results confirm the antibody-dependent conformational differences in the GPGR motif suggested by previously reported solid state NMR measurements of {phi} and {psi} backbone dihedral angles in the RP135/0.5{beta} complex. In addition, we describe REDOR measurements on the helical synthetic peptide MB(i+4)EK in frozen solution that establish our ability to detect {sup 13}C-{sup 15}N dipole-dipole couplings in the distance range appropriate to these hydrogen bonding studies. We also report the results of molecular modeling calculations on the central portion RP135, using a combination of the solid state NMR restraints of Weliky et al. [Nat. Struct. Biol., 6, 141-145, 1999] and the liquid state NMR restraints of Tugarinov et al. (Nat. Struct. Biol., 6, 331-335, 1999]. The dynamics calculations demonstrate the mutual compatibility of the two sets of experimental structural restraints and reduce ambiguities in the solid state NMR restraints that result from symmetry and signal-to-noise considerations.

  12. Probing hydrogen bonds in the antibody-bound HIV-1 gp120 V3 loop by solid state NMR REDOR measurements

    International Nuclear Information System (INIS)

    Balbach, John J.; Yang Jun; Weliky, David P.; Steinbach, Peter J.; Tugarinov, Vitali; Anglister, Jacob; Tycko, Robert

    2000-01-01

    We describe solid state NMR measurements on frozen solutions of the complex of the 24-residue HIV-1 gp120 V3 loop peptide RP135 with the Fab fragment of the anti-gp120 antibody 0.5β, using rotational echo double resonance (REDOR). In order to probe possible hydrogen bonding between arginine side chains and glycine backbone carbonyls in the region of the conserved Gly-Pro-Gly-Arg (GPGR) motif of the V3 loop, RP135 samples were prepared with 15 N labels at the η nitrogen positions of arginine side chains and 13 C labels at glycine carbonyl positions and 13 C-detected 13 C- 15 N REDOR measurements were performed on peptide/antibody complexes of these labeled samples. Such hydrogen bonding was previously observed in a crystal structure of the V3 loop peptide/antibody complex RP142/59.1 [Ghiara et al. (1994) Science, 264, 82-85], but is shown by the REDOR measurements to be absent in the RP135/0.5β complex. These results confirm the antibody-dependent conformational differences in the GPGR motif suggested by previously reported solid state NMR measurements of φ and Ψ backbone dihedral angles in the RP135/0.5β complex. In addition, we describe REDOR measurements on the helical synthetic peptide MB(i+4)EK in frozen solution that establish our ability to detect 13 C- 15 N dipole-dipole couplings in the distance range appropriate to these hydrogen bonding studies. We also report the results of molecular modeling calculations on the central portion RP135, using a combination of the solid state NMR restraints of Weliky et al. [Nat. Struct. Biol., 6, 141-145, 1999] and the liquid state NMR restraints of Tugarinov et al. (Nat. Struct. Biol., 6, 331-335, 1999]. The dynamics calculations demonstrate the mutual compatibility of the two sets of experimental structural restraints and reduce ambiguities in the solid state NMR restraints that result from symmetry and signal-to-noise considerations

  13. Enstrophy-based proper orthogonal decomposition of flow past rotating cylinder at super-critical rotating rate

    Science.gov (United States)

    Sengupta, Tapan K.; Gullapalli, Atchyut

    2016-11-01

    Spinning cylinder rotating about its axis experiences a transverse force/lift, an account of this basic aerodynamic phenomenon is known as the Robins-Magnus effect in text books. Prandtl studied this flow by an inviscid irrotational model and postulated an upper limit of the lift experienced by the cylinder for a critical rotation rate. This non-dimensional rate is the ratio of oncoming free stream speed and the surface speed due to rotation. Prandtl predicted a maximum lift coefficient as CLmax = 4π for the critical rotation rate of two. In recent times, evidences show the violation of this upper limit, as in the experiments of Tokumaru and Dimotakis ["The lift of a cylinder executing rotary motions in a uniform flow," J. Fluid Mech. 255, 1-10 (1993)] and in the computed solution in Sengupta et al. ["Temporal flow instability for Magnus-robins effect at high rotation rates," J. Fluids Struct. 17, 941-953 (2003)]. In the latter reference, this was explained as the temporal instability affecting the flow at higher Reynolds number and rotation rates (>2). Here, we analyze the flow past a rotating cylinder at a super-critical rotation rate (=2.5) by the enstrophy-based proper orthogonal decomposition (POD) of direct simulation results. POD identifies the most energetic modes and helps flow field reconstruction by reduced number of modes. One of the motivations for the present study is to explain the shedding of puffs of vortices at low Reynolds number (Re = 60), for the high rotation rate, due to an instability originating in the vicinity of the cylinder, using the computed Navier-Stokes equation (NSE) from t = 0 to t = 300 following an impulsive start. This instability is also explained through the disturbance mechanical energy equation, which has been established earlier in Sengupta et al. ["Temporal flow instability for Magnus-robins effect at high rotation rates," J. Fluids Struct. 17, 941-953 (2003)].

  14. Corrosion-induced bond strength degradation in reinforced concrete-Analytical and empirical models

    International Nuclear Information System (INIS)

    Bhargava, Kapilesh; Ghosh, A.K.; Mori, Yasuhiro; Ramanujam, S.

    2007-01-01

    The present paper aims to investigate the relationship between the bond strength and the reinforcement corrosion in reinforced concrete (RC). Analytical and empirical models are proposed for the bond strength of corroded reinforcing bars. Analytical model proposed by Cairns.and Abdullah [Cairns, J., Abdullah, R.B., 1996. Bond strength of black and epoxy-coated reinforcement-a theoretical approach. ACI Mater. J. 93 (4), 362-369] for splitting bond failure and later modified by Coronelli [Coronelli, D. 2002. Corrosion cracking and bond strength modeling for corroded bars in reinforced concrete. ACI Struct. J. 99 (3), 267-276] to consider the corroded bars, has been adopted. Estimation of the various parameters in the earlier analytical model has been proposed by the present authors. These parameters include corrosion pressure due to expansive action of corrosion products, modeling of tensile behaviour of cracked concrete and adhesion and friction coefficient between the corroded bar and cracked concrete. Simple empirical models are also proposed to evaluate the reduction in bond strength as a function of reinforcement corrosion in RC specimens. These empirical models are proposed by considering a wide range of published experimental investigations related to the bond degradation in RC specimens due to reinforcement corrosion. It has been found that the proposed analytical and empirical bond models are capable of providing the estimates of predicted bond strength of corroded reinforcement that are in reasonably good agreement with the experimentally observed values and with those of the other reported published data on analytical and empirical predictions. An attempt has also been made to evaluate the flexural strength of RC beams with corroded reinforcement failing in bond. It has also been found that the analytical predictions for the flexural strength of RC beams based on the proposed bond degradation models are in agreement with those of the experimentally

  15. Tools for Predicting Cleaning Efficiency in the LHC

    CERN Document Server

    Assmann, R W; Brugger, M; Hayes, M; Jeanneret, J B; Kain, V; Kaltchev, D I; Schmidt, F

    2003-01-01

    The computer codes SIXTRACK and DIMAD have been upgraded to include realistic models of proton scattering in collimator jaws, mechanical aperture restrictions, and time-dependent fields. These new tools complement long-existing simplified linear tracking programs used up to now for tracking with collimators. Scattering routines from STRUCT and K2 have been compared with one another and the results have been cross-checked to the FLUKA Monte Carlo package. A systematic error is assigned to the predictions of cleaning efficiency. Now, predictions of the cleaning efficiency are possible with a full LHC model, including chromatic effects, linear and nonlinear errors, beam-beam kicks and associated diffusion, and time-dependent fields. The beam loss can be predicted around the ring, both for regular and irregular beam losses. Examples are presented.

  16. Compiled data set of exact NOE distance limits, residual dipolar couplings and scalar couplings for the protein GB3

    Directory of Open Access Journals (Sweden)

    Beat Vögeli

    2015-12-01

    Full Text Available We compiled an NMR data set consisting of exact nuclear Overhauser enhancement (eNOE distance limits, residual dipolar couplings (RDCs and scalar (J couplings for GB3, which forms one of the largest and most diverse data set for structural characterization of a protein to date. All data have small experimental errors, which are carefully estimated. We use the data in the research article Vogeli et al., 2015, Complementarity and congruence between exact NOEs and traditional NMR probes for spatial decoding of protein dynamics, J. Struct. Biol., 191, 3, 306–317, doi:10.1016/j.jsb.2015.07.008 [1] for cross-validation in multiple-state structural ensemble calculation. We advocate this set to be an ideal test case for molecular dynamics simulations and structure calculations.

  17. Scraping beam halo in {mu} {sup +} {mu} {sup minus} colliders

    Energy Technology Data Exchange (ETDEWEB)

    Drozhdin, A.; Mokhov, N.; Johnstone, C.; Wan, W.; Garren, A.

    1998-01-01

    Beam halo scraping schemes have been explored in the 50 x 50 GeV and 2 x 2 TeV {mu}{sup +}{mu}{sup -} colliders using both absorbers and electrostatic deflectors. Utility sections have been specially designed into the rings for scraping. Results of realistic STRUCT- MARS Monte-Carlo simulations show that for the low-energy machine a scheme with a 5 m long steel absorber suppresses losses in the interaction region by three orders of magnitude. The same scraping efficiency at 2 TeV is achieved only by complete extraction of beam halo from the machine. The effect of beam-induced power dissipation in the collider superconducting magnets and detector backgrounds is shown both for the first few turns after injection and for the rest of the cycle.

  18. A second monoclinic polymorph of ethylenediammonium bis(hydrogen squarate monohydrate

    Directory of Open Access Journals (Sweden)

    Louiza Zenkhri

    2011-05-01

    Full Text Available The title compound, C2H10N22+·2HC4O4−·H2O, a new polymorph of ethylenediammonium bis(hydrogen squarate monohydrate, was synthesized by slow evaporation of an acid solution. The asymetric unit contains two hydrogen squarate anions, two half-molecules of protonated ethylenediamine arranged around a twofold axis and one water molecule. In the crystal, N—H...O and O—H...O hydrogen bonds between the hydrogen squarate anions, protonated N atoms from the amine group and water molecules lead to a three-dimensional framework. In particular, the cohesion between the squarate groups is ensured by very short intermolecular hydrogen bonds bonds. The title compound crystallized together with the previously reported polymorph [Mathew et al. (2002. J. Mol. Struct. 641, 263–279].

  19. Redetermination of 2-methyl-4-nitropyridine N-oxide

    Directory of Open Access Journals (Sweden)

    Max Peukert

    2014-04-01

    Full Text Available An improved crystal structure of the title compound, C6H6N2O3, is reported. The structure, previously solved [Li et al. (1987. Jiegou Huaxue (Chin. J. Struct. Chem., 6, 20–24] in the orthorhombic space group Pca21 and refined to R = 0.067, has been solved in the orthorhombic space group Pbcm with data of enhanced quality, giving an improved structure (R = 0.0485. The molecule adopts a planar conformation with all atoms lying on a mirror plane. The crystal structure is composed of molecular sheets extending parallel to the ab plane and connected via C—H...O contacts involving ring H atoms and O atoms of the N-oxide and nitro groups, while van der Waals forces consolidate the stacking of the layers.

  20. Vectorial loading of processive motor proteins: implementing a landscape picture

    International Nuclear Information System (INIS)

    Kim, Young C; Fisher, Michael E

    2005-01-01

    Individual processive molecular motors, of which conventional kinesin is the most studied quantitatively, move along polar molecular tracks and, by exerting a force F = (F x ,F y ,F z ) on a tether, drag cellular cargoes, in vivo, or spherical beads, in vitro, taking up to hundreds of nanometre-scale steps. From observations of velocities and the dispersion of displacements with time, under measured forces and controlled fuel supply (typically ATP), one may hope to obtain insight into the molecular motions undergone in the individual steps. In the simplest situation, the load force F may be regarded as a scalar resisting force, F x z >0, while more recently Block and co-workers (2002 Biophys. J. 83 491, 2003 Proc. Natl Acad. Sci. USA 100 2351) and Carter and Cross (2005 Nature 435 308) have studied assisting (or reverse) loads, F x >0, and also sideways (or transverse) loads F y ≠ 0. We extend previous mechanochemical kinetic models by explicitly implementing a free-energy landscape picture in order to allow for the full vectorial nature of the force F transmitted by the tether. The load-dependence of the various forward and reverse transition rates is embodied in load distribution vectors, θ j + and θ j - , which relate to substeps of the motor, and in next order, in compliance matrices η j + and η j - . The approach is applied specifically to discuss the experiments of Howard and co-workers (1996 Biophys.?J. 70 418) in which the buckling of partially clamped microtubules was measured under the action of bound kinesin molecules which induced determined perpendicular loads. But in the normal single-bead assay it also proves imperative to allow for F z >0: the appropriate analysis for kinesin, suggesting that the motor 'crouches' on binding ATP prior to stepping, is sketched. It yields an expression for the velocity, V (F x ,F z ;[ATP]), needed to address the buckling experiments

  1. RESCUE: An artificial neural network tool for the NMR spectral assignment of proteins

    International Nuclear Information System (INIS)

    Pons, J.L.; Delsuc, M.A.

    1999-01-01

    The assignment of the 1 H spectrum of a protein or a polypeptide is the prerequisite for advanced NMR studies. We present here an assignment tool based on the artificial neural network technology, which determines the type of the amino acid from the chemical shift values observed in the 1 H spectrum. Two artificial neural networks have been trained and extensively tested against a non-redundant subset of the BMRB chemical shift data bank [Seavey, B.R. et al. (1991) J. Biomol. NMR, 1, 217-236]. The most promising of the two accomplishes the analysis in two steps, grouping related amino acids together. It presents a mean rate of success above 80% on the test set. The second network tested separates down to the single amino acid; it presents a mean rate of success of 63%. This tool has been used to assist the manual assignment of peptides and proteins and can also be used as a block in an automated approach to assignment. The program has been called RESCUE and is made publicly available at the following URL: http://www.infobiosud.univ-montp1.fr/rescue

  2. Density functional calculations of backbone 15N shielding tensors in beta-sheet and turn residues of protein G

    International Nuclear Information System (INIS)

    Cai Ling; Kosov, Daniel S.; Fushman, David

    2011-01-01

    We performed density functional calculations of backbone 15 N shielding tensors in the regions of beta-sheet and turns of protein G. The calculations were carried out for all twenty-four beta-sheet residues and eight beta-turn residues in the protein GB3 and the results were compared with the available experimental data from solid-state and solution NMR measurements. Together with the alpha-helix data, our calculations cover 39 out of the 55 residues (or 71%) in GB3. The applicability of several computational models developed previously (Cai et al. in J Biomol NMR 45:245–253, 2009) to compute 15 N shielding tensors of alpha-helical residues is assessed. We show that the proposed quantum chemical computational model is capable of predicting isotropic 15 N chemical shifts for an entire protein that are in good correlation with experimental data. However, the individual components of the predicted 15 N shielding tensor agree with experiment less well: the computed values show much larger spread than the experimental data, and there is a profound difference in the behavior of the tensor components for alpha-helix/turns and beta-sheet residues. We discuss possible reasons for this.

  3. La peroxidación lipídica en la etiopatogenia de la enfermedad periodontal inflamatoria

    Directory of Open Access Journals (Sweden)

    Bárbara E García Triana

    Full Text Available Las especies reactivas del oxígeno están implicadas en la etiopatogenia de la inflamación. Durante la activación de los leucocitos, se liberan grandes cantidades de estas especies, cuya función es la eliminación de los agentes patógenos. Si las defensas antioxidantes de los tejidos no funcionan eficientemente, son inducidas reacciones radicálicas que afectan a las biomoléculas. El ataque a los lípidos de la membrana celular provoca su peroxidación, con la consiguiente formación de nuevas especies radicálicas y metabolitos tóxicos. La presencia de un fuerte infiltrado inflamatorio en los tejidos periodontales, durante la enfermedad periodontal inflamatoria, ha sugerido la posible participación de las especies reactivas del oxígeno en la etiopatogenia de esta enfermedad. Se supone que el ataque de estas sustancias a los tejidos periodontales con deficiente defensa antioxidante, provoca la aparición de la peroxidación lipídica, que puede conducir a la lisis celular y la activación de proteasas.

  4. Combination of Proteasomal Inhibitors Lactacystin and MG132 Induced Synergistic Apoptosis in Prostate Cancer Cells

    Directory of Open Access Journals (Sweden)

    Robert B. Shirley

    2005-12-01

    Full Text Available The proteasome inhibitor Velcade (bortezomib/PS-341 has been shown to block the targeted proteolytic degradation of short-lived proteins that are involved in cell maintenance, growth, division, and death, advocating the use of proteasomal inhibitors as therapeutic agents. Although many studies focused on the use of one proteasomal inhibitor for therapy, we hypothesized that the combination of proteasome inhibitors Lactacystin (AG Scientific, Inc., San Diego, CA and MG132 (Biomol International, Plymouth Meeting, PA may be more effective in inducing apoptosis. Additionally, this regimen would enable the use of sublethal doses of individual drugs, thus reducing adverse effects. Results indicate a significant increase in apoptosis when LNCaP prostate cancer cells were treated with increasing levels of Lactacystin, MG132, or a combination of sublethal doses of these two inhibitors. Furthermore, induction in apoptosis coincided with a significant loss of IKKα, IKKβ, and IKKγ proteins and NFκB activity. In addition to describing effective therapeutic agents, we provide a model system to facilitate the investigation of the mechanism of action of these drugs and their effects on the IKK-NFκB axis.

  5. Crystal structures of 2,6-dibromo-4-methylbenzonitrile and 2,6-dibromo-4-methylphenyl isocyanide

    Directory of Open Access Journals (Sweden)

    Wayland E. Noland

    2017-12-01

    Full Text Available In the title crystals, C8H5Br2N, which are isomorphous, the steric bulk of the methyl group causes neighboring molecules to become mutually inclined. This prevents the formation of planar or nearly planar sheets, which were observed in the trichloro and tribromo analogs. Instead of CN/NC...Br contacts, tetrameric Br...Br contacts are observed. These contacts form tetragonally puckered sheets parallel to (001. The CN/NC and methyl groups are grouped at the peaks and troughs. Both molecules lie across crystallographic mirror planes; thus, the methyl H atoms are disordered over two sets of sites with equal occupancy. The title nitrile is a redetermination. The refinement converged at R[F2 > 2σ(F2] = 0.020, whereas the original determination [Gleason & Britton, (1976. Cryst. Struct. Commun. 5, 229–232] had R = 0.112.

  6. Chemical element abundance in K giant atmospheres

    International Nuclear Information System (INIS)

    Komarov, N.S.; Shcherbak, A.N.

    1980-01-01

    With the help of modified method of differential curves of growth studied are physical parameters of atmospheres of giant stars of KO111 spectral class of the NGC 752, M25 and UMa cluster. Observations have been made on reflector of Crimea astrophysical observatory of Academy of Sciences of the USSR in the period from February to May, 1978. Spectograms are obtained for the wave length range from 5000-5500 A. It is shown that the change of chemical content in the wide range in heavy element composition does not influence the star atmosphere structUre. It follows from the results of the investigation that the abundance of chemical elements in stars of various scattered clusters, is the same in the range of errors of measurements and is similar to the abundance of chemical elements in the Sun atmosphere

  7. A prediction of rate-dependent behaviour in ferroelectric polycrystals

    International Nuclear Information System (INIS)

    Kim, Sang-Joo

    2007-01-01

    Rate-dependent behaviour of a polycrystalline ferroelectric material is predicted based on thermal activation theory and a representative volume element model. First, the behaviour of a ferroelectric single crystal is calculated from a recently proposed three-dimensional free energy model [S.J. Kim, S. Seelecke, Int. J. Solids Struct. 44 (2007) 1196-1209]. Then, from the calculated single crystal responses, poling behaviour of a ferroelectric polycrystal is obtained in three different ways, two representative volume element models and Gaussian integration method. It is found that a dodecahedron representative volume element consisting of 210 crystallites is the best choice among the three methods. Finally, the behaviour of a ferroelectric polycrystal under various electric and stress loads is calculated using the chosen RVE model. The calculated responses are compared qualitatively with experimental observations, and the effects of crystal orientation and polycrystallinity are discussed

  8. A model for the relation between stimulus frequency and spontaneous otoacoustic emissions in lizard papillae.

    Science.gov (United States)

    Wit, Hero P; van Dijk, Pim; Manley, Geoffrey A

    2012-11-01

    Spontaneous otoacoustic emissions (SOAEs) and stimulus frequency otoacoustic emissions (SFOAEs) have been described from lizard ears. Although there are several models for these systems, none has modeled the characteristics of both of these types of otoacoustic emissions based upon their being derived from hair cells as active oscillators. Data from the ears of two lizard species, one lacking a tectorial membrane and one with a chain of tectorial sallets, as described by Bergevin et al. ["Coupled, active oscillators and lizard otoacoustic emissions," AIP Conf. Proc. 1403, 453 (2008)], are modeled as an array of coupled self-sustained oscillators. The model, originally developed by Vilfan and Duke ["Frequency clustering in spontaneous otoacoustic emissions from a lizard's ear," Biophys. J. 95, 4622-4630 (2008)], well describes both the amplitude and phase characteristics of SFOAEs and the relation between SFOAEs and SOAEs.

  9. Group additivity calculations of the thermodynamic properties of unfolded proteins in aqueous solution: a critical comparison of peptide-based and HKF models.

    Science.gov (United States)

    Hakin, A W; Hedwig, G R

    2001-02-15

    A recent paper in this journal [Amend and Helgeson, Biophys. Chem. 84 (2000) 105] presented a new group additivity model to calculate various thermodynamic properties of unfolded proteins in aqueous solution. The parameters given for the revised Helgeson-Kirkham-Flowers (HKF) equations of state for all the constituent groups of unfolded proteins can be used, in principle, to calculate the partial molar heat capacity, C(o)p.2, and volume, V2(0), at infinite dilution of any polypeptide. Calculations of the values of C(o)p.2 and V2(0) for several polypeptides have been carried out to test the predictive utility of the HKF group additivity model. The results obtained are in very poor agreement with experimental data, and also with results calculated using a peptide-based group additivity model. A critical assessment of these two additivity models is presented.

  10. Seismic fragility of RC shear walls in nuclear power plant Part 1: Characterization of uncertainty in concrete constitutive model

    International Nuclear Information System (INIS)

    Syed, Sammiuddin; Gupta, Abhinav

    2015-01-01

    Highlights: • A framework is proposed for seismic fragility assessment of Reinforced Concrete structures. • Experimentally validated finite element models are used to conduct nonlinear simulations. • Critical parameters in concrete constitutive model are identified to conduct nonlinear simulations. • Uncertainties in model parameters of concrete damage plasticity model is characterized. • Closed form expressions are used to compute the damage variables and plasticity. - Abstract: This two part manuscript proposes a framework for seismic fragility assessment of reinforced concrete structures in nuclear energy facilities. The novelty of the proposed approach lies in the characterization of uncertainties in the parameters of the material constitutive model. Concrete constitutive models that comprehensively address different damage states such as tensile cracking, compression failure, stiffness degradation, and recovery of degraded stiffness due to closing of previously formed cracks under dynamic loading are generally defined in terms of a large number of variables to characterize the plasticity and damage at material level. Over the past several years, many different studies have been presented on evaluation of fragility for reinforced concrete structures using nonlinear time history simulations. However, almost all of these studies do not consider uncertainties in the parameters of a comprehensive constitutive model. Part-I of this two-part manuscript presents a study that is used to identify uncertainties associated with the critical parameters in nonlinear concrete damage plasticity model proposed by Lubliner et al. (1989. Int. J. Solids Struct., 25(3), 299) and later modified by Lee and Fenves (1998a. J. Eng. Mech., ASCE, 124(8), 892) and Lee and Fenves (1998b. Earthquake Eng. Struct. Dyn., 27(9), 937) for the purpose of seismic fragility assessment. The limitations in implementation of the damage plasticity model within a finite element framework and

  11. Effect of donor orientation on ultrafast intermolecular electron transfer in coumarin-amine systems

    International Nuclear Information System (INIS)

    Singh, P. K.; Nath, S.; Bhasikuttan, A. C.; Kumbhakar, M.; Mohanty, J.; Sarkar, S. K.; Mukherjee, T.; Pal, H.

    2008-01-01

    Effect of donor amine orientation on nondiffusive ultrafast intermolecular electron transfer (ET) reactions in coumarin-amine systems has been investigated using femtosecond fluorescence upconversion measurements. Intermolecular ET from different aromatic and aliphatic amines used as donor solvents to the excited coumarin-151 (C151) acceptor occurs with ultrafast rates such that the shortest fluorescence lifetime component (τ 1 ) is the measure of the fastest ET rate (τ 1 =τ ET fast =(k ET fast ) -1 ), assigned to the C151-amine contact pairs in which amine donors are properly oriented with respect to C151 to maximize the acceptor-donor electronic coupling (V el ). It is interestingly observed that as the amine solvents are diluted by suitable diluents (either keeping solvent dielectric constant similar or with increasing dielectric constant), the τ 1 remains almost in the similar range as long as the amine dilution does not cross a certain critical limit, which in terms of the amine mole fraction (x A ) is found to be ∼0.4 for aromatic amines and ∼0.8 for aliphatic amines. Beyond these dilutions in the two respective cases of the amine systems, the τ 1 values are seen to increase very sharply. The large difference in the critical x A values involving aromatic and aliphatic amine donors has been rationalized in terms of the largely different orientational restrictions for the ET reactions as imposed by the aliphatic (n-type) and aromatic (π-type) nature of the amine donors [A. K. Satpati et al., J. Mol. Struct. 878, 84 (2008)]. Since the highest occupied molecular orbital (HOMO) of the n-type aliphatic amines is mostly centralized at the amino nitrogen, only some specific orientations of these amines with respect to the close-contact acceptor dye [also of π-character; A. K. Satpati et al., J. Mol. Struct. 878, 84 (2008) and E. W. Castner et al., J. Phys. Chem. A 104, 2869 (2000)] can give suitable V el and thus ultrafast ET reaction. In contrary, the

  12. Understanding and Improving Blind Students' Access to Visual Information in Computer Science Education

    Science.gov (United States)

    Baker, Catherine M.

    Teaching people with disabilities tech skills empowers them to create solutions to problems they encounter and prepares them for careers. However, computer science is typically taught in a highly visual manner which can present barriers for people who are blind. The goal of this dissertation is to understand and decrease those barriers. The first projects I present looked at the barriers that blind students face. I first present the results of my survey and interviews with blind students with degrees in computer science or related fields. This work highlighted the many barriers that these blind students faced. I then followed-up on one of the barriers mentioned, access to technology, by doing a preliminary accessibility evaluation of six popular integrated development environments (IDEs) and code editors. I found that half were unusable and all had some inaccessible portions. As access to visual information is a barrier in computer science education, I present three projects I have done to decrease this barrier. The first project is Tactile Graphics with a Voice (TGV). This project investigated an alternative to Braille labels for those who do not know Braille and showed that TGV was a potential alternative. The next project was StructJumper, which created a modified abstract syntax tree that blind programmers could use to navigate through code with their screen reader. The evaluation showed that users could navigate more quickly and easily determine the relationships of lines of code when they were using StructJumper compared to when they were not. Finally, I present a tool for dynamic graphs (the type with nodes and edges) which had two different modes for handling focus changes when moving between graphs. I found that the modes support different approaches for exploring the graphs and therefore preferences are mixed based on the user's preferred approach. However, both modes had similar accuracy in completing the tasks. These projects are a first step towards

  13. Seismic fragility of RC shear walls in nuclear power plant Part 1: Characterization of uncertainty in concrete constitutive model

    Energy Technology Data Exchange (ETDEWEB)

    Syed, Sammiuddin [Department of Civil, Construction, and Environmental Engineering, North Carolina State University, 426 Mann Hall, Campus Box 7908, Raleigh, NC 27695-7908 (United States); Gupta, Abhinav, E-mail: agupta1@ncsu.edu [Department of Civil, Construction, and Environmental Engineering, North Carolina State University, 413 Mann Hall, Campus Box 7908, Raleigh, NC 27695-7908 (United States)

    2015-12-15

    Highlights: • A framework is proposed for seismic fragility assessment of Reinforced Concrete structures. • Experimentally validated finite element models are used to conduct nonlinear simulations. • Critical parameters in concrete constitutive model are identified to conduct nonlinear simulations. • Uncertainties in model parameters of concrete damage plasticity model is characterized. • Closed form expressions are used to compute the damage variables and plasticity. - Abstract: This two part manuscript proposes a framework for seismic fragility assessment of reinforced concrete structures in nuclear energy facilities. The novelty of the proposed approach lies in the characterization of uncertainties in the parameters of the material constitutive model. Concrete constitutive models that comprehensively address different damage states such as tensile cracking, compression failure, stiffness degradation, and recovery of degraded stiffness due to closing of previously formed cracks under dynamic loading are generally defined in terms of a large number of variables to characterize the plasticity and damage at material level. Over the past several years, many different studies have been presented on evaluation of fragility for reinforced concrete structures using nonlinear time history simulations. However, almost all of these studies do not consider uncertainties in the parameters of a comprehensive constitutive model. Part-I of this two-part manuscript presents a study that is used to identify uncertainties associated with the critical parameters in nonlinear concrete damage plasticity model proposed by Lubliner et al. (1989. Int. J. Solids Struct., 25(3), 299) and later modified by Lee and Fenves (1998a. J. Eng. Mech., ASCE, 124(8), 892) and Lee and Fenves (1998b. Earthquake Eng. Struct. Dyn., 27(9), 937) for the purpose of seismic fragility assessment. The limitations in implementation of the damage plasticity model within a finite element framework and

  14. Redetermination of 2-methyl-4-nitro­pyridine N-oxide

    Science.gov (United States)

    Peukert, Max; Seichter, Wilhelm; Weber, Edwin

    2014-01-01

    An improved crystal structure of the title compound, C6H6N2O3, is reported. The structure, previously solved [Li et al. (1987 ▶). Jiegou Huaxue (Chin. J. Struct. Chem.), 6, 20–24] in the ortho­rhom­bic space group Pca21 and refined to R = 0.067, has been solved in the ortho­rhom­bic space group Pbcm with data of enhanced quality, giving an improved structure (R = 0.0485). The mol­ecule adopts a planar conformation with all atoms lying on a mirror plane. The crystal structure is composed of mol­ecular sheets extending parallel to the ab plane and connected via C—H⋯O contacts involving ring H atoms and O atoms of the N-oxide and nitro groups, while van der Waals forces consolidate the stacking of the layers. PMID:24826136

  15. Beam-induced damage to the Tevatron components and what has been done about it

    International Nuclear Information System (INIS)

    Mokhov, N.V.; Czarapata, P.C.; Drozhdin, A.I.; Still, D.A.; Samulyak, R.V.

    2007-01-01

    A beam-induced damage to the Tevatron collimators happened in December 2003 was induced by a failure in the CDF Roman Pot detector positioning during the collider run. Possible scenarios of this failure resulted in an excessive halo generation and superconducting magnet quench have been studied via realistic simulations using the STRUCT and MARS14 codes. It is shown that the interaction of a misbehaved proton beam with the collimators result in a rapid local heating and a possible damage. A detailed consideration is given to the ablation process for the collimator material taking place in high vacuum. It is shown that ablation of tungsten (primary collimator) and stainless steel (secondary collimator) jaws results in creation of a groove in the jaw surface as was observed after the December's accident. The actions undertaken to avoid such an accident in future are described in detail. (author)

  16. Beam-induced damage to the Tevatron components and what has been done about it

    International Nuclear Information System (INIS)

    Mokhov, N.V.; Czarapata, P.C.; Drozhdin, A.I.; Still, D.A.; Samulyak, R.V.

    2006-01-01

    A beam-induced damage to the Tevatron collimators happened in December 2003 was induced by a failure in the CDF Roman Pot detector positioning during the collider run. Possible scenarios of this failure resulted in an excessive halo generation and superconducting magnet quench have been studied via realistic simulations using the STRUCT and MARS14 codes. It is shown that the interaction of a misbehaved proton beam with the collimators result in a rapid local heating and a possible damage. A detailed consideration is given to the ablation process for the collimator material taking place in high vacuum. It is shown that ablation of tungsten (primary collimator) and stainless steel (secondary collimator) jaws results in creation of a groove in the jaw surface as was observed after the December's accident. The actions undertaken to avoid such an accident in future are described in detail

  17. Handbook of Brain Connectivity

    CERN Document Server

    Jirsa, Viktor K

    2007-01-01

    Our contemporary understanding of brain function is deeply rooted in the ideas of the nonlinear dynamics of distributed networks. Cognition and motor coordination seem to arise from the interactions of local neuronal networks, which themselves are connected in large scales across the entire brain. The spatial architectures between various scales inevitably influence the dynamics of the brain and thereby its function. But how can we integrate brain connectivity amongst these structural and functional domains? Our Handbook provides an account of the current knowledge on the measurement, analysis and theory of the anatomical and functional connectivity of the brain. All contributors are leading experts in various fields concerning structural and functional brain connectivity. In the first part of the Handbook, the chapters focus on an introduction and discussion of the principles underlying connected neural systems. The second part introduces the currently available non-invasive technologies for measuring struct...

  18. 3D Surface Realignment Tracking for Medical Imaging: A Phantom Study with PET Motion Correction

    DEFF Research Database (Denmark)

    Olesen, Oline Vinter; Paulsen, Rasmus Reinhold; Jensen, Rasmus Ramsbøl

    2011-01-01

    We present a complete system for motion correction in high resolution brain positron emission tomography (PET) imaging. It is based on a compact structured light scanner mounted above the patient tunnel of the Siemens High Resolution Research Tomograph PET brain scanner. The structured light system...... is equipped with a near infrared diode and uses phase-shift interferometry to compute 3D representations of the forehead of the patient. These 3D point clouds are progressively aligned to a reference surface and thereby giving the head pose changes. The estimated pose changes are used to reposition a sequence...... of recon- structed PET frames. To align the structured light system with the PET coordinate system a novel registration algorithm based on the PET trans- mission scan and an initial surface has been developed. The performance of the complete setup has been evaluated using a custom made phantom based...

  19. Beam Collimation Studies for the ILC Positron Source

    Energy Technology Data Exchange (ETDEWEB)

    Drozhdin, A.; /Fermilab; Nosochkov, Y.; Zhou, F.; /SLAC

    2008-06-26

    Results of the collimation studies for the ILC positron source beam line are presented. The calculations of primary positron beam loss are done using the ELEGANT code. The secondary positron and electron beam loss, the synchrotron radiation along the beam line and the bremsstrahlung radiation in the collimators are simulated using the STRUCT code. The first part of the collimation system, located right after the positron source target (0.125 GeV), is used for protection of the RF Linac sections from heating and radiation. The second part of the system is used for final collimation before the beam injection into the Damping Ring at 5 GeV. The calculated power loss in the collimation region is within 100 W/m, with the loss in the collimators of 0.2-5 kW. The beam transfer efficiency from the target to the Damping Ring is 13.5%.

  20. Interaction of butylated hydroxyanisole with mitochondrial oxidative phosphorylation.

    Science.gov (United States)

    Fusi, F; Sgaragli, G; Murphy, M P

    1992-03-17

    The antioxidant, butylated hydroxyanisole (BHA), has a number of effects on mitochondrial oxidative phosphorylation. In this study we apply the novel approach developed by Brand (Brand MD, Biochim Biophys Acta 1018: 128-133, 1990) to investigate the site of action of BHA on oxidative phosphorylation in rat liver mitochondria. Using this approach we show that BHA increases the proton leak through the mitochondrial inner membrane and that it also inhibits the delta p (proton motive force across the mitochondrial inner membrane) generating system, but has no effect on the phosphorylation system. This demonstrates that compounds having pleiotypic effects on mitochondrial oxidative phosphorylation in vitro can be analysed and their many effects distinguished. This approach is of general use in analysing many other compounds of pharmacological interest which interact with mitochondria. The implications of these results for the mechanism of interaction of BHA with mitochondrial oxidative phosphorylation are discussed.

  1. Comparison of the thermal stabilization of proteins by oligosaccharides and monosaccharide mixtures: Measurement and analysis in the context of excluded volume theory.

    Science.gov (United States)

    Beg, Ilyas; Minton, Allen P; Islam, Asimul; Hassan, Md Imtaiyaz; Ahmad, Faizan

    2018-06-01

    The thermal stability of apo α-lactalbumin (α-LA) and lysozyme was measured in the presence of mixtures of glucose, fructose, and galactose. Mixtures of these monosaccharides in the appropriate stoichiometric ratio were found to have a greater stabilizing effect on each of the two proteins than equal weight/volume concentrations of di- tri- and tetrasaccharides with identical subunit composition (sucrose, trehalose, raffinose, and stachyose). The excluded volume model for the effect of a single saccharide on the stability of a protein previously proposed by Beg et al. [Biochemistry 54 (2015) 3594] was extended to treat the case of saccharide mixtures. The extended model predicts quantitatively the stabilizing effect of all monosaccharide mixtures on α-LA and lysozyme reported here, as well as previously published results obtained for ribonuclease A [Biophys. Chem. 138 (2008) 120] to within experimental uncertainty. Copyright © 2018 Elsevier B.V. All rights reserved.

  2. Radiation hard 3D diamond sensors for vertex detectors at HL-LHC

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00336619; Quadt, Arnulf; Grosse-Knetter, Jörn; Weingarten, Jens

    Diamond is a good candidate to replace silicon as sensor material in the innermost layer of a tracking detector at HL-LHC, due to its high radiation tolerance. After particle fluences of $10^{16}\\,{\\rm protons/cm^2}$, diamond sensors are expected to achieve a higher signal to noise ratio than silicon. In order to use low grade polycrystalline diamonds as sensors, electrodes inside the diamond bulk, so called 3D electrodes, are produced. Typically, this kind of diamond material has a lower charge collection distance (CCD) than higher grade diamond, which results in a decreased signal amplitude. With 3D electrodes it is possible to achieve full charge collection even in samples with low CCDs by decoupling the spacing of the electrodes from the thickness of the diamond bulk. The electrodes are produced using a femtosecond laser, which changes the phase of the diamond material. The phase changed material is conductive and identified as nanocrystalline graphite using Raman spectroscopy. Due to a crater like struct...

  3. LHCb: F.E.C. for DAQ networks

    CERN Multimedia

    Floros, G; Neufeld, N

    2014-01-01

    The demand for faster and more reliable networks is growing day by day both in commercial and scientific applications, driving many innovations in network protocols, fiber optics and network-controllers. Operating fast links on relatively inexpensive hardware is a very important challenging aspect of this. One important way to enable this is to provide the network with an existing mechanism of error correction, called Forward Error Correction (F.E.C.). Although error-correcting codes exist for over six decades and F.E.C. is applied in various projects, it is still not widespread in Ethernet networks. F.E.C. introduces a very cost effective way to expand the limits of any network based on micro-controllers synthesized on FPGAs, but it is provided only for specific applications, such as backplane systems. Most of the FPGA and/or IP core vendors either do not provide this feature on their Ethernet implementations or their F.E.C. implementations are based on Ethernet micro-controllers that have a different struct...

  4. Modification of Cys-418 of pyruvate formate-lyase by methacrylic acid, based on its radical mechanism.

    Science.gov (United States)

    Plaga, W; Vielhaber, G; Wallach, J; Knappe, J

    2000-01-21

    The recently determined crystal structure of pyruvate formate-lyase (PFL) suggested a new view of the mechanism of this glycyl radical enzyme, namely that intermediary thiyl radicals of Cys-418 and Cys-419 participate in different ways [Becker, A. et al. (1999) Nat. Struct. Biol. 6, 969-975]. We report here a suicide reaction of PFL that occurs with the substrate-analog methacrylate with retention of the protein radical (K(I)=0.42 mM, k(i)=0.14 min(-1)). Using [1-(14)C]methacrylate (synthesized via acetone cyanhydrin), the reaction end-product was identified by peptide mapping and cocrystallization experiments as S-(2-carboxy-(2S)-propyl) substituted Cys-418. The stereoselectivity of the observed Michael addition reaction is compatible with a radical mechanism that involves Cys-418 thiyl as nucleophile and Cys-419 as H-atom donor, thus supporting the functional assignments of these catalytic amino acid residues derived from the protein structure.

  5. Endocytosis of lysosomal acid phosphatase; involvement of mannose receptor and effect of lectins.

    Science.gov (United States)

    Imai, K; Yoshimura, T

    1994-08-01

    Acid phosphatase and beta-glucosidase are unique among lysosomal enzymes in that they have both high mannose and complex type sugasr chains, whereas oligosaccharide chains of lysosomal enzymes in matrix are of high mannose type. We have previously shown that beta-glucosidase was endocytosed into macrophages via an unidentified receptor different from a mannose/fucose receptor (K. Imai, Cell Struct. Funct. 13, 325-332, 1988). Here, we show that uptake of acid phosphatase purified from rat liver lysosomes into rat macrophages was inhibited by ligands for a mannose/fucose receptor and was mediated via an apparently single binding site with Kuptake of 24.7 nM. These results indicate that acid phosphatase and beta-glucosidase recognize different types of receptors even if they have similar sugar chains. Polyvalent concanavalin A which binds both to the enzyme and to macrophages specifically stimulated the uptake in a dose dependent manner, whereas wheat germ agglutinin and phytohaemagglutinin did not.

  6. Effect of Intramolecular Dispersion Interactions on the Conformational Preferences of Monoterpenoids

    Science.gov (United States)

    Loru, Donatella; Vigorito, Annalisa; Santos, Andreia; Tang, Jackson; Sanz, M. Eugenia

    2017-06-01

    The rotational spectra of several monoterpenoids have been reinvestigated with a 2-8 GHz chirped pulse FTMW spectrometer. Axial conformers, in addition to previously reported equatorial conformers, have been detected for carvone, perillaldehyde, and limonene. Observation of the ^{13}C isotopologues of these monoterpenoids in their natural abundances allowed the determination of r_s and r_0 structures. Axial conformers are stabilised by dispersion interactions between the six-membered ring of the monoterpenoids and the isopropenyl group. Comparison of experimental data with ab initio and density functional calculations shows that an accurate description of dispersion interactions is still a challenge for theoretical methods. J. R. Avilés Moreno, F. Partal Ureña, J. J. López González and T. R. Huet, Chem. Phys. Lett., 2009, 473, 17-20. J. R. Avilés Moreno, T. R. Huet and J. J. López González, Struct. Chem., 2013, 24, 1163-1170.

  7. The SAMGrid database server component: its upgraded infrastructure and future development path

    International Nuclear Information System (INIS)

    Loebel-Carpenter, L.; White, S.; Baranovski, A.; Garzoglio, G.; Herber, R.; Illingworth, R.; Kennedy, R.; Kreymer, A.; Kumar, A.; Lueking, L.; Lyon, A.; Merritt, W.; Terekhov, I.; Trumbo, J.; Veseli, S.; Burgon-Lyon, M.; St Denis, R.; Belforte, S.; Kerzel, U.; Bartsch, V.; Leslie, M.

    2004-01-01

    The SAMGrid Database Server encapsulates several important services, such as accessing file metadata and replica catalog, keeping track of the processing information, as well as providing the runtime support for SAMGrid station services. Recent deployment of the SAMGrid system for CDF has resulted in unification of the database schema used by CDF and D0, and the complexity of changes required for the unified metadata catalog has warranted a complete redesign of the DB Server. We describe here the architecture and features of the new server. In particular, we discuss the new CORBA infrastructure that utilizes python wrapper classes around IDL structs and exceptions. Such infrastructure allows us to use the same code on both server and client sides, which in turn results in significantly improved code maintainability and easier development. We also discuss future integration of the new server with an SBIR II project which is directed toward allowing the DB Server to access distributed databases, implemented in different DB systems and possibly using different schema

  8. Redetermination of 1-carboxycyclohexan-1-aminium chloride

    Directory of Open Access Journals (Sweden)

    Teresa González

    2009-02-01

    Full Text Available The crystal structure of the title compound, C7H14NO2+·Cl−, was reported previously [Chacko, Srinivasan & Zand (1975. J. Cryst. Mol. Struct. 5, 353–357] from Weissenberg photographic data with R = 0.113. It has now been redetermined, providing a significant increase in the precision of the derived geometric parameters, viz. mean σ(C—C = 0.003 Å in the present work compared with 0.021 Å for the previous work. The complete cation is generated by crystallographic mirrror symmetry, with three C atoms, two O atoms and the N atom lying on the reflecting plane; the chloride anion also has m site symmetry. The crystal structure is established by a two-dimensional network of O—H...Cl and N—H...Cl hydrogen bonds, generating C12(4 and C12(7 chains, and R24(8 and R24(14 rings.

  9. Development of self-healing polymers via amine–epoxy chemistry: II. Systematic evaluation of self-healing performance

    International Nuclear Information System (INIS)

    Zhang, He; Yang, Jinglei

    2014-01-01

    Part I of this study (H Zhang and J Yang 2014 Smart Mater. Struct. 23 065003) reported the preparation and characterization of epoxy microcapsules (EP-capsules) and amine loaded hollow glass bubbles (AM-HGBs), and the modeling of a two-part self-healing system. In part II, the self-healing performance of this material system is systematically investigated. Various factors including the ratio, the total concentration and the size of the two carriers are studied as well as the healing temperature and the post heat treatment process. The best healing performance is obtained at a ratio of 1:3 of EP-capsules to AM-HGBs. It is observed that a higher concentration of larger carriers, together with a higher healing temperature, enables better healing behavior. Healing efficiency of up to 93% is obtained in these systems. In addition, post heat treatment decreases the healing efficiency due to stoichiometric mismatch of healing agents caused by leakage of amine in the HGBs at elevated temperature. (paper)

  10. Development of self-healing polymers via amine-epoxy chemistry: II. Systematic evaluation of self-healing performance

    Science.gov (United States)

    Zhang, He; Yang, Jinglei

    2014-06-01

    Part I of this study (H Zhang and J Yang 2014 Smart Mater. Struct. 23 065003) reported the preparation and characterization of epoxy microcapsules (EP-capsules) and amine loaded hollow glass bubbles (AM-HGBs), and the modeling of a two-part self-healing system. In part II, the self-healing performance of this material system is systematically investigated. Various factors including the ratio, the total concentration and the size of the two carriers are studied as well as the healing temperature and the post heat treatment process. The best healing performance is obtained at a ratio of 1:3 of EP-capsules to AM-HGBs. It is observed that a higher concentration of larger carriers, together with a higher healing temperature, enables better healing behavior. Healing efficiency of up to 93% is obtained in these systems. In addition, post heat treatment decreases the healing efficiency due to stoichiometric mismatch of healing agents caused by leakage of amine in the HGBs at elevated temperature.

  11. Beam Collimation and Machine-Detector Interface at the International Linear Collider

    CERN Document Server

    Mokhov, Nikolai V; Kostin, Mikhail A

    2005-01-01

    Synchrotron radiation, spray from the dumps and extraction lines, beam-gas and beam halo interactions with collimators and other components in the ILC beam delivery system create fluxes of muons and other secondaries which can exceed the tolerable levels at a detector by a few orders of magnitude. It is shown that with a multi-stage collimation system, magnetized iron spoilers which fill the tunnel and a set of masks in the detector, one can hopefully meet the design goals. Results of modeling with the STRUCT and MARS15 codes of beam loss and energy deposition effects are presented in this paper. We concentrate on collimation system and mask design and optimization, short- and long-term survivability of the critical components (spoilers, absorbers, magnets, separators, dumps), dynamic heat loads and radiation levels in magnets and other components, machine-related backgrounds and damage in collider detectors, and environmental aspects (prompt dose, ground-water and air activation).

  12. The SMC (Short Model Coil) Nb$_{3}$Sn Program: FE Analysis with 3D Modeling

    CERN Document Server

    Kokkinos, C; Guinchard, M; Karppinen, M; Manil, P; Perez, J C; Regis, F

    2012-01-01

    The SMC (Short Model Coil) project aims at testing superconducting coils in racetrack configuration, wound with Nb$_{3}$Sn cable. The degradation of the magnetic properties of the cable is studied by applying different levels of pre-stress. It is an essential step in the validation of procedures for the construction of superconducting magnets with high performance conductor. Two SMC assemblies have been completed and cold tested in the frame of a European collaboration between CEA (FR), CERN and STFC (UK), with the technical support from LBNL (US). The second assembly showed remarkable good quench results, reaching a peak field of 12.5T. This paper details the new 3D modeling method of the SMC, implemented using the ANSYS® Workbench environment. Advanced computer-aided-design (CAD) tools are combined with multi-physics Finite Element Analyses (FEA), in the same integrated graphic interface, forming a fully parametric model that enables simulation driven development of the SMC project. The magnetic and struct...

  13. Detection of Fetal Abnormalities Based on Three Dimensional Nuchal Translucency

    CERN Document Server

    Lai, Khin Wee

    2013-01-01

    Ultrasound (US) prenatal screening has been proposed as the most effective technique for Trisomy 21 early assessment. Assessment of Nuchal Translucency (NT) offers promising non-invasive method for fetal abnormalities detection up to 75%. Nevertheless, current clinician practice of NT examination by locating the sonogram calipers on 2D US image requires highly trained and competent operators by adhering to a standard tedious protocol; therefore it is prone to errors and hence it decreases the reliability in intra- and inter-observer repeatability. This Brief provides the basic knowledge regarding Trisomy 21 diseases and its existing detection methods. The restrictions and disadvantages of each method are discussed accordingly. Therefore, a non-invasive early detection method using 3D ultrasound reconstruction of Nuchal Translucency is introduced. This new method for 3D NT assessments has an edge over the previous 2D methods, and entails the composite function in visualizing the explicit internal marker struct...

  14. Bohman-Frieze-Wormald model on the lattice, yielding a discontinuous percolation transition

    Science.gov (United States)

    Schrenk, K. J.; Felder, A.; Deflorin, S.; Araújo, N. A. M.; D'Souza, R. M.; Herrmann, H. J.

    2012-03-01

    The BFW model introduced by Bohman, Frieze, and Wormald [Random Struct. Algorithms1042-983210.1002/rsa.20038, 25, 432 (2004)], and recently investigated in the framework of discontinuous percolation by Chen and D'Souza [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.106.115701 106, 115701 (2011)], is studied on the square and simple-cubic lattices. In two and three dimensions, we find numerical evidence for a strongly discontinuous transition. In two dimensions, the clusters at the threshold are compact with a fractal surface of fractal dimension df=1.49±0.02. On the simple-cubic lattice, distinct jumps in the size of the largest cluster are observed. We proceed to analyze the tree-like version of the model, where only merging bonds are sampled, for dimension two to seven. The transition is again discontinuous in any considered dimension. Finally, the dependence of the cluster-size distribution at the threshold on the spatial dimension is also investigated.

  15. A dynamic P53-MDM2 model with time delay

    Energy Technology Data Exchange (ETDEWEB)

    Mihalas, Gh.I. [Department of Biophysics and Medical Informatics, University of Medicine and Pharmacy, Piata Eftimie Murgu, nr. 3, 300041 Timisoara (Romania)]. E-mail: mihalas@medinfo.umft.ro; Neamtu, M. [Department of Forecasting, Economic Analysis, Mathematics and Statistics, West University of Timisoara, Str. Pestalozzi, nr. 14A, 300115 Timisoara (Romania)]. E-mail: mihaela.neamtu@fse.uvt.ro; Opris, D. [Department of Applied Mathematics, West University of Timisoara, Bd. V. Parvan, nr. 4, 300223 Timisoara (Romania)]. E-mail: opris@math.uvt.ro; Horhat, R.F. [Department of Biophysics and Medical Informatics, University of Medicine and Pharmacy, Piata Eftimie Murgu, nr. 3, 300041 Timisoara (Romania)]. E-mail: rhorhat@yahoo.com

    2006-11-15

    Specific activator and repressor transcription factors which bind to specific regulator DNA sequences, play an important role in gene activity control. Interactions between genes coding such transcription factors should explain the different stable or sometimes oscillatory gene activities characteristic for different tissues. Starting with the model P53-MDM2 described into [Mihalas GI, Simon Z, Balea G, Popa E. Possible oscillatory behaviour in P53-MDM2 interaction computer simulation. J Biol Syst 2000;8(1):21-9] and the process described into [Kohn KW, Pommier Y. Molecular interaction map of P53 and MDM2 logic elements, which control the off-on switch of P53 in response to DNA damage. Biochem Biophys Res Commun 2005;331:816-27] we enveloped a new model of this interaction. Choosing the delay as a bifurcation parameter we study the direction and stability of the bifurcating periodic solutions. Some numerical examples are finally given for justifying the theoretical results.

  16. Covalent glycoinositolphospholipid (GPI binding to hemoglobin is associated with insulin-activation of erythrocyte membrane protease

    Directory of Open Access Journals (Sweden)

    VESNA NIKETIC

    2004-05-01

    Full Text Available Recently, it was demonstrated that prolonged hyperinsulinism associated with hypoglycemia, both in vivo and in vitro, caused covalent glycoinositolphospholipid (GPI binding to the C termini of both hemoglobin b-chains, which resulted in the formation of a novel, hitherto unrecognized, minor hemoglobin fraction (GPI-Hb (Niketic et al., Biochem. Biophys. Res. Commun. 239 (1997 435. In this study it was demonstrated that exposure of erythrocyte membranes to insulin causes the activation of membrane protease as well as that the formation of GPI-Hb parallels its activity. It is suggested that the insulin-activated protease is able to catalyze, albeit slowly, the transpeptidation, i.e., the replacement of the carboxy-terminal amino acid(s residues of the Hb b-chains with GPI as an exogenous nucleophile. To our knowledge the present results show for the first time that insulin stimulates protease activity in erythrocyte membranes, as well as that insulin-activated protease may be involved in post-translational GPI binding to proteins.

  17. Stochastic modeling of virus capsid assembly pathways

    Science.gov (United States)

    Schwartz, Russell

    2009-03-01

    Virus capsids have become a key model system for understanding self-assembly due to their high complexity, robust and efficient assembly processes, and experimental tractability. Our ability to directly examine and manipulate capsid assembly kinetics in detail nonetheless remains limited, creating a need for computer models that can infer experimentally inaccessible features of the assembly process and explore the effects of hypothetical manipulations on assembly trajectories. We have developed novel algorithms for stochastic simulation of capsid assembly [1,2] that allow us to model capsid assembly over broad parameter spaces [3]. We apply these methods to study the nature of assembly pathway control in virus capsids as well as their sensitivity to assembly conditions and possible experimental interventions. [4pt] [1] F. Jamalyaria, R. Rohlfs, and R. Schwartz. J Comp Phys 204, 100 (2005). [0pt] [2] N. Misra and R. Schwartz. J Chem Phys 129, in press (2008). [0pt] [3] B. Sweeney, T. Zhang, and R. Schwartz. Biophys J 94, 772 (2008).

  18. A dynamic P53-MDM2 model with time delay

    International Nuclear Information System (INIS)

    Mihalas, Gh.I.; Neamtu, M.; Opris, D.; Horhat, R.F.

    2006-01-01

    Specific activator and repressor transcription factors which bind to specific regulator DNA sequences, play an important role in gene activity control. Interactions between genes coding such transcription factors should explain the different stable or sometimes oscillatory gene activities characteristic for different tissues. Starting with the model P53-MDM2 described into [Mihalas GI, Simon Z, Balea G, Popa E. Possible oscillatory behaviour in P53-MDM2 interaction computer simulation. J Biol Syst 2000;8(1):21-9] and the process described into [Kohn KW, Pommier Y. Molecular interaction map of P53 and MDM2 logic elements, which control the off-on switch of P53 in response to DNA damage. Biochem Biophys Res Commun 2005;331:816-27] we enveloped a new model of this interaction. Choosing the delay as a bifurcation parameter we study the direction and stability of the bifurcating periodic solutions. Some numerical examples are finally given for justifying the theoretical results

  19. Carnitine prevents the early mitochondrial damage induced by methylglyoxal bis(guanylhydrazone) in L1210 leukaemia cells.

    Science.gov (United States)

    Nikula, P; Ruohola, H; Alhonen-Hongisto, L; Jänne, J

    1985-06-01

    We previously found that the anti-cancer drug methylglyoxal bis(guanylhydrazone) (mitoguazone) depresses carnitine-dependent oxidation of long-chain fatty acids in cultured mouse leukaemia cells [Nikula, Alhonen-Hongisto, Seppänen & Jänne (1984) Biochem. Biophys. Res. Commun. 120, 9-14]. We have now investigated whether carnitine also influences the development of the well-known mitochondrial damage produced by the drug in L1210 leukaemia cells. Palmitate oxidation was distinctly inhibited in tumour cells exposed to 5 microM-methylglyoxal bis(guanylhydrazone) for only 7 h. Electron-microscopic examination of the drug-exposed cells revealed that more than half of the mitochondria were severely damaged. Similar exposure of the leukaemia cells to the drug in the presence of carnitine not only abolished the inhibition of fatty acid oxidation but almost completely prevented the drug-induced mitochondrial damage. The protection provided by carnitine appeared to depend on the intracellular concentration of methylglyoxal bis(guanylhydrazone), since the mitochondria-sparing effect disappeared at higher drug concentrations.

  20. Active sites of two orthologous cytochromes P450 2E1: Differences revealed by spectroscopic methods

    International Nuclear Information System (INIS)

    Anzenbacherova, Eva; Hudecek, Jiri; Murgida, Daniel; Hildebrandt, Peter; Marchal, Stephane; Lange, Reinhard; Anzenbacher, Pavel

    2005-01-01

    Cytochromes P450 2E1 of human and minipig origin were examined by absorption spectroscopy under high hydrostatic pressure and by resonance Raman spectroscopy. Human enzyme tends to denature to the P420 form more easily than the minipig form; moreover, the apparent compressibility of the heme active site (as judged from a redshift of the absorption maximum with pressure) is greater than that of the minipig counterpart. Relative compactness of the minipig enzyme is also seen in the Raman spectra, where the presence of planar heme conformation was inferred from band positions characteristic of the low-spin heme with high degree of symmetry. In this respect, the CYP2E1 seems to be another example of P450 conformational heterogeneity as shown, e.g., by Davydov et al. for CYP3A4 [Biochem. Biophys. Res. Commun. 312 (2003) 121-130]. The results indicate that the flexibility of the CYP active site is likely one of its basic structural characteristics

  1. A DNA sequence obtained by replacement of the dopamine RNA aptamer bases is not an aptamer.

    Science.gov (United States)

    Álvarez-Martos, Isabel; Ferapontova, Elena E

    2017-08-05

    A unique specificity of the aptamer-ligand biorecognition and binding facilitates bioanalysis and biosensor development, contributing to discrimination of structurally related molecules, such as dopamine and other catecholamine neurotransmitters. The aptamer sequence capable of specific binding of dopamine is a 57 nucleotides long RNA sequence reported in 1997 (Biochemistry, 1997, 36, 9726). Later, it was suggested that the DNA homologue of the RNA aptamer retains the specificity of dopamine binding (Biochem. Biophys. Res. Commun., 2009, 388, 732). Here, we show that the DNA sequence obtained by the replacement of the RNA aptamer bases for their DNA analogues is not able of specific biorecognition of dopamine, in contrast to the original RNA aptamer sequence. This DNA sequence binds dopamine and structurally related catecholamine neurotransmitters non-specifically, as any DNA sequence, and, thus, is not an aptamer and cannot be used neither for in vivo nor in situ analysis of dopamine in the presence of structurally related neurotransmitters. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Dielectric response of biconcave erythrocyte membranes to D- and L-Glucose

    International Nuclear Information System (INIS)

    Livshits, L; Caduff, A; Talary, M S; Feldman, Y

    2007-01-01

    In this paper, we report on the influence of D- and L-glucose on the dielectric properties of native shaped (biconcave) human erythrocytes using time domain dielectric spectroscopy. The dielectric spectra of biconcave cells were analysed using a modified form of the model originally reported for spheroid particle suspensions (Asami and Yonezawa 1995 Biochim. Biophys. Acta. 1245 317-24) The observed increase in the specific membrane capacitance of the biconcave erythrocytes was correlated with an increase in the concentration of D-glucose. In contrast, no associated correlation was found to changes in the membrane capacitance with increasing concentrations of L-glucose. A similar analysis of the dielectric response of osmotically swollen erythrocytes to changes in D-glucose concentration revealed a significantly different calculated specific cell membrane capacitance at elevated (>12 mM) D-glucose concentrations. The paper outlines and discusses the possible biochemical mechanisms that could be responsible for the measured dielectric properties of the erythrocyte membrane capacitances

  3. The distribution of iron between the metal-binding sites of transferrin human serum.

    Science.gov (United States)

    Williams, J; Moreton, K

    1980-02-01

    The Makey & Seal [(1976) Biochim. Biophys. Acta 453, 250--256] method of polyacrylamide-gel electrophoresis in buffer containing 6 M-urea was used to determine the distribution of iron between the N-terminal and C-terminal iron-binding sites of transferrin in human serum. In fresh serum the two sites are unequally occupied; there is preferential occupation of the N-terminal site. On incubation of the serum at 37 degrees C the preference of iron for the N-terminal site becomes more marked. On storage of serum at -15 degrees C the iron distribution changes so that there is a marked preference for the C-terminal site. Dialysis of serum against buffer at pH 7.4 also causes iron to be bound much more strongly by the C-terminal than by the N-terminal site. The original preference for the N-terminal site can be resroted to the dialysed serum by addition of the diffusible fraction.

  4. TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Shen Yang; Delaglio, Frank [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Cornilescu, Gabriel [National Magnetic Resonance Facility (United States); Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: bax@nih.gov

    2009-08-15

    NMR chemical shifts in proteins depend strongly on local structure. The program TALOS establishes an empirical relation between {sup 13}C, {sup 15}N and {sup 1}H chemical shifts and backbone torsion angles {phi} and {psi} (Cornilescu et al. J Biomol NMR 13 289-302, 1999). Extension of the original 20-protein database to 200 proteins increased the fraction of residues for which backbone angles could be predicted from 65 to 74%, while reducing the error rate from 3 to 2.5%. Addition of a two-layer neural network filter to the database fragment selection process forms the basis for a new program, TALOS+, which further enhances the prediction rate to 88.5%, without increasing the error rate. Excluding the 2.5% of residues for which TALOS+ makes predictions that strongly differ from those observed in the crystalline state, the accuracy of predicted {phi} and {psi} angles, equals {+-}13{sup o}. Large discrepancies between predictions and crystal structures are primarily limited to loop regions, and for the few cases where multiple X-ray structures are available such residues are often found in different states in the different structures. The TALOS+ output includes predictions for individual residues with missing chemical shifts, and the neural network component of the program also predicts secondary structure with good accuracy.

  5. Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR.

    Science.gov (United States)

    van der Schot, Gijs; Bonvin, Alexandre M J J

    2015-08-01

    We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on unassigned NOE lists (Huang et al. in J Am Chem Soc 127:1665-1674, 2005b, doi: 10.1021/ja047109h). We compare the original submissions using a previous version of the server based on Rosetta version 2.6 with recalculated targets using the new R3FP fragment picker for fragment selection and implementing a new annotation of prediction reliability (van der Schot et al. in J Biomol NMR 57:27-35, 2013, doi: 10.1007/s10858-013-9762-6), both implemented in the CS-Rosetta3 WeNMR server. In this second round of CASD-NMR, the WeNMR CS-Rosetta server has demonstrated a much better performance than in the first round since only converged targets were submitted. Further, recalculation of all CASD-NMR targets using the new version of the server demonstrates that our new annotation of prediction quality is giving reliable results. Predictions annotated as weak are often found to provide useful models, but only for a fraction of the sequence, and should therefore only be used with caution.

  6. 13C-detected NMR experiments for automatic resonance assignment of IDPs and multiple-fixing SMFT processing

    International Nuclear Information System (INIS)

    Dziekański, Paweł; Grudziąż, Katarzyna; Jarvoll, Patrik; Koźmiński, Wiktor; Zawadzka-Kazimierczuk, Anna

    2015-01-01

    Intrinsically disordered proteins (IDPs) have recently attracted much interest, due to their role in many biological processes, including signaling and regulation mechanisms. High-dimensional 13 C direct-detected NMR experiments have proven exceptionally useful in case of IDPs, providing spectra with superior peak dispersion. Here, two such novel experiments recorded with non-uniform sampling are introduced, these are 5D HabCabCO(CA)NCO and 5D HNCO(CA)NCO. Together with the 4D (HACA)CON(CA)NCO, an extension of the previously published 3D experiments (Pantoja-Uceda and Santoro in J Biomol NMR 59:43–50, 2014. doi: 10.1007/s10858-014-9827-1 10.1007/s10858-014-9827-1 ), they form a set allowing for complete and reliable resonance assignment of difficult IDPs. The processing is performed with sparse multidimensional Fourier transform based on the concept of restricting (fixing) some of spectral dimensions to a priori known resonance frequencies. In our study, a multiple-fixing method was developed, that allows easy access to spectral data. The experiments were tested on a resolution-demanding alpha-synuclein sample. Due to superior peak dispersion in high-dimensional spectrum and availability of the sequential connectivities between four consecutive residues, the overwhelming majority of resonances could be assigned automatically using the TSAR program

  7. Site Energies of Active and Inactive Pheophytins in the Reaction Center of Photosystem II from Chlamydomonas Reinhardtii

    Energy Technology Data Exchange (ETDEWEB)

    Acharya, K.; Neupane, B.; Zazubovich, V.; Sayre, R. T.; Picorel, R.; Seibert, M.; Jankowiak, R.

    2012-03-29

    It is widely accepted that the primary electron acceptor in various Photosystem II (PSII) reaction center (RC) preparations is pheophytin {alpha} (Pheo {alpha}) within the D1 protein (Pheo{sub D1}), while Pheo{sub D2} (within the D2 protein) is photochemically inactive. The Pheo site energies, however, have remained elusive, due to inherent spectral congestion. While most researchers over the past two decades placed the Q{sub y}-states of Pheo{sub D1} and Pheo{sub D2} bands near 678-684 and 668-672 nm, respectively, recent modeling [Raszewski et al. Biophys. J. 2005, 88, 986-998; Cox et al. J. Phys. Chem. B 2009, 113, 12364-12374] of the electronic structure of the PSII RC reversed the assignment of the active and inactive Pheos, suggesting that the mean site energy of Pheo{sub D1} is near 672 nm, whereas Pheo{sub D2} ({approx}677.5 nm) and Chl{sub D1} ({approx}680 nm) have the lowest energies (i.e., the Pheo{sub D2}-dominated exciton is the lowest excited state). In contrast, chemical pigment exchange experiments on isolated RCs suggested that both pheophytins have their Q{sub y} absorption maxima at 676-680 nm [Germano et al. Biochemistry 2001, 40, 11472-11482; Germano et al. Biophys. J. 2004, 86, 1664-1672]. To provide more insight into the site energies of both Pheo{sub D1} and Pheo{sub D2} (including the corresponding Q{sub x} transitions, which are often claimed to be degenerate at 543 nm) and to attest that the above two assignments are most likely incorrect, we studied a large number of isolated RC preparations from spinach and wild-type Chlamydomonas reinhardtii (at different levels of intactness) as well as the Chlamydomonas reinhardtii mutant (D2-L209H), in which the active branch Pheo{sub D1} is genetically replaced with chlorophyll {alpha} (Chl {alpha}). We show that the Q{sub x}-/Q{sub y}-region site energies of Pheo{sub D1} and Pheo{sub D2} are {approx}545/680 nm and {approx}541.5/670 nm, respectively, in good agreement with our previous assignment

  8. Probing DNA in nanopores via tunneling: from sequencing to ``quantum'' analogies

    Science.gov (United States)

    di Ventra, Massimiliano

    2012-02-01

    Fast and low-cost DNA sequencing methods would revolutionize medicine: a person could have his/her full genome sequenced so that drugs could be tailored to his/her specific illnesses; doctors could know in advance patients' likelihood to develop a given ailment; cures to major diseases could be found faster [1]. However, this goal of ``personalized medicine'' is hampered today by the high cost and slow speed of DNA sequencing methods. In this talk, I will discuss the sequencing protocol we suggest which requires the measurement of the distributions of transverse currents during the translocation of single-stranded DNA into nanopores [2-5]. I will support our conclusions with a combination of molecular dynamics simulations coupled to quantum mechanical calculations of electrical current in experimentally realizable systems [2-5]. I will also discuss recent experiments that support these theoretical predictions. In addition, I will show how this relatively unexplored area of research at the interface between solids, liquids, and biomolecules at the nanometer length scale is a fertile ground to study quantum phenomena that have a classical counterpart, such as ionic quasi-particles, ionic ``quantized'' conductance [6,7] and Coulomb blockade [8]. Work supported in part by NIH. [4pt] [1] M. Zwolak, M. Di Ventra, Physical Approaches to DNA Sequencing and Detection, Rev. Mod. Phys. 80, 141 (2008).[0pt] [2] M. Zwolak and M. Di Ventra, Electronic signature of DNA nucleotides via transverse transport, Nano Lett. 5, 421 (2005).[0pt] [3] J. Lagerqvist, M. Zwolak, and M. Di Ventra, Fast DNA sequencing via transverse electronic transport, Nano Lett. 6, 779 (2006).[0pt] [4] J. Lagerqvist, M. Zwolak, and M. Di Ventra, Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport, Biophys. J. 93, 2384 (2007).[0pt] [5] M. Krems, M. Zwolak, Y.V. Pershin, and M. Di Ventra, Effect of noise on DNA sequencing via transverse electronic transport

  9. A etimologia de biomoléculas com metais de transição como auxiliar na aprendizagem de Química Biológica

    OpenAIRE

    Silva, José A. L. da

    2013-01-01

    Numerous functional biomolecules are associated with metals, i.e. the metallobiomolecules; more specifically, some are dependent on transition metals required for several crucial biological roles. Nevertheless, their names can lead to ambiguous interpretations concerning the properties and performances of this group of biological molecules. Their etymology may be useful by providing a more perceptive insight into their features. However, etymology can lead to incongruous conclusions, requirin...

  10. A etimologia de biomoléculas com metais de transição como auxiliar na aprendizagem de Química Biológica

    Directory of Open Access Journals (Sweden)

    José A. L. da Silva

    2013-01-01

    Full Text Available Numerous functional biomolecules are associated with metals, i.e. the metallobiomolecules; more specifically, some are dependent on transition metals required for several crucial biological roles. Nevertheless, their names can lead to ambiguous interpretations concerning the properties and performances of this group of biological molecules. Their etymology may be useful by providing a more perceptive insight into their features. However, etymology can lead to incongruous conclusions, requiring an especially careful approach to prevent errors. Examples illustrating these subjects shall be examined.

  11. Latent interaction effects in the theory of planned behaviour applied to quitting smoking.

    Science.gov (United States)

    Hukkelberg, Silje Sommer; Hagtvet, Knut A; Kovac, Velibor Bobo

    2014-02-01

    This study applies three latent interaction models in the theory of planned behaviour (TPB; Ajzen, 1988, Attitudes, personality, and behavior. Homewood, IL: Dorsey Press; Ajzen, 1991, Organ. Behav. Hum. Decis. Process., 50, 179) to quitting smoking: (1) attitude × perceived behavioural control on intention; (2) subjective norms (SN) × attitude on intention; and (3) perceived behavioural control × intention on quitting behaviour. The data derive from a longitudinal Internet survey of 939 smokers aged 15-74 over a period of 4 months. Latent interaction effects were estimated using the double-mean-centred unconstrained approach (Lin et al., 2010, Struct. Equ. Modeling, 17, 374) in LISREL. Attitude × SN and attitude × perceived behavioural control both showed a significant interaction effect on intention. No significant interaction effect was found for perceived behavioural control × intention on quitting. The latent interaction approach is a useful method for investigating specific conditions between TPB components in the context of quitting behaviour. Theoretical and practical implications of the results are discussed. © 2013 The British Psychological Society.

  12. American Society of Composites, 32nd Technical Conference

    Energy Technology Data Exchange (ETDEWEB)

    Aitharaju, Venkat [General Motors LLC; Wollschlager, Jeffrey; Plakomytis2, Dimitrios; Fish, Jacob

    2018-10-23

    This paper will present a general methodology by which weave draping manufacturing simulation results can be utilized to include the effects of weave draping and scissor angle in a structural multiscale simulation. While the methodology developed is general in nature, this paper will specifically demonstrate the methodology applied to a truncated pyramid, utilizing manufacturing simulation weave draping results from ESI PAM-FORM, and multiscale simulation using Altair Multiscale Designer (MDS) and OptiStruct. From a multiscale simulation perspective, the weave draping manufacturing simulation results will be used to develop a series of woven unit cells which cover the range of weave scissor angles existing within the part. For each unit cell, a multiscale material model will be developed, and applied to the corresponding spatial locations within the structural simulation mesh. In addition, the principal material orientation will be mapped from the wave draping manufacturing simulation mesh to the structural simulation mesh using Altair HyperMesh mapping technology. Results of the coupled simulation will be compared and verified against experimental data of the same available via General Motors (GM) Department of Energy (DOE) project.

  13. Accuracy assessment of the linear Poisson-Boltzmann equation and reparametrization of the OBC generalized Born model for nucleic acids and nucleic acid-protein complexes.

    Science.gov (United States)

    Fogolari, Federico; Corazza, Alessandra; Esposito, Gennaro

    2015-04-05

    The generalized Born model in the Onufriev, Bashford, and Case (Onufriev et al., Proteins: Struct Funct Genet 2004, 55, 383) implementation has emerged as one of the best compromises between accuracy and speed of computation. For simulations of nucleic acids, however, a number of issues should be addressed: (1) the generalized Born model is based on a linear model and the linearization of the reference Poisson-Boltmann equation may be questioned for highly charged systems as nucleic acids; (2) although much attention has been given to potentials, solvation forces could be much less sensitive to linearization than the potentials; and (3) the accuracy of the Onufriev-Bashford-Case (OBC) model for nucleic acids depends on fine tuning of parameters. Here, we show that the linearization of the Poisson Boltzmann equation has mild effects on computed forces, and that with optimal choice of the OBC model parameters, solvation forces, essential for molecular dynamics simulations, agree well with those computed using the reference Poisson-Boltzmann model. © 2015 Wiley Periodicals, Inc.

  14. Design optimization of jacket structures for mass production

    DEFF Research Database (Denmark)

    Sandal, Kasper

    This thesis presents models and applications for structural optimization of jacket structures for offshore wind turbines. The motivation is that automatic design procedures can be used to obtain more cost efficient designs, and thus reduce the levelized cost of energy from offshore wind. A struct......This thesis presents models and applications for structural optimization of jacket structures for offshore wind turbines. The motivation is that automatic design procedures can be used to obtain more cost efficient designs, and thus reduce the levelized cost of energy from offshore wind....... A structural finite element model is developed specifically for the analysis and optimization of jacket structures. The model uses Timoshenko beam elements, and assumes thin walled tubular beams and a linear elastic structural response. The finite element model is implemented in a Matlab package called JADOP...... (Jacket Design Optimization), and the static and dynamic structural response is verified with the commercial finite element software Abaqus. A parametric mesh of the offshore wind turbine structure makes it relatively easy to represent various structures from the literature, as well as exploring...

  15. Cluster protein structures using recurrence quantification analysis on coordinates of alpha-carbon atoms of proteins

    International Nuclear Information System (INIS)

    Zhou Yu; Yu Zuguo; Anh, Vo

    2007-01-01

    The 3-dimensional coordinates of alpha-carbon atoms of proteins are used to distinguish the protein structural classes based on recurrence quantification analysis (RQA). We consider two independent variables from RQA of coordinates of alpha-carbon atoms, %determ1 and %determ2, which were defined by Webber et al. [C.L. Webber Jr., A. Giuliani, J.P. Zbilut, A. Colosimo, Proteins Struct. Funct. Genet. 44 (2001) 292]. The variable %determ2 is used to define two new variables, %determ2 1 and %determ2 2 . Then three variables %determ1, %determ2 1 and %determ2 2 are used to construct a 3-dimensional variable space. Each protein is represented by a point in this variable space. The points corresponding to proteins from the α, β, α+β and α/β structural classes position into different areas in this variable space. In order to give a quantitative assessment of our clustering on the selected proteins, Fisher's discriminant algorithm is used. Numerical results indicate that the discriminant accuracies are very high and satisfactory

  16. A new MARS and its applications

    International Nuclear Information System (INIS)

    Krivosheev, O.E.; Mokhov, N.V.

    1998-01-01

    This paper describes MARS14(98) - the newest version of the MARS Monte Carlo code system for fast simulation of hadronic and electromagnetic cascades in shielding, accelerator and detector components in the energy range from a fraction of an electronvolt up to 30 TeV. The main changes compared to the previous release, MARS 13, concern the hadron production model tuned with evaluated data and the DPMJET-II code, improved photo- and electro- production of hadrons and muons, improved algorithms for the 3-body decays, particle tracking in magnetic fields, synchrotron radiation by electrons and muons, significantly extended histograming capabilities and material description, and improved computational performance. In addition to direct energy deposition calculations, a new set of fluence-to-dose conversion factors for all particles including neutrino are built into the code. The MARS 14(98) system includes links to the MCNP code for neutron transport below 20 MeV, to the ANSYS code for thermal and stress analyses and to the STRUCT code for multi-turn particle tracking in large synchrotrons and collider rings

  17. Control of a flexible beam actuated by macro-fiber composite patches: II. Hysteresis and creep compensation, experimental results

    International Nuclear Information System (INIS)

    Schröck, Johannes; Meurer, Thomas; Kugi, Andreas

    2011-01-01

    This paper considers a flexible cantilever beam, which is actuated by piezoelectric macro-fiber composite (MFC) patch actuators. For accurate positioning tasks, special attention has to be paid to the inherent nonlinear hysteresis and creep behavior of these actuators. A detailed analysis of the MFC-actuated cantilever verifies that these nonlinearities can be efficiently captured by an operator-based model using Prandtl–Ishlinskii's theory. Based on a Hammerstein-like model with the nonlinearities at the input connected in series with a linear infinite-dimensional beam model it follows that hysteresis and creep effects can be compensated by application of the inverse operator. Experimental results prove the feasibility of this approach. With this result, the tracking accuracy of the combination of the compensator with the flatness-based feedforward control design as proposed in the companion paper (Schröck et al 2011 Smart Mater. Struct. 20 015015) can be verified. Measurements demonstrate the applicability of this approach for the realization of highly dynamic trajectories for the beam's tip deflection

  18. The WA105-3x1x1 m3 dual phase LAr-TPC demonstrator

    CERN Document Server

    Murphy, Sebastien

    2016-11-15

    The dual phase Liquid Argon Time Projection Chamber (LAr TPC) is the state-of-art technology for neutrino detection thanks to its superb 3D tracking and calorimetry performance. Its main feature is the charge amplification in gas argon which provides excellent signal-to-noise ratio. Electrons produced in the liquid argon are extracted in the gas phase. Here, a readout plane based on Large Electron Multiplier detectors provides amplification of the charges before its collection onto an anode with strip readout. The charge amplification enables constructing fully homoge- nous giant LAr-TPCs with tuneable gain, excellent charge imaging performance and increased sensitivity to low energy events. Following a staged approach the WA105 collaboration is con- structing a dual phase LAr-TPC with an active volume of 3x1x1m3 that will soon be tested with cosmic rays. Its construction and operation aims to test scalable solutions for the crucial aspects of this technology: ultra high argon purity in non-evacuable tank, la...

  19. A new MARS and its applications

    Energy Technology Data Exchange (ETDEWEB)

    Krivosheev, O.E.; N.V Mokhov, N.V.

    1998-01-01

    This paper describes MARS14(98) - the newest version of the MARS Monte Carlo code system for fast simulation of hadronic and electromagnetic cascades in shielding, accelerator and detector components in the energy range from a fraction of an electronvolt up to 30 TeV. The main changes compared to the previous release, MARS 13, concern the hadron production model tuned with evaluated data and the DPMJET-II code, improved photo- and electro- production of hadrons and muons, improved algorithms for the 3-body decays, particle tracking in magnetic fields, synchrotron radiation by electrons and muons, significantly extended histograming capabilities and material description, and improved computational performance. In addition to direct energy deposition calculations, a new set of fluence-to-dose conversion factors for all particles including neutrino are built into the code. The MARS 14(98) system includes links to the MCNP code for neutron transport below 20 MeV, to the ANSYS code for thermal and stress analyses and to the STRUCT code for multi-turn particle tracking in large synchrotrons and collider rings.

  20. Thermomechanical Analysis of Shape-Memory Composite Tape Spring

    Science.gov (United States)

    Yang, H.; Wang, L. Y.

    2013-06-01

    Intelligent materials and structures have been extensively applied for satellite designs in order to minimize the mass and reduce the cost in the launch of the spacecraft. Elastic memory composites (EMCs) have the ability of high-strain packaging and shape-memory effect, but increase the parts and total weight due to the additional heating system. Shape-memory sandwich structures Li and Wang (J. Intell. Mater. Syst. Struct. 22(14), 1605-1612, 2011) can overcome such disadvantage by using the metal skin acting as the heating element. However, the high strain in the micro-buckled metal skin decreases the deployment efficiency. This paper aims to present an insight into the folding and deployment behaviors of shape-memory composite (SMC) tape springs. A thermomechanical process was analyzed, including the packaging deformation at an elevated temperature, shape frozen at the low temperature and shape recovery after reheating. The result shows that SMC tape springs can significantly decrease the strain concentration in the metal skin, as well as exhibiting excellent shape frozen and recovery behaviors. Additionally, possible failure modes of SMC tape springs were also analyzed.

  1. Fourier transform infrared spectroscopic characterisation of heavy metal-induced metabolic changes in the plant-associated soil bacterium Azospirillum brasilense Sp7

    Science.gov (United States)

    Kamnev, A. A.; Antonyuk, L. P.; Tugarova, A. V.; Tarantilis, P. A.; Polissiou, M. G.; Gardiner, P. H. E.

    2002-06-01

    Structural and compositional features of whole cells of the plant-growth-promoting rhizobacterium Azospirillum brasilense Sp7 under standard and heavy metal-stressed conditions are analysed using Fourier transform infrared (FTIR) spectroscopy and compared with the FT-Raman spectroscopic data obtained previously [J. Mol. Struct. 563-564 (2001) 199]. The structural spectroscopic information is considered together with inductively coupled plasma-mass spectrometric (ICP-MS) analytical data on the content of the heavy metal cations (Co2+, Cu2+ and Zn2+) in the bacterial cells. As a bacterial response to heavy metal stress, all the three metals, being taken up by bacterial cells from the culture medium (0.2 mM) in significant amounts (ca. 0.12, 0.48 and 4.2 mg per gram of dry biomass for Co, Cu and Zn, respectively), are shown to induce essential metabolic changes in the bacterium revealed in the spectra, including the accumulation of polyester compounds in bacterial cells and their enhanced hydration affecting certain IR vibrational modes of functional groups involved.

  2. Frequency-dependent electrodeformation of giant phospholipid vesicles in AC electric field

    Science.gov (United States)

    2010-01-01

    A model of vesicle electrodeformation is described which obtains a parametrized vesicle shape by minimizing the sum of the membrane bending energy and the energy due to the electric field. Both the vesicle membrane and the aqueous media inside and outside the vesicle are treated as leaky dielectrics, and the vesicle itself is modeled as a nearly spherical shape enclosed within a thin membrane. It is demonstrated (a) that the model achieves a good quantitative agreement with the experimentally determined prolate-to-oblate transition frequencies in the kilohertz range and (b) that the model can explain a phase diagram of shapes of giant phospholipid vesicles with respect to two parameters: the frequency of the applied alternating current electric field and the ratio of the electrical conductivities of the aqueous media inside and outside the vesicle, explored in a recent paper (S. Aranda et al., Biophys J 95:L19–L21, 2008). A possible use of the frequency-dependent shape transitions of phospholipid vesicles in conductometry of microliter samples is discussed. PMID:21886342

  3. Cholesterol pathways affected by small molecules that decrease sterol levels in Niemann-Pick type C mutant cells.

    Directory of Open Access Journals (Sweden)

    Madalina Rujoi

    2010-09-01

    Full Text Available Niemann-Pick type C (NPC disease is a genetically inherited multi-lipid storage disorder with impaired efflux of cholesterol from lysosomal storage organelles.The effect of screen-selected cholesterol lowering compounds on the major sterol pathways was studied in CT60 mutant CHO cells lacking NPC1 protein. Each of the selected chemicals decreases cholesterol in the lysosomal storage organelles of NPC1 mutant cells through one or more of the following mechanisms: increased cholesterol efflux from the cell, decreased uptake of low-density lipoproteins, and/or increased levels of cholesteryl esters. Several chemicals promote efflux of cholesterol to extracellular acceptors in both non-NPC and NPC1 mutant cells. The uptake of low-density lipoprotein-derived cholesterol is inhibited by some of the studied compounds.Results herein provide the information for prioritized further studies in identifying molecular targets of the chemicals. This approach proved successful in the identification of seven chemicals as novel inhibitors of lysosomal acid lipase (Rosenbaum et al, Biochim. Biophys. Acta. 2009, 1791:1155-1165.

  4. Regulation of renal function and structure by the signaling Na/K-ATPase.

    Science.gov (United States)

    Xie, Jeffrey X; Li, Xin; Xie, Zijian

    2013-12-01

    The Na/K-ATPase as an essential ion pump was discovered more than 50 years ago (Skou (1989) Biochim. Biophys. Acta 1000, 439-446; Feraille and Doucet (2001) Physiol. Rev. 81, 345-418). The signaling function of Na/K-ATPase has been gradually appreciated over the last 20 years, first from the studies of regulatory effects of ouabain on cardiac cell growth. Several reviews on this topic have been written during the last few years (Schoner and Scheiner-Bobis (2007) Am. J. Physiol. Cell. Physiol. 293, C509-C536; Xie and Cai (2003) Mol. Interv. 3, 157 - 168; Bagrov et al. (2009) Pharmacol. Rev. 61, 9-38; Tian and Xie (2008) Physiology 23, 205-211; Fontana et al. (2013) FEBS J. 280, 5450-5455; Blanco and Wallace (2013) Am. J. Physiol. Renal Physiol. 305, F797-F812). This article will focus on the molecular mechanism of Na/K-ATPase-mediated signal transduction and its potential regulatory role in renal physiology and diseases. © 2013 International Union of Biochemistry and Molecular Biology.

  5. Lipidomic data on lipid droplet triglyceride remodelling associated with protection of breast cancer cells from lipotoxic stress.

    Science.gov (United States)

    Jarc, Eva; Eichmann, Thomas O; Zimmermann, Robert; Petan, Toni

    2018-06-01

    The data presented here is related to the research article entitled "Lipid droplets induced by secreted phospholipase A 2 and unsaturated fatty acids protect breast cancer cells from nutrient and lipotoxic stress" by E. Jarc et al., Biochim. Biophys. Acta 1863 (2018) 247-265. Elevated uptake of unsaturated fatty acids and lipid droplet accumulation are characteristic of aggressive cancer cells and have been associated with the cellular stress response. The present study provides lipidomic data on the triacylglycerol (TAG) and phosphatidylcholine (PC) composition of MDA-MB-231 breast cancer cells exposed to docosahexaenoic acid (DHA; 22:6, ω-3). Datasets provide information on the changes in lipid composition induced by depletion of adipose triglyceride lipase (ATGL) and by exogenous addition of secreted phospholipase A 2 (sPLA 2 ) in DHA-treated cells. The presented alterations in lipid composition, mediated by targeting lipid droplet biogenesis and lipolysis, are associated with protection from lipotoxicity and allow further investigation into the role of lipid droplets in the resistance of cancer cells to lipotoxic stress.

  6. Structural characterization of supramolecular assemblies by {sup 13}C spin dilution and 3D solid-state NMR

    Energy Technology Data Exchange (ETDEWEB)

    Habenstein, Birgit; Loquet, Antoine; Giller, Karin; Becker, Stefan; Lange, Adam, E-mail: adla@nmr.mpibpc.mpg.de [Max Planck Institute for Biophysical Chemistry, Department of NMR-based Structural Biology (Germany)

    2013-01-15

    {sup 13}C spin diluted protein samples can be produced using [1-{sup 13}C] and [2-{sup 13}C]-glucose (Glc) carbon sources in the bacterial growth medium. The {sup 13}C spin dilution results in favorable {sup 13}C spectral resolution and polarization transfer behavior. We recently reported the combined use of [1-{sup 13}C]- and [2-{sup 13}C]-Glc labeling to facilitate the structural analysis of insoluble and non-crystalline biological systems by solid-state NMR (ssNMR), including sequential assignment, detection of long-range contacts and structure determination of macromolecular assemblies. In solution NMR the beneficial properties of sparsely labeled samples using [2-{sup 13}C]-glycerol ({sup 13}C labeled C{alpha} sites on a {sup 12}C diluted background) have recently been exploited to provide a bi-directional assignment method (Takeuchi et al. in J Biomol NMR 49(1):17-26, 2011 ). Inspired by this approach and our own recent results using [2-{sup 13}C]-Glc as carbon sources for the simplification of ssNMR spectra, we present a strategy for a bi-directional sequential assignment of solid-state NMR resonances and additionally the detection of long-range contacts using the combination of {sup 13}C spin dilution and 3D NMR spectroscopy. We illustrate our results with the sequential assignment and the collection of distance restraints on an insoluble and non-crystalline supramolecular assembly, the Salmonella typhimurium type III secretion system needle.

  7. Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR

    Energy Technology Data Exchange (ETDEWEB)

    Schot, Gijs van der [Uppsala University, Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology (Sweden); Bonvin, Alexandre M. J. J., E-mail: a.m.j.j.bonvin@uu.nl [Utrecht University, Faculty of Science – Chemistry, Bijvoet Center for Biomolecular Research (Netherlands)

    2015-08-15

    We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on unassigned NOE lists (Huang et al. in J Am Chem Soc 127:1665–1674, 2005b, doi: 10.1021/ja047109h 10.1021/ja047109h ). We compare the original submissions using a previous version of the server based on Rosetta version 2.6 with recalculated targets using the new R3FP fragment picker for fragment selection and implementing a new annotation of prediction reliability (van der Schot et al. in J Biomol NMR 57:27–35, 2013, doi: 10.1007/s10858-013-9762-6 10.1007/s10858-013-9762-6 ), both implemented in the CS-Rosetta3 WeNMR server. In this second round of CASD-NMR, the WeNMR CS-Rosetta server has demonstrated a much better performance than in the first round since only converged targets were submitted. Further, recalculation of all CASD-NMR targets using the new version of the server demonstrates that our new annotation of prediction quality is giving reliable results. Predictions annotated as weak are often found to provide useful models, but only for a fraction of the sequence, and should therefore only be used with caution.

  8. Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR

    International Nuclear Information System (INIS)

    Schot, Gijs van der; Bonvin, Alexandre M. J. J.

    2015-01-01

    We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on unassigned NOE lists (Huang et al. in J Am Chem Soc 127:1665–1674, 2005b, doi: 10.1021/ja047109h 10.1021/ja047109h ). We compare the original submissions using a previous version of the server based on Rosetta version 2.6 with recalculated targets using the new R3FP fragment picker for fragment selection and implementing a new annotation of prediction reliability (van der Schot et al. in J Biomol NMR 57:27–35, 2013, doi: 10.1007/s10858-013-9762-6 10.1007/s10858-013-9762-6 ), both implemented in the CS-Rosetta3 WeNMR server. In this second round of CASD-NMR, the WeNMR CS-Rosetta server has demonstrated a much better performance than in the first round since only converged targets were submitted. Further, recalculation of all CASD-NMR targets using the new version of the server demonstrates that our new annotation of prediction quality is giving reliable results. Predictions annotated as weak are often found to provide useful models, but only for a fraction of the sequence, and should therefore only be used with caution

  9. Phylogenetic relationships among the European and American bison and seven cattle breeds recon structed using the Bovine SNP50 Illumina Genotyping BeadChip

    DEFF Research Database (Denmark)

    Pertoldi, Cino; Wójcik, Jan M; Kawalko, Agata

    2010-01-01

    amongst bison subspecies and cattle, and (3) de tect loci under positive or stabilizing selection. A Bayesian clustering procedure (STRUCTURE) detected ten genetically distinct clusters, with separation among all seven cattle breeds and European and American bison, but no separation be tween plain......Here we present the first at tempt to use the BovineSNP50 Illumina genotyping BeadChip for genome-wide screening of European bison Bisonbonasus bonasus (EB), two subspecies of American bison: the plains bison (EB), two sub species of American bison: the plains bison Bison bison bison (PB), the wood...... bison Bi on bison athabascae (WB) and seven (PB), the wood bison (WB) and seven cattle Bostaurus breeds. Our aims were to (1) reconstruct their evolutionary relationships, (2) detect any genetic signature of past bottlenecks and to quantify the con sequences of bottle necks on the genetic distances...

  10. Nonlinear dynamics of a nonsmooth shape memory alloy oscillator

    International Nuclear Information System (INIS)

    Cardozo dos Santos, Bruno; Amorim Savi, Marcelo

    2009-01-01

    In the last years, there is an increasing interest in nonsmooth system dynamics motivated by different applications including rotor dynamics, oil drilling and machining. Besides, shape memory alloys (SMAs) have been used in various applications exploring their high dissipation capacity related to their hysteretic behavior. This contribution investigates the nonlinear dynamics of shape memory alloy nonsmooth systems considering a linear oscillator with a discontinuous support built with an SMA element. A constitutive model developed by Paiva et al. [Paiva A, Savi MA, Braga AMB, Pacheco PMCL. A constitutive model for shape memory alloys considering tensile-compressive asymmetry and plasticity. Int J Solids Struct 2005;42(11-12):3439-57] is employed to describe the thermomechanical behavior of the SMA element. Numerical investigations show results where the SMA discontinuous support can dramatically change the system dynamics when compared to those associated with a linear elastic support system. A parametric study is of concern showing the system behavior for different system characteristics, forcing excitation and also gaps. These results show that smart materials can be employed in different kinds of mechanical systems exploring some of the remarkable properties of these alloys.

  11. Prediction of protein subcellular locations by GO-FunD-PseAA predictor.

    Science.gov (United States)

    Chou, Kuo-Chen; Cai, Yu-Dong

    2004-08-06

    The localization of a protein in a cell is closely correlated with its biological function. With the explosion of protein sequences entering into DataBanks, it is highly desired to develop an automated method that can fast identify their subcellular location. This will expedite the annotation process, providing timely useful information for both basic research and industrial application. In view of this, a powerful predictor has been developed by hybridizing the gene ontology approach [Nat. Genet. 25 (2000) 25], functional domain composition approach [J. Biol. Chem. 277 (2002) 45765], and the pseudo-amino acid composition approach [Proteins Struct. Funct. Genet. 43 (2001) 246; Erratum: ibid. 44 (2001) 60]. As a showcase, the recently constructed dataset [Bioinformatics 19 (2003) 1656] was used for demonstration. The dataset contains 7589 proteins classified into 12 subcellular locations: chloroplast, cytoplasmic, cytoskeleton, endoplasmic reticulum, extracellular, Golgi apparatus, lysosomal, mitochondrial, nuclear, peroxisomal, plasma membrane, and vacuolar. The overall success rate of prediction obtained by the jackknife cross-validation was 92%. This is so far the highest success rate performed on this dataset by following an objective and rigorous cross-validation procedure.

  12. DOA Estimation of Multiple LFM Sources Using a STFT-based and FBSS-based MUSIC Algorithm

    Directory of Open Access Journals (Sweden)

    K. B. Cui

    2017-12-01

    Full Text Available Direction of arrival (DOA estimation is an important problem in array signal processing. An effective multiple signal classification (MUSIC method based on the short-time Fourier transform (STFT and forward/ backward spatial smoothing (FBSS techniques for the DOA estimation problem of multiple time-frequency (t-f joint LFM sources is addressed. Previous work in the area e. g. STFT-MUSIC algorithm cannot resolve the t-f completely or largely joint sources because they can only select the single-source t-f points. The proposed method con¬structs the spatial t-f distributions (STFDs by selecting the multiple-source t-f points and uses the FBSS techniques to solve the problem of rank loss. In this way, the STFT-FBSS-MUSIC algorithm can resolve the t-f largely joint or completely joint LFM sources. In addition, the proposed algorithm also owns pretty low computational complexity when resolving multiple LFM sources because it can reduce the times of the feature decomposition and spectrum search. The performance of the proposed method is compared with that of the existing t-f based MUSIC algorithms through computer simulations and the results show its good performance.

  13. NON-LINEAR ANALYSIS OF AN EXPERIMENTAL JOINT OF COLUMN AND BEAMS OF ARMED CONCRETE-STEEL COLUMN FOR FRAME

    Directory of Open Access Journals (Sweden)

    Nelson López

    2017-12-01

    Full Text Available In this research, the nonlinear behavior of a real-scale experimental joint (node is studied, consisting of three reinforced concrete elements, one column and two beams joined to a structural steel column at the upper level. In the numerical analysis the model of the union was analyzed in the inelastic range, this model was elaborated with the finite element program based on fibers, SeismoStruct to analyze as a function of time, the traction and compression efforts in the confined area and not confined area of the concrete column and in the longitudinal reinforcement steel, as well as verification of the design of the base plate that joins the two columns. The results showed that tensile stresses in the unconfined zone surpassed the concrete breaking point, with cracking occurring just below the lower edge of the beams; in the confined area the traction efforts were much lower, with cracks occurring later than in the non-confined area. The concrete column-steel column joint behaved as a rigid node, so the elastic design was consistent with the calculation methodology of base plates for steel columns.

  14. Econometric Methodology of Monopolization Process Evaluation

    Directory of Open Access Journals (Sweden)

    Dmitrijs Skoruks

    2014-06-01

    Full Text Available The research “Econometric Methodology of Monopolization Process Evaluation” gives a perspective description of monopolization process’ nature, occurrence source, development procedure and internal conjuncture specifics, as well as providing an example of modern econometrical method application within a unified framework of market competition analysis for the purpose of conducting a quantitative competition evaluation on an industry level for practical use in both private and public sectors. The main question of the aforementioned research is the definition and quantitative analysis of monopolization effects in modern day globalized markets, while con- structing an empirical model of the econometric analysis, based on the use of in- ternational historical experience of monopoly formations standings, with the goal of introducing a further development scheme for the use of both econometrical and statistical instruments in line with the forecasting and business research need of enterprises and regulatory functions of the public sector. The current research uses a vast variety of monopolization evaluation ratios and their econometrical updates on companies that are involved in the study procedure in order to detect and scallar measure their market monopolizing potential, based on the implemented acquired market positions, turnover shares and competition policies.

  15. Nuclear spin transitions in the kHz range in Rydberg matter clusters give precise values of the internal magnetic field from orbiting Rydberg electrons

    International Nuclear Information System (INIS)

    Holmlid, Leif

    2009-01-01

    Clusters of the electronically excited condensed matter Rydberg matter (RM) are planar and sixfold symmetric with specific magic numbers N as shown by rotational spectroscopy of potassium K N clusters [L. Holmlid, Mol. Phys. 105 (2007) 933; L. Holmlid, J. Mol. Struct. 885 (2008) 122]. In radio frequency emission spectra from such clusters, features are observed that are due to the hyperfine interaction between the atomic nucleus 39 K and two Rydberg electrons. These electrons exist in a doubly excited K atom at n'' = 5 or 6 in a 'sleeping-top' type rotating cluster. Such low excited electrons were observed recently in optical intra-cavity experiments in K(RM), where the electrons in the conduction band are involved in the angular momentum conservation in the stimulated emission. Here we show that the agreement with the theoretical description of circular Rydberg states is excellent within ±0.2% in the magnetic field, invoking angular momentum conservation by electrons in the condensed phase. Sleeping-top clusters may form stacks of clusters, and it is likely that such stacks are the emitting entities involved in the two nuclear spin series observed.

  16. Structural-functional lung imaging using a combined CT-EIT and a Discrete Cosine Transformation reconstruction method.

    Science.gov (United States)

    Schullcke, Benjamin; Gong, Bo; Krueger-Ziolek, Sabine; Soleimani, Manuchehr; Mueller-Lisse, Ullrich; Moeller, Knut

    2016-05-16

    Lung EIT is a functional imaging method that utilizes electrical currents to reconstruct images of conductivity changes inside the thorax. This technique is radiation free and applicable at the bedside, but lacks of spatial resolution compared to morphological imaging methods such as X-ray computed tomography (CT). In this article we describe an approach for EIT image reconstruction using morphologic information obtained from other structural imaging modalities. This leads to recon- structed images of lung ventilation that can easily be superimposed with structural CT or MRI images, which facilitates image interpretation. The approach is based on a Discrete Cosine Transformation (DCT) of an image of the considered transversal thorax slice. The use of DCT enables reduction of the dimensionality of the reconstruction and ensures that only conductivity changes of the lungs are reconstructed and displayed. The DCT based approach is well suited to fuse morphological image information with functional lung imaging at low computational costs. Results on simulated data indicate that this approach preserves the morphological structures of the lungs and avoids blurring of the solution. Images from patient measurements reveal the capabilities of the method and demonstrate benefits in possible applications.

  17. PRODUÇÃO DE BIOCOMPOSTOS A PARTIR DA BIOMASSA: PROSPECÇÃO DE PATENTES NO BRASIL.

    Directory of Open Access Journals (Sweden)

    Katia Iro Altidis Mota

    2017-12-01

    Full Text Available Cada dia mais aumenta a preocupação com a situação do meio ambiente e vários fatores são responsáveis por essa preocupação, dentre eles a qualidade do ar que respiramos, o temor de desastres naturaise até mesmo a preservação do meio ambiente para futuras gerações. Diante deste cenário, órgãos governamentais e indústrias procuram aplicar políticas ambientais que diminuam os impactos negativos à natureza. Indústria e agroindústrias produzem diversos resíduos de alto valor de reutilização que necessitam de destino adequado, pois além de poluírem, representam perdas de matérias-primas e energia, e exigemrecursos significativos em tratamentos para controlar a poluição. É grande a produção científica brasileira sobre a reutilização de resíduos como bagaço de cana-de-açúcar, casca de arroz, borra de café, casca de coco, dentre outros, como substrato para produção compostos de origem biotecnológica. Entretanto, o número de depósitos de pedidos de patentes nesta área ainda é bastante pequeno. Neste trabalho será apresentadoum panorama da relação de pedidos de patentesrelacionados àutilização de biomassa vegetalpara produção de biomoléculas no Brasil.

  18. Whole animal automated platform for drug discovery against multi-drug resistant Staphylococcus aureus.

    Directory of Open Access Journals (Sweden)

    Rajmohan Rajamuthiah

    Full Text Available Staphylococcus aureus, the leading cause of hospital-acquired infections in the United States, is also pathogenic to the model nematode Caenorhabditis elegans. The C. elegans-S. aureus infection model was previously carried out on solid agar plates where the bacteriovorous C. elegans feeds on a lawn of S. aureus. However, agar-based assays are not amenable to large scale screens for antibacterial compounds. We have developed a high throughput liquid screening assay that uses robotic instrumentation to dispense a precise amount of methicillin resistant S. aureus (MRSA and worms in 384-well assay plates, followed by automated microscopy and image analysis. In validation of the liquid assay, an MRSA cell wall defective mutant, MW2ΔtarO, which is attenuated for killing in the agar-based assay, was found to be less virulent in the liquid assay. This robust assay with a Z'-factor consistently greater than 0.5 was utilized to screen the Biomol 4 compound library consisting of 640 small molecules with well characterized bioactivities. As proof of principle, 27 of the 30 clinically used antibiotics present in the library conferred increased C. elegans survival and were identified as hits in the screen. Surprisingly, the antihelminthic drug closantel was also identified as a hit in the screen. In further studies, we confirmed the anti-staphylococcal activity of closantel against vancomycin-resistant S. aureus isolates and other Gram-positive bacteria. The liquid C. elegans-S. aureus assay described here allows screening for anti-staphylococcal compounds that are not toxic to the host.

  19. Whole animal automated platform for drug discovery against multi-drug resistant Staphylococcus aureus.

    Science.gov (United States)

    Rajamuthiah, Rajmohan; Fuchs, Beth Burgwyn; Jayamani, Elamparithi; Kim, Younghoon; Larkins-Ford, Jonah; Conery, Annie; Ausubel, Frederick M; Mylonakis, Eleftherios

    2014-01-01

    Staphylococcus aureus, the leading cause of hospital-acquired infections in the United States, is also pathogenic to the model nematode Caenorhabditis elegans. The C. elegans-S. aureus infection model was previously carried out on solid agar plates where the bacteriovorous C. elegans feeds on a lawn of S. aureus. However, agar-based assays are not amenable to large scale screens for antibacterial compounds. We have developed a high throughput liquid screening assay that uses robotic instrumentation to dispense a precise amount of methicillin resistant S. aureus (MRSA) and worms in 384-well assay plates, followed by automated microscopy and image analysis. In validation of the liquid assay, an MRSA cell wall defective mutant, MW2ΔtarO, which is attenuated for killing in the agar-based assay, was found to be less virulent in the liquid assay. This robust assay with a Z'-factor consistently greater than 0.5 was utilized to screen the Biomol 4 compound library consisting of 640 small molecules with well characterized bioactivities. As proof of principle, 27 of the 30 clinically used antibiotics present in the library conferred increased C. elegans survival and were identified as hits in the screen. Surprisingly, the antihelminthic drug closantel was also identified as a hit in the screen. In further studies, we confirmed the anti-staphylococcal activity of closantel against vancomycin-resistant S. aureus isolates and other Gram-positive bacteria. The liquid C. elegans-S. aureus assay described here allows screening for anti-staphylococcal compounds that are not toxic to the host.

  20. The risk from fast neutron exposure

    International Nuclear Information System (INIS)

    Bond, V.P.

    1979-01-01

    The conclusions and recommendations made by Rossi and Mays in recent papers (Rad. Res. 71, 1, 1977; Rad. Environ. Biophys. 14, 275, 1977; Health Phys. 34, 353, 1978), based on their analysis of recent Japanese data are discussed. They imply that the risk associated with the current annual dose equivalent limit of 5 rem for all radiations is unacceptably high, that this limit must be reduced by a factor of 10 or more, and that the conservative linear, no threshold hypothesis must be abandoned. It is shown in this paper that these recommendations are not supported by the newly-analyzed neutron data, and certainly cannot be applied selectively to the annual absorbed dose limit for neutrons. In particular the judgement that the risk of an annual exposure from 0.5 rad (5 rem) of neutrons is unacceptably high, is a personal opinion of the authors, and does not necessarily follow either from the assumption of a linear-quadratic dose effect relation for low-LET radiation or from other radiobiological considerations. At issue is the level of risk that is to be considered 'acceptable', a question that is societal and thus not resolvable on purely technical or scientific grounds. (author)

  1. Induction of Shikimic Acid Pathway Enzymes by Light in Suspension Cultured Cells of Parsley (Petroselinum crispum) 1

    Science.gov (United States)

    McCue, Kent F.; Conn, Eric E.

    1990-01-01

    Light treatment of suspension cultured cells of parsley (Petroselinum crispum) was shown to increase the activity of the shikimic acid pathway enzyme, 3-deoxy-d-arabino-heptulosonic acid-7-phosphate (DAHP) synthase (EC 4.1.2.15). DAHP synthase activity was assayed for two isoforms, DS-Mn and DS-Co (RJ Ganson, TA d'Amato, RA Jensen [1986] Plant Physiol 82: 203-210). Light increased the enzymatic activity of the plastidic isoform DS-Mn as much as 2-fold, averaging 1.6-fold with >95% confidence. The cytosolic isoform DS-Co was unaffected. Cycloheximide and actinomycin D, translational and transcriptional inhibitors, respectively, both reversed induction of DS-Mn by light suggesting transcriptional regulation of the gene. Chorismate mutase activity was assayed for the two isoforms CM I and CM II (BK Singh, JA Connelly, EE Conn [1985] Arch Biochem Biophys 243: 374-384). Treatment by light did not significantly affect either chorismate mutase isoform. The ratio of the two chorismate mutase isoforms changed during the growth cycle, with an increase in the ratio of plastidic to cytosolic isoforms occurring towards the end of logarithmic growth. PMID:16667741

  2. Cochlear spike synchronization and neuron coincidence detection model

    Science.gov (United States)

    Bader, Rolf

    2018-02-01

    Coincidence detection of a spike pattern fed from the cochlea into a single neuron is investigated using a physical Finite-Difference model of the cochlea and a physiologically motivated neuron model. Previous studies have shown experimental evidence of increased spike synchronization in the nucleus cochlearis and the trapezoid body [Joris et al., J. Neurophysiol. 71(3), 1022-1036 and 1037-1051 (1994)] and models show tone partial phase synchronization at the transition from mechanical waves on the basilar membrane into spike patterns [Ch. F. Babbs, J. Biophys. 2011, 435135]. Still the traveling speed of waves on the basilar membrane cause a frequency-dependent time delay of simultaneously incoming sound wavefronts up to 10 ms. The present model shows nearly perfect synchronization of multiple spike inputs as neuron outputs with interspike intervals (ISI) at the periodicity of the incoming sound for frequencies from about 30 to 300 Hz for two different amounts of afferent nerve fiber neuron inputs. Coincidence detection serves here as a fusion of multiple inputs into one single event enhancing pitch periodicity detection for low frequencies, impulse detection, or increased sound or speech intelligibility due to dereverberation.

  3. Remeasuring HEWL pKa values by NMR spectroscopy 

    DEFF Research Database (Denmark)

    Webb, Helen; Tynan-Connolly, Barbara Mary; Lee, Gregory M

    2011-01-01

    Site-specific pK(a) values measured by NMR spectroscopy provide essential information on protein electrostatics, the pH-dependence of protein structure, dynamics and function, and constitute an important benchmark for protein pK(a) calculation algorithms. Titration curves can be measured by track......Site-specific pK(a) values measured by NMR spectroscopy provide essential information on protein electrostatics, the pH-dependence of protein structure, dynamics and function, and constitute an important benchmark for protein pK(a) calculation algorithms. Titration curves can be measured...... by tracking the NMR chemical shifts of several reporter nuclei versus sample pH. However, careful analysis of these curves is needed to extract residue-specific pK(a) values since pH-dependent chemical shift changes can arise from many sources, including through-bond inductive effects, through-space electric...... protonated carbons and protons in this protein. We extracted pK(a) values from the resulting titration curves using standard fitting methods, and compared these values to each other, and with those measured previously by ¹H NMR (Bartik et al., Biophys J 1994;66:1180–1184). This analysis gives insights...

  4. First evidence of the pore-forming properties of a keratin from skin mucus of rainbow trout (Oncorhynchus mykiss, formerly Salmo gairdneri).

    Science.gov (United States)

    Molle, Virginie; Campagna, Sylvie; Bessin, Yannick; Ebran, Nathalie; Saint, Nathalie; Molle, Gérard

    2008-04-01

    The epidermis of fish is covered with a layer of mucus, which contributes to the defence of the species against parasites, bacteria and fungi. We have previously extracted glycoproteins from various mucus samples from fish and have shown that they present pore-forming activities well correlated with strong antibacterial properties [Ebran, Julien, Orange, Saglio, Lemaitre and Molle(2000) Biochim. Biophys. Acta 1467, 271-280]. The present study focuses on the 65 kDa glycoprotein, Tr65, from the rainbow trout (Oncorhynchus mykiss, formerly Salmo gairdneri).Enzymatic digestion of Tr65 yielded a fragment pattern with strong homology with that of trout type II cytokeratin. Sequence analysis of the cDNA clone obtained by PCR confirmed this homology. We thus constructed a plasmid to overproduce the recombinant Tr65. We extracted and purified this recombinant Tr65, using it for multichannel and single-channel experiments in azolectin bilayers. Our results with recombinant Tr65 confirmed the pore-forming properties already shown with native antibacterial Tr65. These findings offer new insights into the function of keratin proteins present in various mucosal surfaces of animals and human beings.

  5. Lipidomic data on lipid droplet triglyceride remodelling associated with protection of breast cancer cells from lipotoxic stress

    Directory of Open Access Journals (Sweden)

    Eva Jarc

    2018-06-01

    Full Text Available The data presented here is related to the research article entitled “Lipid droplets induced by secreted phospholipase A2 and unsaturated fatty acids protect breast cancer cells from nutrient and lipotoxic stress” by E. Jarc et al., Biochim. Biophys. Acta 1863 (2018 247–265. Elevated uptake of unsaturated fatty acids and lipid droplet accumulation are characteristic of aggressive cancer cells and have been associated with the cellular stress response. The present study provides lipidomic data on the triacylglycerol (TAG and phosphatidylcholine (PC composition of MDA-MB-231 breast cancer cells exposed to docosahexaenoic acid (DHA; 22:6, ω-3. Datasets provide information on the changes in lipid composition induced by depletion of adipose triglyceride lipase (ATGL and by exogenous addition of secreted phospholipase A2 (sPLA2 in DHA-treated cells. The presented alterations in lipid composition, mediated by targeting lipid droplet biogenesis and lipolysis, are associated with protection from lipotoxicity and allow further investigation into the role of lipid droplets in the resistance of cancer cells to lipotoxic stress. Keywords: Lipid droplets, Lipidomics, Adipose triglyceride lipase, Polyunsaturated fatty acid, Cancer, Phospholipase A2

  6. Gaussian curvature elasticity determined from global shape transformations and local stress distributions: a comparative study using the MARTINI model.

    Science.gov (United States)

    Hu, Mingyang; de Jong, Djurre H; Marrink, Siewert J; Deserno, Markus

    2013-01-01

    We calculate the Gaussian curvature modulus kappa of a systematically coarse-grained (CG) one-component lipid membrane by applying the method recently proposed by Hu et al. [Biophys. J., 2012, 102, 1403] to the MARTINI representation of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). We find the value kappa/kappa = -1.04 +/- 0.03 for the elastic ratio between the Gaussian and the mean curvature modulus and deduce kappa(m)/kappa(m) = -0.98 +/- 0.09 for the monolayer elastic ratio, where the latter is based on plausible assumptions for the distance z0 of the monolayer neutral surface from the bilayer midplane and the spontaneous lipid curvature K(0m). By also analyzing the lateral stress profile sigma0(z) of our system, two other lipid types and pertinent data from the literature, we show that determining K(0m) and kappa through the first and second moment of sigma0(z) gives rise to physically implausible values for these observables. This discrepancy, which we previously observed for a much simpler CG model, suggests that the moment conditions derived from simple continuum assumptions miss the effect of physically important correlations in the lipid bilayer.

  7. Target of rapamycin (TOR) plays a critical role in triacylglycerol accumulation in microalgae.

    Science.gov (United States)

    Imamura, Sousuke; Kawase, Yasuko; Kobayashi, Ikki; Sone, Toshiyuki; Era, Atsuko; Miyagishima, Shin-Ya; Shimojima, Mie; Ohta, Hiroyuki; Tanaka, Kan

    2015-10-01

    Most microalgae produce triacylglycerol (TAG) under stress conditions such as nitrogen depletion, but the underlying molecular mechanism remains unclear. In this study, we focused on the role of target of rapamycin (TOR) in TAG accumulation. TOR is a serine/threonine protein kinase that is highly conserved and plays pivotal roles in nitrogen and other signaling pathways in eukaryotes. We previously constructed a rapamycin-susceptible Cyanidioschyzon merolae, a unicellular red alga, by expressing yeast FKBP12 protein to evaluate the results of TOR inhibition (Imamura et al. in Biochem Biophys Res Commun 439:264-269, 2013). By using this strain, we here report that rapamycin-induced TOR inhibition results in accumulation of cytoplasmic lipid droplets containing TAG. Transcripts for TAG synthesis-related genes, such as glycerol-3-phosphate acyltransferase and acyl-CoA:diacylglycerol acyltransferase (DGAT), were increased by rapamycin treatment. We also found that fatty acid synthase-dependent de novo fatty acid synthesis was required for the accumulation of lipid droplets. Induction of TAG and up-regulation of DGAT gene expression by rapamycin were similarly observed in the unicellular green alga, Chlamydomonas reinhardtii. These results suggest the general involvement of TOR signaling in TAG accumulation in divergent microalgae.

  8. Interference of aldehyde metabolizing enzyme with diamine oxidase/histaminase/activity as determined by /sup 14/C putrescine method

    Energy Technology Data Exchange (ETDEWEB)

    Fogel, W A [Polish Academy of Sciences, Cracow (Poland). Inst. of Pharmacology; Bieganski, T; Wozniak, J; Maslinski, C

    1978-01-01

    The ..delta../sup 1/ pyrroline formation, as an indicator of diamine oxidase activity according to Okuyama and Kobayashi /sup 14/C putrescine test (1961, Archs Biochem. Biophys., vol.95, 242), has been investigated in several tissue homogenates. When guinea pig liver homogenate was used as a source of enzyme in the presence of aldehyde dehydrogenase inhibitors chlorate hydrate and acetaldehyde the level of formation ..delta../sup 1/ pyrroline was strongly increased in a dose-dependent manner. Also inhibition of aldehyde reductase by phenobarbital enhanced ..delta../sup 1/ pyrroline formation, but to a lesser degree. In other tissues, with very high initial diamine oxidase activity (rat intestine, dog kidney) or with very low diamine oxidase activity (guinea pig skin, dog liver) the influence of these inhibitors was only slight. Pyrazole, an inhibitor of alcohol dehydrogenase exerted only a small effect on ..delta../sup 1/ pyrroline formation. All aldehyde-metabolizing enzymes inhibitors, except pyrazole, were without effect on purified pea seddling and hog kidney diamine oxidases. The use of aldehyde-metabolizing enzymes inhibitors may help to reveal the real values of diamine oxidase activity, when tissues homogenates are used as a source of enzyme.

  9. Interference of aldehyde metabolizing enzyme with diamine oxidase/histaminase/activity as determined by 14C putrescine method

    International Nuclear Information System (INIS)

    Fogel, W.A.; Bieganski, T.; Wozniak, J.; Maslinski, C.

    1978-01-01

    The Δ 1 pyrroline formation, as an indicator of diamine oxidase activity according to Okuyama and Kobayashi 14 C putrescine test (1961, Archs Biochem. Biophys., vol.95, 242), has been investigated in several tissue homogenates. When guinea pig liver homogenate was used as a source of enzyme in the presence of aldehyde dehydrogenase inhibitors chlorate hydrate and acetaldehyde the level of formation Δ 1 pyrroline was strongly increased in a dose-dependent manner. Also inhibition of aldehyde reductase by phenobarbital enhanced Δ 1 pyrroline formation, but to a lesser degree. In other tissues, with very high initial diamine oxidase activity (rat intestine, dog kidney) or with very low diamine oxidase activity (guinea pig skin, dog liver) the influence of these inhibitors was only slight. Pyrazole, an inhibitor of alcohol dehydrogenase exerted only a small effect on Δ 1 pyrroline formation. All aldehyde-metabolizing enzymes inhibitors, except pyrazole, were without effect on purified pea seddling and hog kidney diamine oxidases. The use of aldehyde-metabolizing enzymes inhibitors may help to reveal the real values of diamine oxidase activity, when tissues homogenates are used as a source of enzyme. (author)

  10. The relationship between the connecting peptide of recombined single chain insulin and its biological function

    Institute of Scientific and Technical Information of China (English)

    HUANG; Yiding; (

    2001-01-01

    ., Harvey, T. S., Camphell, I. D., Solution structure of human insulin-like growth factor I: a nuclear magnetic resonance and restrained molecular dynamics study, Biochemistry, 1991, 30: 5484-5491.［13］Baker, E. N., Blundell, T. L., Cutfield, J. F. et al., The structure of 2Zn pig insulin crystals at 1.5A resolution, Phil. Trans. R. Soc. Lond., 1988, B 319: 369-456.［14］Kobayashi, Y., Nishimura, S., Ohkubo, T. et al., Solution structure of human insulin-like growth factor-I (IGF-I), in Peptide 1990 (eds. Giralt, E., Andreu, D.), Leiden: ESCOM Science Publishers B. V., 1991, 565-567.［15］Wang, P., Cai, R. R., Feng, Y. M. et al., Studies on insulin/IGF-1 hybrid and IGF-1 growth-promoting functional region, IUBMB Life, 2000, 49: 321-325.［16］Zhang, Y. S., Hu, H. M., Cai, R. R. et al., Secretory expression of a single-chain insulin precursor in yeast and its conversion into human insulin, Science in China, Ser. C, 1996, 39(3): 225-233.［17］Sambrook, J., Fritsch, E. F., Maniatis, T., Molecular Cloning: A Laboratory Manual, 2nd ed., New York: Cold Spring Harbor Laboratory Press, 1989.［18］Sanger, F., Nicklen, S., Coulson, A. R., DNA sequencing with chain-terminating inhibitors, Proc. Natl. Acad. Sci. USA, 1977, 74: 5463-5467.［19］Lowrey, O. H., Rosebrough, N. O., Farr, A. L. et al., Protein measurement with the follin-phenol reagent, J. Biol. Chem., 1951, 193: 265-275.［20］Feng, Y. M., Zhu, J. H., Zhang, X. T. et al., Studies on the mechanism of insulin action VIII. The insulin receptor on the membrane of the human placenta, Acta Biochim. Biophys. Sin., 1982, 14: 137-143.［21］Chen, H., Feng, Y. M., Hydrophilic Thr can replace the hydrophobic and absolutely conservative A3Val in insulin, Biochim. Biophys. Acta, 1998, 1429: 69-73.［22］Zhang, X., Xia, S. L., Tomooka, Y. et al., A new assay system for the cell growth promoting effects of insulin and growth factors, Acta Biochim. Biophys. Sin., 1995, 27: 487-492.［23］Ma, J. G., Li, M. Y., Zhen, J. M

  11. Streamlining of the RELAP5-3D Code

    International Nuclear Information System (INIS)

    Mesina, George L; Hykes, Joshua; Guillen, Donna Post

    2007-01-01

    RELAP5-3D is widely used by the nuclear community to simulate general thermal hydraulic systems and has proven to be so versatile that the spectrum of transient two-phase problems that can be analyzed has increased substantially over time. To accommodate the many new types of problems that are analyzed by RELAP5-3D, both the physics and numerical methods of the code have been continuously improved. In the area of computational methods and mathematical techniques, many upgrades and improvements have been made decrease code run time and increase solution accuracy. These include vectorization, parallelization, use of improved equation solvers for thermal hydraulics and neutron kinetics, and incorporation of improved library utilities. In the area of applied nuclear engineering, expanded capabilities include boron and level tracking models, radiation/conduction enclosure model, feedwater heater and compressor components, fluids and corresponding correlations for modeling Generation IV reactor designs, and coupling to computational fluid dynamics solvers. Ongoing and proposed future developments include improvements to the two-phase pump model, conversion to FORTRAN 90, and coupling to more computer programs. This paper summarizes the general improvements made to RELAP5-3D, with an emphasis on streamlining the code infrastructure for improved maintenance and development. With all these past, present and planned developments, it is necessary to modify the code infrastructure to incorporate modifications in a consistent and maintainable manner. Modifying a complex code such as RELAP5-3D to incorporate new models, upgrade numerics, and optimize existing code becomes more difficult as the code grows larger. The difficulty of this as well as the chance of introducing errors is significantly reduced when the code is structured. To streamline the code into a structured program, a commercial restructuring tool, FOR( ) STRUCT, was applied to the RELAP5-3D source files. The

  12. Topology Optimization of Spacecraft Transfer Compartment

    Directory of Open Access Journals (Sweden)

    A. A. Borovikov

    2016-01-01

    Full Text Available IntroductionThe subject of this research is topology optimization of the adapter of a spacecraft transfer compartment. The finite element topology optimization [1] is widely used for simple structure elements [6, 7]. It is argued that using this method in conjunction with additive technology (3D - printing it is possible to create construction designs with the best weight characteristics. However, the paper shows that when applying this method to a complex construction design the optimization results are highly sensitive to optimization algorithm parameters. The goal of this research is to study parameters of the topology optimization algorithm and the influence of their variations on results.1.      Problem formulation   A commercial software Altair HyperWorks/OptiStruct (student’s license performed numerical calculations. The paper presents a detailed description of the finite element model.The main features of the proposed model are as follows:-          Simplicity with non-complicated geometry;-          Building a finite element model in terms of computing time minimization;-          Using the lumped mass elements to simulate the impacts of the conjugates on the adapter;-          A limit of material strength, decreased by an order of magnitude, to eliminate stress concentrators;-          The gravitational load applied corresponds to the loads for the Angara-A5 launcher [8]. 2.      Method of solutionA brief description of the SIMP-method realized in the Altair HyperWorks/OptiStruct software is given.3.      ResultsPerformed numerical calculations, and shown the influence of variations of algorithm parameters (DISCRETE, MATINIT, MINDIM, MAXDIM on construction design as well as the parameters SINGLE and SPLIT used to reveal restrictions on manufacturing.Shown that, depending on variations of parameters, an adapter construction strives to «truss» or «shell» type. Described

  13. Country report: Cuba. Local Production of 90Y And 188Re Radionuclides and Development of Radiopharmaceuticals for Therapy

    International Nuclear Information System (INIS)

    Xiques, Abmel; Hernández, Ignacio; Leyva, René; Pérez, Marylaine; Alonso, Luis Michel; Zamora, Minelys

    2010-01-01

    During the first period of this CRP we could test an efficient and reliable generator system based on ion-chromatography to obtain 90 Y from its parent radionuclide 90 Sr. This production scheme for 90 Y was outlined in the previous CRP related with the development of generator technologies. Quality parameters such as trace metals that can potentially interfere in the labeling of biomoléculas, 90 Y recovery, 90 Sr/ 90 Y ratio and radiation dose to bed matrix were evaluated. The results showed that high recovery and radionuclidic purity could be obtained for 90 Y during its repeated separation from the 90 Sr cow. No replacement or treatment of the cow were necessary and low waste generation and 90 Sr losses less that 0.1% after each run were also observed during the present study. A Fab’ fragment was enzimatically produced and purified from the monoclonal antibody h-R3 (Nimotuzumab®). The fragment and the parent antibody were successfully conjugated with DOTA and labeled with 90 Y. The radioinmunoconjugate thus obtained also exhibited a good 24 h in-vitro stability in an excess of DTPA. A 90 Y radiocoloid was prepared in a cromic phosphate particle for radiosynoviorthesis with promising results in animal models. Two alumina based 188 W/ 188 Re generators were prepared and their eluates were used in the labeling of hR3-DOTA conjugates. Quality control and in vivo evaluation in comparison with 99m Tc-hR3 showed very good results and similar pattern of distribution and pharmacokinetic and will be used in clinical trials for cancer patients. (author)

  14. Aplicación de una técnica de Cromatografía de Exclusión molecular para la purificación de ADN en plantas de Coffea sp. APPLICATION OF A TECHNIQUE OF MOLECULAR EXCLUSION CHROMATOGRAPHY FOR THE PURIFICATION OF DNA FROM Coffea sp. PLANTS

    Directory of Open Access Journals (Sweden)

    Ana María García Cepero

    2006-12-01

    Full Text Available Uno de los mayores inconvenientes en la extracción y purificación de biomoléculas a partir de plantas del género Coffea, es un alto contenido de polifenoles y compuestos tánicos. En el presente artículo se describe una metodología que permite obtener ADN de alta pureza. La extracción del ADN del homogeneizado de tejido foliar en siete genotipos de Coffea sp., se realizó mediante la técnica citada por Chaparro (1993 y su purificación se logró mediante cromatografía de exclusión molecular sobre una fase estacionaria de Sephacryl S-1000. Los resultados muestran que la alta eficiencia de separación de ARN degradado, proteínas, pigmentos y compuestos que absorben entre 220 y 300 nm, permiten obtener un ADN de alta pureza a juzgar por los datos espectrofotométricos y electroforéticos.One of the greatest difficulties in extracting and purifying biomolecules from plants in the genus Coffea is the high polyphenol and tannin contents. In this study a methodology is described that allows obtaining high purity DNA from leaf tissues of seven genotypes of Coffea sp. by means of the technique desribed by Chaparro (1993 and its further purification was achieved by molecular exclusion chromatography on Sephacryl S-1000 (Pharmacia. The results showed that the high separation efficiency of degraded RNA, proteins, pigments, and other compounds that absorb between 220 and 300 nm allowed obtaining high purity DNA as judged by the spectophometric and electroforetic data.

  15. INFLUÊNCIA DA CONCENTRAÇÃO DE OLIGONUCLEOTÍDEOS NO EFEITO DE AGLOMERAÇÃO DE NANOPARTÍCULAS NA PRESENÇA DE SOLUÇÃO SALINA

    Directory of Open Access Journals (Sweden)

    Olavo de Osti Comparato Filho

    2016-08-01

    Full Text Available O desenvolvimento de tecnologias que auxiliam no estudo da interação de nanopartículas com biomoléculas tem proporcionado o surgimento de novas técnicas de diagnóstico de doenças. Nanomateriais possuem características químicas e físicas específicas, como o efeito de ressonância plasmônica de superfície (SPR. Este trabalho parte do princípio da utilização de nanopartículas de Ouro (AuNPs, previamente sintetizadas e padronizadas, para o estudo da influência de concentrações de oligonucleotídeos, em presença de solução salina de Cloreto de Magnésio hidratado (MgCl2.6H2O, na sua estabilidade coloidal, por meio da Espectroscopia de UV-visível. No laboratório de nanossensores, realizaram-se experimentos com nanopartículas, oligonucleotídeos e sal, onde se observou, por meio de testes colorimétricos, a influência da porcentagem de cobertura das superfícies das nanopartículas das soluções finais, nos efeitos da SPR. Os resultados gráficos dos experimentos, dos espectros UV vis que relacionam absorbância e comprimentos de onda, registraram o processo de aglomeração. O objetivo foi analisar comparativamente a influência da concentração dos oligonucleotídeos nas soluções com nanopartículas e sal, para a elaboração das curvas de estabilidade das AuNPs.

  16. An evaluation of the contouring abilities of medical dosimetry students for the anatomy of a prostate cancer patient

    International Nuclear Information System (INIS)

    Collins, Kevin S.

    2012-01-01

    Prostate cancer is one of the most common diseases treated in a radiation oncology department. One of the major predictors of the treatment outcome and patient side effects is the accuracy of the anatomical contours for the treatment plan. Therefore, the purpose of this study was to determine which anatomical structures are most often contoured correctly and incorrectly by medical dosimetry students. The author also wanted to discover whether a review of the contouring rules would increase contouring accuracy. To achieve this, a male computed tomography dataset consisting of 72 transverse slices was sent to students for contouring. The students were instructed to import this dataset into their treatment planning system and contour the following structures: skin, bladder, rectum, prostate, penile bulb, seminal vesicles, left femoral head, and right femoral head. Upon completion of the contours, the contour file was evaluated against a “gold standard” contour set using StructSure software (Standard Imaging, Inc). A review of the initial contour results was conducted and then students were instructed to contour the dataset a second time. The results of this study showed significant differences between contouring sessions. These results and the standardization of contouring rules should benefit all individuals who participate in the treatment planning of cancer patients.

  17. Accounting for Intraligand Interactions in Flexible Ligand Docking with a PMF-Based Scoring Function.

    Science.gov (United States)

    Lizunov, A Y; Gonchar, A L; Zaitseva, N I; Zosimov, V V

    2015-10-26

    We analyzed the frequency with which intraligand contacts occurred in a set of 1300 protein-ligand complexes [ Plewczynski et al. J. Comput. Chem. 2011 , 32 , 742 - 755 .]. Our analysis showed that flexible ligands often form intraligand hydrophobic contacts, while intraligand hydrogen bonds are rare. The test set was also thoroughly investigated and classified. We suggest a universal method for enhancement of a scoring function based on a potential of mean force (PMF-based score) by adding a term accounting for intraligand interactions. The method was implemented via in-house developed program, utilizing an Algo_score scoring function [ Ramensky et al. Proteins: Struct., Funct., Genet. 2007 , 69 , 349 - 357 .] based on the Tarasov-Muryshev PMF [ Muryshev et al. J. Comput.-Aided Mol. Des. 2003 , 17 , 597 - 605 .]. The enhancement of the scoring function was shown to significantly improve the docking and scoring quality for flexible ligands in the test set of 1300 protein-ligand complexes [ Plewczynski et al. J. Comput. Chem. 2011 , 32 , 742 - 755 .]. We then investigated the correlation of the docking results with two parameters of intraligand interactions estimation. These parameters are the weight of intraligand interactions and the minimum number of bonds between the ligand atoms required to take their interaction into account.

  18. Camera-laser fusion sensor system and environmental recognition for humanoids in disaster scenarios

    International Nuclear Information System (INIS)

    Lee, Inho; Oh, Jaesung; Oh, Jun-Ho; Kim, Inhyeok

    2017-01-01

    This research aims to develop a vision sensor system and a recognition algorithm to enable a humanoid to operate autonomously in a disaster environment. In disaster response scenarios, humanoid robots that perform manipulation and locomotion tasks must identify the objects in the environment from those challenged by the call by the United States’ Defense Advanced Research Projects Agency, e.g., doors, valves, drills, debris, uneven terrains, and stairs, among others. In order for a humanoid to undertake a number of tasks, we con- struct a camera–laser fusion system and develop an environmental recognition algorithm. Laser distance sensor and motor are used to obtain 3D cloud data. We project the 3D cloud data onto a 2D image according to the intrinsic parameters of the camera and the distortion model of the lens. In this manner, our fusion sensor system performs functions such as those performed by the RGB-D sensor gener- ally used in segmentation research. Our recognition algorithm is based on super-pixel segmentation and random sampling. The proposed approach clusters the unorganized cloud data according to geometric characteristics, namely, proximity and co-planarity. To assess the feasibility of our system and algorithm, we utilize the humanoid robot, DRC-HUBO, and the results are demonstrated in the accompanying video.

  19. Camera-laser fusion sensor system and environmental recognition for humanoids in disaster scenarios

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Inho [Institute for Human and Machine Cognition (IHMC), Florida (United States); Oh, Jaesung; Oh, Jun-Ho [Korea Advanced Institute of Science and Technology (KAIST), Daejeon (Korea, Republic of); Kim, Inhyeok [NAVER Green Factory, Seongnam (Korea, Republic of)

    2017-06-15

    This research aims to develop a vision sensor system and a recognition algorithm to enable a humanoid to operate autonomously in a disaster environment. In disaster response scenarios, humanoid robots that perform manipulation and locomotion tasks must identify the objects in the environment from those challenged by the call by the United States’ Defense Advanced Research Projects Agency, e.g., doors, valves, drills, debris, uneven terrains, and stairs, among others. In order for a humanoid to undertake a number of tasks, we con- struct a camera–laser fusion system and develop an environmental recognition algorithm. Laser distance sensor and motor are used to obtain 3D cloud data. We project the 3D cloud data onto a 2D image according to the intrinsic parameters of the camera and the distortion model of the lens. In this manner, our fusion sensor system performs functions such as those performed by the RGB-D sensor gener- ally used in segmentation research. Our recognition algorithm is based on super-pixel segmentation and random sampling. The proposed approach clusters the unorganized cloud data according to geometric characteristics, namely, proximity and co-planarity. To assess the feasibility of our system and algorithm, we utilize the humanoid robot, DRC-HUBO, and the results are demonstrated in the accompanying video.

  20. Collective Influence Algorithm to find influencers via optimal percolation in massively large social media

    Science.gov (United States)

    Morone, Flaviano; Min, Byungjoon; Bo, Lin; Mari, Romain; Makse, Hernán A.

    2016-07-01

    We elaborate on a linear-time implementation of Collective-Influence (CI) algorithm introduced by Morone, Makse, Nature 524, 65 (2015) to find the minimal set of influencers in networks via optimal percolation. The computational complexity of CI is O(N log N) when removing nodes one-by-one, made possible through an appropriate data structure to process CI. We introduce two Belief-Propagation (BP) variants of CI that consider global optimization via message-passing: CI propagation (CIP) and Collective-Immunization-Belief-Propagation algorithm (CIBP) based on optimal immunization. Both identify a slightly smaller fraction of influencers than CI and, remarkably, reproduce the exact analytical optimal percolation threshold obtained in Random Struct. Alg. 21, 397 (2002) for cubic random regular graphs, leaving little room for improvement for random graphs. However, the small augmented performance comes at the expense of increasing running time to O(N2), rendering BP prohibitive for modern-day big-data. For instance, for big-data social networks of 200 million users (e.g., Twitter users sending 500 million tweets/day), CI finds influencers in 2.5 hours on a single CPU, while all BP algorithms (CIP, CIBP and BDP) would take more than 3,000 years to accomplish the same task.

  1. On the Tupi-Guaranian prehistory of the Siriono verb

    Directory of Open Access Journals (Sweden)

    Roland Hemmauer

    2007-08-01

    Full Text Available This paper shows that the verbal morphosyntax of Siriono, which is synchronically highly divergent from that of other Tupi-Guaranian (TG languages, can be derived from the recon structed proto-TG (PTG system. Arguments will be presented to show that the SA=A series of person markers (e.g. PTG 1SG *a- has merged with the SO=O series (e.g. PTG 1SG *če- in the 1st and 2nd plural persons in Siriono. In spite of this partial merger of two series of person markers, morphological ele ments that appeared in PTG between the personal prefix and the stem of transitive verbs have been retained in Siriono with an identical distribution. The partial merger of the SA=A series with the SO=O series is explained by a combination of phonological and syntactic motivations. Additional evidence is drawn from Siriono’s closely related sister language Yuki. Apart from this, the prefix k- that occurs on third-person forms of ‘comitative-causative’ verbs in Siriono has retained a trace of the PTG third-person prefix *o- in spite of the emergence of an innovated third-person prefix e-. These facts are taken as evidence of a PTG origin of the Siriono system.

  2. PIV-based estimation of unsteady loads on a flat plate at high angle of attack using momentum equation approaches

    Science.gov (United States)

    Guissart, A.; Bernal, L. P.; Dimitriadis, G.; Terrapon, V. E.

    2017-05-01

    This work presents, compares and discusses results obtained with two indirect methods for the calculation of aerodynamic forces and pitching moment from 2D Particle Image Velocimetry (PIV) measurements. Both methodologies are based on the formulations of the momentum balance: the integral Navier-Stokes equations and the "flux equation" proposed by Noca et al. (J Fluids Struct 13(5):551-578, 1999), which has been extended to the computation of moments. The indirect methods are applied to spatio-temporal data for different separated flows around a plate with a 16:1 chord-to-thickness ratio. Experimental data are obtained in a water channel for both a plate undergoing a large amplitude imposed pitching motion and a static plate at high angle of attack. In addition to PIV data, direct measurements of aerodynamic loads are carried out to assess the quality of the indirect calculations. It is found that indirect methods are able to compute the mean and the temporal evolution of the loads for two-dimensional flows with a reasonable accuracy. Nonetheless, both methodologies are noise sensitive, and the parameters impacting the computation should thus be chosen carefully. It is also shown that results can be improved through the use of dynamic mode decomposition (DMD) as a pre-processing step.

  3. Collective Influence Algorithm to find influencers via optimal percolation in massively large social media

    Science.gov (United States)

    Morone, Flaviano; Min, Byungjoon; Bo, Lin; Mari, Romain; Makse, Hernán A.

    2016-01-01

    We elaborate on a linear-time implementation of Collective-Influence (CI) algorithm introduced by Morone, Makse, Nature 524, 65 (2015) to find the minimal set of influencers in networks via optimal percolation. The computational complexity of CI is O(N log N) when removing nodes one-by-one, made possible through an appropriate data structure to process CI. We introduce two Belief-Propagation (BP) variants of CI that consider global optimization via message-passing: CI propagation (CIP) and Collective-Immunization-Belief-Propagation algorithm (CIBP) based on optimal immunization. Both identify a slightly smaller fraction of influencers than CI and, remarkably, reproduce the exact analytical optimal percolation threshold obtained in Random Struct. Alg. 21, 397 (2002) for cubic random regular graphs, leaving little room for improvement for random graphs. However, the small augmented performance comes at the expense of increasing running time to O(N2), rendering BP prohibitive for modern-day big-data. For instance, for big-data social networks of 200 million users (e.g., Twitter users sending 500 million tweets/day), CI finds influencers in 2.5 hours on a single CPU, while all BP algorithms (CIP, CIBP and BDP) would take more than 3,000 years to accomplish the same task. PMID:27455878

  4. 2-D Difference in gel electrophoresis combined with Pro-Q Diamond staining: a successful approach for the identification of kinase/phosphatase targets.

    Science.gov (United States)

    Orsatti, Laura; Forte, Eleonora; Tomei, Licia; Caterino, Marianna; Pessi, Antonello; Talamo, Fabio

    2009-07-01

    The protein tyrosine phosphatase PRL-3 is an appealing therapeutic cancer target for its well described involvement in the metastasis progression. Nevertheless, very little is known about PRL-3 role in tumorigenesis. In the attempt to identify the protein target of this phosphatase we have devised a model system based on the use of highly invasive HCT116 colon cancer cells over-expressing PRL-3. We used 2-D difference gel electrophoresis combined with the fluorescence staining Pro-Q Diamond selective for phosphorylated proteins to monitor changes in the phosphorylation status of possible substrates. Proteins whose phosphorylation level was negatively affected by PRL-3 over-expression were identified by MS. Two proteins were found to be significantly dephosphorylated in this condition, the cytoskeletal protein ezrin and elongation factor 2. Ezrin has already been described as having a proactive role in cancer metastasis through control of its phosphorylation status, and the PRL-3-induced modulation of ezrin phosphorylation in HCT116 and human umblical vascular endothelial cells is the subject of a separate paper by Forte et al. [Biochim. Biophys. Acta 2008, 1783, 334-344]. The combination of 2-D difference in gel electrophoresis and Pro-Q Diamond was hence confirmed successful in analyzing changes of protein phosphorylation which enable the identification of kinase/phosphatase targets.

  5. ATP-Binding Cassette Proteins: Towards a Computational View of Mechanism

    Science.gov (United States)

    Liao, Jielou

    2004-03-01

    Many large machine proteins can generate mechanical force and undergo large-scale conformational changes (LSCC) to perform varying biological tasks in living cells by utilizing ATP. Important examples include ATP-binding cassette (ABC) transporters. They are membrane proteins that couple ATP binding and hydrolysis to the translocation of substrates across membranes [1]. To interpret how the mechanical force generated by ATP binding and hydrolysis is propagated, a coarse-grained ATP-dependent harmonic network model (HNM) [2,3] is applied to the ABC protein, BtuCD. This protein machine transports vitamin B12 across membranes. The analysis shows that subunits of the protein move against each other in a concerted manner. The lowest-frequency modes of the BtuCD protein are found to link the functionally critical domains, and are suggested to be responsible for large-scale ATP-coupled conformational changes. [1] K. P. Locher, A. T. Lee and D. C. Rees. Science 296, 1091-1098 (2002). [2] Atilgan, A. R., S. R. Durell, R. L. Jernigan, M. C. Demirel, O. Keskin, and I. Bahar. Biophys. J. 80, 505-515(2002); M. M Tirion, Phys. Rev. Lett. 77, 1905-1908 (1996). [3] J. -L. Liao and D. N. Beratan, 2003, to be published.

  6. Hexokinase 2 from Saccharomyces cerevisiae: regulation of oligomeric structure by in vivo phosphorylation at serine-14.

    Science.gov (United States)

    Behlke, J; Heidrich, K; Naumann, M; Müller, E C; Otto, A; Reuter, R; Kriegel, T

    1998-08-25

    Homodimeric hexokinase 2 from Saccharomyces cerevisiae is known to have two sites of phosphorylation: for serine-14 the modification in vivo increases with glucose exhaustion [Kriegel et al. (1994) Biochemistry 33, 148-152], while for serine-157 it occurs in vitro with ATP in the presence of nonphosphorylateable five-carbon analogues of glucose [Heidrich et al. (1997) Biochemistry 36, 1960-1964]. We show now by site-directed mutagenesis and sedimentation analysis that serine-14 phosphorylation affects the oligomeric state of hexokinase, its substitution by glutamate causing complete dissociation; glutamate exchange for serine-157 does not. Phosphorylation of wild-type hexokinase at serine-14 likewise causes dissociation in vitro. In view of the higher glucose affinity of monomeric hexokinase and the high hexokinase concentration in yeast [Womack, F., and Colowick, S. P. (1978) Arch. Biochem. Biophys. 191, 742-747; Mayes, E. L., Hoggett, J. G., and Kellett, G. L. (1983) Eur. J. Biochem. 133, 127-134], we speculate that the in vivo phosphorylation at serine-14 as transiently occurring in glucose derepression might provide a mechanism to improve glucose utilization from low level and/or that nuclear localization of the monomer might be involved in the signal transduction whereby glucose causes catabolite repression.

  7. Interaction of the alpha-toxin of Staphylococcus aureus with the liposome membrane.

    Science.gov (United States)

    Ikigai, H; Nakae, T

    1987-02-15

    When the liposome membrane is exposed to the alpha-toxin of Staphylococcus aureus, fluorescence of the tryptophan residue(s) of the toxin molecule increases concomitantly with the degree of toxin-hexamer formation (Ikigai, H., and Nakae, T. (1985) Biochem. Biophys. Res. Commun. 130, 175-181). In the present study, the toxin-membrane interaction was distinguished from the hexamer formation by the fluorescence energy transfer from the tryptophan residue(s) of the toxin molecule to the dansylated phosphatidylethanolamine in phosphatidylcholine liposome. Measurement of these two parameters yielded the following results. The effect of the toxin concentration and phospholipid concentration on these two parameters showed first order kinetics. The effect of liposome size on the energy transfer and the fluorescence increment of the tryptophan residue(s) was only detectable in small liposomes. Under moderately acidic or basic conditions, the fluorescence energy transfer always preceded the fluorescence increment of the tryptophan residue(s). The fluorescence increment at 336 nm at temperatures below 20 degrees C showed a latent period, whereas the fluorescence energy transfer did not. These results were thought to indicate that when alpha-toxin damages the target membrane, the molecule interacts with the membrane first, and then undergoes oligomerization within the membrane.

  8. Model averaging in the analysis of leukemia mortality among Japanese A-bomb survivors

    International Nuclear Information System (INIS)

    Richardson, David B.; Cole, Stephen R.

    2012-01-01

    Epidemiological studies often include numerous covariates, with a variety of possible approaches to control for confounding of the association of primary interest, as well as a variety of possible models for the exposure-response association of interest. Walsh and Kaiser (Radiat Environ Biophys 50:21-35, 2011) advocate a weighted averaging of the models, where the weights are a function of overall model goodness of fit and degrees of freedom. They apply this method to analyses of radiation-leukemia mortality associations among Japanese A-bomb survivors. We caution against such an approach, noting that the proposed model averaging approach prioritizes the inclusion of covariates that are strong predictors of the outcome, but which may be irrelevant as confounders of the association of interest, and penalizes adjustment for covariates that are confounders of the association of interest, but may contribute little to overall model goodness of fit. We offer a simple illustration of how this approach can lead to biased results. The proposed model averaging approach may also be suboptimal as way to handle competing model forms for an exposure-response association of interest, given adjustment for the same set of confounders; alternative approaches, such as hierarchical regression, may provide a more useful way to stabilize risk estimates in this setting. (orig.)

  9. Modified spectrophotometer for multi-dimensional circular dichroism/fluorescence data acquisition in titration experiments: application to the pH and guanidine-HCI induced unfolding of apomyoglobin.

    Science.gov (United States)

    Ramsay, G; Ionescu, R; Eftink, M R

    1995-01-01

    In a previous paper (Ramsay and Eftink, Biophys. J. 66:516-523) we reported the development of a modified spectrophotometer that can make nearly simultaneous circular dichroism (CD) and fluorescence measurements. This arrangement allows multiple data sets to be collected during a single experiment, resulting in a saving of time and material, and improved correlation between the different types of measurements. The usefulness of the instrument was shown by thermal melting experiments on several different protein systems. This CD/fluorometer spectrophotometer has been further modified by interfacing with a syringe pump and a pH meter. This arrangement allows ligand, pH, and chemical denaturation titration experiments to be performed while monitoring changes in the sample's CD, absorbance, fluorescence, and light scattering properties. Our data acquisition program also has an ability to check whether the signals have approached equilibrium before the data is recorded. For performing pH titrations we have developed a procedure which uses the signal from a pH meter in a feedback circuit in order to collect data at evenly spaced pH intervals. We demonstrate the use of this instrument with studies of the unfolding of sperm whale apomyoglobin, as induced by acid pH and by the addition of guanidine-HCI. Images FIGURE 2 PMID:8527683

  10. Absence of 60-Hz, 0.1-mT magnetic field-induced changes in oncogene transcription rates or levels in CEM-CM3 cells.

    Science.gov (United States)

    Jahreis, G P; Johnson, P G; Zhao, Y L; Hui, S W

    1998-12-22

    Our objective was to assess the reproducibility of the 60-Hz magnetic field-induced, time-dependent transcription changes of c-fos, c-jun and c-myc oncogenes in CEM-CM3 cells reported by Phillips et al. (Biochim. Biophys. Acta, 1132 (1992) 140-144). Cells were exposed to a 60-Hz magnetic field (MF) at 0.1 mT (rms), generated by a pair of Helmholtz coils energized in a reinforcing (MF) mode, or to a null magnetic field when the coils were energized in a bucking (sham) mode. After MF or sham exposure for 15, 30, 60 or 120 min, nuclei and cytoplasmic RNA were extracted. Transcription rates were measured by a nuclear run-on assay, and values were normalized against either their zero-time exposure values, or against those of the c-G3PDH (housekeeping) gene at the same time points. There was no significant difference, at P=0.05, detected between MF and either sham-exposed or control cells at any time point. Transcript levels of the oncogenes were measured by Northern analysis and normalized as above. No significant difference (P=0.05) in transcript levels between MF and either sham-exposed or control cells was detected.

  11. MTH187 from Methanobacterium thermoautotrophicum has three HEAT-like Repeats

    Energy Technology Data Exchange (ETDEWEB)

    Julien, Olivier; Gignac, Isabelle [Universite Laval, Departement de biochimie et de microbiologie and CREFSIP (Canada); Hutton, Anna [University of Alberta, Institute for Biomolecular Design (Canada); Yee, Adelinda; Arrowsmith, Cheryl H. [University of Toronto, Division of Molecular and Structural Biology, Department of Medical Biophysics, Ontario Cancer Institute (Canada); Gagne, Stephane M. [Universite Laval, Departement de biochimie et de microbiologie and CREFSIP (Canada)], E-mail: sgagne@rsvs.ulaval.ca

    2006-06-15

    With the completion of genome sequencing projects, there are a large number of proteins for which we have little or no functional information. Since protein function is closely related to three-dimensional conformation, structural proteomics is one avenue where the role of proteins with unknown function can be investigated. In the present structural project, the structure of MTH187 has been determined by solution-state NMR spectroscopy. This protein of 12.4 kDa is one of the 424 non-membrane proteins that were cloned and purified for the structural proteomic project of Methanobacterium thermoautotrophicum [Christendat, D., Yee, A., Dharamsi, A., Kluger, Y., Gerstein, M., Arrowsmith, C.H. and Edwards, A.M. (2000) Prog. Biophys. Mol. Biol., 73, 339-345]. Methanobacterium thermoautotrophicum is a thermophilic archaeon that grows optimally at 65 deg. C. A particular characteristic of this microorganism is its ability to generate methane from carbon dioxide and hydrogen [Smith, D.R., Doucette-Stamm, L.A., Deloughery, C., Lee, H., Dubois, J., Aldredge, T., Bashirzadeh, R., Blakely, D., Cook, R., Gilbert, K., Harrison, D., Hoang, L., Keagle, P., Lumm, W., Pothier, B., Qiu, D., Spadafora, R., Vicaire, R., Wang, Y., Wierzbowski, J., Gibson, R., Jiwani, N., Caruso, A., Bush, D., Reeve, J. N. et al. (1997) J. Bacteriol., 179, 7135-7155].

  12. Pattern of phylogenetic diversification of the Cychrini ground beetles in the world as deduced mainly from sequence comparisons of the mitochondrial genes.

    Science.gov (United States)

    Su, Zhi-Hui; Imura, Yûki; Okamoto, Munehiro; Osawa, Syozo

    2004-02-04

    The phylogenetic position of the tribe Cychrini within the subfamily Carabinae (the family Carabidae) was estimated by comparing the nucleotide sequences of the mitochondrial NADH dehydrogenase subunit 5 (ND5) gene and the nuclear 28S ribosomal DNA (rDNA). The phylogenetic trees suggest that the Cychrini would most probably be the oldest line within the Carabinae. Phylogenetic trees were constructed by comparing the mitochondrial cytochrome C oxidase subunit I (COI) gene sequences from 33 species of the Cychrini from various localities that include the whole distribution ranges of the representative species within all the known genera in the world. The trees suggest that the Cychrini members radiated into a number of phylogenetic lineages within a short period, starting about 44 million years ago (MYA). Most of the phylogenetic lineages or sublineages are geographically linked, each consisting of a single or only a few species without scarce morphological differentiation in spite of their long evolutionary histories (silent or near-silent evolution [see Adv. Biophys. 36 (1999) 65; J. Mol. Evol. 53 (2001) 517]). The fact suggests that the geographic isolation per se did not bring about conspicuous morphological differentiation. The phylogenetic lineages of the Cychrini well correspond to the taxonomically defined genera and the subgenera.

  13. Dynamics of exciton relaxation in LH2 antenna probed by multipulse nonlinear spectroscopy.

    Science.gov (United States)

    Novoderezhkin, Vladimir I; Cohen Stuart, Thomas A; van Grondelle, Rienk

    2011-04-28

    We explain the relaxation dynamics in the LH2-B850 antenna as revealed by multipulse pump-dump-probe spectroscopy (Th. A. Cohen Stuart, M. Vengris, V. I. Novoderezhkin, R. J. Cogdell, C. N. Hunter, R. van Grondelle, submitted). The theory of pump-dump-probe response is evaluated using the doorway-window approach in combination with the modified Redfield theory. We demonstrate that a simultaneous fit of linear spectra, pump-probe, and pump-dump-probe kinetics can be obtained at a quantitative level using the disordered exciton model, which is essentially the same as used to model the spectral fluctuations in single LH2 complexes (Novoderezhkin, V.; Rutkauskas, D.; van Grondelle, R. Biophys. J. 2006, 90, 2890). The present studies suggest that the observed relaxation rates are strongly dependent on the realization of the disorder. A big spread of the rates (exceeding 3 orders of magnitude) is correlated with the disorder-induced changes in delocalization length and overlap of the exciton wave functions. We conclude that the bulk kinetics reflect a superposition of many pathways corresponding to different physical limits of energy transfer, varying from sub-20 fs relaxation between delocalized and highly spatially overlapping exciton states to >20 ps jumps between states localized at the opposite sides of the ring.

  14. Cooperation of terminal deoxynucleotidyl transferase with DNA polymerase α in the replication of ultraviolet-irradiated DNA

    International Nuclear Information System (INIS)

    Yoshida, S.; Masaki, S.; Nakamura, H.; Morita, T.

    1981-01-01

    The amount of DNA synthesis in vitro with the ultraviolet-irradiated poly(dT).oligo(rA) template initiators catalysed by DNA polymerase α (Masaki, S. and Yoshida, S., Biochim. Biophys. Acta 521, 74-88) decreased with the dose of ultraviolet-irradiation. The ultraviolet irradiation to the template, however, did not affect the rate of incorporation of incorrect deoxynucleotides into the newly synthesized poly(dA). The addition of terminal deoxynucleotidyl transferase to this system enhanced the DNA synthesis to a level which is comparable to that of the control and it concomitantly increased the incorporation of the mismatched deoxynucleotide into the newly synthesized poly(dA) strands. On the other hand, with an unirradiated template initiator, the misincorporation was only slightly enhanced by the addition of terminal deoxynucleotidyl transferase. The sizes of newly synthesized DNA measured by the sedimentation velocities were found to be smaller with the ultraviolet-irradiated templates but they increased to the control level with the addition of terminal deoxynucleotidyl transferase to the systems. These results suggest that terminal deoxynucleotidyl transferase can help DNA polymerase α to bypass thymine dimers in vitro by the formation of mismatched regions at the positions opposite to pyrimidine dimers on the template. (Auth.)

  15. Nanodevices in nature: Electrochemical aspects

    International Nuclear Information System (INIS)

    Volkov, Alexander G.; Volkova-Gugeshashvili, Maya I.; Brown-McGauley, Courtney L.; Osei, Albert J.

    2007-01-01

    Electrochemical multielectron reactions in photosynthesis and respiration are evaluated by thermodynamic and kinetic analysis. Kharkats and Volkov [Yu.I. Kharkats, A.G. Volkov, Biochim. Biophys. Acta 891 (1987) 56] were the first to present proof that cytochrome c oxidase reduces molecular oxygen by synchronous multielectron mechanism without O 2 - intermediate formation. After this pioneering observation, it became clear that the first step of oxygen reduction is two-electron concerted process. The energy for the H + -pump of cytochrome oxidase is liberated when the third and fourth electrons are added in the last two steps of water formation independent of the reaction pathway. Electrochemical principles govern many biological properties of organisms, such as the generation of electric fields, and the conduction of fast excitation waves. These properties are supported by the function of a variety of natural nanodevices. Ionic channels, as natural nanodevices, control the plasma membrane potential, and the movement of ions across membranes; thereby, regulating various biological functions. Some voltage-gated ion channels work as plasma membrane nanopotentiostats. In plants, excitation waves are possible mechanisms for intercellular and intracellular communication in response to environmental changes. The role of electrified nanointerface of the plasma membrane in signal transduction is discussed as well

  16. Binding properties of Clostridium botulinum type C progenitor toxin to mucins.

    Science.gov (United States)

    Nakamura, Toshio; Takada, Noriko; Tonozuka, Takashi; Sakano, Yoshiyuki; Oguma, Keiji; Nishikawa, Atsushi

    2007-04-01

    It has been reported that Clostridium botulinum type C 16S progenitor toxin (C16S toxin) first binds to the sialic acid on the cell surface of mucin before invading cells [A. Nishikawa, N. Uotsu, H. Arimitsu, J.C. Lee, Y. Miura, Y. Fujinaga, H. Nakada, T. Watanabe, T. Ohyama, Y. Sakano, K. Oguma, The receptor and transporter for internalization of Clostridium botulinum type C progenitor toxin into HT-29 cells, Biochem. Biophys. Res. Commun. 319 (2004) 327-333]. In this study we investigated the binding properties of the C16S toxin to glycoproteins. Although the toxin bound to membrane blotted mucin derived from the bovine submaxillary gland (BSM), which contains a lot of sialyl oligosaccharides, it did not bind to neuraminidase-treated BSM. The binding of the toxin to BSM was inhibited by N-acetylneuraminic acid, N-glycolylneuraminic acid, and sialyl oligosaccharides strongly, but was not inhibited by neutral oligosaccharides. Both sialyl alpha2-3 lactose and sialyl alpha2-6 lactose prevented binding similarly. On the other hand, the toxin also bound well to porcine gastric mucin. In this case, neutral oligosaccharides might play an important role as ligand, since galactose and lactose inhibited binding. These results suggest that the toxin is capable of recognizing a wide variety of oligosaccharide structures.

  17. Cultured Chinese hamster cells undergo apoptosis after exposure to cold but nonfreezing temperatures.

    Science.gov (United States)

    Nagle, W A; Soloff, B L; Moss, A J; Henle, K J

    1990-08-01

    Cultured Chinese hamster V79 fibroblast cells at the transition from logarithmic to stationary growth have been shown to undergo apoptosis (programmed cell death) after cold shock [B. L. Soloff, W. A. Nagle, A. J. Moss, Jr., K. J. Henle, and J. T. Crawford, Biochem. Biophys. Res. Commun. 145, 876-883 (1987)]. In this report, we show that about 95% of the cell population was susceptible to cold-induced apoptosis, and the amount of cell killing was dependent on the duration of hypothermia. Cells treated for 0-90 min at 0 degrees C exhibited an exponential survival curve with a D0 of 32 min; thus, even short exposures to the cold (e.g., 5 min) produced measurable cell killing. The cold-induced injury was not produced by freezing, because similar results were observed at 6 degrees C, and cell killing was not influenced by the cryoprotective agent dimethyl sulfoxide. Cold-induced apoptosis was inhibited by rewarming at 23 degrees C, compared to 37 degrees C, by inhibitors of macromolecular synthesis, such as cycloheximide, and by 0.8 mM zinc sulfate. The results suggest that apoptosis represents a new manifestation of cell injury after brief exposure to 0-6 degrees C hypothermia.

  18. Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor

    International Nuclear Information System (INIS)

    D'Auvergne, Edward J.; Gooley, Paul R.

    2008-01-01

    Finding the dynamics of an entire macromolecule is a complex problem as the model-free parameter values are intricately linked to the Brownian rotational diffusion of the molecule, mathematically through the autocorrelation function of the motion and statistically through model selection. The solution to this problem was formulated using set theory as an element of the universal set U-the union of all model-free spaces (d'Auvergne EJ and Gooley PR (2007) Mol BioSyst 3(7), 483-494). The current procedure commonly used to find the universal solution is to initially estimate the diffusion tensor parameters, to optimise the model-free parameters of numerous models, and then to choose the best model via model selection. The global model is then optimised and the procedure repeated until convergence. In this paper a new methodology is presented which takes a different approach to this diffusion seeded model-free paradigm. Rather than starting with the diffusion tensor this iterative protocol begins by optimising the model-free parameters in the absence of any global model parameters, selecting between all the model-free models, and finally optimising the diffusion tensor. The new model-free optimisation protocol will be validated using synthetic data from Schurr JM et al. (1994) J Magn Reson B 105(3), 211-224 and the relaxation data of the bacteriorhodopsin (1-36)BR fragment from Orekhov VY (1999) J Biomol NMR 14(4), 345-356. To demonstrate the importance of this new procedure the NMR relaxation data of the Olfactory Marker Protein (OMP) of Gitti R et al. (2005) Biochem 44(28), 9673-9679 is reanalysed. The result is that the dynamics for certain secondary structural elements is very different from those originally reported

  19. Evaluación de la actividad antioxidante de extractos de Palicourea guianensis (Rubiaceae

    Directory of Open Access Journals (Sweden)

    Lina Marcela Giraldo Vásquez

    Full Text Available Introducción: la proliferación de radicales libres en el cuerpo humano induce daños oxidativos a las biomoléculas que provocan daños a nivel celular y generan diversas anomalías en el organismo, como arterosclerosis, envejecimiento y cáncer. Actualmente, la búsqueda por moléculas con características antioxidantes es cada vez mayor, donde las plantas representan una de las principales fuentes de compuestos. Objetivo: determinar la actividad antioxidante y el contenido de fenoles de los extractos de diferentes polaridades de la parte aérea de la especie Palicourea guianensis (Rubiaceae. Métodos: para la evaluación de la actividad biológica, se calcularon los valores de concentración media inhibitoria (IC50 de los extractos más activos mediante los métodos de captura de electrones DPPH (2,2-difenil-1-picrilhidracilo y ABTS (ácido 2,2'azinobis-(3-etilbenzotiazolina-6-sulfónico. Adicionalmente, se determinó la concentración de fenoles totales presentes en los extractos a través del método de Folin-Ciocalteu. Resultados: los extractos en acetato de etilo (PgAEF y en agua (PgAF presentaron mayor actividad antioxidante con valores de IC50 de 5 207 y 3 912 mg/L respectivamente. Asimismo, se observó una relación directamente proporcional entre la concentración de fenoles totales presentes en los extractos y la actividad antioxidante exhibida. Conclusiones: las especies de la familia Rubiaceae, especialmente P. guianensis, son una fuente promisoria e importante de metabolitos secundarios con capacidad antioxidante, por lo cual se requieren de mayores estudios que permitan identificar dichas sustancias e integrarlas a programas de terapia antioxidante en el área de la salud.

  20. Tillandsia recurvata L. (Bromeliaceae: aspectos farmacognósticos

    Directory of Open Access Journals (Sweden)

    Alex Lucena de Vasconcelos

    2013-01-01

    Full Text Available A cobertura superior das florestas tropicais, formada pelas copas das árvores, constitui um ambiente de extrema diversidade vegetal. Contribuindo com a grande riqueza dessas florestas encontram-se as espécies botânicas epífitas, cuja importância pode ser observada do ponto de vista ecológico, faunístico, etnobotânico e até mesmo farmacológico. Dentre as espécies adaptadas à vida epifítica podemos citar as bromeliáceas, que compõem uma das famílias mais representativas dessa flora com elevada variabilidade genética. Tillandsia recurvata é uma espécie epífita cosmopolita, nativa, adaptada a habitats áridos, utilizada para o tratamento de diversas doenças, mas pouco se tem publicado a respeito das comprovações científicas de suas propriedades. O presente trabalho revisa os aspectos etnofarmacológicos, atividades biológicas e compostos químicos relacionados à espécie em questão, pertencente à Bromeliaceae. A partir do levantamento de dados realizado, observa-se que esta se trata de uma espécie de conhecido uso popular no tratamento de diferentes distúrbios, com alguns estudos farmacológicos que comprovam suas propriedades terapêuticas. Do ponto de vista químico observa-se a presença de terpenos, flavonoides e derivados cinâmicos em sua constituição, em que alguns compostos isolados ilustram a potencialidade desta espécie como fonte de biomoléculas de interesse. Todos estes aspectos considerados nesta revisão contribuem para o conhecimento a respeito da importância biológica e o potencial terapêutico acerca dos metabólitos desta promissora espécie.

  1. Country report: Cuba. Local Production of {sup 90}Y And {sup 188}Re Radionuclides and Development of Radiopharmaceuticals for Therapy

    Energy Technology Data Exchange (ETDEWEB)

    Xiques, Abmel; Hernández, Ignacio; Leyva, René; Pérez, Marylaine; Alonso, Luis Michel; Zamora, Minelys [Centro de Isotopos (CENTIS) (Cuba)

    2010-07-01

    During the first period of this CRP we could test an efficient and reliable generator system based on ion-chromatography to obtain {sup 90}Y from its parent radionuclide {sup 90}Sr. This production scheme for {sup 90}Y was outlined in the previous CRP related with the development of generator technologies. Quality parameters such as trace metals that can potentially interfere in the labeling of biomoléculas, {sup 90}Y recovery, {sup 90}Sr/{sup 90}Y ratio and radiation dose to bed matrix were evaluated. The results showed that high recovery and radionuclidic purity could be obtained for {sup 90}Y during its repeated separation from the {sup 90}Sr cow. No replacement or treatment of the cow were necessary and low waste generation and {sup 90}Sr losses less that 0.1% after each run were also observed during the present study. A Fab’ fragment was enzimatically produced and purified from the monoclonal antibody h-R3 (Nimotuzumab®). The fragment and the parent antibody were successfully conjugated with DOTA and labeled with {sup 90}Y. The radioinmunoconjugate thus obtained also exhibited a good 24 h in-vitro stability in an excess of DTPA. A {sup 90}Y radiocoloid was prepared in a cromic phosphate particle for radiosynoviorthesis with promising results in animal models. Two alumina based {sup 188}W/{sup 188}Re generators were prepared and their eluates were used in the labeling of hR3-DOTA conjugates. Quality control and in vivo evaluation in comparison with {sup 99m}Tc-hR3 showed very good results and similar pattern of distribution and pharmacokinetic and will be used in clinical trials for cancer patients. (author)

  2. Relación entre indicadores clínicos del espermograma y variables redox en infertilidad masculina

    Directory of Open Access Journals (Sweden)

    Akel Mallok

    2011-09-01

    Full Text Available En conjunción a los factores convencionales que originan la infertilidad se ha identificado el estrés oxidativo, asociado como el factor causal que ocasiona daño al espermatozoide, pero los métodos para su determinación a nivel clínico no han sido desarrollados. El presente estudio tuvo como objetivo evaluar la existencia de una correlación entre indicadores globales del estado redox a muestras de suero sanguíneo, lisado de eritrocitos, plasma seminal y lisado de espermatozoides con la finalidad de identificar posibles biomarcadores. Se analizaron muestras que procedían de 31 pacientes con diagnóstico de infertilidad masculina y 30 voluntarios aparentemente sanos. Se confirmó que en todas las muestras analizadas los indicadores de daño a biomoléculas se encontraban significativamente (p< 0,01 incrementados en los pacientes cuando se compararon con el grupo control. Los indicadores de daño se acompañaron con bajos niveles de la capacidad antioxidante total en la fase lipídica y un desbalance en la actividad de las enzimas catalasa y superóxido dismutasa (relación catalasa/superóxido dismutasa 10 veces superior en plasma seminal de pacientes con respecto al valor control. El incremento de indicadores como malonindialdehído y organoperóxidos totales medidos en plasma seminal se correlacionaron con el incremento de indicadores de hipofunción espermática como movilidad y características morfológicas. El comportamiento de las variables redox en el plasma seminal resultó de gran valor diagnóstico y se propone para que sea usado en el seguimiento de intervenciones nutricionales o farmacológicas a estos pacientes.

  3. Accessing ns-μs side chain dynamics in ubiquitin with methyl RDCs

    International Nuclear Information System (INIS)

    Fares, Christophe; Lakomek, Nils-Alexander; Walter, Korvin F. A.; Frank, Benedikt T. C.; Meiler, Jens; Becker, Stefan; Griesinger, Christian

    2009-01-01

    This study presents the first application of the model-free analysis (MFA) (Meiler in J Am Chem Soc 123:6098-6107, 2001; Lakomek in J Biomol NMR 34:101-115, 2006) to methyl group RDCs measured in 13 different alignment media in order to describe their supra-τ c dynamics in ubiquitin. Our results indicate that methyl groups vary from rigid to very mobile with good correlation to residue type, distance to backbone and solvent exposure, and that considerable additional dynamics are effective at rates slower than the correlation time τ c . In fact, the average amplitude of motion expressed in terms of order parameters S 2 associated with the supra-τ c window brings evidence to the existence of fluctuations contributing as much additional mobility as those already present in the faster ps-ns time scale measured from relaxation data. Comparison to previous results on ubiquitin demonstrates that the RDC-derived order parameters are dominated both by rotameric interconversions and faster libration-type motions around equilibrium positions. They match best with those derived from a combined J-coupling and residual dipolar coupling approach (Chou in J Am Chem Soc 125:8959-8966, 2003) taking backbone motion into account. In order to appreciate the dynamic scale of side chains over the entire protein, the methyl group order parameters are compared to existing dynamic ensembles of ubiquitin. Of those recently published, the broadest one, namely the EROS ensemble (Lange in Science 320:1471-1475, 2008), fits the collection of methyl group order parameters presented here best. Last, we used the MFA-derived averaged spherical harmonics to perform highly-parameterized rotameric searches of the side chains conformation and find expanded rotamer distributions with excellent fit to our data. These rotamer distributions suggest the presence of concerted motions along the side chains

  4. Vertical Object Layout and Compression for Fixed Heaps

    Science.gov (United States)

    Titzer, Ben L.; Palsberg, Jens

    Research into embedded sensor networks has placed increased focus on the problem of developing reliable and flexible software for microcontroller-class devices. Languages such as nesC [10] and Virgil [20] have brought higher-level programming idioms to this lowest layer of software, thereby adding expressiveness. Both languages are marked by the absence of dynamic memory allocation, which removes the need for a runtime system to manage memory. While nesC offers code modules with statically allocated fields, arrays and structs, Virgil allows the application to allocate and initialize arbitrary objects during compilation, producing a fixed object heap for runtime. This paper explores techniques for compressing fixed object heaps with the goal of reducing the RAM footprint of a program. We explore table-based compression and introduce a novel form of object layout called vertical object layout. We provide experimental results that measure the impact on RAM size, code size, and execution time for a set of Virgil programs. Our results show that compressed vertical layout has better execution time and code size than table-based compression while achieving more than 20% heap reduction on 6 of 12 benchmark programs and 2-17% heap reduction on the remaining 6. We also present a formalization of vertical object layout and prove tight relationships between three styles of object layout.

  5. Major facilitator superfamily porters, LacY, FucP and XylE of Escherichia coli appear to have evolved positionally dissimilar catalytic residues without rearrangement of 3-TMS repeat units.

    Science.gov (United States)

    Västermark, Ake; Lunt, Bryan; Saier, Milton

    2014-01-01

    Based on alleged functional residue correspondences between FucP and LacY, a recent study has resulted in a proposed model of 3-TMS unit rearrangements [Madej et al.: Proc Natl Acad Sci USA 2013;110:5870-5874]. We rebut this theory, using 7 different lines of evidence. Our observations suggest that these two transporters are homologous throughout their lengths, having evolved from a common ancestor without repeat unit rearrangements. We exploit the availability of the high-resolution XylE crystal structures in multiple conformations including the inward-facing state to render possible direct comparisons with LacY. Based on a Δdistance map, we confirm the conclusion of Quistgaard et al. [Nat Struct Mol Biol 2013;20:766-768] that the N-terminal 6 TMS halves of these transporters are internally less mobile than the second halves during the conformational transition from the outward occluded state to the inward occluded state and inward occluded state to inward open state. These observations, together with those of Madej et al. [2013], lead to the suggestion that functionally equivalent catalytic residues involved in substrate binding and transport catalysis have evolved in dissimilar positions, but apparently often in similar positions in the putative 3-TMS repeat units, from a single structural scaffold without intragenic rearrangement. © 2014 S. Karger AG, Basel.

  6. From Medieval Philosophy to the Virtual Library: a descriptive framework for scientific knowledge and documentation as basis for document retrieval

    Directory of Open Access Journals (Sweden)

    Frances Morrissey

    2001-11-01

    Full Text Available This paper examines the conceptual basis of document retrieval systems for the Virtual Library in science and technology. It does so through analysing some cognitive models for scientific knowledge, drawing on philosophy, sociology and linguistics. It is important to consider improvements in search/ retrieval functionalities for scientific documents because knowledge creation and transfer are integral to the functioning of scientific communities, and on a larger scale, science and technology are central to the knowledge economy. This paper proposes four new and innovative understandings. Firstly, it is proposed that formal scientific communication constitutes the documentation and dissemination of concepts, and that conceptualism is a useful philosophical basis for study. Second, it is proposed that the scientific document is a dyadic con-struct, being both the physical manifestation as an encoded medium, and also being the associated knowledge, or intangible ideation, that is carried within the document. Third, it is shown that major philosophers of science divide science into three main activities, dealing with data, derived or inferred laws, and the axioms or the paradigm. Fourth, it is demonstrated that the data, information and conceptual frameworks carried by a scientific document, as different levels of signification or semiotic systems, can each be characterised in ways assisting in search and retrieval functionalities for the Virtual Library.

  7. Etude structurale et vibrationnelle d'un nouveau composé complexe de cobalt: [Co(imidazole)4Cl]Cl.

    Science.gov (United States)

    Derbel, Amira; Mhiri, Tahar; Graia, Mohsen

    2015-10-01

    In the title complex, chlorido-tetra-kis-(1H-imidazole-κN (3))cobalt(II) chloride, [CoCl(C3H4N2)4]Cl, the Co(II) cation has a distorted square-pyramidal coordination environment. It is coordinated by four N atoms of four imidazole (Im) groups in the basal plane, and by a Cl atom in the apical position. It is isostructural with [Cu(Im)4Cl]Cl [Morzyk-Ociepa et al. (2012 ▸). J. Mol. Struct. 1028, 49-56] and [Cu(Im)4Br]Br [Hossaini Sadr et al. (2004 ▸). Acta Cryst. E60, m1324-m1326]. In the crystal, the [CoCl(C3H4N2)4](+) cations and Cl(-) anions are linked via N-H⋯Cl hydrogen bonds, forming layers parallel to (010). These layers are linked via C-H⋯Cl hydrogen bonds and C-H⋯π and π-π [inter-centroid distance = 3.794 (2) Å] inter-actions, forming a three-dimensional framework. The IR spectrum shows vibrational bands typical for imidazol groups. The monoclinic unit cell of the title compound emulates an ortho-rhom-bic cell as its β angle is close to 90°. The crystal is twinned, with the refined ratio of twin components being 0.569 (1):0.431 (1).

  8. On the Elastic behavior of Sodium Borate Glasses

    Science.gov (United States)

    Vignarooban, K.; Boolchand, P.; Kerner, R.; Micoulaut, M.

    2010-03-01

    Alkali Borates are industrial glasses and their physical properties are of general interest. We have made a special effort to synthesize dry (Na2O)x(B2O3)100-x glasses over a wide composition range, 0 modulated-DSC, Raman scattering, FTIR, and molar volume experiments. The enthalpy of relaxation at Tg shows a global minimum in the 20% < x < 40% range, which we identify with the rigid but stress-free Intermediate Phase (IP). The Boroxyl ring vibrational mode near 808 cm-1 in B2O3, steadily softens by about 4 cm-1 as the soda content increases to about 20%. A vibrational mode of mixed ringsfootnotetextKamitsos et al., Jour. Mol. Struct 247, 1 (1996). (containing 3-fold and 4-fold B) is also observed near 775 cm-1 at low x, and it also steadily softens by nearly 10 cm-1 as x increases in the 20% < x < 40% soda range (IP). We are examining the underlying optical elasticity power-laws to ascertain the nature of the elastic phases. IR reflectance experiments provide the 4-fold coordinated B fraction to increase from 0.17 near x = 20% to 0.44 near x = 40% in broad agreement with NMR results. Evolution of physical properties of these glasses with soda content will be reviewed.

  9. Assessing the influence of project management on quality during the early phases of construction projects

    Directory of Open Access Journals (Sweden)

    Ljevo Žanesa

    2018-12-01

    Full Text Available Although the quality of a process affects the quality of the end product, there is currently an insignif­icant amount of knowledge about the quality of project management (PM processes that directly affect the quality of the delivered product (constructed building. This study presents a proposal for modeling the impact of the quality of the PM process on the quality of the con­structed building. The quality of the PM process is rep­resented by the main quality factors and product quality indicators. It presents the results of the interviews that were conducted and study cases that were analyzed in Bosnia and Herzegovina with a variety of project partici­pants (with different managerial perspectives in terms of the indicators of quality of the delivered product. All par­ticipants, regardless of managerial perspective, believe that the most important indicator of the quality of prod­ucts for each phase of the project is “customer satisfaction in the end phase”, the measurement of which is different for each project phase that is presented. The results of the factor analysis of the definition and the planning phases show that 11 variables, namely, the quality factors of the PM process, can be grouped into three new factors, which is described as 66.61% (77.046% of the basic set of vari­ables.

  10. Nondestructive Damage Assessment of Composite Structures Based on Wavelet Analysis of Modal Curvatures: State-of-the-Art Review and Description of Wavelet-Based Damage Assessment Benchmark

    Directory of Open Access Journals (Sweden)

    Andrzej Katunin

    2015-01-01

    Full Text Available The application of composite structures as elements of machines and vehicles working under various operational conditions causes degradation and occurrence of damage. Considering that composites are often used for responsible elements, for example, parts of aircrafts and other vehicles, it is extremely important to maintain them properly and detect, localize, and identify the damage occurring during their operation in possible early stage of its development. From a great variety of nondestructive testing methods developed to date, the vibration-based methods seem to be ones of the least expensive and simultaneously effective with appropriate processing of measurement data. Over the last decades a great popularity of vibration-based structural testing has been gained by wavelet analysis due to its high sensitivity to a damage. This paper presents an overview of results of numerous researchers working in the area of vibration-based damage assessment supported by the wavelet analysis and the detailed description of the Wavelet-based Structural Damage Assessment (WavStructDamAs Benchmark, which summarizes the author’s 5-year research in this area. The benchmark covers example problems of damage identification in various composite structures with various damage types using numerous wavelet transforms and supporting tools. The benchmark is openly available and allows performing the analysis on the example problems as well as on its own problems using available analysis tools.

  11. Fabrication of a polyvinylidene difluoride fiber with a metal core and its application as directional air flow sensor

    Science.gov (United States)

    Bian, Yixiang; Liu, Rongrong; Hui, Shen

    2016-09-01

    We fabricated a sensitive air flow detector that mimic the sensing mechanism found at the tail of some insects. [see Y. Yang, A. Klein, H. Bleckmann and C. Liu, Appl. Phys. Lett. 99(2) (2011); J. J. Heys, T. Gedeon, B. C. Knott and Y. Kim, J. Biomech. 41(5), 977 (2008); J. Tao and X. Yu, Smart Mat. Struct. 21(11) (2012)]. Our bionic airflow sensor uses a polyvinylidene difluoride (PVDF) microfiber with a molybdenum core which we produced with the hot extrusion tensile method. The surface of the fiber is partially coated with conductive silver adhesive that serve as surface electrodes. A third electrode, the metal core is used to polarize polyvinylidene difluoride (PVDF) under the surface electrodes. The cantilever beam structure of the prepared symmetric electrodes of metal core piezoelectric fiber (SMPF) is used as the artificial hair airflow sensor. The surface electrodes are used to measure output voltage. Our theoretical and experimental results show that the SMPF responds fast to air flow changes, the output charge has an exponential correlation with airflow velocity and a cosine relation with the direction of airflow. Our bionic airflow sensor with directional sensing ability can also measure air flow amplitude. [see H. Droogendijk, R. G. P. Sanders and G. J. M. Krijnen, New J. Phys. 15 (2013)]. By using two surface electrodes, our sensing circuit further improves sensitivity.

  12. 3dRPC: a web server for 3D RNA-protein structure prediction.

    Science.gov (United States)

    Huang, Yangyu; Li, Haotian; Xiao, Yi

    2018-04-01

    RNA-protein interactions occur in many biological processes. To understand the mechanism of these interactions one needs to know three-dimensional (3D) structures of RNA-protein complexes. 3dRPC is an algorithm for prediction of 3D RNA-protein complex structures and consists of a docking algorithm RPDOCK and a scoring function 3dRPC-Score. RPDOCK is used to sample possible complex conformations of an RNA and a protein by calculating the geometric and electrostatic complementarities and stacking interactions at the RNA-protein interface according to the features of atom packing of the interface. 3dRPC-Score is a knowledge-based potential that uses the conformations of nucleotide-amino-acid pairs as statistical variables and that is used to choose the near-native complex-conformations obtained from the docking method above. Recently, we built a web server for 3dRPC. The users can easily use 3dRPC without installing it locally. RNA and protein structures in PDB (Protein Data Bank) format are the only needed input files. It can also incorporate the information of interface residues or residue-pairs obtained from experiments or theoretical predictions to improve the prediction. The address of 3dRPC web server is http://biophy.hust.edu.cn/3dRPC. yxiao@hust.edu.cn.

  13. Inclusion of Moloney murine leukemia virus elements upstream of the transgene cassette in an E1-deleted adenovirus leads to an unusual genomic integration in epithelial cells

    International Nuclear Information System (INIS)

    Zheng Changyu; O'Connell, Brian C.; Baum, Bruce J.

    2003-01-01

    Classically, the 5' and 3' long terminal repeats (LTRs) are considered necessary but not sufficient for retroviral integration. Recently, we reported that inclusion of these and additional elements from Moloney murine leukemia virus (MoMLV) facilitated transgene integration, without retroviral integrase, when placed in an adenoviral context (AdLTR-luc vector) (Nat. Biotech. 18 (2000), 176; Biochem. Biophys. Res. Commun. 300 (2003), 115). To help understand this nonhomologous DNA recombination event, we constructed another vector, AdELP-luc, with 2.7 kb of MoMLV elements identically placed into an E1-deleted adenovirus type 5 backbone upstream of a luciferase cDNA reporter gene. Unlike AdLTR-luc, no MoMLV elements were placed downstream of the expression cassette. AdELP-luc readily infected epithelial cells in vitro. Southern hybridizations with DNA from cloned cells showed that disruption of the MoMLV sequences occurred. One cell clone, grown in vitro without any special selection medium for 9 months, exhibited stable vector integration and luciferase activity. Importantly, both Southern hybridization and FISH analyses showed that in addition to the MoMLV elements and expression cassette, substantial adenoviral sequence downstream of the luciferase cDNA was genomically integrated. These results suggest that the 2.7 kb of MoMLV sequence included in AdELP-luc have cis-acting functions and mediates an unusual integration event

  14. Atypical rapid progression of osteoarticular amyloidosis involving the hip in a patient on hemodialysis using polyacrylonitrile membranes

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Kenneth S. [University of Wisconsin School of Medicine and Public Health, Department of Radiology, University of Wisconsin Hospital and Clinics, Madison, WI (United States); Holsbeeck, Marnix T. van [Wayne State School of Medicine, Department of Radiology, Henry Ford Hospital, Detroit, MI (United States); Abbud, Alexander [Wayne State School of Medicine, Department of Pathology, Henry Ford Hospital, Detroit, MI (United States)

    2010-01-15

    Amyloidosis related to dialysis is a well-known complication affecting many organ systems, in particular the musculoskeletal system. In 1985 Shirahama et al. (Biochem Biophys Res Commun 53:705-709, 1985) identified beta-2 microglobulin (MG) as the offending constituent by using protein purification techniques. Amyloidosis has been increasing in prevalence because of longer life spans and increased chronic medical conditions such as end-stage renal disease. When dialysis-related amyloidosis involves the musculoskeletal system, it affects the shoulder girdle, the so called shoulder pad sign, the wrist, hip, knee, and spine (Resnick, Diagnosis of bone and joint disorders, 4th edn., pp. 2054-2058 and 2176-2183, 2002). Other osteoarticular manifestations of amyloidosis include osteoporosis, lytic lesions, and pathologic fractures. It has been well documented that the prevalence of amyloid is dependent on duration of dialysis - over 90% in patients on dialysis for over 7 years (Jadoul, Nephrol Dial Transplant 13:61-64, 1998). However, a recent changeover to high-flux membranes used in hemofiltration has been reported to delay its onset (Campistol et al., Contrib Nephrol 125:76-85, 1999). We report on the radiographic, nuclear medicine, and computed tomography (CT) findings of osteoarticular amyloidosis involving the hip, and sequence its atypical rapid onset. The imaging, histopathological findings, and differential diagnosis are discussed. (orig.)

  15. Co-operation of the transcription factor hepatocyte nuclear factor-4 with Sp1 or Sp3 leads to transcriptional activation of the human haem oxygenase-1 gene promoter in a hepatoma cell line.

    Science.gov (United States)

    Takahashi, Shigeru; Matsuura, Naomi; Kurokawa, Takako; Takahashi, Yuji; Miura, Takashi

    2002-11-01

    We reported previously that the 5'-flanking region (nucleotides -1976 to -1655) of the human haem oxygenase-1 ( hHO-1 ) gene enhances hHO-1 promoter activity in human hepatoma HepG2 cells, but not in HeLa cells [Takahashi, Takahashi, Ito, Nagano, Shibahara and Miura (1999) Biochim. Biophys. Acta 1447, 231-235]. To define more precisely the regulatory elements involved, in the present study we have functionally dissected this region and localized the enhancer to a 50 bp fragment (-1793 to -1744). Site-direct mutagenesis analysis revealed that two regions were responsible for this enhancer activity, i.e. a hepatocyte nuclear factor-4 (HNF-4) homologous region and a GC box motif homologous region. Mutation in either region alone moderately decreased enhancer activity. However, mutations in both regions reduced promoter activity to the basal level. Electrophoretic mobility-shift assays demonstrated that the P5-2 fragment (-1793 to -1744) interacted with at least two nuclear factors, i.e. HNF-4 and Sp1/Sp3. Co-transfection experiments using Drosophila SL2 cells revealed that HNF-4 and Sp1/Sp3 synergistically stimulated the enhancer activity of the P5-2 fragment. These results indicate that co-operation of HNF-4 with Sp1 or Sp3 leads to the activation of hHO-1 gene expression in hepatoma cells.

  16. Iron induction of ferritin synthesis in soybean cell suspensions.

    Science.gov (United States)

    Proudhon, D; Briat, J F; Lescure, A M

    1989-06-01

    In animal cells specialized for iron storage, iron-induced accumulation of ferritin is known to result from a shift of stored mRNA from the ribonucleoprotein fraction to polysomes. Previous reports with bean leaves suggested that in plants iron induction of ferritin synthesis would result from a regulation at the transcriptional level (F van der Mark, F Bienfait, H van der Ende [1983] Biochem Biophys Res Commun 115:463-469). Soybean (Glycine max, cv Mandarin) cell suspension cultures have been used here to support these findings. Ferritin induction is obtained by addition of Fe-citrate to the culture medium. A good correlation is found between cellular iron content and the amount of ferritin accumulation. This protein accumulation corresponds to an increase of in vitro translatable ferritin mRNA. Addition of 4 micrograms actinomycin D per milliliter to the cultures inhibits completely in vivo RNA synthesis, whereas protein synthesis was poorly affected, at least for 24 hours. During the same time, this concentration of actinomycin D strongly inhibits the iron-induced synthesis of ferritin. These results show that in soybean cell cultures, the mechanism of regulation of ferritin synthesis in response to iron does not result from recruitment of preexisting mRNA. They confirm that in plant systems, ferritin synthesis results from increased transcription of the corresponding genes.

  17. Modulation of the transducer function of Na+,K+-ATPase: new mechanism of heart remodeling.

    Science.gov (United States)

    Lopatina, Ekaterina V; Kipenko, Anna V; Pasatetskaya, Natalia A; Penniyaynen, Valentina A; Krylov, Boris V

    2016-10-01

    Endogenous digitalis-like factors were found in the mammalian and human blood. It was the starting point for the elucidation of the new non-pumping function of the Na + ,K + -ATPase. It was previously well known that Na + ,K + -ATPase is a pharmacological target receptor for cardiac glycosides (J.C. Skou. 1957. Biochim. Biophys. Acta, 23: 394-401). We have investigated the trophotropic effects of such agents as ouabain, epinephrine, norepinephrine, atenolol, and comenic acid using the organotypic tissue culture combined with the reconstruction of optical cross sections and confocal microscopy. It was shown that the growth zone of organotypic culture forms a multidimensional structure. Our results indicate that the cardiac glycoside ouabain applied in endogenous concentrations (10 -8 , 10 -10 mol/L) can modulate transducer function of Na + ,K + -ATPase and control the cell growth and proliferation. It was also shown that Src-kinase is involved in "endogenous" ouabain activated intracellular pathways as a series unit. Epinephrine (10 -9 -10 -14 mol/L) and comenic acid (10 -6 -10 -10 mol/L) were demonstrated to modulate the growth of 10- to 12-day-old chicken embryo cardiac tissue explants in a dose-dependent manner. Epinephrine and comenic acid regulate growth and proliferation of the cardiac tissue via receptor-mediated modulation Na + ,K + -ATPase as a signal transducer. The trophotropic effects of the investigated agents specifically control the heart remodeling phenomenon.

  18. Transepithelial transport of flavanone in intestinal Caco-2 cell monolayers

    International Nuclear Information System (INIS)

    Kobayashi, Shoko; Konishi, Yutaka

    2008-01-01

    Our recent study [S. Kobayashi, S. Tanabe, M. Sugiyama, Y. Konishi, Transepithelial transport of hesperetin and hesperidin in intestinal Caco-2 cell monolayers, Biochim. Biophys. Acta, 1778 (2008) 33-41] shows that the mechanism of absorption of hesperetin involves both proton-coupled active transport and transcellular passive diffusion. Here, as well as analyzing the cell permeability of hesperetin, we also study the transport of other flavanones, naringenin and eriodictyol, using Caco-2 cell monolayers. Similar to hesperetin mentioned, naringenin and eriodictyol showed proton-coupled polarized transport in apical-to-basolateral direction in non-saturable manner, constant permeation in the apical-to-basolateral direction (J ap→bl ) irrespective of the transepithelial electrical resistance (TER), and preferable distribution into the basolateral side after apical loading in the presence of a proton gradient. Furthermore, the proton-coupled J ap→bl of hesperetin, naringenin and eriodictyol, were inhibited by substrates of the monocarboxylic acid transporter (MCT), such as benzoic acid, but not by ferulic acid. In contrast, both benzoic and ferulic acids have no stimulatory effect on J ap→bl of each flavanone by trans-stimulation analysis. These results indicates that proton-driven active transport is commonly participated in the absorption of flavanone in general, and that its transport is presumed to be unique other than MCT-mediated transport for absorption of phenolic acids (PAs), sodium-dependent MCT (SMCT) nor anion exchanger-mediated transport

  19. Sensitivity of Rabbit Ventricular Action Potential and Ca2+ Dynamics to Small Variations in Membrane Currents and Ion Diffusion Coefficients

    Directory of Open Access Journals (Sweden)

    Yuan Hung Lo

    2013-01-01

    Full Text Available Little is known about how small variations in ionic currents and Ca2+ and Na+ diffusion coefficients impact action potential and Ca2+ dynamics in rabbit ventricular myocytes. We applied sensitivity analysis to quantify the sensitivity of Shannon et al. model (Biophys. J., 2004 to 5%–10% changes in currents conductance, channels distribution, and ion diffusion in rabbit ventricular cells. We found that action potential duration and Ca2+ peaks are highly sensitive to 10% increase in L-type Ca2+ current; moderately influenced by 10% increase in Na+-Ca2+ exchanger, Na+-K+ pump, rapid delayed and slow transient outward K+ currents, and Cl− background current; insensitive to 10% increases in all other ionic currents and sarcoplasmic reticulum Ca2+ fluxes. Cell electrical activity is strongly affected by 5% shift of L-type Ca2+ channels and Na+-Ca2+ exchanger in between junctional and submembrane spaces while Ca2+-activated Cl−-channel redistribution has the modest effect. Small changes in submembrane and cytosolic diffusion coefficients for Ca2+, but not in Na+ transfer, may alter notably myocyte contraction. Our studies highlight the need for more precise measurements and further extending and testing of the Shannon et al. model. Our results demonstrate usefulness of sensitivity analysis to identify specific knowledge gaps and controversies related to ventricular cell electrophysiology and Ca2+ signaling.

  20. Recycling Frank: Spontaneous emergence of homochirality in noncatalytic systems

    Science.gov (United States)

    Plasson, Raphaël; Bersini, Hugues; Commeyras, Auguste

    2004-01-01

    In this work, we introduce a prebiotically relevant protometabolic pattern corresponding to an engine of deracemization by using an external energy source. The spontaneous formation of a nonracemic mixture of chiral compounds can be observed in out-of-equilibrium systems via a symmetry-breaking phenomenon. This observation is possible thanks to chirally selective autocatalytic reactions (Frank's model) [Frank, F. C. (1953) Biochim. Biophys. Acta 11, 459–463]. We show that the use of a Frank-like model in a recycled system composed of reversible chemical reactions, rather than the classical irreversible system, allows for the emergence of a synergetic autoinduction from simple reactions, without any autocatalytic or even catalytic reaction. This model is described as a theoretical framework, based on the stereoselective reactivity of preexisting chiral monomeric building blocks (polymerization, epimerization, and depolymerization) maintained out of equilibrium by a continuous energy income, via an activation reaction. It permits the self-conversion of all monomeric subunits into a single chiral configuration. Real prebiotic systems of amino acid derivatives can be described on this basis. They are shown to be able to spontaneously reach a stable nonracemic state in a few centuries. In such systems, the presence of epimerization reactions is no more destructive, but in contrast is the central driving force of the unstabilization of the racemic state. PMID:15548617

  1. Immunochemical analysis of Micrococcus lysodeikticus (luteus) F1-ATPase and its subunits.

    Science.gov (United States)

    Urban, C; Salton, M R

    1983-08-31

    The F1-ATPase from Micrococcus lysodeikticus has been purified to 95% protein homogeneity in this laboratory and as all other bacterial F1S, possesses five distinct subunits with molecular weights ranging from 60 000 to 10 000 (Huberman, M. and Salton, M.R.J. (1979) Biochim. Biophys. Acta 547, 230-240). In this communication, we demonstrate the immunochemical reactivities of antibodies to native and SDS-dissociated subunits with the native and dissociated F1-ATPase and show that: (1) the antibodies generated to the native or SDS-dissociated subunits react with the native molecule; (2) all of the subunits comprising the F1 are antigenically unique as determined by crossed immunoelectrophoresis and the Ouchterlony double-diffusion techniques; (3) antibodies to the SDS-denatured individual delta- and epsilon-subunits can be used to destabilize the interaction of these specific subunits with the rest of the native F1; and (4) all subunit antibodies as well as anti-native F1 were found to inhibit ATPase activity to varying degrees, the strongest inhibition being seen with antibodies to the total F1 and anti-alpha- and anti-beta-subunit antibodies. The interaction of specific subunit antibodies may provide a new and novel way to study further and characterize the catalytic portions of F1-ATPases and in general may offer an additional method for the examination of multimeric proteins.

  2. Développement d'une stratégie d'adressage sur or par chimie "click" électro-catalysée : application à la détection sans marquage de biomolécules

    OpenAIRE

    Ripert , Micaël

    2013-01-01

    This production of microsystem for label-free multi detection of biomolecules is fundamental for the realization of rapid tests dedicated to laboratory diagnosis. A viable method is requires to both address capture probes and to be associates with a sensitive analysis on multiplexed platform. In this study, the method chosen for detection on electrode is cyclic voltammetry, and ferrocene was used to modify stem-loop oligonucleotides. A strategy was developed for the electroadressing of probes...

  3. Using support vector machine to predict beta- and gamma-turns in proteins.

    Science.gov (United States)

    Hu, Xiuzhen; Li, Qianzhong

    2008-09-01

    By using the composite vector with increment of diversity, position conservation scoring function, and predictive secondary structures to express the information of sequence, a support vector machine (SVM) algorithm for predicting beta- and gamma-turns in the proteins is proposed. The 426 and 320 nonhomologous protein chains described by Guruprasad and Rajkumar (Guruprasad and Rajkumar J. Biosci 2000, 25,143) are used for training and testing the predictive model of the beta- and gamma-turns, respectively. The overall prediction accuracy and the Matthews correlation coefficient in 7-fold cross-validation are 79.8% and 0.47, respectively, for the beta-turns. The overall prediction accuracy in 5-fold cross-validation is 61.0% for the gamma-turns. These results are significantly higher than the other algorithms in the prediction of beta- and gamma-turns using the same datasets. In addition, the 547 and 823 nonhomologous protein chains described by Fuchs and Alix (Fuchs and Alix Proteins: Struct Funct Bioinform 2005, 59, 828) are used for training and testing the predictive model of the beta- and gamma-turns, and better results are obtained. This algorithm may be helpful to improve the performance of protein turns' prediction. To ensure the ability of the SVM method to correctly classify beta-turn and non-beta-turn (gamma-turn and non-gamma-turn), the receiver operating characteristic threshold independent measure curves are provided. (c) 2008 Wiley Periodicals, Inc.

  4. Instabilities in dynamic anti-plane sliding of an elastic layer on a dissimilar elastic half-space

    Science.gov (United States)

    Kunnath, R.

    2012-12-01

    The stability of dynamic anti-plane sliding at an interface between an elastic layer and an elastic half-space with dissimilar elastic properties is studied. Friction at the interface is assumed to follow a rate- and state-dependent law, with a positive instantaneous dependence on slip velocity and a rate weakening behavior in the steady state. The perturbations are of the form exp(ikx+pt), where k is the wavenumber, x is the coordinate along the interface, p is the time response to the perturbation and t is time. The results of the stability analysis are shown in Figs. 1 and 2 with the velocity weakening parameter b/a=5, shear wave speed ratio cs'/cs=1.2, shear modulus ratio μ'/μ=1.2 and non-dimensional layer thickness H=100. The normalized instability growth rate and normalized phase velocity are plotted as a function of wavenumber. Fig.1 is for a non-dimensional unperturbed slip velocity ɛ=5 (rapid sliding) while Fig. 2 is for ɛ=0.05 (slow sliding). The results show the destabilization of interfacial waves. For slow sliding, destabilization of interfacial waves is still seen, indicating that the quasi-static approximation to slow sliding is not valid. This is in agreement with the result of Ranjith (Int. J. Solids and Struct., 2009, 46, 3086-3092) who predicted an instability of long-wavelength Love waves in slow sliding.

  5. Influence of boundary conditions on the response of multilayered plates with cohesive interfaces and delaminations using a homogenized approach

    Directory of Open Access Journals (Sweden)

    R. Massabò

    2014-07-01

    Full Text Available Stress and displacement fields in multilayered composites with interfacial imperfections, such as imperfect bonding of the layers or delaminations, or where the plies are separated by thin interlayers allowing relative motion, have large variations in the thickness, with characteristic zigzag patterns and jumps at the layer interfaces. These effects are well captured by a model recently formulated by the author for multilayered plates with imperfect interfaces and affine interfacial traction laws (Massabò & Campi, Meccanica, 2014, in press; Compos Struct, 2014, 116, 311-324. The model defines a homogenized displacement field, which satisfies interfacial continuity, and uses a variational technique to derive equilibrium equations depending on only six generalized displacement functions, for any arbitrary numbers of layers and interfaces. The model accurately predicts stresses and displacements in simply supported, highly anisotropic, thick plates with continuous, sliding interfaces. In this paper the model is applied to wide plates with clamped edges and some inconsistencies, which have been noted in the literature for models based on similar approaches and have limited their utilization, are explained. A generalized transverse shear force is introduced as the gross stress resultant which is directly related to the bending moment in the equilibrium equations of multilayered structures with imperfect interfaces and substitutes for the shear force of single-layer theory. An application to a delaminated wide plate highlights the potential and limitations of the proposed model for the solution of fracture mechanics problems.

  6. Analysis of the Relevant Factors of Retaining Women in Judo

    Directory of Open Access Journals (Sweden)

    Joško Sindik

    2014-09-01

    Full Text Available This study aimed to determine the latent dimensions of all relevant factors about engagement of women in judo, to determine the intercorrelations among these latent dimensions, as well as the correlations with three relevant variables. Final goal was to determine the differences in revealed latent dimensions, in relation to several independent variables: educational level, marital status, impulses to engage in judo, then depending are the women athletes (competitors or not, members of the Board or not, trainers or not. A total of 50 female judokas from a larger number of Croatian clubs were examined, by specially composed the survey. The results showed that all seven questionnaires showed medium to high satisfactory reliability, together with good con¬struct validity, in 15 latent dimensions that are revealed. It can be noticed that relatively older women have more obligations and more barriers that oppose to their engagement in judo. Only small number of differences are found among women engaged in judo, mainly among participants who are members of the Board in the club or Croatian Judo Federation, as compared with those who are not. Small number of statistically significant differences (as well as the correlations can be also observed as the fact that all women partially share similar problems, while the media strategies are perceived as the most powerful to increase women’s persistence in judo, in any type of engagement.

  7. Magnetocaloric properties of as-quenched Ni{sub 50.4}Mn{sub 34.9}In{sub 14.7} ferromagnetic shape memory alloy ribbons

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez Llamazares, J.L. [Instituto Potosino de Investigacion Cientifica y Tecnologica (IPICYT), San Luis Potosi, S.L.P. (Mexico); Garcia, C. [MIT, Department of Materials Science and Engineering, Massachusetts (United States); Hernando, B.; Prida, V.M. [Universidad de Oviedo, Departamento de Fisica, Facultad de Ciencias, Oviedo (Spain); Baldomir, D.; Serantes, D. [Universidade de Santiago de Compostela, Departamento de Fisica Aplicada, Facultad de Fisica, Santiago de Compostela (Spain); Gonzalez, J. [UPV, Departamento Fisica de Materiales, Facultad de Quimica, San Sebastian (Spain)

    2011-06-15

    The temperature dependences of magnetic entropy change and refrigerant capacity have been calculated for a maximum field change of {delta} H=30 kOe in as-quenched ribbons of the ferromagnetic shape memory alloy Ni{sub 50.4}Mn{sub 34.9}In{sub 14.7} around the structural reverse martensitic transformation and magnetic transition of austenite. The ribbons crystallize into a single-phase austenite with the L2{sub 1}-type crystal structure and Curie point of 284 K. At 262 K austenite starts its transformation into a 10-layered structurally modulated monoclinic martensite. The first- and second-order character of the structural and magnetic transitions was confirmed by the Arrott plot method. Despite the superior absolute value of the maximum magnetic entropy change obtained in the temperature interval where the reverse martensitic transformation occurs ({delta}S{sub M} {sup max}=7.2 Jkg{sup -1}K{sup -1}) with respect to that obtained around the ferromagnetic transition of austenite ({delta} S{sub M} {sup max}=2.6 Jkg{sup -1}K{sup -1}), the large average hysteretic losses due to the effect of the magnetic field on the phase transformation as well as the narrow thermal dependence of the magnetic entropy change make the temperature interval around the ferromagnetic transition of austenite of a higher effective refrigerant capacity (RC{sup magn}{sub eff}=95Jkg{sup -1} versus RC{sup struct}{sub eff}=60Jkg{sup -1}). (orig.)

  8. EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments

    Science.gov (United States)

    Zhao, Huiying; Yu, Jiafeng; Guo, Chengang; Dou, Xianghua; Song, Feng; Hu, Guodong; Cao, Zanxia; Qu, Yuanxu

    2018-01-01

    Abstract Long non-coding RNAs (lncRNAs) play important functional roles in various biological processes. Early databases were utilized to deposit all lncRNA candidates produced by high-throughput experimental and/or computational techniques to facilitate classification, assessment and validation. As more lncRNAs are validated by low-throughput experiments, several databases were established for experimentally validated lncRNAs. However, these databases are small in scale (with a few hundreds of lncRNAs only) and specific in their focuses (plants, diseases or interactions). Thus, it is highly desirable to have a comprehensive dataset for experimentally validated lncRNAs as a central repository for all of their structures, functions and phenotypes. Here, we established EVLncRNAs by curating lncRNAs validated by low-throughput experiments (up to 1 May 2016) and integrating specific databases (lncRNAdb, LncRANDisease, Lnc2Cancer and PLNIncRBase) with additional functional and disease-specific information not covered previously. The current version of EVLncRNAs contains 1543 lncRNAs from 77 species that is 2.9 times larger than the current largest database for experimentally validated lncRNAs. Seventy-four percent lncRNA entries are partially or completely new, comparing to all existing experimentally validated databases. The established database allows users to browse, search and download as well as to submit experimentally validated lncRNAs. The database is available at http://biophy.dzu.edu.cn/EVLncRNAs. PMID:28985416

  9. APD detectors for biological fluorescence spectroscopy

    International Nuclear Information System (INIS)

    Mazeres, S.; Borrel, V.; Magenc, C.; Courrech, J.L.; Bazer-Bachi, R.

    2006-01-01

    Fluorescence spectroscopy is a very convenient and widely used method for studying the molecular background of biological processes [L. Salome, J.L. Cazeil, A. Lopez, J.F. Tocanne, Eur. Biophys. J. 27 (1998) 391-402]. Chromophores are included in the structure under study and a flash of laser light induces fluorescence (Fluorescence Recovery After Photo-bleaching), the decay of which yields information on the polarity, the speed of rotation, and the speed of diffusion as well as on the temporal and spatial evolution of interactions between molecular species. The method can even be used to study living cells [J.F. Tocanne, L. Cezanne, A. Lopez, Prog. Lipid Res. 33 (1994) 203-237, L. Cezanne, A. Lopez, F. Loste, G. Parnaud, O. Saurel, P. Demange, J.F. Tocanne, Biochemistry 38 (1999) 2779-2786]. This is classically performed with a PM-based system. For biological reasons a decrease of the excitation of the cells is highly desirable. Because the fluorescence response then becomes fainter a significant improvement in detector capability would be welcome. We present here results obtained with an Avalanche Photo Diode (APD)-based system. The small sensitive area of detection allows a very significant improvement in signal/noise ratio, improvement in gain, and the opening-up of a new parameter space. With these new detectors we can begin the study of information transmission between cells through morphine receptors. This work involves both electronics engineers and biophysicists, so results and techniques in both fields will be presented here

  10. A simple theory of motor protein kinetics and energetics. II.

    Science.gov (United States)

    Qian, H

    2000-01-10

    A three-state stochastic model of motor protein [Qian, Biophys. Chem. 67 (1997) pp. 263-267] is further developed to illustrate the relationship between the external load on an individual motor protein in aqueous solution with various ATP concentrations and its steady-state velocity. A wide variety of dynamic motor behavior are obtained from this simple model. For the particular case of free-load translocation being the most unfavorable step within the hydrolysis cycle, the load-velocity curve is quasi-linear, V/Vmax = (cF/Fmax-c)/(1-c), in contrast to the hyperbolic relationship proposed by A.V. Hill for macroscopic muscle. Significant deviation from the linearity is expected when the velocity is less than 10% of its maximal (free-load) value--a situation under which the processivity of motor diminishes and experimental observations are less certain. We then investigate the dependence of load-velocity curve on ATP (ADP) concentration. It is shown that the free load Vmax exhibits a Michaelis-Menten like behavior, and the isometric Fmax increases linearly with ln([ATP]/[ADP]). However, the quasi-linear region is independent of the ATP concentration, yielding an apparently ATP-independent maximal force below the true isometric force. Finally, the heat production as a function of ATP concentration and external load are calculated. In simple terms and solved with elementary algebra, the present model provides an integrated picture of biochemical kinetics and mechanical energetics of motor proteins.

  11. Sensitive detection and separation of fluorescent derivatives using capillary electrophoresis with laser-induced fluorescence detection with 532nm Nd:YAG laser

    International Nuclear Information System (INIS)

    Vrabel, Patrik; Taborsky, Petr; Ryvolova, Marketa; Havel, Josef; Preisler, Jan

    2006-01-01

    Capillary electrophoresis with laser-induced fluorescence detection (CELIF) is a powerful tool for separation and sensitive determination of fluorescent species. Biologically active compounds, such as amino acids, peptides and proteins may exhibit native fluorescence, which is however often low and/or an expensive laser is required for excitation in UV. Therefore, labelling of the analytes with a fluorescent dye is usually necessary. In this work, a home-built CELIF instrument with diode pumped frequency-doubled continuous wave Nd:YAG excitation laser with feedback power regulation (532nm) was constructed. The suitability of this type of laser for LIF detection in a separation method was found excellent. A limit of detection (LOD) (S/N=3) of 2x10 -13 mol/l was achieved with rhodamine B, which is comparable to those obtained using similar instruments with Ar + laser [Y.F. Cheng, N.J. Dovichi, Science 242 (1988) 562, E.S. Yeung et al., J. Chromatogr. 608 (1992) 73]. LOD of a protein derivatized according to modified procedures [M.J. Little et al., Anal. Chim. Acta 339 (1997) 279, A. Chersi et al., Biochim. Biophys. Acta 1336 (1997) 83] was determined. Detection of the derivatives was found to be limited by insufficient reaction recovery at low analyte concentration, chemical noise, separation efficiency and quality of the derivatizing reagent rather than by the detector performance. As a consequence, a huge gap between the detection ability of CELIF instruments and LOD determined in real samples is revealed

  12. Determination, at equilibrium, of association constants of labelled or unlabelled ligands by a non-graphical method

    International Nuclear Information System (INIS)

    Goertz, G.; Longchampt, J.; Crepy, O.; Judas, O.; Jayle, M.-F.

    1976-01-01

    Determination, at equilibrium of association constants of labelled or unlabelled ligands by a non-graphical method are described. This work deals with the determination of association constants at equilibrium by a non-graphical method in binding systems containing one specific receptor. Equations have been derived from that originally described by Lea (Biochim. Biophys. Acta, 322, 68-74), the terms of which are obtained from the data of simple displacement curves of a bound radioactive ligand by unlabelled competitors identical or different in nature. By knowing the function relating the variations of the bound ligand (B) to the affinity constant (Ksub(i)) and the quantity (Msub(i)) of competitor for a given system, it is possible to calculate any of these parameters when the two others are measured. Thus, it becomes easy to compare the relative affinities of different receptors for the same ligand or that of one receptor for various labelled or unlabelled ligands. Furthermore, theoretical displacement curves can be drawn and compared to experimental data, only when knowing the affinity constant of a specific binding system in given conditions. These modes of calculation have been tested in a study of interactions between various steroids and a fraction of human serum proteins precipitated by ammonium sulfate (30-45%) and containing the sex hormone-binding globulin. Association constants thus obtained agree well with those reported in the literature and determined by graphical procedures

  13. Halogenated benzimidazole inhibitors of phosphorylation, ''in vitro'' and ''in vivo'', of the surface acidic proteins of the yeast ribosomal 60S subunit by endogenous protein kinases CK-II and PK60S

    International Nuclear Information System (INIS)

    Szyszka, Ryszard; Boguszewska, Aleksandra; Grankowski, Nikodem; Shugar, David

    1996-01-01

    Several halogeno benzimidazoles and 2-azabenzimidazoles, previously shown to be relatively selective inhibitors of protein kinases CK-I and/or CK-II from various sources, including CK-II from yeast [Szyszka et al. (1995) Biochem. Biophys. Res. Commun. 208, 418-424] inhibit also the yeast ribosomal protein kinase PK60S. The most effective inhibitor of CK-II and PK60S was tetrabromo-2-azabenzimidazole (TetraBr-2-azaBz), which was competitive with respect to ATP (and GTP in the case of CK-II) with K i values of 0.7 μM for CK-II, and 0.1 μM for PK60S. PK60S phosphorylates only three (YP1β, YB1β', YP2α) out of five polypeptides of pp13 kDa acidic proteins of 60S subunit phosphorylated by CK-II [Szyszka et al. (1995) Acta Biochim. Polon. 42, 357-362]. Accordingly, TetraBr-azaBz inhibits phosphorylation only of these polypeptides, catalysed by PK60S. Addition of TetraBr-2Bz to cultures of yeast cells, at concentrations which were without effect on cell growth, led to inhibition of intracellular phosphorylation of ribosomal acidic proteins, paralleling that observed ''in vitro''. TetraBr-2-azaBz is shown to be a useful tool for studies on the intracellular regulation of phosphorylation of the ribosomal 60S acidic proteins, which are involved in formation of active ribosomes. (author). 36 refs, 4 figs, 2 tabs

  14. Translational step inhibited in vivo by aflatoxin B1 in rat-liver polysomes

    International Nuclear Information System (INIS)

    Sarasin, A.; Moule, Y.

    1975-01-01

    Aflatoxin B 1 strongly inhibits protein synthesis in rat liver cells. This paper confirms the foregoing results and represents an attempt to localize the translational step inhibited in vivo by aflatoxin B 1 . We used the simulation study developed by Li, Kisilevsky, Wasan and Hammond, 1972 (Biochim. Biophys. Acta, 272, 451-462) to determine precisely the site inhibited in vivo after drug intoxication. This analysis is based on two parameters: the kinetics of polysome labeling to follow the nascent peptide synthesis, and the kinetics of supernatant labeling to follow the completed protein synthesis. Up to 5 h after dosing, aflatoxin specifically inhibits the elongation and/or termination steps during protein synthesis; after longer periods of time inhibition occurs essentially at the initiation step. When the intracellular concentration of aflatoxin is too high, particularly 2 h after dosing, each step of protein synthesis is blocked. Polypeptide synthesis by the postmitochondrial supernatants isolated from aflatoxin-treated animals is impaired in the same proportion as protein synthesis in vivo. The damage caused by aflatoxin is mostly observed on microsomes. However, purified polysomes isolated from aflatoxin-treated rats synthesize proteins in vitro to the same extent as those from controls. These results suggest that aflatoxin metabolite(s) are bound to polysomes with noncovalent bonds. These active metabolites are probably lost during polysome isolation procedures. Finally, relationships between protein metabolism and aflatoxin carcinogenesis are discussed. (orig./BSC) [de

  15. Organization and alternative splicing of the Caenorhabditis elegans cAMP-dependent protein kinase catalytic-subunit gene (kin-1).

    Science.gov (United States)

    Tabish, M; Clegg, R A; Rees, H H; Fisher, M J

    1999-04-01

    The cAMP-dependent protein kinase (protein kinase A, PK-A) is multifunctional in nature, with key roles in the control of diverse aspects of eukaryotic cellular activity. In the case of the free-living nematode, Caenorhabditis elegans, a gene encoding the PK-A catalytic subunit has been identified and two isoforms of this subunit, arising from a C-terminal alternative-splicing event, have been characterized [Gross, Bagchi, Lu and Rubin (1990) J. Biol. Chem. 265, 6896-6907]. Here we report the occurrence of N-terminal alternative-splicing events that, in addition to generating a multiplicity of non-myristoylatable isoforms, also generate the myristoylated variant(s) of the catalytic subunit that we have recently characterized [Aspbury, Fisher, Rees and Clegg (1997) Biochem. Biophys. Res. Commun. 238, 523-527]. The gene spans more than 36 kb and is divided into a total of 13 exons. Each of the mature transcripts contains only 7 exons. In addition to the already characterized exon 1, the 5'-untranslated region and first intron actually contain 5 other exons, any one of which may be alternatively spliced on to exon 2 at the 5' end of the pre-mRNA. This N-terminal alternative splicing occurs in combination with either of the already characterized C-terminal alternative exons. Thus, C. elegans expresses at least 12 different isoforms of the catalytic subunit of PK-A. The significance of this unprecedented structural diversity in the family of PK-A catalytic subunits is discussed.

  16. Data set for mass spectrometric analysis of recombinant human serum albumin from various expression systems

    Directory of Open Access Journals (Sweden)

    Daryl G.S. Smith

    2015-09-01

    Full Text Available Human serum albumin (HSA is a versatile and important protein for the pharmaceutical industry (Fanali et al., Mol. Aspects Med. 33(3 (2012 209–290. Due to the potential transmission of pathogens from plasma sourced albumin, numerous expression systems have been developed to produce recombinant HSA (rHSA (Chen et al., Biochim. Biophys. Acta (BBA—Gen. Subj. 1830(12 (2013 5515–5525; Kobayashi, Biologicals 34(1 (2006 55–59. Based on our previous study showing increased glycation of rHSA expressed in Asian rice (Frahm et al., J. Phys. Chem. B 116(15 (2012 4661–4670, both supplier-to-supplier and lot-to-lot variability of rHSAs from a number of expression systems were evaluated using reversed phase liquid chromatography linked with MS and MS/MS analyses. The data are associated with the research article ‘Determination of Supplier-to-Supplier and Lot-to-Lot Variability in Glycation of Recombinant Human Serum Albumin Expressed in Oryza sativa’ where further analysis of rHSA samples with additional biophysical methods can be found (Frahm et al., PLoS ONE 10(9 (2014 e109893. We determined that all rHSA samples expressed in rice showed elevated levels of arginine and lysine hexose glycation compared to rHSA expressed in yeast, suggesting that the extensive glycation of the recombinant proteins is a by-product of either the expression system or purification process and not a random occurrence.

  17. Potencial de los quito-oligosacáridos generados de quitina y quitosana Potencial de los quito-oligosacáridos generados de quitina y quitosana

    Directory of Open Access Journals (Sweden)

    José Eleazar Barboza Corona

    2012-01-01

    Full Text Available Las quitinasas sintetizadas por plantas, hongos, insectos y bacterias tienen un gran poten­cial debido a su amplio espectro de aplicaciones. En este trabajo revisamos generalidades sobre las quitinasas y quitosanasas bacterianas y su uso en la producción de quito-oligo­sacáridos. Este tipo de biomoléculas han creado un mercado biotecnológico diversificado e ilimitado que incluye aplicaciones en alimentos como aditivos y bioconservadores, asi­mismo en múltiples aplicaciones biomédicas enfocadas a la actividad anti-tumoral, a la capacidad como agentes antioxidantes y como antidiabéticos. Además, en la agricultura se han aplicado como factores de nodulación, como agentes osmoprotectores y antioxidan­tes para beneficiar el crecimiento de cultivos. Es importante destacar el potencial de las quitinasas sintetizadas por Bacillus thuringiensis, el bioinsecticida mas importante mun­dialmente. Las quitinasas de B. thuringiensis se han empleado recientemente para generar quito-oligosacáridos que tienen actividad antimicrobiana, particularmente contra diversas bacterias patógenas de importancia en salud pública transmitidas por alimentos.Chitinases synthesized by plants, fungi, insects and bacteria have a huge potential owing to its wide range of applications. In this work we review generalities about chitin, chitosane, chitinases and chitosanases from bacteria and their use in the production of chitin-oligosaccharides. This kind of biomolecules has created a diversified biotechnology market, including unlimited applications such as food additives and biopreservative, in biomedical applications focused mainly on anti-tumor activities, as antioxidants and anti-diabetics. In agriculture chitin-oligosaccharides has been applied as nodulation factors, osmoprotectors agents and antioxidants to benefit crop growth. It is important to note the potential use of chitinases biosynthesized by Bacillus thuringiensis, the most important biopesticide

  18. AISLAMIENTO, CLONACIÓN Y EXPRESIÓN DE UNA ENZIMA LIPOLÍTICA DE Natronococcus sp. TC6, A PARTIR DE UNA LIBRERÍA GENÓMICA

    Directory of Open Access Journals (Sweden)

    Alberto López Barrera

    2017-01-01

    Full Text Available Los procesos biotecnológicos e industriales demandan de biocatalizadores robustos. Para conseguir este atributo, se recurre a la búsqueda de enzimas de microorganismos que naturalmente se han adaptado a ambientes inhóspitos. La generación de bibliotecas genómicas y el análisis genómico son herramientas moleculares poderosas para descubrir biomoléculas con características únicas y sobresalientes. Empleando el genoma fragmentado mecánicamente de un arquea halófila, Natronococcus sp. TC6, se construyó una genoteca de cósmidos, los cuales fueron usados para transformar a la cepa E. coli. En total, fueron generados 2181 clones, de los cuales, se seleccionaron seis con actividad lipolítica, ya que hidrolizaron ésteres de p-nitrofenilo como sustratos, en un medio de reacción conteniendo 2.5 M de NaCl. Las clonas que hidrolizaron ambos sustratos (clonas positivas fueron aisladas y los cósmidos fueron purificados y fragmentados para posteriores análisis enzimáticos. Los fragmentos de DNA de las clonas positivas, fueron subclonados y secuenciados. El análisis bioinformático de las secuencias obtenidas permitió identificar una tioesterasa putativa, la cual fue ligada en un vector de expresión, y éste utilizado para su introducción en células de E. coli BL21 para la producción de la proteína recombinante. La tioesterasa identificada posee 158 aminoácidos con un peso molecular de 15.4 kDa y con una similitud del 99% con el gene de la bacteria Stenotrophomonas maltophilia. La tioesterasa putativa de Natronococcus sp. TC6, presenta tres sitios altamente conservados como en S. maltophilia, posee dos motivos cercanos al extremo N-terminal, GHVNN y YXEXAR. También presenta una variante del pentapéptido involucrado en el sitio activo y característico de la mayoría de las éster hidrolasas, GXSXV.

  19. Karyotype Learning Center: A Software For Teaching And Learning Cytogenetics

    Directory of Open Access Journals (Sweden)

    Joelma Freire De Mesquita

    2004-05-01

    Full Text Available The in vitro cultivation of human cells is an essential part of the work of every diagnostic cytoge-netics laboratory. Almost all human cytogenetic studies involve the examination of dividing bloodcell population by blocking cell division at metaphase with subsequent processing and staining bybanding techniques. The chromosome constitution is described as Karyotype that states the totalnumber of chromosomes and the sex chromosome constitution. Karyotypes are prepared by cuttingup a photograph of the spread metaphase chromosomes, matching up homologous chromosomes andsticking them back down on a card or nowadays more often by getting an image analysis computerto do the job. Chromosomes are identied by their size, centromere position and banding pattern.Teaching a student how to detect and interpret even the most common chromosome abnormaliti-es is a major challenge: mainly, in a developing country where the laboratorial facilities are notalways available for a big number of students. Therefore, in this work we present an educationalsoftware for teaching undergraduate students of Medical and Life Sciences Courses how to arrangenormal and abnormal chromosomes in the form of karyotype. The user, using drag-and-drop, is da-red to match up homologous chromosome. For that, we have developed a free full access web site(http://www.biomol.net/cariotipo/ for hosting the software. The latter has proved to be light andfast even under slow dial-up connections. This web site also oers a theoretical introductory sectionwith basic concepts about karyotype. Up to now the software has been successfully applied to un-dergraduate courses at the University of Rio de Janeiro (UNIRIO. The students have approved thesoftware; to them the similarities with the well-known game solitaire turns the exercise more excitingand provides additional stimulus to learn and understand karyotype. Professors have also used thesoftware as complementary material in their regular classes

  20. Los péptidos antimicrobianos de origen vegetal con un breve enfoque en las proteínas de transferencia de lípidos: minirevisión

    Directory of Open Access Journals (Sweden)

    Silvio Alejandro López-Pazos

    2014-06-01

    Full Text Available Los sistemas de defensa de los organismos vivientes abarcan una gran gama de biomoléculas, un importante grupo de estas, son los péptidos antimicrobianos (AMP del inglés Antimicrobial Peptides. Estas péptidos forman parte de la inmunidad no específica e innata de los seres vivos y son activos contra patógenos(bacterias, hongos, virus y protozoarios. Las plantas, al ser una fuente de alimento, son atacadas pormuchas clases de microorganismos, aunque solo unos pocos les pueden causar enfermedades. Las plantas y los organismos patógenos han coevolucionado, así las primeras han logrado estrategias efectivas de resistirel ataque de sus invasores. Las proteínas relacionadas con patogénesis (PR hacen parte de un mecanismo inducible de resistencia, las cuales se expresanen gran proporción, en tejidos vegetales parasitados. Las PR tienen un peso molecular de entre 5 a 75 kDa, aquellas con pesos inferiores a 10 kDa se denominanAMP, entre las que se cuentan las quitinasas, endoproteasas, peroxidasas, heveinas, oxalato oxidasas, proteínas de transferencia de lípidos (LTP del inglés Lipid Transfer Protein o Lipid Transfer Peptide y defensinas,entre otras. Las LTP presentan un tamaño de 7-10 kDa, se caracterizan por participar en intercambio de lípidos entre membranas, ser ricas en residuosde cisteína y por poseer una conformación cationica. Las LTP tienen capacidad de inhibir el crecimiento de bacterias y de hongos por su interacción con fosfolípidos de la membrana del patógeno y también por lacompetencia con moléculas señalizadoras del agente invasor por el receptor de la planta, y así la LTP evitaría el reconocimiento planta-patógeno. Aquí se presentan algunas consideraciones importantes acercade esta temática y su perspectiva en la agricultura comercial colombiana.

  1. La peroxidación lipídica en la etiopatogenia de la enfermedad periodontal inflamatoria

    Directory of Open Access Journals (Sweden)

    Bárbara E García Triana

    1998-04-01

    Full Text Available Las especies reactivas del oxígeno están implicadas en la etiopatogenia de la inflamación. Durante la activación de los leucocitos, se liberan grandes cantidades de estas especies, cuya función es la eliminación de los agentes patógenos. Si las defensas antioxidantes de los tejidos no funcionan eficientemente, son inducidas reacciones radicálicas que afectan a las biomoléculas. El ataque a los lípidos de la membrana celular provoca su peroxidación, con la consiguiente formación de nuevas especies radicálicas y metabolitos tóxicos. La presencia de un fuerte infiltrado inflamatorio en los tejidos periodontales, durante la enfermedad periodontal inflamatoria, ha sugerido la posible participación de las especies reactivas del oxígeno en la etiopatogenia de esta enfermedad. Se supone que el ataque de estas sustancias a los tejidos periodontales con deficiente defensa antioxidante, provoca la aparición de la peroxidación lipídica, que puede conducir a la lisis celular y la activación de proteasas.The reative oxygen species are involved in the pathogenesis of inflammation. Leukocyte activation released a great amount of these species the function of which is to eliminate pathogen agents. If antioxidant tissue defenses do not act properly, then radical reactions affecting biomolecules are induced. The attack on cell membrane lipids caused their peroxidation followed by the formation of new radical species and toxic metabolites. The existence of a strong inflammatory infiltrate in periodontal tissues in the course of the periodontal disease suggest the possible involvement of reactive oxygen species in the pathogenesis of this disease. It is supposed that the attack of these substances on the poorly antioxidant defended periodontal tissues makes the lipid peroxidation take place, which may lead to cellular lysis and proteases activation.

  2. The utility of cancer-related cultural constructs to understand colorectal cancer screening among African Americans

    Directory of Open Access Journals (Sweden)

    Vetta L. Sanders Thompson

    2013-09-01

    Full Text Available Background. Data suggest that colorectal cancer could be cut by approximately 60% if all people aged 50 years or older received regular screening. Studies have identified socio-cultural attitudes that might inform cancer education and screening promotion campaigns. This article applies item response theory (IRT to a set of survey items selected to assess sociocultural attitudes in order to determine how current measures may affect what we know about how these attitudes affect colorectal cancer screening (CRCS.Design and Methods. A survey of colorectal cancer screening, screening attitudes and cultural beliefs was administered to 1021 African Americans – 683 women and 338 men, ages 50 to 75. Eligibility crite ria for participation included being born in the United States, self-identified African American male or female, age 50 to 75 years. The IRT analysis was performed on 655 individuals with complete data for the 43 observed variables. Results. Twenty-nine items comprise the Multi-construct African American Cultural Survey (MAACS that addresses seven cultural con- structs: mistrust/distrust, privacy, ethnic identity, collectivism, empowerment, and male gender roles. The items provide adequate information about the attitudes of the population across most levels of the constructs assessed. Among the sociocultural variables considered, empowerment (OR=1.078; 95% CI: 1.008, 1.151 had the strongest association with CRCS adherence and privacy showed promise. Conclusions. The MAACS provides a fixed length questionnaire to assess African American CRCS attitudes, two new constructs that might assist in CRCS promotion, and a suggested focus for identification of additional constructs of interest.

  3. On the nature of dissipative Timoshenko systems at light of the second spectrum of frequency

    Science.gov (United States)

    Almeida Júnior, D. S.; Ramos, A. J. A.

    2017-12-01

    In the present work, we prove that there exists a relation between a physical inconsistence known as second spectrum of frequency or non-physical spectrum and the exponential decay of a dissipative Timoshenko system where the damping mechanism acts on angle rotation. The so-called second spectrum is addressed into stabilization scenario and, in particular, we show that the second spectrum of the classical Timoshenko model can be truncated by taking a damping mechanism. Also, we show that dissipative Timoshenko type systems which are free of the second spectrum [based on important physical and historical observations made by Elishakoff (Advances mathematical modeling and experimental methods for materials and structures, solid mechanics and its applications, Springer, Berlin, pp 249-254, 2010), Elishakoff et al. (ASME Am Soc Mech Eng Appl Mech Rev 67(6):1-11 2015) and Elishakoff et al. (Int J Solids Struct 109:143-151, 2017)] are exponential stable for any values of the coefficients of system. In this direction, we provide physical explanations why weakly dissipative Timoshenko systems decay exponentially according to equality between velocity of wave propagation as proved in pioneering works by Soufyane (C R Acad Sci 328(8):731-734, 1999) and also by Muñoz Rivera and Racke (Discrete Contin Dyn Syst B 9:1625-1639, 2003). Therefore, the second spectrum of the classical Timoshenko beam model plays an important role in explaining some results on exponential decay and our investigations suggest to pay attention to the eventual consequences of this spectrum on stabilization setting for dissipative Timoshenko type systems.

  4. Autofocus algorithm for curvilinear SAR imaging

    Science.gov (United States)

    Bleszynski, E.; Bleszynski, M.; Jaroszewicz, T.

    2012-05-01

    We describe an approach to autofocusing for large apertures on curved SAR trajectories. It is a phase-gradient type method in which phase corrections compensating trajectory perturbations are estimated not directly from the image itself, but rather on the basis of partial" SAR data { functions of the slow and fast times { recon- structed (by an appropriate forward-projection procedure) from windowed scene patches, of sizes comparable to distances between distinct targets or localized features of the scene. The resulting partial data" can be shown to contain the same information on the phase perturbations as that in the original data, provided the frequencies of the perturbations do not exceed a quantity proportional to the patch size. The algorithm uses as input a sequence of conventional scene images based on moderate-size subapertures constituting the full aperture for which the phase corrections are to be determined. The subaperture images are formed with pixel sizes comparable to the range resolution which, for the optimal subaperture size, should be also approximately equal the cross-range resolution. The method does not restrict the size or shape of the synthetic aperture and can be incorporated in the data collection process in persistent sensing scenarios. The algorithm has been tested on the publicly available set of GOTCHA data, intentionally corrupted by random-walk-type trajectory uctuations (a possible model of errors caused by imprecise inertial navigation system readings) of maximum frequencies compatible with the selected patch size. It was able to eciently remove image corruption for apertures of sizes up to 360 degrees.

  5. Chimeric β-Lactamases: Global Conservation of Parental Function and Fast Time-Scale Dynamics with Increased Slow Motions

    Science.gov (United States)

    Clouthier, Christopher M.; Morin, Sébastien; Gobeil, Sophie M. C.; Doucet, Nicolas; Blanchet, Jonathan; Nguyen, Elisabeth; Gagné, Stéphane M.; Pelletier, Joelle N.

    2012-01-01

    Enzyme engineering has been facilitated by recombination of close homologues, followed by functional screening. In one such effort, chimeras of two class-A β-lactamases – TEM-1 and PSE-4 – were created according to structure-guided protein recombination and selected for their capacity to promote bacterial proliferation in the presence of ampicillin (Voigt et al., Nat. Struct. Biol. 2002 9:553). To provide a more detailed assessment of the effects of protein recombination on the structure and function of the resulting chimeric enzymes, we characterized a series of functional TEM-1/PSE-4 chimeras possessing between 17 and 92 substitutions relative to TEM-1 β-lactamase. Circular dichroism and thermal scanning fluorimetry revealed that the chimeras were generally well folded. Despite harbouring important sequence variation relative to either of the two ‘parental’ β-lactamases, the chimeric β-lactamases displayed substrate recognition spectra and reactivity similar to their most closely-related parent. To gain further insight into the changes induced by chimerization, the chimera with 17 substitutions was investigated by NMR spin relaxation. While high order was conserved on the ps-ns timescale, a hallmark of class A β-lactamases, evidence of additional slow motions on the µs-ms timescale was extracted from model-free calculations. This is consistent with the greater number of resonances that could not be assigned in this chimera relative to the parental β-lactamases, and is consistent with this well-folded and functional chimeric β-lactamase displaying increased slow time-scale motions. PMID:23284969

  6. Vortex dynamics in the wake of a pivoted cylinder undergoing vortex-induced vibrations with elliptic trajectories

    Science.gov (United States)

    Marble, Erik; Morton, Christopher; Yarusevych, Serhiy

    2018-05-01

    Vortex-induced vibrations of a pivoted cylinder are investigated experimentally at a fixed Reynolds number of 3100, a mass ratio of 10.8, and a range of reduced velocities, 4.42 ≤ U^* ≤ 9.05. For these conditions, the cylinder traces elliptic trajectories, with the experimental conditions producing three out of four possible combinations of orbiting direction and primary axis alignment relative to the incoming flow. The study focuses on the quantitative analysis of wake topology and its relation to this type of structural response. Velocity fields were measured using time-resolved, two-component particle image velocimetry (TR-PIV). These results show that phase-averaged wake topology generally agrees with the Morse and Williamson (J Fluids Struct 25(4):697-712, 2009) shedding map for one-degree-of-freedom vortex-induced vibrations, with 2S, 2{P}o, and 2P shedding patterns observed within the range of reduced velocities studied here. Vortex tracking and vortex strength quantification are used to analyze the vortex shedding process and how it relates to cylinder response. In the case of 2S vortex shedding, vortices are shed when the cylinder is approaching the maximum transverse displacement and reaches the streamwise equilibrium. 2P vortices are shed approximately half a period earlier in the cylinder's elliptic trajectory. Leading vortices shed immediately after the peak in transverse oscillation and trailing vortices shed near the equilibrium of transverse oscillation. The orientation and direction of the cylinder's elliptic trajectory are shown to influence the timing of vortex shedding, inducing changes in the 2P wake topology.

  7. Far Infrared High Resolution Synchrotron FTIR Spectroscopy of the Low Frequency Bending Modes of Dmso

    Science.gov (United States)

    Cuisset, Arnaud; Smirnova, Irina; Bocquet, Robin; Hindle, Francis; Mouret, Gael; Sadovskii, Dmitrii A.; Pirali, Olivier; Roy, Pascale

    2010-06-01

    In addition to its importance for industrial and environmental studies, the monitoring of DiMethylSulfOxyde (DMSO, (CH_3)_2SO) concentrations is of considerable interest for civil protection. The existing high resolution gas phase spectroscopic data of DMSO only concerned the pure rotational transitions in the ground state. In the Far-IR domain, the low-frequency rovibrational transitions have never previously resolved. The high brightness of the AILES beamline of the synchrotron SOLEIL and the instrumental sensitivity provided by the multipass cell allowed to measure for the first time these transitions. 1581 A-type and C-type transitions in the ν11 band have been assigned and 25 molecular constants of Watson's s-form hamiltonian developed to degree 8 have been fitted within the experimental accuracy. The use of then synchrotron radiation has opened many possibilities for new spectroscopic studies. Together with several other recent studies, our successful measurement and analysis of DMSO convincingly demonstrates the potential of the AILES beamline for high resolution FIR spectroscopy. Thus our present work is just at the beginning of unraveling the rovibrational structure of low frequency bending and torsional vibrational states of DMSO and yielding important comprehensive structural and spectroscopic information on this molecule. L. Margules, R. A. Motienko, E. A. Alekseev, J. Demaison, J. Molec. Spectrosc., 260(23),2009 V. Typke, M. Dakkouri, J. Molec. Struct., 599(177),2001 A. Cuisset, L. Nanobashvili, I. Smirnova, R. Bocquet, F. Hindle, G. Mouret, O. Pirali, P. Roy, D. Sadovskii, Chem. Phys. Lett., accepted for publication

  8. E-MSD: improving data deposition and structure quality.

    Science.gov (United States)

    Tagari, M; Tate, J; Swaminathan, G J; Newman, R; Naim, A; Vranken, W; Kapopoulou, A; Hussain, A; Fillon, J; Henrick, K; Velankar, S

    2006-01-01

    The Macromolecular Structure Database (MSD) (http://www.ebi.ac.uk/msd/) [H. Boutselakis, D. Dimitropoulos, J. Fillon, A. Golovin, K. Henrick, A. Hussain, J. Ionides, M. John, P. A. Keller, E. Krissinel et al. (2003) E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. Nucleic Acids Res., 31, 458-462.] group is one of the three partners in the worldwide Protein DataBank (wwPDB), the consortium entrusted with the collation, maintenance and distribution of the global repository of macromolecular structure data [H. Berman, K. Henrick and H. Nakamura (2003) Announcing the worldwide Protein Data Bank. Nature Struct. Biol., 10, 980.]. Since its inception, the MSD group has worked with partners around the world to improve the quality of PDB data, through a clean up programme that addresses inconsistencies and inaccuracies in the legacy archive. The improvements in data quality in the legacy archive have been achieved largely through the creation of a unified data archive, in the form of a relational database that stores all of the data in the wwPDB. The three partners are working towards improving the tools and methods for the deposition of new data by the community at large. The implementation of the MSD database, together with the parallel development of improved tools and methodologies for data harvesting, validation and archival, has lead to significant improvements in the quality of data that enters the archive. Through this and related projects in the NMR and EM realms the MSD continues to improve the quality of publicly available structural data.

  9. Corrigendum to "Synthesis and spectral characterization of new homologous 1,3,5-triaryl-2-pyrazolines: Influence of alkyloxy chain length on fluorescence" [Spectrochim. Acta Part A: Mol. Biomol. Spectrosc. 133 (2014) 182-189

    Science.gov (United States)

    Abbas, Asghar; Hussain, Safdar; Hafeez, Noureen; Naseer, Muhammad Moazzam

    2015-03-01

    The authors regret to inform that the affiliation of one of the authors, namely, Noureen Hafeez has been written as Department of Forensic Medicine & Toxicology, Rawalpindi Institute of Health Sciences (RIHS), Bahria University, Islamabad, Pakistan in the published article. The correct address is shown above.

  10. Decommissioning of a Radioactive Facility Used for Biomolecule Labeling and Biological Effects; Desclasificación de una Instalación Radiactiva Dedicada al Marcado de Biomoléculas y Efectos Biológicos

    Energy Technology Data Exchange (ETDEWEB)

    Yagüe, L.; Navarro, N.; Álvarez, A.; Quiñones, J.

    2015-07-01

    This paper presents the measurement methodology designed for the final status survey of an old radioactive facility, used as radiolabeling lab. Its declassification as radioactive facility required the radiological characterization of all walls, structures and materials at the facility in order to reuse its outbuilding for conventional use. To demonstrate compliance with the declassification criteria, the design of the final status survey was performed applying MARSSIM(1) (Multi-Agency Radiation Survey and Site Investigation Manual) methodology and using different measurement techniques depending on the radioactive isotopes in the inventory of the facility, their half-lives and emission characteristics.

  11. A look at the effect of sequence complexity on pressure destabilisation of DNA polymers.

    Science.gov (United States)

    Rayan, Gamal; Macgregor, Robert B

    2015-04-01

    Our previous studies on the helix-coil transition of double-stranded DNA polymers have demonstrated that molar volume change (ΔV) accompanying the thermally-induced transition can be positive or negative depending on the experimental conditions, that the pressure-induced transition is more cooperative than the heat-induced transition [Rayan and Macgregor, J Phys Chem B2005, 109, 15558-15565], and that the pressure-induced transition does not occur in the absence of water [Rayan and Macgregor, Biophys Chem, 2009, 144, 62-66]. Additionally, we have shown that ΔV values obtained by pressure-dependent techniques differ from those obtained by ambient pressure techniques such as PPC [Rayan et al. J Phys Chem B2009, 113, 1738-1742] thus shedding light on the effects of pressure on DNA polymers. Herein, we examine the effect of sequence complexity, and hence cooperativity on pressure destabilisation of DNA polymers. Working with Clostridium perfringes DNA under conditions such that the estimated ΔV of the helix-coil transition corresponds to -1.78 mL/mol (base pair) at atmospheric pressure, we do not observe the pressure-induced helix-coil transition of this DNA polymer, whereas synthetic copolymers poly[d(A-T)] and poly[d(I-C)] undergo cooperative pressure-induced transitions at similar ΔV values. We hypothesise that the reason for the lack of pressure-induced helix-coil transition of C. perfringens DNA under these experimental conditions lies in its sequence complexity. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Synthesis, kinetic evaluation, and utilization of a biotinylated dipeptide proline diphenyl phosphonate for the disclosure of dipeptidyl peptidase IV-like serine proteases.

    Science.gov (United States)

    Gilmore, Brendan F; Carson, Louise; McShane, Laura L; Quinn, Derek; Coulter, Wilson A; Walker, Brian

    2006-08-18

    In this study, we report on the synthesis, kinetic characterisation, and application of a novel biotinylated and active site-directed inactivator of dipeptidyl peptidase IV (DPP-IV). Thus, the dipeptide-derived proline diphenyl phosphonate NH(2)-Glu(biotinyl-PEG)-Pro(P)(OPh)(2) has been prepared by a combination of classical solution- and solid-phase methodologies and has been shown to be an irreversible inhibitor of porcine DPP-IV, exhibiting an over all second-order rate constant (k(i)/K(i)) for inhibition of 1.57 x 10(3) M(-1) min(-1). This value compares favourably with previously reported rates of inactivation of DPP-IV by dipeptides containing a P(1) proline diphenyl phosphonate grouping [B. Boduszek, J. Oleksyszyn, C.M. Kam, J. Selzler, R.E. Smith, J.C. Powers, Dipeptide phophonates as inhibitors of dipeptidyl peptidase IV, J. Med. Chem. 37 (1994) 3969-3976; B.F. Gilmore, J.F. Lynas, C.J. Scott, C. McGoohan, L. Martin, B. Walker, Dipeptide proline diphenyl phosphonates are potent, irreversible inhibitors of seprase (FAPalpha), Biochem, Biophys. Res. Commun. 346 (2006) 436-446.], thus demonstrating that the incorporation of the side-chain modified (N-biotinyl-3-(2-(2-(3-aminopropyloxy)-ethoxy)-ethoxy)-propyl) glutamic acid residue at the P(2) position is compatible with inhibitor efficacy. The utilisation of this probe for the detection of both purified dipeptidyl peptidase IV and the disclosure of a dipeptidyl peptidase IV-like activity from a clinical isolate of Porphyromonas gingivalis, using established electrophoretic and Western blotting techniques previously developed by our group, is also demonstrated.

  13. Non-cooperative immobilization of residual water bound in lyophilized photosynthetic lamellae.

    Science.gov (United States)

    Harańczyk, Hubert; Baran, Ewelina; Nowak, Piotr; Florek-Wojciechowska, Małgorzata; Leja, Anna; Zalitacz, Dorota; Strzałka, Kazimierz

    2015-12-01

    This study applied 1H-NMR in time and in frequency domain measurements to monitor the changes that occur in bound water dynamics at decreased temperature and with increased hydration level in lyophilizates of native wheat photosynthetic lamellae and in photosynthetic lamellae reconstituted from lyophilizate. Proton relaxometry (measured as free induction decay = FID) distinguishes a Gaussian component S within the NMR signal (o). This comes from protons of the solid matrix of the lamellae and consists of (i) an exponentially decaying contribution L1 from mobile membrane protons, presumably from lipids, and from water that is tightly bound to the membrane surface and thus restricted in mobility; and (ii) an exponentially decaying component L2 from more mobile, loosely bound water pool. Both proton relaxometry data and proton spectroscopy show that dry lyophilizate incubated in dry air, i.e., at a relative humidity (p/p0) of 0% reveals a relatively high hydration level. The observed liquid signal most likely originates from mobile membrane protons and a tightly bound water fraction that is sealed in pores of dry lyophilizate and thus restricted in mobility. The estimations suggest that the amount of sealed water does not exceed the value characteristic for the main hydration shell of a phospholipid. Proton spectra collected for dry lyophilizate of photosynthetic lamellae show a continuous decrease in the liquid signal component without a distinct freezing transition when it is cooled down to -60ºC, which is significantly lower than the homogeneous ice nucleation temperature [Bronshteyn, V.L. et al. Biophys. J. 65 (1993) 1853].

  14. Ion channels in a skeletal muscle cell line from a Duchenne muscular dystrophy patient.

    Science.gov (United States)

    Caviedes, R; Caviedes, P; Liberona, J L; Jaimovich, E

    1994-09-01

    A cell line (RCDMD), derived from a muscle biopsy taken from a 7-year-old patient with Duchenne muscular dystrophy (DMD), was established in vitro using conditioned media from the UCHT1 thyroid cell line as described elsewhere (Biochim Biophys Acta 1992; 1134:247-255). Unlike other cell lines established by the same procedure, RCDMD cells were highly refractory to transformation and the resulting cell line grew slowly with a doubling time of approximately 72 h. Further, cells continue to grow after more than 20 doublings and 15 passages. Some of the characteristics of the cell line include lack of reaction with antidystrophin antibodies and the presence of receptors for the dihydropyridine PN200-110 (Kd) = 0.3 +/- 0.05 nmol/L and Bmax = 1.06 +/- 0.03 pmol/mg protein) and for alpha-bungarotoxin (Kd = 1.02 +/- 0.17 nmol/L and Bmax = 4.2 +/- 0.37 pmol/mg protein). Patch clamped cells in the voltage clamp configuration lack ion currents when growing in complete medium with high serum, but they can be induced to differentiate by serum deprivation and addition of hormones and trace elements. After 5 days in differentiating medium, noninactivating, delayed rectifier potassium currents are seen. At day 12, A-type, inactivating potassium currents as well as transient inward currents are seen. In conditions in which sodium and potassium currents are absent, a very fast activating and fast inactivating calcium current was evident. The cell line offers the possibility of studying cellular mechanisms in the pathophysiology of DMD.

  15. Simulation of the effect of rogue ryanodine receptors on a calcium wave in ventricular myocytes with heart failure

    International Nuclear Information System (INIS)

    Lu, Luyao; Xia, Ling; Ye, Xuesong; Cheng, Heping

    2010-01-01

    Calcium homeostasis is considered to be one of the most important factors for the contraction and relaxation of the heart muscle. However, under some pathological conditions, such as heart failure (HF), calcium homeostasis is disordered, and spontaneous waves may occur. In this study, we developed a mathematical model of formation and propagation of a calcium wave based upon a governing system of diffusion–reaction equations presented by Izu et al (2001 Biophys. J. 80 103–20) and integrated non-clustered or 'rogue' ryanodine receptors (rogue RyRs) into a two-dimensional (2D) model of ventricular myocytes isolated from failing hearts in which sarcoplasmic reticulum (SR) Ca 2+ pools are partially unloaded. The model was then used to simulate the effect of rogue RyRs on initiation and propagation of the calcium wave in ventricular myocytes with HF. Our simulation results show that rogue RyRs can amplify the diastolic SR Ca 2+ leak in the form of Ca 2+ quarks, increase the probability of occurrence of spontaneous Ca 2+ waves even with smaller SR Ca 2+ stores, accelerate Ca 2+ wave propagation, and hence lead to delayed afterdepolarizations (DADs) and cardiac arrhythmia in the diseased heart. This investigation suggests that incorporating rogue RyRs in the Ca 2+ wave model under HF conditions provides a new view of Ca 2+ dynamics that could not be mimicked by adjusting traditional parameters involved in Ca 2+ release units and other ion channels, and contributes to understanding the underlying mechanism of HF

  16. Kinetics of hydrogen peroxide elimination by astrocytes and C6 glioma cells analysis based on a mathematical model.

    Science.gov (United States)

    Makino, Nobuo; Mise, Takeshi; Sagara, Jun-Ichi

    2008-06-01

    Oxidative stress is implicated in a variety of disorders including neurodegenerative diseases, and H(2)O(2) is important in the generation of reactive oxygen and oxidative stress. In this study, we have examined the rate of extracellular H(2)O(2) elimination and relevant enzyme activities in cultured astrocytes and C6 glioma cells and have analyzed the results based on a mathematical model. As compared with other types of cultured cells, astrocytes showed higher activity of glutathione peroxidase (GPx) but lower activities for GSH recycling. C6 cells showed relatively low GPx activity, and treatment of C6 cells with dibutyryl-cAMP, which induces astrocytic differentiation, increased catalase activity and H(2)O(2) permeation rate but exerted little effect on other enzyme activities. A mathematical model [N. Makino, K. Sasaki, N. Hashida, Y. Sakakura, A metabolic model describing the H(2)O(2) elimination by mammalian cells including H(2)O(2) permeation through cytoplasmic and peroxisomal membranes: comparison with experimental data, Biochim. Biophys. Acta 1673 (2004) 149-159.], which includes relevant enzymes and H(2)O(2) permeation through membranes, was found to be fitted well to the H(2)O(2) concentration dependences of removal reaction with the permeation rate constants as variable parameters. As compared with PC12 cells as a culture model for neuron, H(2)O(2) removal activity of astrocytes was considerably higher at physiological H(2)O(2) concentrations. The details of the mathematical model are presented in Appendix.

  17. Modelling Ca2+ bound Troponin in Excitation Contraction Coupling

    Directory of Open Access Journals (Sweden)

    Henry G. Zot

    2016-09-01

    Full Text Available To explain disparate decay rates of cytosolic Ca2+ and structural changes in the thin filaments during a twitch, we model the time course of Ca2+ bound troponin (Tn resulting from the free Ca2+ transient of fast skeletal muscle. In fibers stretched beyond overlap, the decay of Ca2+ as measured by a change in fluo 3 fluorescence is significantly slower than the intensity decay of the meridional 1/38.5 nm-1 reflection of Tn; this is not simply explained by considering only the Ca2+ binding properties of Tn alone (Matsuo, T., Iwamoto, H., and Yagi, N. (2010. Biophys. J. 99, 193-200. We apply a comprehensive model that includes the known Ca2+ binding properties of Tn in the context of the thin filament with and without cycling crossbridges. Calculations based on the model predict that the transient of Ca2+ bound Tn correlates with either the fluo 3 time course in muscle with overlapping thin and thick filaments or the intensity of the meridional 1/38.5 nm-1 reflection in overstretched muscle. Hence, cycling crossbridges delay the dissociation of Ca2+ from Tn. Correlation with the fluo 3 fluorescence change is not causal given that the transient of Ca2+ bound Tn depends on sarcomere length, whereas the fluo-3 fluorescence change does not. Transient positions of tropomyosin calculated from the time course of Ca2+ bound Tn are in reasonable agreement with the transient of measured perturbations of the Tn repeat in overlap and non-overlap muscle preparations.

  18. New ribosome-inactivating proteins with polynucleotide:adenosine glycosidase and antiviral activities from Basella rubra L. and bougainvillea spectabilis Willd.

    Science.gov (United States)

    Bolognesi, A; Polito, L; Olivieri, F; Valbonesi, P; Barbieri, L; Battelli, M G; Carusi, M V; Benvenuto, E; Del Vecchio Blanco, F; Di Maro, A; Parente, A; Di Loreto, M; Stirpe, F

    1997-12-01

    New single-chain (type 1) ribosome-inactivating proteins (RIPs) were isolated from the seeds of Basella rubra L. (two proteins) and from the leaves of Bougainvillea spectabilis Willd. (one protein). These RIPs inhibit protein synthesis both in a cell-free system, with an IC50 (concentration causing 50% inhibition) in the 10(-10) M range, and by various cell lines, with IC50S in the 10(-8)-10(-6) M range. All three RIPs released adenine not only from rat liver ribosomes but also from Escherichia coli rRNA, polyadenylic acid, herring sperm DNA, and artichoke mottled crinkle virus (AMCV) genomic RNA, thus being polynucleotide:adenosine glycosidases. The proteins from Basella rubra had toxicity to mice similar to that of most type 1 RIPs (Barbieri et al., 1993, Biochim Biophys Acta 1154: 237-282) with an LD50 (concentration that is 50% lethal) Bougainvillea spectabilis had an LD50 > 32 mg.kg-1. The N-terminal sequence of the two RIPs from Basella rubra had 80-93% identity, whereas it differed from the sequence of the RIP from Bougainvillea spectabilis. When tested with antibodies against various RIPs, the RIPs from Basella gave some cross-reactivity with sera against dianthin 32, and weak cross-reactivity with momordin I and momorcochin-S, whilst the RIP from Bougainvillea did not cross-react with any antiserum tested. An RIP from Basella rubra and one from Bougainvillea spectabilis were tested for antiviral activity, and both inhibited infection of Nicotiana benthamiana by AMCV.

  19. Evolutionary, kinetic and thermodynamic aspects on the bioenergetics of inorganic pyrophosphate (PPi) and adenosine triphosphate (ATP)

    International Nuclear Information System (INIS)

    Baltscheffsky, H.; Baltscheffsky, M.

    1995-01-01

    Energy barriers for energy carriers are of fundamental significance for the successful operation of the bioenergetic reactions in living cells. PPi and ATP are outstanding ''energy-rich'' examples of molecular ''energy currencies'' in biological systems, with kinetic barriers preventing excessively fast thermodynamically feasible hydrolysis from occurring. The barriers may be considered to facilitate the energy coupling roles of these phosphate compounds, which are to secure growth and maintain numerous other energy requiring functions. The enzymes involved in overcoming the energies of activation of the bioenergetic reactions have evolved to be very well tuned for their roles. Three aspects will be discussed in some detail. The first is the fact that ATP at neutral pH is considerably more energy-rich than PPi, which thus has been called a ''poor man's ATP''. This is exemplified by the kinetic and thermodynamic differences observed between the requirements for the photosynthetic formation of PPi and ATP in certain photobacterial chromatophores by varying levels of energy supply. At lower pH, PPi and ATP are equally energy-rich, which may be of significance for acidophiles. The second concerns the possible evolutionary significance of the finding that, in the dark, a pH gradient suffices to drive extensive PPi synthesis, whereas ATP synthesis requires both a pH gradient and a membrane potential (Strid et al, Biochim. Biophys. Acta 892 (1987) 236-244). Thirdly, PPi as the most plausible predecessor to ATP in the origin and early evolution of life, will be discussed. (author). Abstract only

  20. Simulation of the effect of rogue ryanodine receptors on a calcium wave in ventricular myocytes with heart failure

    Science.gov (United States)

    Lu, Luyao; Xia, Ling; Ye, Xuesong; Cheng, Heping

    2010-06-01

    Calcium homeostasis is considered to be one of the most important factors for the contraction and relaxation of the heart muscle. However, under some pathological conditions, such as heart failure (HF), calcium homeostasis is disordered, and spontaneous waves may occur. In this study, we developed a mathematical model of formation and propagation of a calcium wave based upon a governing system of diffusion-reaction equations presented by Izu et al (2001 Biophys. J. 80 103-20) and integrated non-clustered or 'rogue' ryanodine receptors (rogue RyRs) into a two-dimensional (2D) model of ventricular myocytes isolated from failing hearts in which sarcoplasmic reticulum (SR) Ca2+ pools are partially unloaded. The model was then used to simulate the effect of rogue RyRs on initiation and propagation of the calcium wave in ventricular myocytes with HF. Our simulation results show that rogue RyRs can amplify the diastolic SR Ca2+ leak in the form of Ca2+ quarks, increase the probability of occurrence of spontaneous Ca2+ waves even with smaller SR Ca2+ stores, accelerate Ca2+ wave propagation, and hence lead to delayed afterdepolarizations (DADs) and cardiac arrhythmia in the diseased heart. This investigation suggests that incorporating rogue RyRs in the Ca2+ wave model under HF conditions provides a new view of Ca2+ dynamics that could not be mimicked by adjusting traditional parameters involved in Ca2+ release units and other ion channels, and contributes to understanding the underlying mechanism of HF.

  1. Control of a flexible beam actuated by macro-fiber composite patches: I. Modeling and feedforward trajectory control

    International Nuclear Information System (INIS)

    Schröck, Johannes; Meurer, Thomas; Kugi, Andreas

    2011-01-01

    This paper considers a systematic approach for motion planning and feedforward control design for a flexible cantilever actuated by piezoelectric macro-fiber composite (MFC) patches. For accurate feedforward tracking control, special attention has to be paid to the inherent nonlinear hysteresis and creep behavior of these actuators. In order to account for these effects an appropriate compensator is applied which allows us to perform the tracking controller design on the basis of a linear infinite-dimensional model. A detailed analysis of the nonlinear actuator behavior as well as the compensator design and the overall experimental validation is presented in the companion paper (Schröck et al 2011 Smart Mater. Struct. 20 015016). The governing equations of motion of the hysteresis and creep compensated cantilever are determined by means of the extended Hamilton's principle. This allows us to consider the influence of the bonded patch actuators on the mechanical properties of the underlying beam structure in a straightforward manner and results in a model with spatially varying system parameters. For the solution of the motion planning and feedforward control problem a flatness-based methodology is proposed. In a first step, the infinite-dimensional system of the MFC-actuated flexible cantilever is approximated by a finite-dimensional model, where all system variables, i.e. the states, input and output, can be parameterized in terms of a so-called flat output. In a second step, it is shown by numerical simulations that these parameterizations converge with increasing system order of the finite-dimensional model such that the feedforward control input can be directly calculated in order to realize prescribed output trajectories

  2. 论《春季日语教程》中普特帕特的种族身份越界%A Study of Puttputt’ s Transgression of Ethnical Identity in Japanese by Spring

    Institute of Scientific and Technical Information of China (English)

    石嘉璇

    2014-01-01

    The novel Japanese by Spring shows the difference of black intellectuals in the process of con-structing their ethnical identities by depicting the character Puttputt as“a black professor with white con-sciousness”. Based on transgression, this thesis analyzes Puttbutt ’ s transgression of ethnical identity which results from political correctness and ethnical negotiation, and it aims to show these black intellec-tuals’ efforts in dealing with ethnical relationship. Besides, transgression, as a writing technique, helps Reed express his satire to racism and opportunism under the background of multiculturalism.%小说《春季日语教程》中塑造的“白人意识的黑人学者”，形象生动地体现了黑人的种族身份越界，阐释了黑人知识分子在种族身份构建过程中所表现出的与众不同。基于种族越界叙事，分析黑人教授普特帕特在“政治正确”以及“种族协商”策略之下的种族身份越界，可以展现黑人知识分子为寻求种族关系发展做出的努力。同时种族身份越界方法的使用，也有效传递了里德对于种族主义以及文化多元主义背景下产生的各种投机行为的讽刺。

  3. Heterobifunctional crosslinkers for tethering single ligand molecules to scanning probes

    International Nuclear Information System (INIS)

    Riener, Christian K.; Kienberger, Ferry; Hahn, Christoph D.; Buchinger, Gerhard M.; Egwim, Innocent O.C.; Haselgruebler, Thomas; Ebner, Andreas; Romanin, Christoph; Klampfl, Christian; Lackner, Bernd; Prinz, Heino; Blaas, Dieter; Hinterdorfer, Peter; Gruber, Hermann J.

    2003-01-01

    Single molecule recognition force microscopy (SMRFM) is a versatile atomic force microscopy (AFM) method to probe specific interactions of cognitive molecules on the single molecule level. It allows insights to be gained into interaction potentials and kinetic barriers and is capable of mapping interaction sites with nm positional accuracy. These applications require a ligand to be attached to the AFM tip, preferably by a distensible poly(ethylene glycol) (PEG) chain between the measuring tip and the ligand molecule. The PEG chain greatly facilitates specific binding of the ligand to immobile receptor sites on the sample surface. The present study contributes to tip-PEG-ligand tethering in three ways: (i) a convenient synthetic route was found to prepare NH 2 -PEG-COOH which is the key intermediate for long heterobifunctional crosslinkers; (ii) a variety of heterobifunctional PEG derivatives for tip-PEG-ligand linking were prepared from NH 2 -PEG-COOH; (iii) in particular, a new PEG crosslinker with one thiol-reactive end and one terminal nitrilotriacetic acid (NTA) group was synthesized and successfully used to tether His 6 -tagged protein molecules to AFM tips via noncovalent NTA-Ni 2+ -His 6 bridges. The new crosslinker was applied to link a recombinant His 6 -tagged fragment of the very-low density lipoprotein receptor to the AFM tip whereupon specific docking to the capsid of human rhinovirus particles was observed by force microscopy. In a parallel study, the specific interaction of the small GTPase Ran with the nuclear import receptor importin β1 was studied in detail by SMRFM, using the new crosslinker to link His 6 -tagged Ran to the measuring tip [Nat. Struct. Biol. (2003), 10, 553-557

  4. Engineering the future of military tactical vehicles and systems with modeling and simulation

    Science.gov (United States)

    Loew, Matthew; Watters, Brock

    2005-05-01

    Stewart & Stevenson has developed a Modeling and Simulation approach based on Systems Engineering principles for the development of future military vehicles and systems. This approach starts with a requirements analysis phase that captures and distills the design requirements into a list of parameterized values. A series of executable engineering models are constructed to allow the requirements to be transformed into systems with definable architectures with increasing levels of fidelity. Required performance parameters are available for importation into a variety of modeling and simulation tools including PTC Pro/ENGINEER (for initial engineering models, mechanisms, packaging, and detailed 3-Dimensional solid models), LMS International Virtual.Lab Motion (for vehicle dynamics and ride analysis) and AVL Cruise (Powertrain simulations). Structural analysis and optimization (performed in ANSYS, Pro/MECHANICA, and Altair OptiStruct) is based on the initial geometry from Pro/ENGINEER. Spreadsheets are used for requirements analysis, design documentation and first-order studies. Collectively, these models serve as templates for all design activities. Design variables initially studied within a simplified system model can be cascaded down as the new requirements for a sub-system model. By utilizing this approach premature decisions on systems architectures can be avoided. Ultimately, the systems that are developed are optimally able to meet the requirements by utilizing this top-down approach. Additionally, this M&S approach is seen as a life-cycle tool useful in initially assisting with project management activities through the initial and detail design phases and serves as a template for testing and validation/verification activities. Furthermore, because of the multi-tiered approach, there is natural re-use possible with the models as well.

  5. Temperature driven annealing of perforations in bicellar model membranes.

    Science.gov (United States)

    Nieh, Mu-Ping; Raghunathan, V A; Pabst, Georg; Harroun, Thad; Nagashima, Kazuomi; Morales, Hannah; Katsaras, John; Macdonald, Peter

    2011-04-19

    Bicellar model membranes composed of 1,2-dimyristoylphosphatidylcholine (DMPC) and 1,2-dihexanoylphosphatidylcholine (DHPC), with a DMPC/DHPC molar ratio of 5, and doped with the negatively charged lipid 1,2-dimyristoylphosphatidylglycerol (DMPG), at DMPG/DMPC molar ratios of 0.02 or 0.1, were examined using small angle neutron scattering (SANS), (31)P NMR, and (1)H pulsed field gradient (PFG) diffusion NMR with the goal of understanding temperature effects on the DHPC-dependent perforations in these self-assembled membrane mimetics. Over the temperature range studied via SANS (300-330 K), these bicellar lipid mixtures exhibited a well-ordered lamellar phase. The interlamellar spacing d increased with increasing temperature, in direct contrast to the decrease in d observed upon increasing temperature with otherwise identical lipid mixtures lacking DHPC. (31)P NMR measurements on magnetically aligned bicellar mixtures of identical composition indicated a progressive migration of DHPC from regions of high curvature into planar regions with increasing temperature, and in accord with the "mixed bicelle model" (Triba, M. N.; Warschawski, D. E.; Devaux, P. E. Biophys. J.2005, 88, 1887-1901). Parallel PFG diffusion NMR measurements of transbilayer water diffusion, where the observed diffusion is dependent on the fractional surface area of lamellar perforations, showed that transbilayer water diffusion decreased with increasing temperature. A model is proposed consistent with the SANS, (31)P NMR, and PFG diffusion NMR data, wherein increasing temperature drives the progressive migration of DHPC out of high-curvature regions, consequently decreasing the fractional volume of lamellar perforations, so that water occupying these perforations redistributes into the interlamellar volume, thereby increasing the interlamellar spacing. © 2011 American Chemical Society

  6. The substructure of immunoglobulin G resolved to 25 kDa using amplitude modulation AFM in air

    International Nuclear Information System (INIS)

    Thomson, Neil H.

    2005-01-01

    Amplitude modulation (or tapping-mode) atomic force microscopy (AM AFM or TM AFM) in air can reveal sub-molecular details of isolated multi-subunit proteins, such as immunoglobulin G (IgG) antibodies, on atomically flat support surfaces such as mica [A. San Paulo, R. Garcia, Biophys. J. 78(3) (2000) 1599]. This is achieved by controlling the microscope imaging parameters (e.g. cantilever drive frequency and set-point amplitude) to keep the AFM tip predominantly in the attractive force regime. Under these conditions, the 50 kDa F c and F ab subunits can be resolved when the molecule has the appropriate orientation on the surface. The presence of a water layer on hydrophilic mica is an important factor affecting imaging contrast, a consequence of capillary neck formation between tip and surface [L. Zitzler, S. Herminghaus, F. Mugele, Phys. Rev. B 66(15) (2002) 155436]. Desiccation of samples to remove surface bound water layers can yield reproducible imaging of the IgG substructure [N.H. Thomson, J. Microsc. (Oxford) 217(3) (2004) 193]. This approach has also given higher resolution than previously achieved, down to about 25 kDa, and these data are detailed here. These subdomains are formed as two immunoglobulin folds from the light and heavy peptide chains of the IgG crossover. This result has been validated by comparing the AFM images with X-ray crystallography data from the protein data bank. These data show that the AFM can obtain 25 kDa resolution on isolated protein molecules with commercially available silicon tips, but, as expected for a local probe technique, resolution is highly dependent on the macromolecular orientation on the support surface

  7. Non invasive radiofrequency diagnostics of cancer. The Bioscanner — Trimprob technology and clinical applications

    Science.gov (United States)

    Vedruccio, Clarbruno; Ricci Vedruccio, Carla

    2011-12-01

    A new paper by Pokorny, Vedruccio, Cifra, Kucera, titled Cancer physics: Diagnostics based on damped cellular elasto-electrical vibrations in microtubules, recently available on Eur. Biophys. J., discloses the mechanism of active grown cancer tissues interaction with a Non- Linear Resonance Interaction (NLRI) Bioscanner Trimprob diagnostic device that is certified and ready to be used to investigate suspected cases of disease and cancer. This technology spreads early capabilities of cancer detection by means of low level radiofrequency oscillations in UHF band. The system is based on an unique and extremely innovative non- linear radiofrequency oscillator working on 462-465 MHz plus the harmonics. The diseased tissues suspected of cancer, are irradiated by means of a handy probe near field emission, while a spectrum analyzer placed in the far field detects by means of a small antenna, the oscillator interaction within the tissues. The Bioscanner is characterized by a high dynamic range, in the order of 30 or more decibel, and is useful for detection of small cancer agglomerates, if used by a well trained operator. At the resonance, the free running oscillator locks-in on the specific interaction frequency, in a sharp frequency window centered on 462 MHz; the resulting effect is evidenced by a deep decrease of the 462 MHz spectral line propagation in the far field around the oscillator probe. The NLRI provides a selective characterization, like a sort of a electronic biopsy response of biologic tissues in support of modern imaging diagnostics. Further to existing literature describing methods for cancer detections by means of electromagnetic fields this paper shows this innovative in vivo medical diagnostic equipment and some clinical applications.

  8. A translational study "case report" on the small molecule "energy blocker" 3-bromopyruvate (3BP) as a potent anticancer agent: from bench side to bedside.

    Science.gov (United States)

    Ko, Y H; Verhoeven, H A; Lee, M J; Corbin, D J; Vogl, T J; Pedersen, P L

    2012-02-01

    The small alkylating molecule, 3-bromopyruvate (3BP), is a potent and specific anticancer agent. 3BP is different in its action from most currently available chemo-drugs. Thus, 3BP targets cancer cells' energy metabolism, both its high glycolysis ("Warburg Effect") and mitochondrial oxidative phosphorylation. This inhibits/ blocks total energy production leading to a depletion of energy reserves. Moreover, 3BP as an "Energy Blocker", is very rapid in killing such cells. This is in sharp contrast to most commonly used anticancer agents that usually take longer to show a noticeable effect. In addition, 3BP at its effective concentrations that kill cancer cells has little or no effect on normal cells. Therefore, 3BP can be considered a member, perhaps one of the first, of a new class of anticancer agents. Following 3BP's discovery as a novel anticancer agent in vitro in the Year 2000 (Published in Ko et al. Can Lett 173:83-91, 2001), and also as a highly effective and rapid anticancer agent in vivo shortly thereafter (Ko et al. Biochem Biophys Res Commun 324:269-275, 2004), its efficacy as a potent anticancer agent in humans was demonstrated. Here, based on translational research, we report results of a case study in a young adult cancer patient with fibrolamellar hepatocellular carcinoma. Thus, a bench side discovery in the Department of Biological Chemistry at Johns Hopkins University, School of Medicine was taken effectively to bedside treatment at Johann Wolfgang Goethe University Frankfurt/Main Hospital, Germany. The results obtained hold promise for 3BP as a future cancer therapeutic without apparent cyto-toxicity when formulated properly.

  9. The cytotoxicity of 3-bromopyruvate in breast cancer cells depends on extracellular pH.

    Science.gov (United States)

    Azevedo-Silva, João; Queirós, Odília; Ribeiro, Ana; Baltazar, Fátima; Young, Ko H; Pedersen, Peter L; Preto, Ana; Casal, Margarida

    2015-04-15

    Although the anti-cancer properties of 3BP (3-bromopyruvate) have been described previously, its selectivity for cancer cells still needs to be explained [Ko et al. (2001) Cancer Lett. 173, 83-91]. In the present study, we characterized the kinetic parameters of radiolabelled [14C] 3BP uptake in three breast cancer cell lines that display different levels of resistance to 3BP: ZR-75-1 < MCF-7 < SK-BR-3. At pH 6.0, the affinity of cancer cells for 3BP transport correlates with their sensitivity, a pattern that does not occur at pH 7.4. In the three cell lines, the uptake of 3BP is dependent on the protonmotive force and is decreased by MCTs (monocarboxylate transporters) inhibitors. In the SK-BR-3 cell line, a sodium-dependent transport also occurs. Butyrate promotes the localization of MCT-1 at the plasma membrane and increases the level of MCT-4 expression, leading to a higher sensitivity for 3BP. In the present study, we demonstrate that this phenotype is accompanied by an increase in affinity for 3BP uptake. Our results confirm the role of MCTs, especially MCT-1, in 3BP uptake and the importance of cluster of differentiation (CD) 147 glycosylation in this process. We find that the affinity for 3BP transport is higher when the extracellular milieu is acidic. This is a typical phenotype of tumour microenvironment and explains the lack of secondary effects of 3BP already described in in vivo studies [Ko et al. (2004) Biochem. Biophys. Res. Commun. 324, 269-275].

  10. Replacement of Ser108 in Plasmodium falciparum enolase results in weak Mg(II) binding: role of a parasite-specific pentapeptide insert in stabilizing the active conformation of the enzyme.

    Science.gov (United States)

    Dutta, Sneha; Mukherjee, Debanjan; Jarori, Gotam K

    2015-06-01

    A distinct structural feature of Plasmodium falciparum enolase (Pfeno) is the presence of a five amino acid insert -104EWGWS108- that is not found in host enolases. Its conservation among apicomplexan enolases has raised the possibility of its involvement in some important physiological function(s). Deletion of this sequence is known to lower k(cat)/K(m), increase K(a) for Mg(II) and convert dimer into monomers (Vora HK, Shaik FR, Pal-Bhowmick I, Mout R & Jarori GK (2009) Arch Biochem Biophys 485, 128-138). These authors also raised the possibility of the formation of an H-bond between Ser108 and Leu49 that could stabilize the apo-Pfeno in an active closed conformation that has high affinity for Mg(II). Here, we examined the effect of replacement of Ser108 with Gly/Ala/Thr on enzyme activity, Mg(II) binding affinity, conformational states and oligomeric structure and compared it with native recombinant Pfeno. The results obtained support the view that Ser108 is likely to be involved in the formation of certain crucial H-bonds with Leu49. The presence of these interactions can stabilize apo-Pfeno in an active closed conformation similar to that of Mg(II) bound yeast enolase. As predicted, S108G/A-Pfeno variants (where Ser108-Leu49 H-bonds are likely to be disrupted) were found to exist in an open conformation and had low affinity for Mg(II). They also required Mg(II) induced conformational changes to acquire the active closed conformational state essential for catalysis. The possible physiological relevance of apo-Pfeno being in such an active state is discussed. © 2015 FEBS.

  11. Heme orientational disorder in human adult hemoglobin reconstituted with a ring fluorinated heme and its functional consequences

    International Nuclear Information System (INIS)

    Nagao, Satoshi; Hirai, Yueki; Kawano, Shin; Imai, Kiyohiro; Suzuki, Akihiro; Yamamoto, Yasuhiko

    2007-01-01

    A ring fluorinated heme, 13,17-bis(2-carboxylatoethyl)-3,8-diethyl-2-fluoro-7,12, 18-trimethyl-porphyrin-atoiron(III), has been incorporated into human adult hemoglobin (Hb A). The heme orientational disorder in the individual subunits of the protein has been readily characterized using 19 F NMR and the O 2 binding properties of the protein have been evaluated through the oxygen equilibrium analysis. The equilibrated orientations of hemes in α- and β- subunits of the reconstituted protein were found to be almost completely opposite to each other, and hence were largely different from those of the native and the previously reported reconstituted proteins [T. Jue, G.N. La Mar, Heme orientational heterogeneity in deuterohemin-reconstituted horse and human hemoglobin characterized by proton nuclear magnetic resonance spectroscopy, Biochem. Biophys. Res. Commun. 119 (1984) 640-645]. Despite the large difference in the degree of the heme orientational disorder in the subunits of the proteins, the O 2 affinity and the cooperativity of the protein reconstituted with 2-MF were similar to those of the proteins reconstituted with a series of hemes chemically modified at the heme 3- and 8-positions [K. Kawabe, K. Imaizumi, Z. Yoshida, K. Imai, I. Tyuma, Studies on reconstituted myoglobins and hemoglobins II. Role of the heme side chains in the oxygenation of hemoglobin, J. Biochem. 92 (1982) 1713-1722], whose O 2 affinity and cooperativity were higher and lower, respectively, relative to those of native protein. These results indicated that the heme orientational disorder could exert little effect, if any, on the O 2 affinity properties of Hb A. This finding provides new insights into structure-function relationship of Hb A

  12. Non invasive radiofrequency diagnostics of cancer. The Bioscanner — Trimprob technology and clinical applications

    International Nuclear Information System (INIS)

    Vedruccio, Clarbruno; Vedruccio, Carla Ricci

    2011-01-01

    A new paper by Pokorny, Vedruccio, Cifra, Kucera, titled Cancer physics: Diagnostics based on damped cellular elasto-electrical vibrations in microtubules, recently available on Eur. Biophys. J., discloses the mechanism of active grown cancer tissues interaction with a Non- Linear Resonance Interaction (NLRI) Bioscanner Trimprob diagnostic device that is certified and ready to be used to investigate suspected cases of disease and cancer. This technology spreads early capabilities of cancer detection by means of low level radiofrequency oscillations in UHF band. The system is based on an unique and extremely innovative non- linear radiofrequency oscillator working on 462-465 MHz plus the harmonics. The diseased tissues suspected of cancer, are irradiated by means of a handy probe near field emission, while a spectrum analyzer placed in the far field detects by means of a small antenna, the oscillator interaction within the tissues. The Bioscanner is characterized by a high dynamic range, in the order of 30 or more decibel, and is useful for detection of small cancer agglomerates, if used by a well trained operator. At the resonance, the free running oscillator locks-in on the specific interaction frequency, in a sharp frequency window centered on 462 MHz; the resulting effect is evidenced by a deep decrease of the 462 MHz spectral line propagation in the far field around the oscillator probe. The NLRI provides a selective characterization, like a sort of a electronic biopsy response of biologic tissues in support of modern imaging diagnostics. Further to existing literature describing methods for cancer detections by means of electromagnetic fields this paper shows this innovative in vivo medical diagnostic equipment and some clinical applications.

  13. Apocrustacyanin C(1) crystals grown in space and on earth using vapour-diffusion geometry: protein structure refinements and electron-density map comparisons.

    Science.gov (United States)

    Habash, Jarjis; Boggon, Titus J; Raftery, James; Chayen, Naomi E; Zagalsky, Peter F; Helliwell, John R

    2003-07-01

    Models of apocrustacyanin C(1) were refined against X-ray data recorded on Bending Magnet 14 at the ESRF to resolutions of 1.85 and 2 A from a space-grown and an earth-grown crystal, respectively, both using vapour-diffusion crystal-growth geometry. The space crystals were grown in the APCF on the NASA Space Shuttle. The microgravity crystal growth showed a cyclic nature attributed to Marangoni convection, thus reducing the benefits of the microgravity environment, as reported previously [Chayen et al. (1996), Q. Rev. Biophys. 29, 227-278]. A subsequent mosaicity evaluation, also reported previously, showed only a partial improvement in the space-grown crystals over the earth-grown crystals [Snell et al. (1997), Acta Cryst. D53, 231-239], contrary to the case for lysozyme crystals grown in space with liquid-liquid diffusion, i.e. without any major motion during growth [Snell et al. (1995), Acta Cryst. D52, 1099-1102]. In this paper, apocrustacyanin C(1) electron-density maps from the two refined models are now compared. It is concluded that the electron-density maps of the protein and the bound waters are found to be better overall for the structures of apocrustacyanin C(1) studied from the space-grown crystal compared with those from the earth-grown crystal, even though both crystals were grown using vapour-diffusion crystal-growth geometry. The improved residues are on the surface of the protein, with two involved in or nearby crystal lattice-forming interactions, thus linking an improved crystal-growth mechanism to the molecular level. The structural comparison procedures developed should themselves be valuable for evaluating crystal-growth procedures in the future.

  14. Factors contributing to troponin exchange in myofibrils and in solution.

    Science.gov (United States)

    She, M; Trimble, D; Yu, L C; Chalovich, J M

    2000-01-01

    The troponin complex in a muscle fiber can be replaced with exogenous troponin by using a gentle exchange procedure in which the actin-tropomyosin complex is never devoid of a full complement of troponin (Brenner et al. (1999) Biophys J 77: 2677-2691). The mechanism of this exchange process and the factors that influence this exchange are poorly understood. In this study, the exchange process has now been examined in myofibrils and in solution. In myofibrils under rigor conditions, troponin exchange occurred preferentially in the region of overlap between actin and myosin when the free Ca2+ concentration was low. At higher concentrations of Ca2+, the exchange occurred uniformly along the actin. Ca2+ also accelerated troponin exchange in solution but the effect of S1 could not be confirmed in solution experiments. The rate of exchange in solution was insensitive to moderate changes in pH or ionic strength. Increasing the temperature resulted in a two-fold increase in rate with each 10 degrees C increase in temperature. A sequential two step model of troponin binding to actin-tropomyosin could simulate the observed association and dissociation transients. In the absence of Ca2+ or rigor S1, the following rate constants could describe the binding process: k1 = 7.12 microM(-1) s(-1), k(-1) = 0.65 s(-1), k2 = 0.07 s(-1), k(-2) = 0.0014 s(-1). The slow rate of detachment of troponin from actin (k(-2)) limits the rate of exchange in solution and most likely contributes to the slow rate of exchange in fibers.

  15. On small things in water moving around: Purcell's contributions to biology

    Science.gov (United States)

    Berg, Howard

    2012-02-01

    I went to see Purcell after finishing my course work for the Ph.D. (1961) to ask whether I might join his group. ``But I don't have any graduate students,`` he said. ``Why is that?'' I asked. ``I can't think of anything to do,'' he replied. That was a wipe out. After I had finished my Ph.D. with Ramsey on the hydrogen maser (1964), Ed and I came up with an idea that led to work on sedimentation field-flow fractionation (PNAS 1967). We had hoped this method would be useful for biology, but problems of adsorption of proteins to surfaces stood in the way. Then I moved over to the biology department and got interested in the motile behavior of bacteria (1968). Here was a subject that I thought Ed would really enjoy. There were wonderful movies made by Norbert Pfennig of experiments done by Theodor Engelmann in the 1880's. We found a 16-mm projector and looked at these movies on Ed's office wall. Ed's first comment proved seminal, ''How can such a small cell swim in a straight line?'' We thought about how cells count molecules in their environment and wrote ``Physics of chemoreception,'' (Biophys. J.,1977). In the meantime, Ed gave a memorable lecture at Viki Weisskopf's retirement symposium, his classic ``Life at low Reynolds number'' (Am. J. Phys. 1977). Ed really wanted to understand what it would be like to swim like a bacterium! He wasn't very interested in what the literature had to say about such a problem, he wanted to think it through for himself. My role was straight man. I very much enjoyed the ride.

  16. Contamination of current-clamp measurement of neuron capacitance by voltage-dependent phenomena

    Science.gov (United States)

    White, William E.

    2013-01-01

    Measuring neuron capacitance is important for morphological description, conductance characterization, and neuron modeling. One method to estimate capacitance is to inject current pulses into a neuron and fit the resulting changes in membrane potential with multiple exponentials; if the neuron is purely passive, the amplitude and time constant of the slowest exponential give neuron capacitance (Major G, Evans JD, Jack JJ. Biophys J 65: 423–449, 1993). Golowasch et al. (Golowasch J, Thomas G, Taylor AL, Patel A, Pineda A, Khalil C, Nadim F. J Neurophysiol 102: 2161–2175, 2009) have shown that this is the best method for measuring the capacitance of nonisopotential (i.e., most) neurons. However, prior work has not tested for, or examined how much error would be introduced by, slow voltage-dependent phenomena possibly present at the membrane potentials typically used in such work. We investigated this issue in lobster (Panulirus interruptus) stomatogastric neurons by performing current clamp-based capacitance measurements at multiple membrane potentials. A slow, voltage-dependent phenomenon consistent with residual voltage-dependent conductances was present at all tested membrane potentials (−95 to −35 mV). This phenomenon was the slowest component of the neuron's voltage response, and failure to recognize and exclude it would lead to capacitance overestimates of several hundredfold. Most methods of estimating capacitance depend on the absence of voltage-dependent phenomena. Our demonstration that such phenomena make nonnegligible contributions to neuron responses even at well-hyperpolarized membrane potentials highlights the critical importance of checking for such phenomena in all work measuring neuron capacitance. We show here how to identify such phenomena and minimize their contaminating influence. PMID:23576698

  17. USO DA eCG PARA FORMAÇÃO DO CORPO LÚTEO EQÜINO E PRODUÇÃO DE PROGESTERONA

    Directory of Open Access Journals (Sweden)

    Tiago Gomes RODRIGUES

    2015-12-01

    Full Text Available Este estudo foi conduzido com a finalidade de avaliar o uso da gonadotrofina coriônica eqüina (eCG logo após a ovulação de éguas com o objetivo avaliar a formação do corpo lúteo e produção de progesterona. Utilizou-se 50 éguas durante 2 estações de monta 2011/2012 e 2012/2013. Com auxílio da ultrassonografia as éguas foram monitoradas as características dos órgãos genitais durante o estro até o dia da ovulação (D0 e no diestro em D2, D4 e D8. O experimento foi dividido em 2 tratamentos: Tratamento I (n=25 – éguas com ovulação natural e tratamento II (n=25  – éguas com ovulação induzida. Verificada a ovulação, os tratamentos foram sub divididas em 5 grupos de 5 animais, obedecendo a administração do fármaco estudado (eCG, sendo GI: controle; GII: 250 UI eCG no DO; GIII: 250 UI eCG no DO + 250 UI eCG no D2; GIV: 500 UI no Do; e GV: 500 UI eCG no D0 + 500 UI no D2. Para a avaliação do efeito dose resposta do fármaco e influência do eCG sob a glândula luteínica, foram coletados os dados: tônus uterino, ecogenicidade e tamanho do corpo lúteo (CL e concentração de progesterona. Na análise estatística somente quando comparando o GV entre os dois tratamentos há diferença estatística para o D8 na concentração de progesterona. Portanto o uso da eCG no momento da ovulação, não produziu efeito significativo esperado, mas este trabalho inicial abre portas para novas investigações a respeito desta biomolécula, e que venha contribuir na biotecnologia reprodutiva equina.

  18. Impact initiation of explosives and propellants via statistical crack mechanics

    Science.gov (United States)

    Dienes, J. K.; Zuo, Q. H.; Kershner, J. D.

    2006-06-01

    A statistical approach has been developed for modeling the dynamic response of brittle materials by superimposing the effects of a myriad of microcracks, including opening, shear, growth and coalescence, taking as a starting point the well-established theory of penny-shaped cracks. This paper discusses the general approach, but in particular an application to the sensitivity of explosives and propellants, which often contain brittle constituents. We examine the hypothesis that the intense heating by frictional sliding between the faces of a closed crack during unstable growth can form a hot spot, causing localized melting, ignition, and fast burn of the reactive material adjacent to the crack. Opening and growth of a closed crack due to the pressure of burned gases inside the crack and interactions of adjacent cracks can lead to violent reaction, with detonation as a possible consequence. This approach was used to model a multiple-shock experiment by Mulford et al. [1993. Initiation of preshocked high explosives PBX-9404, PBX-9502, PBX-9501, monitored with in-material magnetic gauging. In: Proceedings of the 10th International Detonation Symposium, pp. 459-467] involving initiation and subsequent quenching of chemical reactions in a slab of PBX 9501 impacted by a two-material flyer plate. We examine the effects of crack orientation and temperature dependence of viscosity of the melt on the response. Numerical results confirm our theoretical finding [Zuo, Q.H., Dienes, J.K., 2005. On the stability of penny-shaped cracks with friction: the five types of brittle behavior. Int. J. Solids Struct. 42, 1309-1326] that crack orientation has a significant effect on brittle behavior, especially under compressive loading where interfacial friction plays an important role. With a reasonable choice of crack orientation and a temperature-dependent viscosity obtained from molecular dynamics calculations, the calculated particle velocities compare well with those measured using

  19. On employing H216O, H217O, H218O, and D216O lines as frequency standards in the 15-170 cm-1 window

    International Nuclear Information System (INIS)

    Furtenbacher, Tibor; Csaszar, Attila G.

    2008-01-01

    The protocol MARVEL, standing for measured active rotational-vibrational energy levels, is used to study high-accuracy measurements of rotational lines of four isotopologues of water, H 2 16 O, H 2 17 O, H 2 18 O, and D 2 16 O, obtained by spectroscopy in the far-infrared (FIR) region of 15-170 cm -1 by Matsushima et al. [Matsushima F, Odashima H, Iwasaki T, Tsunekawa S, Takagi K. Frequency measurement of pure rotational transitions of H 2 O from 0.5 to 5 THz. J Mol Struct 1995; 352/353, 371-8; Matsushima F, Nagase H, Nakauchi T, Odashima H, Takagi K. Frequency measurement of pure rotational transitions of H 2 17 O and H 2 18 O from 0.5 to 5 THz. J Mol Spectrosc 1999;193: 217-23; Matsushima F, Matsunaga M, Qian GY, Ohtaki Y, Wang RL, Takagi K. Frequency measurement of pure rotational transitions of D 2 O from 0.5 to 5 THz. J Mol Spectrosc 2001;206: 41-6; Matsushima F, Tomatsu N, Nagai T, Moriwaki Y, Takagi K. Frequency measurement of pure rotational transitions in the v 2 =1 state of H 2 O. J Mol Spectrosc 2006;235: 190-5]. MARVEL validates the high accuracy of most of the measured line positions. It results in a considerable number of energy levels with an average internal uncertainty of only 40 kHz (2σ). It also supports serious inaccuracy problems when Watson-type A-reduced Hamiltonians are used for predicting the highly accurate rotational measurements for water. Finally, MARVEL suggests a large number of para-water levels, for example 41 for H 2 16 O, which are candidates for becoming frequency standards in the FIR region of 15-170 cm -1 (the 0.5-5 THz window) when an accuracy of about 0.1 MHz is deemed to be sufficient

  20. False discovery rate control incorporating phylogenetic tree increases detection power in microbiome-wide multiple testing.

    Science.gov (United States)

    Xiao, Jian; Cao, Hongyuan; Chen, Jun

    2017-09-15

    Next generation sequencing technologies have enabled the study of the human microbiome through direct sequencing of microbial DNA, resulting in an enormous amount of microbiome sequencing data. One unique characteristic of microbiome data is the phylogenetic tree that relates all the bacterial species. Closely related bacterial species have a tendency to exhibit a similar relationship with the environment or disease. Thus, incorporating the phylogenetic tree information can potentially improve the detection power for microbiome-wide association studies, where hundreds or thousands of tests are conducted simultaneously to identify bacterial species associated with a phenotype of interest. Despite much progress in multiple testing procedures such as false discovery rate (FDR) control, methods that take into account the phylogenetic tree are largely limited. We propose a new FDR control procedure that incorporates the prior structure information and apply it to microbiome data. The proposed procedure is based on a hierarchical model, where a structure-based prior distribution is designed to utilize the phylogenetic tree. By borrowing information from neighboring bacterial species, we are able to improve the statistical power of detecting associated bacterial species while controlling the FDR at desired levels. When the phylogenetic tree is mis-specified or non-informative, our procedure achieves a similar power as traditional procedures that do not take into account the tree structure. We demonstrate the performance of our method through extensive simulations and real microbiome datasets. We identified far more alcohol-drinking associated bacterial species than traditional methods. R package StructFDR is available from CRAN. chen.jun2@mayo.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  1. Structural Basis of Low-Affinity Nickel Binding to the Nickel-Responsive Transcription Factor NikR from Escherichia coli

    International Nuclear Information System (INIS)

    Phillips, C.; Schreiter, E.; Stultz, C.; Drennan, C.

    2010-01-01

    Escherichia coli NikR regulates cellular nickel uptake by binding to the nik operon in the presence of nickel and blocking transcription of genes encoding the nickel uptake transporter. NikR has two binding affinities for the nik operon: a nanomolar dissociation constant with stoichiometric nickel and a picomolar dissociation constant with excess nickel (Bloom, S. L., and Zamble, D. B. (2004) Biochemistry 43, 10029-10038; Chivers, P. T., and Sauer, R. T. (2002) Chem. Biol. 9, 1141-1148). While it is known that the stoichiometric nickel ions bind at the NikR tetrameric interface (Schreiter, E. R., et al. (2003) Nat. Struct. Biol. 10, 794-799; Schreiter, E. R., et al. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 13676-13681), the binding sites for excess nickel ions have not been fully described. Here we have determined the crystal structure of NikR in the presence of excess nickel to 2.6 (angstrom) resolution and have obtained nickel anomalous data (1.4845 (angstrom)) in the presence of excess nickel for both NikR alone and NikR cocrystallized with a 30-nucleotide piece of double-stranded DNA containing the nik operon. These anomalous data show that excess nickel ions do not bind to a single location on NikR but instead reveal a total of 22 possible low-affinity nickel sites on the NikR tetramer. These sites, for which there are six different types, are all on the surface of NikR, and most are found in both the NikR alone and NikR-DNA structures. Using a combination of crystallographic data and molecular dynamics simulations, the nickel sites can be described as preferring octahedral geometry, utilizing one to three protein ligands (typically histidine) and at least two water molecules.

  2. Perspectives of biomolecular NMR in drug discovery: the blessing and curse of versatility

    International Nuclear Information System (INIS)

    Jahnke, Wolfgang

    2007-01-01

    The versatility of NMR and its broad applicability to several stages in the drug discovery process is well known and generally considered one of the major strengths of NMR (Pellecchia et al., Nature Rev Drug Discov 1:211-219, 2002; Stockman and Dalvit, Prog Nucl Magn Reson Spectrosc 41:187-231, 2002; Lepre et al., Comb Chem High throughput screen 5:583-590, 2002; Wyss et al., Curr Opin Drug Discov Devel 5:630-647, 2002; Jahnke and Widmer, Cell Mol Life Sci 61:580-599, 2004; Huth et al., Methods Enzymol 394:549-571, 2005b; Klages et al., Mol Biosyst 2:318-332, 2006; Takeuchi and Wagner, Curr Opin Struct Biol 16:109-117, 2006; Zartler and Shapiro, Curr Pharm Des 12:3963-3972, 2006). Indeed, NMR is the only biophysical technique which can detect and quantify molecular interactions, and at the same time provide detailed structural information with atomic level resolution. NMR should therefore be ideally suited and widely requested as a tool for drug discovery research, and numerous examples of drug discovery projects which have substantially benefited from NMR contributions or were even driven by NMR have been described in the literature. However, not all pharmaceutical companies have rigorously implemented NMR as integral tool of their research processes. Some companies invest with limited resources, and others do not use biomolecular NMR at all. This discrepancy in assessing the value of a technology is striking, and calls for clarification-under which circumstances can NMR provide added value to the drug discovery process? What kind of contributions can NMR make, and how is it implemented and integrated for maximum impact? This perspectives article suggests key areas of impact for NMR, and a model of integrating NMR with other technologies to realize synergies and maximize their value for drug discovery

  3. Inference and Analysis of Population Structure Using Genetic Data and Network Theory.

    Science.gov (United States)

    Greenbaum, Gili; Templeton, Alan R; Bar-David, Shirli

    2016-04-01

    prior conditions. The method is implemented in the software NetStruct (available at https://giligreenbaum.wordpress.com/software/). Copyright © 2016 by the Genetics Society of America.

  4. Corrigendum to ;Dipole moment and solvatochromism of benzoic acid liquid crystals: Tuning the dipole moment and molecular orbital energies by substituted Au under external electric field; [J. Mol. Struct. 1137 (2017) 440-452

    Science.gov (United States)

    Sıdır, Yadigar Gülseven; Sıdır, İsa; Demiray, Ferhat

    2017-08-01

    The authors regret to inform that three references in the article titled ;Dipole moment and solvatochromism of benzoic acid liquid crystals: Tuning the dipole moment and molecular orbital energies by substituted Au under external electric field; are not given in the manuscript. This is purely an oversight mistake. The references are as shown in this correction. The authors would like to apologize for any inconvenience caused.

  5. Cross-linking in collagen by nonenzymatic glycation increases the matrix stiffness in rabbit achilles tendon.

    Science.gov (United States)

    Reddy, G Kesava

    2004-01-01

    Nonenzymatic glycation of connective tissue matrix proteins is a major contributor to the pathology of diabetes and aging. Previously the author and colleagues have shown that nonenzymatic glycation significantly enhances the matrix stability in the Achilles tendon (Reddy et al., 2002, Arch. Biochem. Biophys., 399, 174-180). The present study was designed to gain further insight into glycation-induced collagen cross-linking and its relationship to matrix stiffness in the rabbit Achilles tendon. The glycation process was initiated by incubating the Achilles tendons (n = 6) in phosphate-buffered saline containing ribose, whereas control tendons (n = 6) were incubated in phosphate-buffered saline without ribose. Eight weeks following glycation, the biomechanical attributes as well as the degree of collagen cross-linking were determined to examine the potential associations between matrix stiffness and molecular properties of collagen. Compared to nonglycated tendons, the glycated tendons showed increased maximum load, stress, strain, Young's modulus of elasticity, and toughness indicating that glycation increases the matrix stiffness in the tendons. Glycation of tendons resulted in a considerable decrease in soluble collagen content and a significant increase in insoluble collagen and pentosidine. Analysis of potential associations between the matrix stiffness and degree of collagen cross-linking showed that both insoluble collagen and pentosidine exhibited a significant positive correlation with the maximum load, stress, and strain, Young's modulus of elasticity, and toughness (r values ranging from.61 to.94) in the Achilles tendons. However, the soluble collagen content present in neutral salt buffer, acetate buffer, and acetate buffer containing pepsin showed an inverse relation with the various biomechanical attributes tested (r values ranging from.22 to.84) in the Achilles tendons. The results of the study demonstrate that glycation-induced collagen cross

  6. Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation

    Energy Technology Data Exchange (ETDEWEB)

    Kekenes-Huskey, P. M., E-mail: pkekeneshuskey@ucsd.edu [Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0636 (United States); Gillette, A. K. [Department of Mathematics, University of Arizona, Tucson, Arizona 85721-0089 (United States); McCammon, J. A. [Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0636 (United States); Department of Chemistry, Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0636 (United States)

    2014-05-07

    The macroscopic diffusion constant for a charged diffuser is in part dependent on (1) the volume excluded by solute “obstacles” and (2) long-range interactions between those obstacles and the diffuser. Increasing excluded volume reduces transport of the diffuser, while long-range interactions can either increase or decrease diffusivity, depending on the nature of the potential. We previously demonstrated [P. M. Kekenes-Huskey et al., Biophys. J. 105, 2130 (2013)] using homogenization theory that the configuration of molecular-scale obstacles can both hinder diffusion and induce diffusional anisotropy for small ions. As the density of molecular obstacles increases, van der Waals (vdW) and electrostatic interactions between obstacle and a diffuser become significant and can strongly influence the latter's diffusivity, which was neglected in our original model. Here, we extend this methodology to include a fixed (time-independent) potential of mean force, through homogenization of the Smoluchowski equation. We consider the diffusion of ions in crowded, hydrophilic environments at physiological ionic strengths and find that electrostatic and vdW interactions can enhance or depress effective diffusion rates for attractive or repulsive forces, respectively. Additionally, we show that the observed diffusion rate may be reduced independent of non-specific electrostatic and vdW interactions by treating obstacles that exhibit specific binding interactions as “buffers” that absorb free diffusers. Finally, we demonstrate that effective diffusion rates are sensitive to distribution of surface charge on a globular protein, Troponin C, suggesting that the use of molecular structures with atomistic-scale resolution can account for electrostatic influences on substrate transport. This approach offers new insight into the influence of molecular-scale, long-range interactions on transport of charged species, particularly for diffusion-influenced signaling events

  7. Thermodynamic and fluorescence studies of the underlying factors in benzyl alcohol-induced lipid interdigitated phase.

    Science.gov (United States)

    Chen, C H; Hoye, K; Roth, L G

    1996-09-15

    To further investigate factors contributing to the action of alcohol in the solute-induced lipid interdigitation phase, thermodynamic and fluorescence polarization measurements were carried out to study the interaction of benzyl alcohol with dipalmitoyl phosphatidylcholine bilayer vesicles. The obtained results were compared with those previously reported for ethanol and cyclohexanol (L. G. Roth and C-H. Chen, Arch. Biochem. Biophys. 296, 207, 1992). Similar to ethanol, benzyl alcohol was found to exhibit a biphasic effect on the enthalpy (delta Hm) and the temperature (tm) of the lipid-phase transition and the steady-state fluorescence polarization (P) monitored by 1,6-diphenyl-1,3,5-hexatriene. At a total concentration of benzyl alcohol delta Hm and P, which were correlated with the formation of a lipid interdigitated phase, as evidenced by reported X-ray diffraction data. Combining the results with benzyl alcohol and ethanol suggested that simultaneously large changes in delta Hm and P can be used as an indication of the occurrence of a solute-induced lipid interdigitated phase. The overall interacting force in the formation of this lipid phase, as derived from the interactions of the hydroxyl portion of an alcohol with the lipid phosphate head group and the hydrophobic portion of an alcohol with the lipid hydrocarbon chains, may or may not be dominated by hydrophobic interaction. Although lipid/water partition coefficients and the contribution of hydrophobic interaction to the overall interacting force were comparable between benzyl alcohol and cyclohexanol, benzyl alcohol induced lipid interdigitated phase, but not for cyclohexanol. This was due to the ability of benzyl alcohol to be more effective than cyclohexanol in simultaneously interacting with the phosphate head group and the hydrocarbon chains of lipid.

  8. Role of ions in the regulation of light-harvesting

    Directory of Open Access Journals (Sweden)

    Radek Kana

    2016-12-01

    Full Text Available Regulation of photosynthetic light harvesting in the thylakoids is one of the major key factors affecting the efficiency of photosynthesis. Thylakoid membrane is negatively charged and influences both the structure and the function of the primarily photosynthetic reactions through its electrical double layer. Further, there is a heterogeneous organization of soluble ions (K+, Mg2+, Cl- attached to the thylakoid membrane that, together with fixed charges (negatively charged amino acids, lipids, provides an electrical field. The electrical double layer is affected by the valence of the ions and interferes with the regulation of state transitions, protein interactions, and excitation energy spillover from Photosystem II to Photosystem I. These effects are reflected in changes in the intensity of chlorophyll a fluorescence, which is also a measure of photoprotective non-photochemical quenching of the excited state of chlorophyll a. A triggering of non-photochemical quenching proceeds via lumen acidification and is coupled to the export of positive counter-ions (Mg2+, K+ to the stroma or/and negative ions (e.g., Cl- into the lumen. The effect of protons and anions in the lumen and of the cations (Mg2+, K+ in the stroma are, thus, functionally tightly interconnected. In this review, we discuss the consequences of the model of electrical double layer, proposed by James Barber (J. Barber (1980 Biochim Biophys Acta 594:253-308 in light of light-harvesting regulation. Further, we explain differences between electrostatic screening and neutralization, and we emphasize the opposite effect of monovalent (K+ and divalent (Mg2+ ions on light-harvesting and on screening of the negative charges on the thylakoid membrane; this effect needs to be incorporated in all future models of photosynthetic regulation by ion channels and transporters.

  9. Differential Control of Heme Reactivity in Alpha and Beta Subunits of Hemoglobin: A Combined Raman Spectroscopic and Computational Study

    Science.gov (United States)

    2015-01-01

    The use of hybrid hemoglobin (Hb), with mesoheme substituted for protoheme, allows separate monitoring of the α or β hemes along the allosteric pathway. Using resonance Raman (rR) spectroscopy in silica gel, which greatly slows protein motions, we have observed that the Fe–histidine stretching frequency, νFeHis, which is a monitor of heme reactivity, evolves between frequencies characteristic of the R and T states, for both α or β chains, prior to the quaternary R–T and T–R shifts. Computation of νFeHis, using QM/MM and the conformational search program PELE, produced remarkable agreement with experiment. Analysis of the PELE structures showed that the νFeHis shifts resulted from heme distortion and, in the α chain, Fe–His bond tilting. These results support the tertiary two-state model of ligand binding (Henry et al., Biophys. Chem.2002, 98, 149). Experimentally, the νFeHis evolution is faster for β than for α chains, and pump–probe rR spectroscopy in solution reveals an inflection in the νFeHis time course at 3 μs for β but not for α hemes, an interval previously shown to be the first step in the R–T transition. In the α chain νFeHis dropped sharply at 20 μs, the final step in the R–T transition. The time courses are fully consistent with recent computational mapping of the R–T transition via conjugate peak refinement by Karplus and co-workers (Fischer et al., Proc. Natl. Acad. Sci. U. S. A.2011, 108, 5608). The effector molecule IHP was found to lower νFeHis selectively for α chains within the R state, and a binding site in the α1α2 cleft is suggested. PMID:24991732

  10. Computer modeling of the optical properties and heating of spherical gold and silica-gold nanoparticles for laser combined imaging and photothermal treatment

    International Nuclear Information System (INIS)

    Pustovalov, V; Astafyeva, L; Jean, B

    2009-01-01

    Recently, several groups of investigators (Anderson, Halas, Zharov, El-Sayed and their co-workers (Pitsillides et al 2003 Biophys. J. 84 4023-31, Zharov et al 2003 Appl. Phys. Lett. 83 4897-9, Zharov et al 2004 Proc. SPIE 5319 291-9, Loo et al 2005 Nano Lett. 5 709-11, Gobin et al 2007 Nano Lett. 7 1929-34, Fu et al 2008 Nanotechnology 19 045103, Huang et al 2006 J. Am. Chem. Soc. 128 2115-20, Jain et al 2006 J. Phys. Chem. B 110 7238-48, Jain et al 2007 Nano Today 2 18-29)) demonstrated, through pioneering results, the great potential of laser thermal therapy of cells and tissues conjugated with gold nanoparticles. It was also proposed to use combined diagnostics and therapy on the basis of nanoparticle selection for achievement of efficient contrast for laser imaging applications, as well as for photothermal therapy. However, the current understanding of the relationship between optical properties (absorption, backscattering) of nanoparticles, the efficiency of nanoparticle heating and the possibility to use them for combined imaging and therapy is limited. Here, we report the results of computer modeling of optical absorption and backscattering properties and laser heating of gold and silica-gold spherical nanoparticles for laser combined imaging and photothermal treatment of cells and tissues conjugated with nanoparticles. The efficiencies of nanoparticle heating and backscattering by nanoparticles, depending upon their radii, structure and optical properties of the metal, were investigated. This paper focuses on the analysis and determination of appropriate ranges of nanoparticle sizes for the purposes of laser combined imaging and photothermal treatment. The possibility to use spherical gold and silica-gold nanoparticles in determined ranges of radii for these purposes for laser wavelengths 532 and 800 nm is investigated.

  11. Immune stimulation by a CpG-containing oligodeoxynucleotide is enhanced when encapsulated and delivered in lipid particles.

    Science.gov (United States)

    Mui, B; Raney, S G; Semple, S C; Hope, M J

    2001-09-01

    The therapeutic benefit from phosphorothioate oligodeoxynucleotides (PS ODN) containing immune stimulatory sequences (ISS) has been demonstrated in animal models of cancer and infection. In particular, when CpG-containing PS ODN are administered to mice, activation of macrophages and dendritic, NK, T, and B cells occurs, resulting in the release of an array of cytokines, including interleukin-12 (IL-12), interferon-gamma (IFN-gamma), and tumor necrosis factor-alpha (TNF-alpha). We have previously described stabilized antisense-lipid particles (SALP) for the i.v. administration of antisense ODN [Biochim Biophys Acta (2001) 1510:152--166]. Given the propensity for SALP to target macrophages in vivo it was of interest to determine whether they could enhance the potency of CpG ODN to induce an immune response. In this report we show that when CpG-containing SALP are administered intravenously to ICR mice the plasma concentrations of IL-12, IFN-gamma, IL-6, monocyte chemoattractant protein-1, and TNF-alpha are greatly increased compared with the same dose of free ODN. The pattern of cytokine induction indicates that the immune response is T helper cell type 1-biased, similar to that observed for PS CpG ODN ISS in general. Furthermore, when phosphodiester (PO) ODN is substituted for PS ODN in the SALP formulation cytokine induction is even greater at the early time points, in marked contrast to free PO ODN, which is inactive. These results demonstrate that the immunogenicity of ISS is not only enhanced by encapsulation in lipid particles, which more closely mimic the way ISS DNA would normally be presented to antigen presenting cells by pathogens in vivo, but also SALP enable unmodified PO CpG ODN to be used as immune stimulants.

  12. Factors determining the oxygen consumption rate (VO2) on-kinetics in skeletal muscles.

    Science.gov (United States)

    Korzeniewski, Bernard; Zoladz, Jerzy A

    2004-05-01

    Using a computer model of oxidative phosphorylation developed previously [Korzeniewski and Mazat (1996) Biochem. J. 319, 143-148; Korzeniewski and Zoladz (2001) Biophys. Chem. 92, 17-34], we analyse the effect of several factors on the oxygen-uptake kinetics, especially on the oxygen consumption rate (VO2) and half-transition time t(1/2), at the onset of exercise in skeletal muscles. Computer simulations demonstrate that an increase in the total creatine pool [PCr+/-Cr] (where Cr stands for creatine and PCr for phosphocreatine) and in glycolytic ATP supply lengthen the half-transition time, whereas increase in mitochondrial content, in parallel activation of ATP supply and ATP usage, in oxygen concentration, in proton leak, in resting energy demand, in resting cytosolic pH and in initial alkalization decrease this parameter. Theoretical studies show that a decrease in the activity of creatine kinase (CK) [displacement of this enzyme from equilibrium during on-transient (rest-to-work transition)] accelerates the first stage of the VO2 on-transient, but slows down the second stage of this transient. It is also demonstrated that a prior exercise terminated a few minutes before the principal exercise shortens the transition time. Finally, it is shown that at a given ATP demand, and under conditions where CK works near the thermodynamic equilibrium, the half-transition time of VO2 kinetics is determined by the amount of PCr that has to be transformed into Cr during rest-to-work transition; therefore any factor that diminishes the difference in [PCr] between rest and work at a given energy demand will accelerate the VO2 on-kinetics. Our conclusions agree with the general idea formulated originally by Easterby [(1981) Biochem. J. 199, 155-161] that changes in metabolite concentrations determine the transition times between different steady states in metabolic systems.

  13. Transformation of cooperative free energies between ligation systems of hemoglobin: resolution of the carbon monoxide binding intermediates.

    Science.gov (United States)

    Huang, Y; Ackers, G K

    1996-01-23

    A strategy has been developed for quantitatively "translating" the distributions of cooperative free energy between different oxygenation analogs of hemoglobin (Hb). The method was used to resolve the cooperative free energies of all eight carbon monoxide binding intermediates. These parameters of the FeCOHb system were determined by thermodynamic transformation of corresponding free energies obtained previously for all species of the Co/FeCO system, i.e., where cobalt-substituted hemes comprise the unligated sites [Speros, P. C., et al. (1991) Biochemistry 30, 7254-7262]. Using hybridized combinations of normal and cobalt-substituted Hb, ligation analog systems Co/FeX (X = CO, CN) were constructed and experimentally quantified. Energetics of cobalt-induced structural perturbation were determined for all species of both the "mixed metal" Co/Fe system and also the ligated Co/FeCN system. It was found that major energetic perturbations of the Co/Fe hybrid species originate from a pure cobalt substitution effect on the alpha subunits. These perturbations are transduced to the beta subunit within the same dimeric half-tetramer, resulting in alteration of the free energies for binding at the nonsubstituted (Fe) sites. Using the linkage strategy developed in this study along with the determined energetics of these couplings, the experimental assembly free energies for the Co/FeCO species were transformed into cooperative free energies of the 10 Fe/FeCO species. The resulting values were found to distribute according to predictions of a symmetry rule mechanism proposed previously [Ackers, G. K., et al. (1992) Science 255, 54-63]. Their distribution is consistent with accurate CO binding data of normal Hb [Perrella, M., et al. (1990b) Biophys. Chem. 37, 211-223] and also with accurate O2 binding data obtained under the same conditions [Chu, A. H., et al. (1984) Biochemistry 23, 604-617].

  14. Modifications in cell cycle kinetics and in expression of G1 phase-regulating proteins in human amniotic cells after exposure to electromagnetic fields and ionizing radiation.

    Science.gov (United States)

    Lange, S; Viergutz, T; Simkó, M

    2004-10-01

    Low-frequency electromagnetic fields are suspected of being involved in carcinogenesis, particularly in processes that could be related to cancer promotion. Because development of cancer is associated with deregulated cell growth and we previously observed a magnetic field-induced decrease in DNA synthesis [Lange et al. (2002) Alterations in the cell cycle and in the protein level of cyclin D1p, 21CIP1, and p16INK4a after exposure to 50 HZ. MF in human cells. Radiat. Environ. Biophys.41, 131], this study aims to document the influence of 50 Hz, 1 mT magnetic fields (MF), with or without initial gamma-ionizing radiation (IR), on the following cell proliferation-relevant parameters in human amniotic fluid cells (AFC): cell cycle distribution, expression of the G1 phase-regulating proteins Cdk4, cyclin D1, p21CIP1 and p16INK4a, and Cdk4 activity. While IR induced a G1 delay and a dose-dependent G2 arrest, no discernible changes in cell cycle kinetics were observed due to MF exposure. However, a significant decrease in the protein expression of cyclin D1 and an increase in p21CIP1- and p16INK4a-expression could be detected after exposure to MF alone. IR-exposure caused an augmentation of p21CIP1- and p16INK4a- levels as well, but did not alter cyclin D1 expression. A slight diminution of Cdk4 activity was noticed after MF exposure only, indicating that Cdk4 appears not to act as a mediator of MF- or IR-induced changes in the cell cycle of AFC cells. Co-exposure to MF/IR affected neither cell cycle distribution nor protein expression or kinase activity additionally or synergistically, and therefore MF seems not to modify the mutagenic potency of IR.

  15. Lipid-protein interactions in plasma membranes of fiber cells isolated from the human eye lens.

    Science.gov (United States)

    Raguz, Marija; Mainali, Laxman; O'Brien, William J; Subczynski, Witold K

    2014-03-01

    The protein content in human lens membranes is extremely high, increases with age, and is higher in the nucleus as compared with the cortex, which should strongly affect the organization and properties of the lipid bilayer portion of intact membranes. To assess these effects, the intact cortical and nuclear fiber cell plasma membranes isolated from human lenses from 41- to 60-year-old donors were studied using electron paramagnetic resonance spin-labeling methods. Results were compared with those obtained for lens lipid membranes prepared from total lipid extracts from human eyes of the same age group [Mainali, L., Raguz, M., O'Brien, W. J., and Subczynski, W. K. (2013) Biochim. Biophys. Acta]. Differences were considered to be mainly due to the effect of membrane proteins. The lipid-bilayer portions of intact membranes were significantly less fluid than lipid bilayers of lens lipid membranes, prepared without proteins. The intact membranes were found to contain three distinct lipid environments termed the bulk lipid domain, boundary lipid domain, and trapped lipid domain. However, the cholesterol bilayer domain, which was detected in cortical and nuclear lens lipid membranes, was not detected in intact membranes. The relative amounts of bulk and trapped lipids were evaluated. The amount of lipids in domains uniquely formed due to the presence of membrane proteins was greater in nuclear membranes than in cortical membranes. Thus, it is evident that the rigidity of nuclear membranes is greater than that of cortical membranes. Also the permeability coefficients for oxygen measured in domains of nuclear membranes were significantly lower than appropriate coefficients measured in cortical membranes. Relationships between the organization of lipids into lipid domains in fiber cells plasma membranes and the organization of membrane proteins are discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Isolation and characterization of a mannan from mesosomal membrane vesicles of Micrococcus lysodeikticus.

    Science.gov (United States)

    Owen, P; Salton, M R

    1975-10-06

    The carbohydrate content of mesosomal membranes of Micrococcus lysodeikticus has been shown to be consistently higher (about four times) than that of corresponding plasma membrane preparations. Analysis of washed membrane fractions by gas-liquid chromatography indicated that mannose was the major neutral sugar of both types of membrane (accounting for 95 and 89%, respectively, of the mesosomal and plasma membrane carbohydrate). Small amounts of inositol, glucose and ribose were also detected. We have shown by polyacrylamide gel electrophoresis in sodium dodecylsulphate and by precipitation and agar gel diffusion experiments with concanavalin A that a mannan is the major carbohydrate component of both types of membrane. This polymer can be selectively released from mesosomal membranes by a simple procedure involving low ionic strength-shock and heating to 80 degrees C for 1 min, and purified by ultrafiltration and ethanol precipitation. The mannan contains mannose as the only neutral carbohydrate, is not phosphorylated and does not contain significant amounts of amino sugars or uronic acids. Agar gel electrophoresis experiments, however, indicate an anionic polymer whose acidic properties are eliminated upon mild base hydrolysis. Analysis of native mannan by infrared spectroscopy reveals absorption bands attributable to ester carbonyl groups and to carboxylate ions, consistent with the presence of succinyl residues in the polymer (Owen, P. and Salton, M.R.J. (1975) Biochem, Biophys. Res. Commun. 63, 875--800). A sedimentation coefficient of 1.39 S was obtained by analytical ultracentrifugation in 1.0 M NaCl and a value of one reducing equivalent per 50 mannose residues by reduction with NaB3H4. The polysaccharide was only slightly degraded (2%) by jack bean alpha-mannosidase and could precipitate 15 times its own weight of concanavalin A. The acidic polymers was also detected in the cell "periplasm" and was secreted from cells grown in defined media during the

  17. Accuracy and precision of protein–ligand interaction kinetics determined from chemical shift titrations

    International Nuclear Information System (INIS)

    Markin, Craig J.; Spyracopoulos, Leo

    2012-01-01

    NMR-monitored chemical shift titrations for the study of weak protein–ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K D ) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K D value of a 1:1 protein–ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125–138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of 1 H– 15 N 2D HSQC NMR spectra acquired using precise protein–ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k off ). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k off ∼ 3,000 s −1 in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k off from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k off values over a wide range, from 100 to 15,000 s −1 . The validity of line shape analysis for k off values approaching intermediate exchange (∼100 s −1 ), may be facilitated by more accurate K D measurements from NMR

  18. Identification of new drug candidates against Borrelia burgdorferi using high-throughput screening

    Directory of Open Access Journals (Sweden)

    Pothineni VR

    2016-04-01

    Full Text Available Venkata Raveendra Pothineni,1 Dhananjay Wagh,1 Mustafeez Mujtaba Babar,1 Mohammed Inayathullah,1 David Solow-Cordero,2 Kwang-Min Kim,1 Aneesh V Samineni,1 Mansi B Parekh,1 Lobat Tayebi,3 Jayakumar Rajadas1 1Biomaterials and Advanced Drug Delivery Laboratory, Stanford Cardiovascular Pharmacology Division, Cardiovascular Institute, Stanford University School of Medicine, Palo Alto, 2Chemical & Systems Biology, Stanford University School of Medicine, Stanford, CA, 3Department of Developmental Sciences, Marquette University School of Dentistry, Milwaukee, WI, USA Abstract: Lyme disease is the most common zoonotic bacterial disease in North America. It is estimated that >300,000 cases per annum are reported in USA alone. A total of 10%–20% of patients who have been treated with antibiotic therapy report the recrudescence of symptoms, such as muscle and joint pain, psychosocial and cognitive difficulties, and generalized fatigue. This condition is referred to as posttreatment Lyme disease syndrome. While there is no evidence for the presence of viable infectious organisms in individuals with posttreatment Lyme disease syndrome, some researchers found surviving Borrelia burgdorferi population in rodents and primates even after antibiotic treatment. Although such observations need more ratification, there is unmet need for developing the therapeutic agents that focus on removing the persisting bacterial form of B. burgdorferi in rodent and nonhuman primates. For this purpose, high-throughput screening was done using BacTiter-Glo assay for four compound libraries to identify candidates that stop the growth of B. burgdorferi in vitro. The four chemical libraries containing 4,366 compounds (80% Food and Drug Administration [FDA] approved that were screened are Library of Pharmacologically Active Compounds (LOPAC1280, the National Institutes of Health Clinical Collection, the Microsource Spectrum, and the Biomol FDA. We subsequently identified 150

  19. Biochemical analysis of the Hormoconis resinae fungal mycelium in the corrosion of aeronautical aluminium alloys

    Directory of Open Access Journals (Sweden)

    Araya, R.

    2007-06-01

    ón. De las fracciones de biomoléculas separadas y analizadas durante este estudio preliminar, sólo, las fracciones proteicas revelaron cambios de una a otra generación. Cuando esta cepa del hongo se cultivó en presencia de probetas de los metales, las modificaciones en la electroforesis de las respectivas fracciones proteicas fueron correlativas del comportamiento del micelio frente a la corrosión del aluminio y sus aleaciones.

  20. Cardiac Regeneration using Growth Factors: Advances and Challenges.

    Science.gov (United States)

    Rebouças, Juliana de Souza; Santos-Magalhães, Nereide Stela; Formiga, Fabio Rocha

    2016-09-01

    Myocardial infarction is the most significant manifestation of ischemic heart disease and is associated with high morbidity and mortality. Novel strategies targeting at regenerating the injured myocardium have been investigated, including gene therapy, cell therapy, and the use of growth factors. Growth factor therapy has aroused interest in cardiovascular medicine because of the regeneration mechanisms induced by these biomolecules, including angiogenesis, extracellular matrix remodeling, cardiomyocyte proliferation, stem-cell recruitment, and others. Together, these mechanisms promote myocardial repair and improvement of the cardiac function. This review aims to address the strategic role of growth factor therapy in cardiac regeneration, considering its innovative and multifactorial character in myocardial repair after ischemic injury. Different issues will be discussed, with emphasis on the regeneration mechanisms as a potential therapeutic resource mediated by growth factors, and the challenges to make these proteins therapeutically viable in the field of cardiology and regenerative medicine. Resumo O infarto do miocárdio representa a manifestação mais significativa da cardiopatia isquêmica e está associado a elevada morbimortalidade. Novas estratégias vêm sendo investigadas com o intuito de regenerar o miocárdio lesionado, incluindo a terapia gênica, a terapia celular e a utilização de fatores de crescimento. A terapia com fatores de crescimento despertou interesse em medicina cardiovascular, devido aos mecanismos de regeneração induzidos por essas biomoléculas, incluindo angiogênese, remodelamento da matriz extracelular, proliferação de cardiomiócitos e recrutamento de células-tronco, dentre outros. Em conjunto, tais mecanismos promovem a reparação do miocárdio e a melhora da função cardíaca. Esta revisão pretende abordar o papel estratégico da terapia, com fatores de crescimento, para a regeneração cardíaca, considerando seu car

  1. Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations.

    Science.gov (United States)

    Markin, Craig J; Spyracopoulos, Leo

    2012-12-01

    NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K ( D )) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K ( D ) value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of (1)H-(15)N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k ( off )). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k ( off ) ~ 3,000 s(-1) in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k ( off ) from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k ( off ) values over a wide range, from 100 to 15,000 s(-1). The validity of line shape analysis for k ( off ) values approaching intermediate exchange (~100 s(-1)), may be facilitated by more accurate K ( D ) measurements

  2. Interface Evolution During Transient Pressure Solution Creep

    Science.gov (United States)

    Dysthe, D. K.; Podladchikov, Y. Y.; Renard, F.; Jamtveit, B.; Feder, J.

    When aggregates of small grains are pressed together in the presence of small amounts of solvent the aggregate compacts and the grains tend to stick together. This hap- pens to salt and sugar in humid air, and to sediments when buried in the Earths crust. Stress concentration at the grain contacts cause local dissolution, diffusion of the dissolved material out of the interface and deposition on the less stressed faces of the grains{1}. This process, in geology known as pressure solution, plays a cen- tral role during compaction of sedimentary basins{1,2}, during tectonic deformation of the Earth's crust{3}, and in strengthening of active fault gouges following earth- quakes{4,5}. Experimental data on pressure solution has so far not been sufficiently accurate to understand the transient processes at the grain scale. Here we present ex- perimental evidence that pressure solution creep does not establish a steady state inter- face microstructure as previously thought. Conversely, cumulative creep strain and the characteristic size of interface microstructures grow as the cubic root of time. A sim- ilar transient phenomenon is known in metallurgy (Andrade creep) and is explained here using an analogy with spinodal dewetting. 1 Weyl, P. K., Pressure solution and the force of crystallization - a phenomenological theory. J. Geophys. Res., 64, 2001-2025 (1959). 2 Heald, M. T., Cementation of Simpson and St. Peter Sandstones in parts of Okla- homa, Arkansas and Missouri, J. Geol. Chicago, 14, 16-30 (1956). 3 Schwartz, S., Stöckert, B., Pressure solution in siliciclastic HP-LT metamorphic rocks constraints on the state of stress in deep levels of accretionary complexes. Tectonophysics, 255, 203-209 (1996). 4 Renard, F., Gratier, J.P., Jamtveit, B., Kinetics of crack-sealing, intergranular pres- sure solution, and compaction around active faults. J. Struct. Geol., 22, 1395-1407, (2000). 5 Miller, S. A., BenZion, Y., Burg, J. P.,A three-dimensional fluid-controlled earth

  3. Watching proteins function with time-resolved x-ray crystallography

    Science.gov (United States)

    Šrajer, Vukica; Schmidt, Marius

    2017-09-01

    Macromolecular crystallography was immensely successful in the last two decades. To a large degree this success resulted from use of powerful third generation synchrotron x-ray sources. An expansive database of more than 100 000 protein structures, of which many were determined at resolution better than 2 Å, is available today. With this achievement, the spotlight in structural biology is shifting from determination of static structures to elucidating dynamic aspects of protein function. A powerful tool for addressing these aspects is time-resolved crystallography, where a genuine biological function is triggered in the crystal with a goal of capturing molecules in action and determining protein kinetics and structures of intermediates (Schmidt et al 2005a Methods Mol. Biol. 305 115-54, Schmidt 2008 Ultrashort Laser Pulses in Biology and Medicine (Berlin: Springer) pp 201-41, Neutze and Moffat 2012 Curr. Opin. Struct. Biol. 22 651-9, Šrajer 2014 The Future of Dynamic Structural Science (Berlin: Springer) pp 237-51). In this approach, short and intense x-ray pulses are used to probe intermediates in real time and at room temperature, in an ongoing reaction that is initiated synchronously and rapidly in the crystal. Time-resolved macromolecular crystallography with 100 ps time resolution at synchrotron x-ray sources is in its mature phase today, particularly for studies of reversible, light-initiated reactions. The advent of the new free electron lasers for hard x-rays (XFELs; 5-20 keV), which provide exceptionally intense, femtosecond x-ray pulses, marks a new frontier for time-resolved crystallography. The exploration of ultra-fast events becomes possible in high-resolution structural detail, on sub-picosecond time scales (Tenboer et al 2014 Science 346 1242-6, Barends et al 2015 Science 350 445-50, Pande et al 2016 Science 352 725-9). We review here state-of-the-art time-resolved crystallographic experiments both at synchrotrons and XFELs. We also outline

  4. Characterization of frictional melting processes in subduction zone faults by trace element and isotope analyses

    Science.gov (United States)

    Ishikawa, T.; Ujiie, K.

    2017-12-01

    Pseudotachylytes found in exhumed accretionary complexes, which are considered to be formed originally at seismogenic depths, are of great importance for elucidating frictional melting and concomitant dynamic weakening of the fault during earthquake in subduction zones. However, fluid-rich environment of the subduction zone faults tends to cause extensive alteration of the pseudotachylyte glass matrix in later stages, and thus it has been controversial that pseudotachylytes are rarely formed or rarely preserved. Chemical analysis of the fault rocks, especially on fluid-immobile trace elements and isotopes, can be a useful means to identify and quantify the frictional melting occurred in subduction zone faults. In this paper, we report major and trace element and Sr isotope compositions for pseudotachylyte-bearing dark veins and surrounding host rocks from the Mugi area of the Shimanto accretionary complex (Ujiie et al., J. Struct. Geol. 2007). Samples were collected from a rock chip along the microstructure using a micro-drilling technique, and then analyzed by ICP-MS and TIMS. Major element compositions of the dark veins showed a clear shift from the host rock composition toward the illite composition. The dark veins, either unaltered or completely altered, were also characterized by extreme enrichment in some of the trace elements such as Ti, Zr, Nb and Th. These results are consistent with disequilibrium melting of the fault zone. Model calculations revealed that the compositions of the dark veins can be produced by total melting of clay-rich matrix in the source rock, leaving plagioclase and quartz grains almost unmolten. The calculations also showed that the dark veins are far more enriched in melt component than that expected from the source rock compositions, suggesting migration and concentration of frictional melt during the earthquake faulting. Furthermore, Sr isotope data of the dark veins implied the occurrence of frictional melting in multiple stages

  5. The Equivalence of the Methyl Groups in Puckered 3,3-DIMETHYL Oxetane

    Science.gov (United States)

    Macario, Alberto; Blanco, Susana; Lopez, Juan Carlos

    2016-06-01

    The spectroscopic study of molecules with large amplitude vibrations have led to reconsider the concept of molecular structure. Sometimes identifying definite bond lengths and angles is not enough to reproduce the experimental data so one must have information on the large amplitude molecular vibration potential energy function and dynamics. 3,3-dimethyloxetane (DMO) has non-planar ring equilibrium configuration and a double minimum potential function for ring-puckering with a barrier of 47 cm-1. The observation of endocyclic 13C and 18O monosubstituted isotopologues allow to conclude that the ring is puckered. However an interesting feature was observed for the 13C substitutions at the methyl carbon atoms. While two different axial and equatorial 13C-methyl groups spectra are predicted from a rigid non-planar ring DMO model, only one species was found. The observed rotational transitions appear at a frequency close to the average of the frequencies predicted for each isotopologue. The observed lines have the same intensity as that found for the 13C_α isotopomer and double that that found for the 13C_β isotopomer.^c This behaviour evidences that the two methyl groups of DMO are equivalent as could be expected for a planar ring. In this work we show how consideration of the potential function and the path for ring puckering motion to calculate the proper kinetic energy terms allow to reproduce the experimental results. Ab initio computations at the CCSD/6-311++G(d,p) level, tested on related systems, have been done for this purpose. J. A. Duckett, T. L. Smithson, and H. Wieser, J. Mol. Spectrosc. 1978, 69 , 159; J. Mol. Struct. 1979, 56, 157 J. C. López, A. G. Lesarri, R. M. Villamañán and J. L. Alonso, J. Mol. Spectrosc. 1990, 141, 231 R. Sánchez, S. Blanco, A. Lesarri, J. C. López and J. L. Alonso, Phys. Chem. Chem. Phys. 2005, 7, 1157

  6. Influence of membrane composition on its flexibility

    International Nuclear Information System (INIS)

    Gerbelli, B.B.; Teixeira da Silva, E.R.; Oliveira, C.L.P.; Oliveira, E.A.

    2012-01-01

    Full text: Lamellar phases and vesicles composed of lipids have been used as model systems to investigate biological process related to cell membrane as well as promising carriers for drugs and gene therapy. The composition of the membrane determines its three dimensional shape and its properties such as rigidity and compressibility which play an important role on membrane fusion, protein adhesion, interactions between proteins, etc. We present systematic study of a lamellar system composed mainly of lecithin which is a biocompatible phospholipid and simusol, which is a mixture of fatty acids that acts as a cosurfactant introducing flexibility to the membrane. Using X ray scattering we determine the lamellar periodicity as a function of the hydration for different formulations of the membrane; ranging from 100 % to 50 % mass fraction of lecithin. The X-ray spectra are fitted using a 4 Gaussian model [1]that allows us to determine the lamellar periodicity and the Caille parameter [2]. The ideal swelling law relating the membrane volume fraction (φ m ) to the lamellar periodicity (D) is given by φ m =δ m /D, where δ m is the thickness membrane, however, when steric interactions are dominant with respect to electrostatic and van der Waals interactions, deviations from this behavior are expected [3]. We present experimental data illustrating the swelling behavior for the membrane compositions and the respective behavior of the hydration limit, membrane Luzzati [4], of the Caille parameter and qualitative interpretation of the interaction forces the systems studying the parameter membrane square amplitude fluctuation[5]. [1] Private communication with Prof. Dr. Cristiano Luis Pinto de Oliveira. [2] Caille A. et all, Acad. Sci. Paris B274 (1972) 891. [3] E. Kurtisovski et all, PRL 98, 258103 (2007). [4] Nagle et all, Curr Opin Struct Biol. 2000 Aug;10(4):474-80. [5] H. I. Petrache. Structure and interactions of fluid phospholipids bilayers measured by high resolution

  7. Influence of membrane composition on its flexibility

    Energy Technology Data Exchange (ETDEWEB)

    Gerbelli, B.B.; Teixeira da Silva, E.R.; Oliveira, C.L.P.; Oliveira, E.A. [Universidade de Sao Paulo (USP), SP (Brazil)

    2012-07-01

    Full text: Lamellar phases and vesicles composed of lipids have been used as model systems to investigate biological process related to cell membrane as well as promising carriers for drugs and gene therapy. The composition of the membrane determines its three dimensional shape and its properties such as rigidity and compressibility which play an important role on membrane fusion, protein adhesion, interactions between proteins, etc. We present systematic study of a lamellar system composed mainly of lecithin which is a biocompatible phospholipid and simusol, which is a mixture of fatty acids that acts as a cosurfactant introducing flexibility to the membrane. Using X ray scattering we determine the lamellar periodicity as a function of the hydration for different formulations of the membrane; ranging from 100 % to 50 % mass fraction of lecithin. The X-ray spectra are fitted using a 4 Gaussian model [1]that allows us to determine the lamellar periodicity and the Caille parameter [2]. The ideal swelling law relating the membrane volume fraction ({phi}{sub m}) to the lamellar periodicity (D) is given by {phi}{sub m} ={delta}{sub m}/D, where {delta}{sub m} is the thickness membrane, however, when steric interactions are dominant with respect to electrostatic and van der Waals interactions, deviations from this behavior are expected [3]. We present experimental data illustrating the swelling behavior for the membrane compositions and the respective behavior of the hydration limit, membrane Luzzati [4], of the Caille parameter and qualitative interpretation of the interaction forces the systems studying the parameter membrane square amplitude fluctuation[5]. [1] Private communication with Prof. Dr. Cristiano Luis Pinto de Oliveira. [2] Caille A. et all, Acad. Sci. Paris B274 (1972) 891. [3] E. Kurtisovski et all, PRL 98, 258103 (2007). [4] Nagle et all, Curr Opin Struct Biol. 2000 Aug;10(4):474-80. [5] H. I. Petrache. Structure and interactions of fluid phospholipids

  8. 政务社交媒体的公众接受模型研究%User Acceptance Model for Social Media of Government Agencies

    Institute of Scientific and Technical Information of China (English)

    吴云; 胡广伟

    2014-01-01

    Based on UTAUT, a user acceptance model for social media of government was established, in which three hypothetical con-structs were spotlighted:anxiety of privacy and comments (ANX), perceived credibility (PC) and social evaluation (SE). By means of CFA we found, SE and social influence (SI) were main factors affecting user intention (UI), while performance expectation (PE) and PC had impact on SE, however influences of ANX and effort expectation (EE) on UI were not significant. It was concluded that, firstly, public users were not sensitive to preserving their personal privacy and managing information on the internet;secondly, social relationship would be a good channel for promoting usage of governments' social media; last but not the least, public user expected social media to benefit the whole society such as improving government transparency and democracy.%根据UTAUT提供的影响结构，加入了焦虑、感知可信性、社会评价三个因素，构建了政务社交媒体公众接受模型。通过验证性因子分析发现，社会影响和社会评价是影响用户使用意愿的主要因素，绩效预期和感知可信性通过社会评价产生影响，而焦虑和付出预期影响不显著。研究结论如下：公众对个人隐私保护及言论管理方面存在的潜在问题不敏感；社会关系对政务社交媒体的推广效果有显著影响；公众期望政务社交媒体对整个社会有益(如提高政府透明度等)。

  9. Cohesive zone model for intergranular slow crack growth in ceramics: influence of the process and the microstructure

    International Nuclear Information System (INIS)

    Romero de la Osa, M; Olagnon, C; Chevalier, J; Estevez, R; Tallaron, C

    2011-01-01

    Ceramic polycrystals are prone to slow crack growth (SCG) which is stress and environmentally assisted, similarly to observations reported for silica glasses. The kinetics of fracture are known to be dependent on the load level, the temperature and the relative humidity. In addition, evidence is available on the influence of the microstructure on the SCG rate with an increase in the crack velocity with decreasing the grain size. Crack propagation takes place beyond a load threshold, which is grain size dependent. We present a cohesive zone model for the intergranular failure process. The methodology accounts for an intrinsic opening that governs the length of the cohesive zone and allows the investigation of grain size effects. A rate and temperature-dependent cohesive model is proposed (Romero de la Osa M, Estevez R et al 2009 J. Mech. Adv. Mater. Struct. 16 623–31) to mimic the reaction–rupture mechanism. The formulation is inspired by Michalske and Freiman's picture (Michalske and Freiman 1983 J. Am. Ceram. Soc. 66 284–8) together with a recent study by Zhu et al (2005 J. Mech. Phys. Solids 53 1597–623) of the reaction–rupture mechanism. The present investigation extends a previous work (Romero de la Osa et al 2009 Int. J. Fracture 158 157–67) in which the problem is formulated. Here, we explore the influence of the microstructure in terms of grain size, their elastic properties and residual thermal stresses originating from the cooling from the sintering temperature down to ambient conditions. Their influence on SCG for static loadings is reported and the predictions compared with experimental trends. We show that the initial stress state is responsible for the grain size dependence reported experimentally for SCG. Furthermore, the account for the initial stresses enables the prediction of a load threshold below which no crack growth is observed: a crack arrest takes place when the crack path meets a region in compression

  10. Terahertz Rotational Spectroscopy of the so Radical

    Science.gov (United States)

    Martin-Drumel, M. A.; Cuisset, A.; Eliet, S.; Mouret, G.; Hindle, F.; Pirali, O.

    2013-06-01

    Sulfur monoxide SO (X^3Σ^-) is a well-known interstellar radical identified in a wide variety of astrophysical environments. Due to its high reactivity and its role in chemical reactions involving O and S atoms, SO is also a reaction intermediate in combustion processes and chemistry of the Earth atmosphere. We have recorded pure rotational transitions of SO in the THz spectral range using synchrotron-based Fourier-Transform (FT) FIR and continous wave (CW) THz techniques. A FT-FIR spectrum of SO has been recorded at the AILES beamline of SOLEIL synchrotron in the spectral range 44-93 wn using a resolution of 0.001 wn allowing an accuracy on line position of 0.00007 wn (≃ 2 MHz). A multipass absorption discharge cell aligned to an absorption path length of 24 m has been used. A continuous electrical discharge (1 A / 980 V) in a flowing mixture of H_2S, He, H_2 and air (respectively at pressure of 0.01, 1.15, 0.14 and 0.06 mbar) was used to produce SO. On this spectrum, 102 transitions of SO have been identified with N=31 to 65. Among the observed lines, 99 are detected for the first time (22 new transitions belong to the HIFI spectral windows). Due to our limited instrumental resolution, transitions involving N ranging from 31 to 43 show unresolved fine structure triplets. Recently, in order to observe all fine structure components in the HIFI spectral windows, we have recorded a high resolution CW-THz spectrum of SO. At the time of the writing, this spectrum was under analysis. C. A. Gottlieb and J. A. Ball, Astrophys. J. 184, L59 (1973) G.A. Blake et al., Astrophys. J. 315, 621 (1987) J. B. Burkholder et al., J. Mol. Spectrosc. 124, 379 (1987) M. A. Martin-Drumel et al., Rev. Sci. Instrum. 82, 113106 (2011) S. Eliet et al., J. Mol. Struct. 1006, 13 (2011)

  11. Monitoring the bio-stimulation of hydrocarbon-contaminated soils by measurements of soil electrical properties, and CO2 content and its 13C/12C isotopic signature

    Science.gov (United States)

    Noel, C.; Gourry, J.; Ignatiadis, I.; Colombano, S.; Dictor, M.; Guimbaud, C.; Chartier, M.; Dumestre, A.; Dehez, S.; Naudet, V.

    2013-12-01

    Hydrocarbon contaminated soils represent an environmental issue as it impacts on ecosystems and aquifers. Where significant subsurface heterogeneity exists, conventional intrusive investigations and groundwater sampling can be insufficient to obtain a robust monitoring of hydrocarbon contaminants, as the information they provide is restricted to vertical profiles at discrete locations, with no information between sampling points. In order to obtain wider information in space volume on subsurface modifications, complementary methods can be used like geophysics. Among geophysical methods, geoelectrical techniques such as electrical resistivity (ER) and induced polarization (IP) seem the more promising, especially to study the effects of biodegradation processes. Laboratory and field geoelectrical experiments to characterize soils contaminated by oil products have shown that mature hydrocarbon-contaminated soils are characterized by enhanced electrical conductivity although hydrocarbons are electrically resistive. This high bulk conductivity is due to bacterial impacts on geological media, resulting in changes in the chemical and physical properties and thus, to the geophysical properties of the ground. Moreover, microbial activity induced CO2 production and isotopic deviation of carbon. Indeed, produced CO2 will reflect the pollutant isotopic signature. Thus, the ratio δ13C(CO2) will come closer to δ13C(hydrocarbon). BIOPHY, project supported by the French National Research Agency (ANR), proposes to use electrical methods and gas analyses to develop an operational and non-destructive method for monitoring in situ biodegradation of hydrocarbons in order to optimize soil treatment. Demonstration field is located in the South of Paris (France), where liquid fuels (gasoline and diesel) leaked from some tanks in 1997. In order to stimulate biodegradation, a trench has been dug to supply oxygen to the water table and thus stimulate aerobic metabolic bioprocesses. ER and

  12. The effects of methylglyoxal-bis(guanylhydrazone) on spermine binding and transport in liver mitochondria.

    Science.gov (United States)

    Toninello, A; Via, L D; Di Noto, V; Mancon, M

    1999-12-15

    This study evaluated the effect of the anticancer drug methylglyoxal-bis(guanylhydrazone) (MGBG) on the binding of the polyamine spermine to the mitochondrial membrane and its transport into the inner compartment of this organelle. Spermine binding was studied by applying a new thermodynamic treatment of ligand-receptor interactions (Di Noto et al., Macromol Theory Simul 5: 165-181, 1996). Results showed that MGBG inhibited the binding of spermine to the site competent for the first step in polyamine transport; the interaction of spermine with this site, termed S1, also mediates the inhibitory effect of the polyamine on the mitochondrial permeability transition (Dalla Via et al., Biochim Biophys Acta 1284: 247-252, 1996). In the presence of 1 mM MGBG, the binding capacity and affinity of this site were reduced by about 2.6-fold; on the contrary, the binding capacity of the S2 site, which is most likely responsible for the internalization of cytoplasmic proteins (see Dalla Via et al., reference cited above), increased by about 1.3-fold, and its binding affinity remained unaffected. MGBG also inhibited the initial rate of spermine transport in a dose-dependent manner by establishing apparently sigmoidal kinetics. Consequently, the total extent of spermine accumulation inside mitochondria was inhibited. This inhibition in transport seems to reflect a conformational change at the level of the channel protein constituting the polyamine transport system, rather than competitive inhibition at the inner active site of the channel, thereby excluding the possibility that the polyamine and drug use the same transport pathway. Furthermore, it is suggested that, in the presence of MGBG, the S2 site is able to participate in residual spermine transport. MGBG also strongly inhibits deltapH-dependent spermine efflux, resulting in a complete block in the bidirectional flux of the polyamine and its sequestration inside the matrix space. The effects of MGBG on spermine accumulation

  13. Scaling of Dielectric Breakdown Thresholds in Earth's and CO2-rich atmospheres: Impact for Predictions of Extraterrestrial Transient Luminous Events and Lightning Discharges

    Science.gov (United States)

    Riousset, J. A.

    2016-12-01

    which may be of biological importance [Miller, Science, 117, 528-529, 1953; Biochem. Biophys. Acta, 23, 480-489, 1957].

  14. Co-ordinate induction of hepatic mitochondrial and peroxisomal carnitine acyltransferase synthesis by diet and drugs.

    Science.gov (United States)

    Brady, P S; Marine, K A; Brady, L J; Ramsay, R R

    1989-01-01

    The present studies examined the effect of agents that induce peroxisomal and mitochondrial beta-oxidation on hepatic mitochondrial carnitine palmitoyltransferase (CPT) and peroxisomal carnitine acyltransferase [CPTs of Ramsay (1988) Biochem. J. 249, 239-245; COT of Farrell & Bieber (1983) Arch. Biochem. Biophys. 222, 123-132 and Miyazawa, Ozasa, Osumi & Hashimoto (1983) J. Biochem. 94, 529-542]. In the first studies, high fat diets containing corn oil or fish oil were used to induce peroxisomal and mitochondrial enzymes. Rats were fed one of three diets for 4 weeks: (1) low fat, with corn oil as 11% of energy (kJ); (2) high fat, with corn oil as 45% of kJ; (3) high fat, with fish oil as 45% of kJ. At the end of 4 weeks, both mitochondrial CPT and peroxisomal CPTs exhibited increases in activity, immunoreactive protein, mRNA levels and transcription rates in livers of rats fed either high-fat diet compared to the low fat diet. Riboflavin deficiency or starvation for 48 h also increased the peroxisomal CPTs mRNA. A second set of studies used the plasticizer 2-(diethylhexyl)phthalate (DEHP), 0.5% clofibrate or 1% acetylsalicylic acid (fed for 3 weeks) to alter peroxisomal and mitochondrial fatty acid oxidation. With DEHP, the mitochondrial CPT and peroxisomal CPTs activity, immunoreactive protein, mRNA levels and and transcription rate were all increased by 3-5-fold. The peroxisomal CPTs activity, immunoreactive protein, mRNA levels and transcription rate were increased 2-3-fold by clofibrate and acetylsalicylic acid, again similar to mitochondrial CPT. The results of the combined studies using both diet and drugs to cause enzyme induction suggest that the synthesis of the carnitine acyltransferases (mitochondrial CPT and peroxisomal CPTs) may be co-ordinated with each other; however, the co-ordinate regulatory factors have not yet been identified. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 5. PMID:2775196

  15. Measurement of nucleotide exchange rate constants in single rabbit soleus myofibrils during shortening and lengthening using a fluorescent ATP analog.

    Science.gov (United States)

    Shirakawa, I; Chaen, S; Bagshaw, C R; Sugi, H

    2000-02-01

    The kinetics of displacement of a fluorescent nucleotide, 2'(3')-O-[N[2-[[Cy3]amido]ethyl]carbamoyl]-adenosine 5'-triphosphate (Cy3-EDA-ATP), bound to rabbit soleus muscle myofibrils were studied using flash photolysis of caged ATP. Use of myofibrils from this slow twitch muscle allowed better resolution of the kinetics of nucleotide exchange than previous studies with psoas muscle myofibrils (, Biophys. J. 73:2033-2042). Soleus myofibrils in the presence of Cy3-EDA-nucleotides (Cy3-EDA-ATP or Cy3-EDA-ADP) showed selective fluorescence staining of the A-band. The K(m) for Cy3-EDA-ATP and the K(d) for Cy3-EDA-ADP binding to the myofibril A-band were 1.9 microM and 3.8 microM, respectively, indicating stronger binding of nucleotide to soleus cross-bridges compared to psoas cross-bridges (2.6 microM and 50 microM, respectively). After flash photolysis of caged ATP, the A-band fluorescence of the myofibril in the Cy3-EDA-ATP solution under isometric conditions decayed exponentially with a rate constant of 0.045 +/- 0.007 s(-1) (n = 32) at 10 degrees C, which was about seven times slower than that for psoas myofibrils. When a myofibril was allowed to shorten with a constant velocity, the nucleotide displacement rate constant increased from 0.066 s(-1) (isometric) to 0.14 s(-1) at 20 degrees C with increasing shortening velocity up to 0.1 myofibril length/s (V(max), the shortening velocity under no load was approximately 0. 2 myofibril lengths/s). The rate constant was not significantly affected by an isovelocity stretch of up to 0.1 myofibril lengths/s. These results suggest that the cross-bridge kinetics are not significantly affected at higher strain during lengthening but depend on the lower strain during shortening. These data also indicate that the interaction distance between a cross-bridge and the actin filament is at least 16 nm for a single cycle of the ATPase.

  16. As to the clastogenic-, sister-chromatid exchange inducing-and cytotoxic activity of inosine triphosphate in cultures of human peripheral lymphocytes.

    Science.gov (United States)

    Vormittag, W; Brannath, W

    2001-05-09

    The influence of commercial inosine triphosphate (ITP) on the chromosome aberration rate, the mitotic rate, sister-chromatid exchange (SCE) frequency, and the proportion of first (X1), second (X2) and third (X3) division metaphases was investigated in 72h cultures of human peripheral lymphocytes. The blood donors had mild inactive arthrosis and a normal health check-up. All cultures of each volunteer were set-up simultaneously. In contrast to a previous report [Arch. Biochem. Biophys. 278 (1990) 238-244], it was demonstrated in two preliminary studies (number of subjects, n=5 each) that ITP at a final concentration of 100 microM does not induce chromosomal aberrations and, furthermore, that not ITP concentrations higher than 100 microM but ITP doses higher than 3.8mM prohibit culture growth. Based on these results, cultures with a final ITP concentration of 3.6mM (max.) and 1.8mM (max./2) were compared with control cultures (number of subjects n=10; three males and seven females, mean age x=57.6 years). Whereas no increase in the chromosomal breakage rate was observed in cultures with an ITP concentration of 1.8mM and only a marginally significant one (P=0.048) for 3.6mM ITP cultures, a highly significant induction of SCEs, not only at an ITP concentration of 3.6mM (Prate from 0 to 1.8mM as well as from 1.8 to 3.6mM in the aberration studies (all P values are equal to smallest possible one for a sample size of 10, namely, 0.002), and in the SCE studies there is a significant decrease in the X3 frequency when ITP is increased (0-1.8mM: P=0.0061 and 1.8-3.6mM: Pchanges significantly only at the second dose step (0-1.8mM ITP: P=0.22 and 1.8-3.6mM ITP: P<0.0001). The results are discussed.

  17. Physical-chemical basis of the protection of slowly frozen human erythrocytes by glycerol

    Energy Technology Data Exchange (ETDEWEB)

    Rall, W.F.; Mazur, P.; Souzu, H.

    1978-07-01

    One theory of freezing damage suggests that slowly cooled cells are killed by being exposed to increasing concentrations of electrolytes as the suspending medium freezes. A corollary to this view is that protective additives such as glycerol protect cells by acting colligatively to reduce the electrolyte concentration at any subzero temperature. Recently published phase-diagram data for the ternary system glycerol-NaCl-water by M.L. Shepard et al. (Cryobiology, 13: 9-23, 1976), in combination with the data on human red cell survival vs. subzero temperature presented here and in the companion study of Souzu and Mazur (Biophys. J., 23: 89-100), permit a precise test of this theory. Appropriate liquidus phase-diagram information for the solutions used in the red cell freezing experiments was obtained by interpolation of liquidus data of Shepard and his co-workers. The results of phase-diagram analysis of red cell survival indicate that the correlation between the temperature that yields 50% hemolysis (LT/sub 50/) and the electrolyte concentration attained at that temperature in various concentrations of glycerol is poor. With increasing concentrations of glycerol, the cells were killed at progressively lower concentrations of NaCl. For example, the LT/sub 50/ for cells frozen in the absence of glycerol corresponds to a NaCl concentration of 12 weight percent (2.4 molal), while for cells frozen in 1.75 M glycerol in buffered saline the LT/sub 50/ corresponds to 3.0 weight percent NaCl (1.3 molal). The data, in combination with other findings, lead to two conclusions: (a) The protection from glycerol is due to its colligative ability to reduce the concentration of sodium chloride in the external medium, but (b) the protection is less than that expected from colligative effects; apparently glycerol itself can also be a source of damage, probably because it renders the red cells susceptible to osmotic shock during thawing.

  18. Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations

    Energy Technology Data Exchange (ETDEWEB)

    Markin, Craig J.; Spyracopoulos, Leo, E-mail: leo.spyracopoulos@ualberta.ca [University of Alberta, Department of Biochemistry (Canada)

    2012-12-15

    NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K{sub D}) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K{sub D} value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of {sup 1}H-{sup 15}N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k{sub off}). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k{sub off} {approx} 3,000 s{sup -1} in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k{sub off} from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k{sub off} values over a wide range, from 100 to 15,000 s{sup -1}. The validity of line shape analysis for k{sub off} values approaching intermediate exchange ({approx}100 s{sup -1}), may be facilitated by

  19. The Tutorial Program in Biochemistry at UFV: Improvement of the Activities and Performance of the Enrolled Students

    Directory of Open Access Journals (Sweden)

    T.R. Costa

    2005-07-01

    Full Text Available The Tutorial Program in Biochemistry  at UFV is reaching  the objectives  since the creation,  in 2001. Based  on the  accomplishment  of weekly sessions (2h,  which  tutor and  programs  students reunite to effects the  apprenticeship marked  by the  inter-activity,  the  Program  aims to give support to stu- dents  with  deficiency of basic knowledge.  For  this  reason,  reproved  students or students with  poor performance  in pre-requisites  subjects  are  automatically inscribed.   The  attending students receive satisfactory grade (S, frequency greater  than  75%, or not satisfactory grade (N. The work method- ology has been modified to obtain  better results.   This  study  aimed  evaluate  the  performance  of the Programs students through  modifications,  as the  elimination  of the theoretical session of 1h-weekly and the implantation of didactic  little-books containing  script classes and exercise lists.  Satisfactory results  indicated  that in 7 analyzed  semesters  (from I-2001 to I-2004, the attending students (S got similar  average  final-grade  (70.48  if compared  with  students not  enrolled  in the  Program  (71.64; not attending students (N, 56.81 got significantly  lower final-grade.  The failure rate  for S grade stu- dents  (8.69% was similar to the rate  of not-enrolled  students (8.97%, both  very lower than  N grade students (30.71%.  Based on the  necessity  of additional didactic material, two didactics  little-books were prepared  to  be used  in sessions.   The  little-books  Tutoria em Bioqu´ımica:  Biomol´eculas  and Tutoria em Bioqu´ımica:  Metabolismo  Celular  guide discussions  in classes, emphasizing  exercises.  It constitutes a considerable  advance,  according  to Programs students:  it  guides  and  encourages  the studies.  A questionnaire revealed  the  high acceptance  degree (97

  20. Refinement of NMR structures using implicit solvent and advanced sampling techniques.

    Science.gov (United States)

    Chen, Jianhan; Im, Wonpil; Brooks, Charles L

    2004-12-15

    NMR biomolecular structure calculations exploit simulated annealing methods for conformational sampling and require a relatively high level of redundancy in the experimental restraints to determine quality three-dimensional structures. Recent advances in generalized Born (GB) implicit solvent models should make it possible to combine information from both experimental measurements and accurate empirical force fields to improve the quality of NMR-derived structures. In this paper, we study the influence of implicit solvent on the refinement of protein NMR structures and identify an optimal protocol of utilizing these improved force fields. To do so, we carry out structure refinement experiments for model proteins with published NMR structures using full NMR restraints and subsets of them. We also investigate the application of advanced sampling techniques to NMR structure refinement. Similar to the observations of Xia et al. (J.Biomol. NMR 2002, 22, 317-331), we find that the impact of implicit solvent is rather small when there is a sufficient number of experimental restraints (such as in the final stage of NMR structure determination), whether implicit solvent is used throughout the calculation or only in the final refinement step. The application of advanced sampling techniques also seems to have minimal impact in this case. However, when the experimental data are limited, we demonstrate that refinement with implicit solvent can substantially improve the quality of the structures. In particular, when combined with an advanced sampling technique, the replica exchange (REX) method, near-native structures can be rapidly moved toward the native basin. The REX method provides both enhanced sampling and automatic selection of the most native-like (lowest energy) structures. An optimal protocol based on our studies first generates an ensemble of initial structures that maximally satisfy the available experimental data with conventional NMR software using a simplified

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