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Sample records for repeating unit structure

  1. Structural determination of Streptococcus pneumoniae repeat units in serotype 41A and 41F capsular polysaccharides to probe gene functions in the corresponding capsular biosynthetic loci

    DEFF Research Database (Denmark)

    Petersen, Bent O.; Skovsted, Ian C.; Paulsen, Berit Smestad

    2014-01-01

    We report the repeating unit structures ofthe native capsular polysaccharidesof S. pneumoniaeserotypes 41A and 41F. Structuraldeterminationsyieldedsix carbohydrate units in the doubly branched repeating unit to givethe following structure for serotype 41A:The structure determinations were motivat...

  2. Modelling Structure-Property Relationship for Copolymers by Structured Representation of Repeating Units

    Science.gov (United States)

    Bertinetto, Carlo; Duce, Celia; Micheli, Alessio; Starita, Antonina; Solaro, Roberto; Tiné, Maria R.

    2009-08-01

    We report here a recent study on the prediction by recursive neural network of the glass transition temperature of (meth)acrylic copolymers, for which appropriate structured representations are proposed. It is shown that the flexibility of such description allows for simultaneously treating different classes of compounds as well as accounting for different average properties such as tacticity and molar composition.

  3. Impacts of Repeat Unit Structure and Copolymer Architecture on Thermal and Solution Properties in Homopolymers, Copolymers, and Copolymer Blends

    Science.gov (United States)

    Marrou, Stephen Raye

    Gradient copolymers are a relatively new type of copolymer architecture in which the distribution of comonomers gradually varies over the length of the copolymer chain, resulting in a number of unusual properties derived from the arrangement of repeat units. For example, nanophase-segregated gradient copolymers exhibit extremely broad glass transition temperatures (Tgs) resulting from the wide range of compositions present in the nanostructure. This dissertation presents a number of studies on how repeat unit structure and copolymer architecture dictate bulk and solution properties, specifically taking inspiration from the gradient copolymer architecture and comparing the response from this compositionally heterogeneous material to other more conventional materials. The glass transition behavior of a range of common homopolymers was studied to determine the effects of subunit structure on Tg breadth, observing a significant increase in T g breadth with increasing side chain length in methacrylate-based homopolymers and random copolymers. Additionally, increasing the composition distribution of copolymers, either by blending individual random copolymers of different overall composition or synthesizing random copolymers to high conversion, resulted in significant increases to Tg breadth. Plasticization of homopolymers and random copolymers with low molecular weight additives also served to increase the Tg breadth; the most dramatic effect was observed in the selective plasticization of a styrene/4-vinylpyridine gradient copolymer with increases in T g breadth to values above 100 °C. In addition, the effects of repeat unit structure and copolymer architecture on other polymer properties besides Tg were also investigated. The intrinsic fluorescence of styrene units in styrene-containing copolymers was studied, noting the impact of repeat unit structure and copolymer architecture on the resulting fluorescence spectra in solution. The impact of repeat unit structure on

  4. The dependence of the electrochemical properties of perfluorosulfonic acid membrane/water systems on repeat unit structure

    Science.gov (United States)

    Kim, Young Gyun; Bae, Young Chan

    2009-07-01

    We developed a molecular thermodynamic framework to describe the dependence of the electrochemical properties of a perfluorosulfonic acid (PFSA) membrane/water system on the polymer structure. To better understand the behavior of the polymer membrane/water system, we developed a lattice model based on lattice cluster theory. We performed hypothetical calculations for a variety of repeat unit structures. We also investigated the correlation between the interaction energy and extending or reducing the chain length of the polymer repeat unit using COMPASS force fields. Our results indicate that the ionic conductivity of the nonpolar CF2CF2 group in the main chain varies with the length of the chain. In addition, the ionic conductivity of different CF2CF2 group chain lengths fluctuates according to hydration level. When OCF2CF3CF groups are substituted at 0 and 1, the predictions of the PFSA membrane agreed well with the experimental data from a Dow membrane. To obtain good ionic conductivity at a high vapor equilibrated hydration level, the nonpolar group in the polymer repeat unit and the substituted group chain connecting the nonpolar group length should both be short, and the substituted group chain connected with the sulfonic group should be long.

  5. Controlled growth of DNA structures from repeating units using the vernier mechanism.

    Science.gov (United States)

    Greschner, Andrea A; Bujold, Katherine E; Sleiman, Hanadi F

    2014-08-11

    In this report, we demonstrate the assembly of length-programmed DNA nanostructures using a single 16 base sequence and its complement as building blocks. To achieve this, we applied the Vernier mechanism to DNA assembly, which uses a mismatch in length between two monomers to dictate the final length of the product. Specifically, this approach relies on the interaction of two DNA strands containing a different number (n, m) of complementary binding sites: these two strands will keep binding to each other until they come into register, thus generating a larger assembly whose length (n × m) is encoded by the number of binding sites in each strand. While the Vernier mechanism has been applied to other areas of supramolecular chemistry, here we present an application of its principles to DNA nanostructures. Using a single 16 base repeat and its complement, and varying the number of repeats on a given DNA strand, we show the consistent construction of duplexes up to 228 base pairs (bp) in length. Employing specific annealing protocols, strand capping, and intercalator chaperones allows us to further grow the duplex to 392 base pairs. We demonstrate that the Vernier method is not only strand-efficient, but also produces a cleaner, higher-yielding product than conventional designs.

  6. Structural Analysis and Anticoagulant Activities of the Novel Sulfated Fucan Possessing a Regular Well-Defined Repeating Unit from Sea Cucumber

    OpenAIRE

    Mingyi Wu; Li Xu; Longyan Zhao; Chuang Xiao; Na Gao; Lan Luo; Lian Yang; Zi Li; Lingyun Chen; Jinhua Zhao

    2015-01-01

    Sulfated fucans, the complex polysaccharides, exhibit various biological activities. Herein, we purified two fucans from the sea cucumbers Holothuria edulis and Ludwigothurea grisea. Their structures were verified by means of HPGPC, FT-IR, GC–MS and NMR. As a result, a novel structural motif for this type of polymers is reported. The fucans have a unique structure composed of a central core of regular (1→2) and (1→3)-linked tetrasaccharide repeating units. Approximately 50% of the units from...

  7. Structural determination of Streptococcus pneumoniae repeat units in serotype 41A and 41F capsular polysaccharides to probe gene functions in the corresponding capsular biosynthetic loci.

    Science.gov (United States)

    Petersen, Bent O; Skovsted, Ian C; Paulsen, Berit Smestad; Redondo, Antonio R; Meier, Sebastian

    2014-12-05

    We report the repeating unit structures of the native capsular polysaccharides of Streptococcus pneumoniae serotypes 41A and 41F. Structural determinations yielded six carbohydrate units in the doubly branched repeating unit to give the following structure for serotype 41A: The structure determinations were motivated (1) by an ambition to help close the remaining gaps in S. pneumoniae capsular polysaccharide structures, and (2) by the attempt to derive functional annotations of carbohydrate active enzymes in the biosynthesis of bacterial polysaccharides from the determined structures. An activity present in 41F but not 41A is identified as an acetyltransferase acting on the rhamnopyranosyl sidechain E. The genes encoding the formation of the six glycosidic bonds in serogroup 41 were determined from the capsular polysaccharide structures of serotype 41A, 41F, and genetically related serotypes, in conjunction with corresponding genomic information and computational homology searches. In combination with complementary information, NMR spectroscopy considerably simplifies the functional annotation of carbohydrate active enzymes in the biosynthesis of bacterial polysaccharides.

  8. Structural analysis and anticoagulant activities of the novel sulfated fucan possessing a regular well-defined repeating unit from sea cucumber.

    Science.gov (United States)

    Wu, Mingyi; Xu, Li; Zhao, Longyan; Xiao, Chuang; Gao, Na; Luo, Lan; Yang, Lian; Li, Zi; Chen, Lingyun; Zhao, Jinhua

    2015-04-13

    Sulfated fucans, the complex polysaccharides, exhibit various biological activities. Herein, we purified two fucans from the sea cucumbers Holothuria edulis and Ludwigothurea grisea. Their structures were verified by means of HPGPC, FT-IR, GC-MS and NMR. As a result, a novel structural motif for this type of polymers is reported. The fucans have a unique structure composed of a central core of regular (1→2) and (1→3)-linked tetrasaccharide repeating units. Approximately 50% of the units from L. grisea (100% for H. edulis fucan) contain sides of oligosaccharides formed by nonsulfated fucose units linked to the O-4 position of the central core. Anticoagulant activity assays indicate that the sea cucumber fucans strongly inhibit human blood clotting through the intrinsic pathways of the coagulation cascade. Moreover, the mechanism of anticoagulant action of the fucans is selective inhibition of thrombin activity by heparin cofactor II. The distinctive tetrasaccharide repeating units contribute to the anticoagulant action. Additionally, unlike the fucans from marine alga, although the sea cucumber fucans have great molecular weights and affluent sulfates, they do not induce platelet aggregation. Overall, our results may be helpful in understanding the structure-function relationships of the well-defined polysaccharides from invertebrate as new types of safer anticoagulants.

  9. Structural Analysis and Anticoagulant Activities of the Novel Sulfated Fucan Possessing a Regular Well-Defined Repeating Unit from Sea Cucumber

    Directory of Open Access Journals (Sweden)

    Mingyi Wu

    2015-04-01

    Full Text Available Sulfated fucans, the complex polysaccharides, exhibit various biological activities. Herein, we purified two fucans from the sea cucumbers Holothuria edulis and Ludwigothurea grisea. Their structures were verified by means of HPGPC, FT-IR, GC–MS and NMR. As a result, a novel structural motif for this type of polymers is reported. The fucans have a unique structure composed of a central core of regular (1→2 and (1→3-linked tetrasaccharide repeating units. Approximately 50% of the units from L. grisea (100% for H. edulis fucan contain sides of oligosaccharides formed by nonsulfated fucose units linked to the O-4 position of the central core. Anticoagulant activity assays indicate that the sea cucumber fucans strongly inhibit human blood clotting through the intrinsic pathways of the coagulation cascade. Moreover, the mechanism of anticoagulant action of the fucans is selective inhibition of thrombin activity by heparin cofactor II. The distinctive tetrasaccharide repeating units contribute to the anticoagulant action. Additionally, unlike the fucans from marine alga, although the sea cucumber fucans have great molecular weights and affluent sulfates, they do not induce platelet aggregation. Overall, our results may be helpful in understanding the structure-function relationships of the well-defined polysaccharides from invertebrate as new types of safer anticoagulants.

  10. Effect of repeat unit structure and molecular mass of lactic acid bacteria hetero-exopolysaccharides on binding to milk proteins

    DEFF Research Database (Denmark)

    Birch, Johnny; HarÐarson, HörÐur Kári; Khan, Sanaullah

    2017-01-01

    -exopolysaccharides (HePSs) of 0.14–4.9 MDa from lactic acid bacteria to different milk proteins (β-casein, κ-casein, native and heat-treated β-lactoglobulin) at pH 4.0–5.0. Maximum binding capacity (RUmax) and apparent affinity (KA,app) were HePS- and protein-dependent and varied for example 10- and 600-fold......Interactions of exopolysaccharides and proteins are of great importance in food science, but complicated to analyze and quantify at the molecular level. A surface plasmon resonance procedure was established to characterize binding of seven structure-determined, branched hetero...

  11. RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures

    Science.gov (United States)

    Paladin, Lisanna; Hirsh, Layla; Piovesan, Damiano; Andrade-Navarro, Miguel A.; Kajava, Andrey V.; Tosatto, Silvio C.E.

    2017-01-01

    RepeatsDB 2.0 (URL: http://repeatsdb.bio.unipd.it/) is an update of the database of annotated tandem repeat protein structures. Repeat proteins are a widespread class of non-globular proteins carrying heterogeneous functions involved in several diseases. Here we provide a new version of RepeatsDB with an improved classification schema including high quality annotations for ∼5400 protein structures. RepeatsDB 2.0 features information on start and end positions for the repeat regions and units for all entries. The extensive growth of repeat unit characterization was possible by applying the novel ReUPred annotation method over the entire Protein Data Bank, with data quality is guaranteed by an extensive manual validation for >60% of the entries. The updated web interface includes a new search engine for complex queries and a fully re-designed entry page for a better overview of structural data. It is now possible to compare unit positions, together with secondary structure, fold information and Pfam domains. Moreover, a new classification level has been introduced on top of the existing scheme as an independent layer for sequence similarity relationships at 40%, 60% and 90% identity. PMID:27899671

  12. A Structured Group Program for Repeat Dieters.

    Science.gov (United States)

    McNamara, Kathleen

    1989-01-01

    Describes a structured group program for women who repeatedly diet and may be at risk of developing more serious eating disorders. Discusses sessions focusing on eating behavior as well as internal factors that contribute to low body esteem and food and weight preoccupation. Evaluates effectiveness of program by self-reports of members of two…

  13. Fuel cell repeater unit including frame and separator plate

    Energy Technology Data Exchange (ETDEWEB)

    Yamanis, Jean; Hawkes, Justin R; Chiapetta, Jr., Louis; Bird, Connie E; Sun, Ellen Y; Croteau, Paul F

    2013-11-05

    An example fuel cell repeater includes a separator plate and a frame establishing at least a portion of a flow path that is operative to communicate fuel to or from at least one fuel cell held by the frame relative to the separator plate. The flow path has a perimeter and any fuel within the perimeter flow across the at least one fuel cell in a first direction. The separator plate, the frame, or both establish at least one conduit positioned outside the flow path perimeter. The conduit is outside of the flow path perimeter and is configured to direct flow in a second, different direction. The conduit is fluidly coupled with the flow path.

  14. Structural segmentation of music based on repeated harmonies

    NARCIS (Netherlands)

    de Haas, W.B.; Volk, A.; Wiering, F.

    2013-01-01

    In this paper we present a simple, yet powerful method for deriving the structural segmentation of a musical piece based on repetitions in chord sequences, called FORM. Repetition in harmony is a fundamental factor in constituting musical form. However, repeated pattern discovery in music still rema

  15. Evolutionary Origin of Higher-Order Repeat Structure in Alpha-Satellite DNA of Primate Centromeres

    Science.gov (United States)

    Koga, Akihiko; Hirai, Yuriko; Terada, Shoko; Jahan, Israt; Baicharoen, Sudarath; Arsaithamkul, Visit; Hirai, Hirohisa

    2014-01-01

    Alpha-satellite DNA (AS) is a main DNA component of primate centromeres, consisting of tandemly repeated units of ∼170 bp. The AS of humans contains sequences organized into higher-order repeat (HOR) structures, in which a block of multiple repeat units forms a larger repeat unit and the larger units are repeated tandemly. The presence of HOR in AS is widely thought to be unique to hominids (family Hominidae; humans and great apes). Recently, we have identified an HOR-containing AS in the siamang, which is a small ape species belonging to the genus Symphalangus in the family Hylobatidae. This result supports the view that HOR in AS is an attribute of hominoids (superfamily Hominoidea) rather than hominids. A single example is, however, not sufficient for discussion of the evolutionary origin of HOR-containing AS. In the present study, we developed an efficient method for detecting signs of large-scale HOR and demonstrated HOR of AS in all the three other genera. Thus, AS organized into HOR occurs widely in hominoids. Our results indicate that (i) HOR-containing AS was present in the last common ancestor of hominoids or (ii) HOR-containing AS emerged independently in most or all basal branches of hominoids. We have also confirmed HOR occurrence in centromeric AS in the Hylobatidae family, which remained unclear in our previous study because of the existence of AS in subtelomeric regions, in addition to centromeres, of siamang chromosomes. PMID:24585002

  16. Formation of functional CENP-B boxes at diverse locations in repeat units of centromeric DNA in New World monkeys.

    Science.gov (United States)

    Kugou, Kazuto; Hirai, Hirohisa; Masumoto, Hiroshi; Koga, Akihiko

    2016-06-13

    Centromere protein B, which is involved in centromere formation, binds to centromeric repetitive DNA by recognizing a nucleotide motif called the CENP-B box. Humans have large numbers of CENP-B boxes in the centromeric repetitive DNA of their autosomes and X chromosome. The current understanding is that these CENP-B boxes are located at identical positions in the repeat units of centromeric DNA. Great apes also have CENP-B boxes in locations that are identical to humans. The purpose of the present study was to examine the location of CENP-B box in New World monkeys. We recently identified CENP-B box in one species of New World monkeys (marmosets). In this study, we found functional CENP-B boxes in CENP-A-assembled repeat units of centromeric DNA in 2 additional New World monkeys (squirrel monkeys and tamarins) by immunostaining and ChIP-qPCR analyses. The locations of the 3 CENP-B boxes in the repeat units differed from one another. The repeat unit size of centromeric DNA of New World monkeys (340-350 bp) is approximately twice that of humans and great apes (171 bp). This might be, associated with higher-order repeat structures of centromeric DNA, a factor for the observed variation in the CENP-B box location in New World monkeys.

  17. Comparison of xanthans by the relative abundance of its six constituent repeating units

    NARCIS (Netherlands)

    Kool, M.M.; Gruppen, H.; Sworn, G.; Schols, H.A.

    2013-01-01

    Five xanthans were hydrolyzed to their repeating units using cellulases. Hydrophilic interaction chromatography with online electrospray ionization ion trap mass spectrometry and evaporative light scattering detection was used to analyze the oligomers released. It was concluded that six different pe

  18. Mechanical properties of regular porous biomaterials made from truncated cube repeating unit cells: Analytical solutions and computational models.

    Science.gov (United States)

    Hedayati, R; Sadighi, M; Mohammadi-Aghdam, M; Zadpoor, A A

    2016-03-01

    Additive manufacturing (AM) has enabled fabrication of open-cell porous biomaterials based on repeating unit cells. The micro-architecture of the porous biomaterials and, thus, their physical properties could then be precisely controlled. Due to their many favorable properties, porous biomaterials manufactured using AM are considered as promising candidates for bone substitution as well as for several other applications in orthopedic surgery. The mechanical properties of such porous structures including static and fatigue properties are shown to be strongly dependent on the type of the repeating unit cell based on which the porous biomaterial is built. In this paper, we study the mechanical properties of porous biomaterials made from a relatively new unit cell, namely truncated cube. We present analytical solutions that relate the dimensions of the repeating unit cell to the elastic modulus, Poisson's ratio, yield stress, and buckling load of those porous structures. We also performed finite element modeling to predict the mechanical properties of the porous structures. The analytical solution and computational results were found to be in agreement with each other. The mechanical properties estimated using both the analytical and computational techniques were somewhat higher than the experimental data reported in one of our recent studies on selective laser melted Ti-6Al-4V porous biomaterials. In addition to porosity, the elastic modulus and Poisson's ratio of the porous structures were found to be strongly dependent on the ratio of the length of the inclined struts to that of the uninclined (i.e. vertical or horizontal) struts, α, in the truncated cube unit cell. The geometry of the truncated cube unit cell approaches the octahedral and cube unit cells when α respectively approaches zero and infinity. Consistent with those geometrical observations, the analytical solutions presented in this study approached those of the octahedral and cube unit cells when

  19. Repeater F-waves are signs of motor unit pathology in polio survivors.

    Science.gov (United States)

    Hachisuka, Akiko; Komori, Tetsuo; Abe, Tatsuya; Hachisuka, Kenji

    2015-05-01

    The purpose of this study was to determine whether F-waves reveal electrophysiological features of anterior horn cells in polio survivors. Forty-three polio survivors and 20 healthy controls underwent motor nerve conduction studies of the median and tibial nerves bilaterally, including sampling of F-waves elicited by 100 stimuli and the determination of motor unit number estimation (MUNE). A significant increase in abnormally stereotyped ("repeater") F-waves and a reduction of F-wave persistence were observed in both nerves in the polio group as compared with the control group. Repeater F-waves had a negative correlation with MUNE. These trends in F-wave persistence and repeater F-waves after motor unit loss are characteristic findings in polio survivors. Repeater F-waves are a sign of motor unit pathology. © 2014 The Authors. Muscle & Nerve Published by Wiley Periodicals, Inc.

  20. Synthesis and conformational analysis of the repeating units of bacterial spore peptidoglycan.

    Science.gov (United States)

    Keglević, Dina; Kojić-Prodić, Biserka; Tomisić, Zrinka Banić

    2003-06-16

    Deprotection of the fully blocked disacharide allyl O-(2-amino-4,6-O-benzylidene-3-O-[(R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranosyl-1',2-lactam)-(1-->4)-2-acetamido-3,6-di-O-benzyl-2-deoxy-beta-D-glucopyranoside by selective de-O-allylation and parallel removal of the benzylidene and O-benzyl groups is described. The resulting beta-muramyl lactam-(1-->4)-GlcNAc disaccharide is characterised as the per-O-acetylated derivative by 1H and 13C NMR spectroscopy and X-ray structure analysis. Conformational analysis about glycosidic bond of repeating units of bacterial spore cortex is based on experimental data and molecular modelling.

  1. Distinct C9orf72-Associated Dipeptide Repeat Structures Correlate with Neuronal Toxicity

    Science.gov (United States)

    Krans, Amy; Sawaya, Michael R.; Paulson, Henry L.; Todd, Peter K.; Barmada, Sami J.; Ivanova, Magdalena I.

    2016-01-01

    Hexanucleotide repeat expansions in C9orf72 are the most common inherited cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The expansions elicit toxicity in part through repeat-associated non-AUG (RAN) translation of the intronic (GGGGCC)n sequence into dipeptide repeat-containing proteins (DPRs). Little is known, however, about the structural characteristics and aggregation propensities of the dipeptide units comprising DPRs. To address this question, we synthesized dipeptide units corresponding to the three sense-strand RAN translation products, analyzed their structures by circular dichroism, electron microscopy and dye binding assays, and assessed their relative toxicity when applied to primary cortical neurons. Short, glycine-arginine (GR)3 dipeptides formed spherical aggregates and selectively reduced neuronal survival compared to glycine-alanine (GA)3 and glycine-proline (GP)3 dipeptides. Doubling peptide length had little effect on the structure of GR or GP peptides, but (GA)6 peptides formed β-sheet rich aggregates that bound thioflavin T and Congo red yet lacked the typical fibrillar morphology of amyloids. Aging of (GA)6 dipeptides increased their β-sheet content and enhanced their toxicity when applied to neurons. We also observed that the relative toxicity of each tested dipeptide was proportional to peptide internalization. Our results demonstrate that different C9orf72-related dipeptides exhibit distinct structural properties that correlate with their relative toxicity. PMID:27776165

  2. Organometallic macromolecules with piano stool coordination repeating units: chain configuration and stimulated solution behaviour.

    Science.gov (United States)

    Cao, Kai; Ward, Jonathan; Amos, Ryan C; Jeong, Moon Gon; Kim, Kyoung Taek; Gauthier, Mario; Foucher, Daniel; Wang, Xiaosong

    2014-09-11

    Theoretical calculations illustrate that organometallic macromolecules with piano stool coordination repeating units (Fe-acyl complex) adopt linear chain configuration with a P-Fe-C backbone surrounded by aromatic groups. The macromolecules show molecular weight-dependent and temperature stimulated solution behaviour in DMSO.

  3. Identification of a highly sulfated fucoidan from sea cucumber Pearsonothuria graeffei with well-repeated tetrasaccharides units.

    Science.gov (United States)

    Hu, Yaqin; Li, Shan; Li, Junhui; Ye, Xingqian; Ding, Tian; Liu, Donghong; Chen, Jianchu; Ge, Zhiwei; Chen, Shiguo

    2015-12-10

    Sea cucumber fucoidan is a major bioactive component of sea cucumber. The structures of fucoidans have significant influences on their biological activities. The present study clarified the delicate structure of a fucoidan from Pearsonothuria graeffei. Fucoidan was obtained after papain digestion and purified by ion chromatography. The carbohydrate sequence of fucoidan was firstly determined by negative-ion electrospray tandem mass spectrometry (ES-MS) with collision-induced dissociation of the oligosaccharide fragments, which were obtained by mild acid hydrolysis, and completed by NMR for assignment of the anomeric conformation. It was unambiguously identified as a tetrasaccharide repeating unit with a backbone of [ → 3Fuc (2S, 4S) α1 → 3Fucα1→ 3Fuc (4S) α1 → 3Fuc#7 × 10#]n. The glycosidic bonds between the non-sulfated and 2,4-O-disulfated fucose residues were selectively cleaved, and highly ordered oligosaccharide fragments with a tetrasaccharide repeating unit were obtained. The highly 4-O- and 2, 4-di-O-sulfated polysaccharide deserves further developments for Pharmacia use.

  4. Associations between inverted repeats and the structural evolution of bacterial genomes.

    Science.gov (United States)

    Achaz, Guillaume; Coissac, Eric; Netter, Pierre; Rocha, Eduardo P C

    2003-08-01

    The stability of the structure of bacterial genomes is challenged by recombination events. Since major rearrangements (i.e., inversions) are thought to frequently operate by homologous recombination between inverted repeats, we analyzed the presence and distribution of such repeats in bacterial genomes and their relation to the conservation of chromosomal structure. First, we show that there is a strong under-representation of inverted repeats, relative to direct repeats, in most chromosomes, especially among the ones regarded as most stable. Second, we show that the avoidance of repeats is frequently associated with the stability of the genomes. Closely related genomes reported to differ in terms of stability are also found to differ in the number of inverted repeats. Third, when using replication strand bias as a proxy for genome stability, we find a significant negative correlation between this strand bias and the abundance of inverted repeats. Fourth, when measuring the recombining potential of inverted repeats and their eventual impact on different features of the chromosomal structure, we observe a tendency of repeats to be located in the chromosome in such a way that rearrangements produce a smaller strand switch and smaller asymmetries than expected by chance. Finally, we discuss the limitations of our analysis and the influence of factors such as the nature of repeats, e.g., transposases, or the differences in the recombination machinery among bacteria. These results shed light on the challenges imposed on the genome structure by the presence of inverted repeats.

  5. Accuracy and repeatability of an inertial measurement unit system for field-based occupational studies.

    Science.gov (United States)

    Schall, Mark C; Fethke, Nathan B; Chen, Howard; Oyama, Sakiko; Douphrate, David I

    2016-04-01

    The accuracy and repeatability of an inertial measurement unit (IMU) system for directly measuring trunk angular displacement and upper arm elevation were evaluated over eight hours (i) in comparison to a gold standard, optical motion capture (OMC) system in a laboratory setting, and (ii) during a field-based assessment of dairy parlour work. Sample-to-sample root mean square differences between the IMU and OMC system ranged from 4.1° to 6.6° for the trunk and 7.2°-12.1° for the upper arm depending on the processing method. Estimates of mean angular displacement and angular displacement variation (difference between the 90th and 10th percentiles of angular displacement) were observed to change IMU system may serve as an acceptable instrument for directly measuring trunk and upper arm postures in field-based occupational exposure assessment studies with long sampling durations. Practitioner Summary: Few studies have evaluated inertial measurement unit (IMU) systems in the field or over long sampling durations. Results of this study indicate that the IMU system evaluated has reasonably good accuracy and repeatability for use in a field setting over a long sampling duration.

  6. Solution structure of the spectrin repeat: a left-handed antiparallel triple-helical coiled-coil.

    Science.gov (United States)

    Pascual, J; Pfuhl, M; Walther, D; Saraste, M; Nilges, M

    1997-10-31

    Cytoskeletal proteins belonging to the spectrin family have an elongated structure composed of repetitive units. The three-dimensional solution structure of the 16th repeat from chicken brain alpha-spectrin (R16) has been determined by NMR spectroscopy and distance geometry-simulated annealing calculations. We used a total of 1035 distance restraints, which included 719 NOE-based values obtained by applying the ambiguous restraints for iterative assignment (ARIA) method. In addition, we performed a direct refinement against 1H-chemical shifts. The final ensemble of 20 structures shows an average RMSD of 1.52 A from the mean for the backbone atoms, excluding loops and N and C termini. R16 is made up of three antiparallel alpha-helices separated by two loops, and folds into a left-handed coiled-coil. The basic unit of spectrin is an antiparallel heterodimer composed of two homologous chains, beta and alpha. These assemble a tetramer via a mechanism that relies on the completion of a single repeat by association of the partial repeats located at the C terminus of the beta-chain (two helices) and at the N terminus of the alpha-chain (one helix). This tetramer is the assemblage able to cross-link actin filaments. Model building by homology of the "tetramerization" repeat from human erythrocyte spectrin illuminates the possible role of point mutations which cause hemolytic anemias.

  7. Local chromatin structure of heterochromatin regulates repeated DNA stability, nucleolus structure, and genome integrity

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Jamy C. [Univ. of California, Berkeley, CA (United States)

    2007-01-01

    Heterochromatin constitutes a significant portion of the genome in higher eukaryotes; approximately 30% in Drosophila and human. Heterochromatin contains a high repeat DNA content and a low density of protein-encoding genes. In contrast, euchromatin is composed mostly of unique sequences and contains the majority of single-copy genes. Genetic and cytological studies demonstrated that heterochromatin exhibits regulatory roles in chromosome organization, centromere function and telomere protection. As an epigenetically regulated structure, heterochromatin formation is not defined by any DNA sequence consensus. Heterochromatin is characterized by its association with nucleosomes containing methylated-lysine 9 of histone H3 (H3K9me), heterochromatin protein 1 (HP1) that binds H3K9me, and Su(var)3-9, which methylates H3K9 and binds HP1. Heterochromatin formation and functions are influenced by HP1, Su(var)3-9, and the RNA interference (RNAi) pathway. My thesis project investigates how heterochromatin formation and function impact nuclear architecture, repeated DNA organization, and genome stability in Drosophila melanogaster. H3K9me-based chromatin reduces extrachromosomal DNA formation; most likely by restricting the access of repair machineries to repeated DNAs. Reducing extrachromosomal ribosomal DNA stabilizes rDNA repeats and the nucleolus structure. H3K9me-based chromatin also inhibits DNA damage in heterochromatin. Cells with compromised heterochromatin structure, due to Su(var)3-9 or dcr-2 (a component of the RNAi pathway) mutations, display severe DNA damage in heterochromatin compared to wild type. In these mutant cells, accumulated DNA damage leads to chromosomal defects such as translocations, defective DNA repair response, and activation of the G2-M DNA repair and mitotic checkpoints that ensure cellular and animal viability. My thesis research suggests that DNA replication, repair, and recombination mechanisms in heterochromatin differ from those in

  8. Total synthesis of a Streptococcus pneumoniae serotype 12F CPS repeating unit hexasaccharide

    Directory of Open Access Journals (Sweden)

    Peter H. Seeberger

    2017-01-01

    Full Text Available The Gram-positive bacterium Streptococcus pneumoniae causes severe disease globally. Vaccines that prevent S. pneumoniae infections induce antibodies against epitopes within the bacterial capsular polysaccharide (CPS. A better immunological understanding of the epitopes that protect from bacterial infection requires defined oligosaccharides obtained by total synthesis. The key to the synthesis of the S. pneumoniae serotype 12F CPS hexasaccharide repeating unit that is not contained in currently used glycoconjugate vaccines is the assembly of the trisaccharide β-D-GalpNAc-(1→4-[α-D-Glcp-(1→3]-β-D-ManpNAcA, in which the branching points are equipped with orthogonal protecting groups. A linear approach relying on the sequential assembly of monosaccharide building blocks proved superior to a convergent [3 + 3] strategy that was not successful due to steric constraints. The synthetic hexasaccharide is the starting point for further immunological investigations.

  9. Total synthesis of a Streptococcus pneumoniae serotype 12F CPS repeating unit hexasaccharide

    Science.gov (United States)

    Pereira, Claney L; Govindan, Subramanian

    2017-01-01

    The Gram-positive bacterium Streptococcus pneumoniae causes severe disease globally. Vaccines that prevent S. pneumoniae infections induce antibodies against epitopes within the bacterial capsular polysaccharide (CPS). A better immunological understanding of the epitopes that protect from bacterial infection requires defined oligosaccharides obtained by total synthesis. The key to the synthesis of the S. pneumoniae serotype 12F CPS hexasaccharide repeating unit that is not contained in currently used glycoconjugate vaccines is the assembly of the trisaccharide β-D-GalpNAc-(1→4)-[α-D-Glcp-(1→3)]-β-D-ManpNAcA, in which the branching points are equipped with orthogonal protecting groups. A linear approach relying on the sequential assembly of monosaccharide building blocks proved superior to a convergent [3 + 3] strategy that was not successful due to steric constraints. The synthetic hexasaccharide is the starting point for further immunological investigations.

  10. Inulin isoforms differ by repeated additions of one crystal unit cell.

    Science.gov (United States)

    Cooper, Peter D; Barclay, Thomas G; Ginic-Markovic, Milena; Gerson, Andrea R; Petrovsky, Nikolai

    2014-03-15

    Inulin isoforms, especially delta inulin, are important biologically as immune activators and clinically as vaccine adjuvants. In exploring action mechanisms, we previously found regular increments in thermal properties of the seven-member inulin isoform series that suggested regular additions of some energetic structural unit. Because the previous isolates carried additional longer chains that masked defining ranges, these were contrasted with new isoform isolates comprising only inulin chain lengths defining that isoform. The new series began with 19 fructose units per chain (alpha-1 inulin), increasing regularly by 6 fructose units per isoform. Thus the 'energetic unit' equates to 6 fructose residues per chain. All isoforms showed indistinguishable X-ray diffraction patterns that were also identical with known inulin crystals. We conclude that an 'energetic unit' equates to one helix turn of 6 fructose units per chain as found in one unit cell of the inulin crystal. Each isoform chain comprised progressively more helix turns plus one additional fructose and glucose residues per chain.

  11. Unusual structures are present in DNA fragments containing super-long Huntingtin CAG repeats.

    Directory of Open Access Journals (Sweden)

    Daniel Duzdevich

    Full Text Available BACKGROUND: In the R6/2 mouse model of Huntington's disease (HD, expansion of the CAG trinucleotide repeat length beyond about 300 repeats induces a novel phenotype associated with a reduction in transcription of the transgene. METHODOLOGY/PRINCIPAL FINDINGS: We analysed the structure of polymerase chain reaction (PCR-generated DNA containing up to 585 CAG repeats using atomic force microscopy (AFM. As the number of CAG repeats increased, an increasing proportion of the DNA molecules exhibited unusual structural features, including convolutions and multiple protrusions. At least some of these features are hairpin loops, as judged by cross-sectional analysis and sensitivity to cleavage by mung bean nuclease. Single-molecule force measurements showed that the convoluted DNA was very resistant to untangling. In vitro replication by PCR was markedly reduced, and TseI restriction enzyme digestion was also hindered by the abnormal DNA structures. However, significantly, the DNA gained sensitivity to cleavage by the Type III restriction-modification enzyme, EcoP15I. CONCLUSIONS/SIGNIFICANCE: "Super-long" CAG repeats are found in a number of neurological diseases and may also appear through CAG repeat instability. We suggest that unusual DNA structures associated with super-long CAG repeats decrease transcriptional efficiency in vitro. We also raise the possibility that if these structures occur in vivo, they may play a role in the aetiology of CAG repeat diseases such as HD.

  12. Triplet repeat DNA structures and human genetic disease: dynamic mutations from dynamic DNA

    Indian Academy of Sciences (India)

    Richard R Sinden; Vladimir N Potaman; Elena A Oussatcheva; Christopher E Pearson; Yuri L Lyubchenko; Luda S Shlyakhtenko

    2002-02-01

    Fourteen genetic neurodegenerative diseases and three fragile sites have been associated with the expansion of (CTG)n•(CAG)n, (CGG)n•(CCG)n, or (GAA)n•(TTC)n repeat tracts. Different models have been proposed for the expansion of triplet repeats, most of which presume the formation of alternative DNA structures in repeat tracts. One of the most likely structures, slipped strand DNA, may stably and reproducibly form within triplet repeat sequences. The propensity to form slipped strand DNA is proportional to the length and homogeneity of the repeat tract. The remarkable stability of slipped strand DNA may, in part, be due to loop-loop interactions facilitated by the sequence complementarity of the loops and the dynamic structure of three-way junctions formed at the loop-outs.

  13. Large cryptic internal sequence repeats in protein structures from Homo sapiens

    Indian Academy of Sciences (India)

    R Sarani; N A Udayaprakash; R Subashini; P Mridula; T Yamane; K Sekar

    2009-03-01

    Amino acid sequences are known to constantly mutate and diverge unless there is a limiting condition that makes such a change deleterious. However, closer examination of the sequence and structure reveals that a few large, cryptic repeats are nevertheless sequentially conserved. This leads to the question of why only certain repeats are conserved at the sequence level. It would be interesting to find out if these sequences maintain their conservation at the three-dimensional structure level. They can play an active role in protein and nucleotide stability, thus not only ensuring proper functioning but also potentiating malfunction and disease. Therefore, insights into any aspect of the repeats – be it structure, function or evolution – would prove to be of some importance. This study aims to address the relationship between protein sequence and its three-dimensional structure, by examining if large cryptic sequence repeats have the same structure.

  14. Repeatability of gait pattern variables measured by use of extremity-mounted inertial measurement units in nonlame horses during trotting.

    Science.gov (United States)

    Cruz, Antonio M; Maninchedda, Ugo E; Burger, Dominik; Wanda, Sabine; Vidondo, Beatriz

    2017-09-01

    OBJECTIVE To determine repeatability of gait variables measured by use of extremity-mounted inertial measurement units (IMUs) in nonlame horses during trotting under controlled conditions of treadmill exercise. ANIMALS 10 horses. PROCEDURES Six IMUs were strapped to the metacarpal, metatarsal, and distal tibial regions of each horse. Data were collected in a standardized manner (3 measurements/d on 3 d/wk over a 3-week period) while each horse was trotted on a treadmill. Every measurement consisted of a minimum of 20 strides from which a minimum of 10 strides was selected for analysis. Spatial and temporal variables were derived from the IMUs. Repeatability coefficients based on the within-subject SD were computed for each gait analysis variable at each week. RESULTS Most of the temporal and spatial variables had high repeatability (repeatability coefficients variables, specifically the symmetry variables (which were calculated from other variables), had somewhat higher repeatability coefficients (ie, lower repeatability) only in the last week. CONCLUSIONS AND CLINICAL RELEVANCE With the exceptions of some symmetry variables, which may reflect individual variations during movement, the extremity-mounted IMUs provided data with high repeatability for nonlame horses trotting under controlled conditions of treadmill exercise. Repeatability was achieved for each instrumented limb segment with regard to the spatial relationship between 2 adjacent segments (joint angles) and the temporal relationship among all segments (limb phasing). Extremity-mounted IMUs could have the potential to become a method for gait analysis in horses.

  15. Crystal Structure of a Designed Tetratricopeptide Repeat Module in Complex with its Peptide Ligand

    Energy Technology Data Exchange (ETDEWEB)

    Cortajarena, A.; Wang, J; Regan, L

    2010-01-01

    Tetratricopeptide repeats (TPRs) are protein domains that mediate key protein-protein interactions in cells. Several TPR domains bind the C-termini of the chaperones heat shock protein (Hsp)90 and/or Hsp70, and exchange of such binding partners is key for the heat shock response. We have previously described the design of a TPR protein that binds tightly and specifically to the C-terminus of Hsp90, and in doing so, is able to inhibit chaperone function in vivo. Here we present the X-ray crystal structure of the designed TPR domain (CTPR390) in complex with its peptide ligand - the C-terminal residues of Hsp90 (peptide MEEVD). This structure reveals two interesting aspects of the TPR modules. First, a new packing arrangement of 3-TPR modules is observed. The TPR units stack against each other in an unusual fashion to form infinite superhelices in the crystal. Second, the structure provides insights into the molecular basis of TPR-ligand recognition.

  16. Chromatin structure of repeating CTG/CAG and CGG/CCG sequences in human disease.

    Science.gov (United States)

    Wang, Yuh-Hwa

    2007-05-01

    In eukaryotic cells, chromatin structure organizes genomic DNA in a dynamic fashion, and results in regulation of many DNA metabolic processes. The CTG/CAG and CGG/CCG repeating sequences involved in several neuromuscular degenerative diseases display differential abilities for the binding of histone octamers. The effect of the repeating DNA on nucleosome assembly could be amplified as the number of repeats increases. Also, CpG methylation, and sequence interruptions within the triplet repeats exert an impact on the formation of nucleosomes along these repeating DNAs. The two most common triplet expansion human diseases, myotonic dystrophy 1 and fragile X syndrome, are caused by the expanded CTG/CAG and CGG/CCG repeats, respectively. In addition to the expanded repeats and CpG methylation, histone modifications, chromatin remodeling factors, and noncoding RNA have been shown to coordinate the chromatin structure at both myotonic dystrophy 1 and fragile X loci. Alterations in chromatin structure at these two loci can affect transcription of these disease-causing genes, leading to disease symptoms. These observations have brought a new appreciation that a full understanding of disease gene expression requires a knowledge of the structure of the chromatin domain within which the gene resides.

  17. Tetrahedral Units: For Dodecahedral Super-Structures

    CERN Document Server

    Ortiz, Y; Liebman, J F

    2016-01-01

    Different novel organic-chemical possibilities for tetrahedral building units are considered, with attention to their utility in constructing different super-structures. As a representative construction we consider the use of sets of 20 such identical tetrahedral units to form a super-dodecahedron.

  18. Location of the O-acetyl substituents on a nonasaccharide repeating unit of sycamore extracellular xyloglucan.

    Science.gov (United States)

    York, W S; Oates, J E; van Halbeek, H; Darvill, A G; Albersheim, P; Tiller, P R; Dell, A

    1988-02-15

    The locations of the O-acetyl substituents on the major nonasaccharide repeating unit of the xyloglucan isolated from sycamore extracellular polysaccharides were determined by a combination of analytical methods, including f.a.b.-m.s. and 1H-n.m.r. spectroscopy. The O-2-linked-beta-D-galactosyl residue of the nonasaccharide was found to be the dominant site of O-acetyl substitution. Both mono-O-acetylated and di-O-acetylated beta-D-galactosyl residues were detected. The degree of O-acetylation of the beta-D-galactosyl residue, was estimated by 1H-n.m.r. spectroscopy to be 55-60% at O-6, 15-20% at O-4, and 20-25% at O-3. 1H-n.m.r. spectroscopy also indicated that approximately 50% of the beta-D-galactosyl residues are mono-O-acetylated, 25-30% are di-O-acetylated, and 20% are not acetylated.

  19. The four-transmembrane protein IP39 of Euglena forms strands by a trimeric unit repeat.

    Science.gov (United States)

    Suzuki, Hiroshi; Ito, Yasuyuki; Yamazaki, Yuji; Mineta, Katsuhiko; Uji, Masami; Abe, Kazuhiro; Tani, Kazutoshi; Fujiyoshi, Yoshinori; Tsukita, Sachiko

    2013-01-01

    Euglenoid flagellates have striped surface structures comprising pellicles, which allow the cell shape to vary from rigid to flexible during the characteristic movement of the flagellates. In Euglena gracilis, the pellicular strip membranes are covered with paracrystalline arrays of a major integral membrane protein, IP39, a putative four-membrane-spanning protein with the conserved sequence motif of the PMP-22/EMP/MP20/Claudin superfamily. Here we report the three-dimensional structure of Euglena IP39 determined by electron crystallography. Two-dimensional crystals of IP39 appear to form a striated pattern of antiparallel double-rows in which trimeric IP39 units are longitudinally polymerised, resulting in continuously extending zigzag-shaped lines. Structural analysis revealed an asymmetric molecular arrangement in the trimer, and suggested that at least four different interactions between neighbouring protomers are involved. A combination of such multiple interactions would be important for linear strand formation of membrane proteins in a lipid bilayer.

  20. Structural analysis of the KRIT1 ankyrin repeat and FERM domains reveals a conformationally stable ARD-FERM interface

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Rong [Yale Univ., New Haven, CT (United States); Li, Xiaofeng [Yale Univ., New Haven, CT (United States); Boggon, Titus J. [Yale Univ., New Haven, CT (United States)

    2015-10-14

    Cerebral cavernous malformations (CCM) are vascular dysplasias that usually occur in the brain and are associated with mutations in the KRIT1/CCM1, CCM2/MGC4607/OSM/Malcavernin, and PDCD10/CCM3/ TFAR15 genes. Here we report the 2.9 Å crystal structure of the ankyrin repeat domain (ARD) and FERM domain of the protein product of KRIT1 (KRIT1; Krev interaction trapped 1). The crystal structure reveals that the KRIT1 ARD contains 4 ankyrin repeats. There is also an unusual conformation in the ANK4 repeat that is stabilized by Trp-404, and the structure reveals a solvent exposed ankyrin groove. Domain orientations of the three copies within the asymmetric unit suggest a stable interaction between KRIT1 ARD and FERM domains, indicating a globular ARD–FERM module. It resembles the additional F0 domain found N-terminal to the FERM domain of talin. Structural analysis of KRIT1 ARD–FERM highlights surface regions of high evolutionary conservation, and suggests potential sites that could mediate interaction with binding partners. The structure therefore provides a better understanding of KRIT1 at the molecular level.

  1. Structural analysis of the KRIT1 ankyrin repeat and FERM domains reveals a conformationally stable ARD-FERM interface.

    Science.gov (United States)

    Zhang, Rong; Li, Xiaofeng; Boggon, Titus J

    2015-12-01

    Cerebral cavernous malformations (CCM) are vascular dysplasias that usually occur in the brain and are associated with mutations in the KRIT1/CCM1, CCM2/MGC4607/OSM/Malcavernin, and PDCD10/CCM3/TFAR15 genes. Here we report the 2.9 Å crystal structure of the ankyrin repeat domain (ARD) and FERM domain of the protein product of KRIT1 (KRIT1; Krev interaction trapped 1). The crystal structure reveals that the KRIT1 ARD contains 4 ankyrin repeats. There is an unusual conformation in the ANK4 repeat that is stabilized by Trp-404, and the structure reveals a solvent exposed ankyrin groove. Domain orientations of the three copies within the asymmetric unit suggest a stable interaction between KRIT1 ARD and FERM domains, indicating a globular ARD-FERM module. This resembles the additional F0 domain found N-terminal to the FERM domain of talin. Structural analysis of KRIT1 ARD-FERM highlights surface regions of high evolutionary conservation, and suggests potential sites that could mediate interaction with binding partners. The structure therefore provides a better understanding of KRIT1 at the molecular level.

  2. The repeat domain of the type III effector protein PthA shows a TPR-like structure and undergoes conformational changes upon DNA interaction.

    Science.gov (United States)

    Murakami, Mário Tyago; Sforça, Mauricio Luis; Neves, Jorge Luiz; Paiva, Joice Helena; Domingues, Mariane Noronha; Pereira, André Luiz Araujo; Zeri, Ana Carolina de Mattos; Benedetti, Celso Eduardo

    2010-12-01

    Many plant pathogenic bacteria rely on effector proteins to suppress defense and manipulate host cell mechanisms to cause disease. The effector protein PthA modulates the host transcriptome to promote citrus canker. PthA possesses unusual protein architecture with an internal region encompassing variable numbers of near-identical tandem repeats of 34 amino acids termed the repeat domain. This domain mediates protein-protein and protein-DNA interactions, and two polymorphic residues in each repeat unit determine DNA specificity. To gain insights into how the repeat domain promotes protein-protein and protein-DNA contacts, we have solved the structure of a peptide corresponding to 1.5 units of the PthA repeat domain by nuclear magnetic resonance (NMR) and carried out small-angle X-ray scattering (SAXS) and spectroscopic studies on the entire 15.5-repeat domain of PthA2 (RD2). Consistent with secondary structure predictions and circular dichroism data, the NMR structure of the 1.5-repeat peptide reveals three α-helices connected by two turns that fold into a tetratricopeptide repeat (TPR)-like domain. The NMR structure corroborates the theoretical TPR superhelix predicted for RD2, which is also in agreement with the elongated shape of RD2 determined by SAXS. Furthermore, RD2 undergoes conformational changes in a pH-dependent manner and upon DNA interaction, and shows sequence similarities to pentatricopeptide repeat (PPR), a nucleic acid-binding motif structurally related to TPR. The results point to a model in which the RD2 structure changes its compactness as it embraces the DNA with the polymorphic diresidues facing the interior of the superhelix oriented toward the nucleotide bases.

  3. Variability of United States isolates of Macrophomina phaseolina based on simple sequence repeats and cross genus transferability to related Botryosphaeraceae

    Science.gov (United States)

    Twelve simple sequence repeat (SSRs) loci were used to evaluate genetic diversity of 109 isolates of Macrophomina phaseolina collected from different geographical regions and host species throughout the United States (U.S.). Genetic diversity was assessed using Nei’s minimum genetic distance and th...

  4. The influence of the six constituent xanthan repeating units on the order–disorder transition of xanthan

    NARCIS (Netherlands)

    Kool, M.M.; Gruppen, H.; Sworn, G.; Schols, H.A.

    2014-01-01

    Xanthans occurring in different levels of disordered conformation were enzymatically hydrolyzed to their six pentamer repeating units (RUs). The RUs present in the enzyme digests were analyzed using LC–MS. As only disordered xanthan segments are degraded by cellulases, the influence of the six diffe

  5. Sulfated fucans from echinoderms have a regular tetrasaccharide repeating unit defined by specific patterns of sulfation at the 0-2 and 0-4 positions.

    Science.gov (United States)

    Mulloy, B; Ribeiro, A C; Alves, A P; Vieira, R P; Mourão, P A

    1994-09-02

    Sulfated fucans from echinoderms (sea cucumber and sea urchin) have a linear backbone of 1-->3-linked alpha-L-fucopyranose with some sulfate substitution at the 2- and 4-positions. NMR spectroscopy indicates that both polysaccharides have a tetrasaccharide repeat unit in which the separate residues differ only in the extent and position of their sulfate substitution. The sea urchin fucan has the structure, [formula: see text] This type of regular structure has not previously been described, and is in contrast with the random arrangement of substituents on the similar 1-->3-linked alpha-L-fucopyranose backbone of the fucoidans from brown algae.

  6. Direct Repeat Unit (dru) Typing of Methicillin-Resistant Staphylococcus pseudintermedius from Dogs and Cats.

    Science.gov (United States)

    Kadlec, Kristina; Schwarz, Stefan; Goering, Richard V; Weese, J Scott

    2015-12-01

    Methicillin-resistant Staphylococcus pseudintermedius (MRSP) has emerged in a remarkable manner as an important problem in dogs and cats. However, limited molecular epidemiological information is available. The aims of this study were to apply direct repeat unit (dru) typing in a large collection of well-characterized MRSP isolates and to use dru typing to analyze a collection of previously uncharacterized MRSP isolates. Two collections of MRSP isolates from dogs and cats were included in this study. The first collection comprised 115 well-characterized MRSP isolates from North America and Europe. The data for these isolates included multilocus sequence typing (MLST) and staphylococcal protein A gene (spa) typing results as well as SmaI macrorestriction patterns after pulsed-field gel electrophoresis (PFGE). The second collection was a convenience sample of 360 isolates from North America. The dru region was amplified by PCR, sequenced, and analyzed. For the first collection, the discriminatory indices of the typing methods were calculated. All isolates were successfully dru typed. The discriminatory power for dru typing (D = 0.423) was comparable to that of spa typing (D = 0.445) and of MLST (D = 0.417) in the first collection. Occasionally, dru typing was able to further discriminate between isolates that shared the same spa type. Among all 475 isolates, 26 different dru types were identified, with 2 predominant types (dt9a and dt11a) among 349 (73.4%) isolates. The results of this study underline that dru typing is a useful tool for MRSP typing, being an objective, standardized, sequence-based method that is relatively cost-efficient and easy to perform.

  7. Efficient Procedures of Sensitivity Analysis for Structural Vibration Systems with Repeated Frequencies

    Directory of Open Access Journals (Sweden)

    Shijia Zhao

    2013-01-01

    Full Text Available Derivatives of eigenvectors with respect to structural parameters play an important role in structural design, identification, and optimization. Particularly, calculation of eigenvector sensitivity is considered when the eigenvalues are repeated. A relaxation factor embedded in the combined approximations (CA method makes it effective to the structural response at various modified designs. The proposed method is feasible after overcoming the defection of irreversibility of the characteristic matrix. Numerical examples show that it is easy to implement the computational procedure, and the method presented in this paper is efficient for the general linear vibration damped systems with repeated frequencies.

  8. Evolutionary conservation of sequence and secondary structures inCRISPR repeats

    Energy Technology Data Exchange (ETDEWEB)

    Kunin, Victor; Sorek, Rotem; Hugenholtz, Philip

    2006-09-01

    Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel class of direct repeats, separated by unique spacer sequences of similar length, that are present in {approx}40% of bacterial and all archaeal genomes analyzed to date. More than 40 gene families, called CRISPR-associated sequences (CAS), appear in conjunction with these repeats and are thought to be involved in the propagation and functioning of CRISPRs. It has been proposed that the CRISPR/CAS system samples, maintains a record of, and inactivates invasive DNA that the cell has encountered, and therefore constitutes a prokaryotic analog of an immune system. Here we analyze CRISPR repeats identified in 195 microbial genomes and show that they can be organized into multiple clusters based on sequence similarity. All individual repeats in any given cluster were inferred to form characteristic RNA secondary structure, ranging from non-existent to pronounced. Stable secondary structures included G:U base pairs and exhibited multiple compensatory base changes in the stem region, indicating evolutionary conservation and functional importance. We also show that the repeat-based classification corresponds to, and expands upon, a previously reported CAS gene-based classification including specific relationships between CRISPR and CAS subtypes.

  9. Structural Studies of a Four-MBT Repeat Protein MBTD1

    Energy Technology Data Exchange (ETDEWEB)

    Eryilmaz, Jitka; Pan, Patricia; Amaya, Maria F.; Allali-Hassani, Abdellah; Dong, Aiping; Adams-Cioaba, Melanie A.; MacKenzie, Farrell; Vedadi, Masoud; Min, Jinrong; (Toronto); (Toronto)

    2010-08-17

    The Polycomb group (PcG) of proteins is a family of important developmental regulators. The respective members function as large protein complexes involved in establishment and maintenance of transcriptional repression of developmental control genes. MBTD1, Malignant Brain Tumor domain-containing protein 1, is one such PcG protein. MBTD1 contains four MBT repeats. We have determined the crystal structure of MBTD1 (residues 130-566aa covering the 4 MBT repeats) at 2.5 {angstrom} resolution by X-ray crystallography. The crystal structure of MBTD1 reveals its similarity to another four-MBT-repeat protein L3MBTL2, which binds lower methylated lysine histones. Fluorescence polarization experiments confirmed that MBTD1 preferentially binds mono- and di-methyllysine histone peptides, like L3MBTL1 and L3MBTL2. All known MBT-peptide complex structures characterized to date do not exhibit strong histone peptide sequence selectivity, and use a 'cavity insertion recognition mode' to recognize the methylated lysine with the deeply buried methyl-lysine forming extensive interactions with the protein while the peptide residues flanking methyl-lysine forming very few contacts. Nevertheless, our mutagenesis data based on L3MBTL1 suggested that the histone peptides could not bind to MBT repeats in any orientation. The four MBT repeats in MBTD1 exhibits an asymmetric rhomboid architecture. Like other MBT repeat proteins characterized so far, MBTD1 binds mono- or dimethylated lysine histones through one of its four MBT repeats utilizing a semi-aromatic cage.

  10. Investigation of the population structure of Legionella pneumophila by analysis of tandem repeat copy number and internal sequence variation.

    Science.gov (United States)

    Visca, Paolo; D'Arezzo, Silvia; Ramisse, Françoise; Gelfand, Yevgeniy; Benson, Gary; Vergnaud, Gilles; Fry, Norman K; Pourcel, Christine

    2011-09-01

    The population structure of the species Legionella pneumophila was investigated by multilocus variable number of tandem repeats (VNTR) analysis (MLVA) and sequencing of three VNTRs (Lpms01, Lpms04 and Lpms13) in selected strains. Of 150 isolates of diverse origins, 136 (86 %) were distributed into eight large MLVA clonal complexes (VACCs) and the rest were either unique or formed small clusters of up to two MLVA genotypes. In spite of the lower degree of genome-wide linkage disequilibrium of the MLVA loci compared with sequence-based typing, the clustering achieved by the two methods was highly congruent. The detailed analysis of VNTR Lpms04 alleles showed a very complex organization, with five different repeat unit lengths and a high level of internal variation. Within each MLVA-defined VACC, Lpms04 was endowed with a common recognizable pattern with some interesting exceptions. Evidence of recombination events was suggested by analysis of internal repeat variations at the two additional VNTR loci, Lpms01 and Lpms13. Sequence analysis of L. pneumophila VNTR locus Lpms04 alone provides a first-line assay for allocation of a new isolate within the L. pneumophila population structure and for epidemiological studies.

  11. Convergent synthesis of the tetrasaccharide repeating unit of the O-antigen of Shigella boydii type 9

    Directory of Open Access Journals (Sweden)

    Abhishek Santra

    2011-08-01

    Full Text Available A convenient synthesis of the tetrasaccharide repeating unit of the O-antigen of Shigella boydii type 9 has been achieved in excellent yield using a [2 + 2] block glycosylation strategy. TEMPO-mediated selective oxidation of the primary alcohol of the tetrasaccharide derivative 8 to the carboxylic group followed by deprotection of the functional groups furnished target tetrasaccharide 1 as its 4-methoxyphenyl glycoside in high yield.

  12. Structure of thrombospondin type 3 repeats in bacterial outer membrane protein A reveals its intra-repeat disulfide bond-dependent calcium-binding capability

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Shuyan; Sun, Cancan; Tan, Kemin; Ye, Sheng; Zhang, Rongguang

    2017-09-01

    Eukaryotic thrombospondin type 3 repeat (TT3R) is an efficient calcium ion (Ca2+) binding motif only found in mammalian thrombospondin family. TT3R has also been found in prokaryotic cellulase Cel5G, which was thought to forfeit the Ca2+-binding capability due to the formation of intra-repeat disulfide bonds, instead of the inter-repeat ones possessed by eukaryotic TT3Rs. In this study, we have identified an enormous number of prokaryotic TT3R-containing proteins belonging to several different protein families, including outer membrane protein A (OmpA), an important structural protein connecting the outer membrane and the periplasmic peptidoglycan layer in gram-negative bacteria. Here, we report the crystal structure of the periplasmic region of OmpA from Capnocytophaga gingivalis, which contains a linker region comprising five consecutive TT3Rs. The structure of OmpA-TT3R exhibits a well-ordered architecture organized around two tightly-coordinated Ca2+ and confirms the presence of abnormal intra-repeat disulfide bonds. Further mutagenesis studies showed that the Ca2+-binding capability of OmpA-TT3R is indeed dependent on the proper formation of intra-repeat disulfide bonds, which help to fix a conserved glycine residue at its proper position for Ca2+ coordination. Additionally, despite lacking inter repeat disulfide bonds, the interfaces between adjacent OmpA-TT3Rs are enhanced by both hydrophobic and conserved aromatic-proline interactions.

  13. Repeating Patterns: Strategies to Assist Young Students to Generalise the Mathematical Structure

    Science.gov (United States)

    Warren, Elizabeth; Miller, Jodie; Cooper, Thomas

    2012-01-01

    This paper focuses on very young students' ability to engage in repeating pattern tasks and identifying strategies that assist them to ascertain the structure of the pattern. It describes results of a study which is part of the Early Years Generalising Project (EYGP) and involves Australian students in Years 1 to 4 (ages 5-10). This paper reports…

  14. Effect of repeated contact on adhesion measurements involving polydimethylsiloxane structural material

    Science.gov (United States)

    Kroner, E.; Maboudian, R.; Arzt, E.

    2009-09-01

    During the last few years several research groups have focused on the fabrication of artificial gecko inspired adhesives. For mimicking these structures, different polymers are used as structure material, such as polydimethylsiloxanes (PDMS), polyurethanes (PU), and polypropylene (PP). While these polymers can be structured easily and used for artificial adhesion systems, the effects of repeated adhesion testing have never been investigated closely. In this paper we report on the effect of repeated adhesion measurements on the commercially available poly(dimethylsiloxane) polymer kit Sylgard 184 (Dow Corning). We show that the adhesion force decreases as a function of contact cycles. The rate of change and the final value of adhesion are found to depend on the details of the PDMS synthesis and structuring.

  15. Effect of repeated contact on adhesion measurements involving polydimethylsiloxane structural material

    Energy Technology Data Exchange (ETDEWEB)

    Kroner, E; Arzt, E [INM-Leibniz Institute for New Materials, Campus D2 2, 66125 Saarbruecken (Germany); Maboudian, R, E-mail: elmar.kroner@inm-gmbh.de [Department of Chem. Eng., 201 Gilman Hall, University of California, Berkeley, CA 94720-1462 (United States)

    2009-09-15

    During the last few years several research groups have focused on the fabrication of artificial gecko inspired adhesives. For mimicking these structures, different polymers are used as structure material, such as polydimethylsiloxanes (PDMS), polyurethanes (PU), and polypropylene (PP). While these polymers can be structured easily and used for artificial adhesion systems, the effects of repeated adhesion testing have never been investigated closely. In this paper we report on the effect of repeated adhesion measurements on the commercially available poly(dimethylsiloxane) polymer kit Sylgard 184 (Dow Corning). We show that the adhesion force decreases as a function of contact cycles. The rate of change and the final value of adhesion are found to depend on the details of the PDMS synthesis and structuring.

  16. Giant repeater F-wave in patients with anterior horn cell disorders. Role of motor unit size.

    Science.gov (United States)

    Ibrahim, I K; el-Abd, M A

    1997-01-01

    Conventional F-wave responses as well as single motor unit F-wave responses together with the volitionally recruited motor unit action potentials (MUAP) were studied in hand and feet muscles of 10 healthy subjects and 32 patients with anterior horn cell disorders. The amplitude of the largest F-wave (Fl) was significantly greater in the affected patients compared with healthy subjects. Giant repeater F-wave responses "up to 4 mV" were recorded in muscles having volitionally recruited giant MUAPs. Although, the group mean percentage of motor unit F-wave responses per stimulation in all tested orthodromic MUAPs was significantly decreased in amyotrophic lateral sclerosis patients, the group mean percentage of motor unit F-wave responses per stimulation in all tested orthodromic MUAPs that gave motor unit F-wave response was significantly increased compared with healthy subjects. The responding orthodromic MUAP gave identical motor unit F-wave response, even for complex polyphasic units. Enhanced monosynaptic (H-) reflex, proximal axon reflex (A-wave), and repetitive muscle response as possible explanations for the giant F-wave responses could be discounted. The electrophysiologic behavior of the giant late responses described here fits well with the criteria of F-waves modulated by newly formed distal (and or proximal) axonal branching.

  17. Primary and Repeat Cesarean Deliveries: A Population-based Study in the United States, 1979-2010.

    Science.gov (United States)

    Ananth, Cande V; Friedman, Alexander M; Keyes, Katherine M; Lavery, Jessica A; Hamilton, Ava; Wright, Jason D

    2017-07-01

    Despite the temporal increase in cesarean deliveries, the extent to which maternal age, period, and maternal birth cohorts may have contributed to these trends remains unknown. We performed an analysis of 123 million singleton deliveries in the United States (1979-2010). We estimated rate ratio (RR) with 95% confidence interval (CI) for primary and repeat cesarean deliveries. We examined changes in cesarean rates with weighted Poisson regression models across three time-scales: maternal age, year of delivery, and birth cohort (mother's birth year). The primary cesarean rate increased by 68% (95% confidence interval [CI]: 67%, 69%) between 1979 (11.0%) and 2010 (18.5%). Repeat cesarean deliveries increased by 178% (95% CI: 176, 179) from 5.2% in 1979 to 14.4% in 2010. Cesarean rates increased with advancing age. Compared with 1979, the RR for the period effect in primary and repeat cesarean deliveries increased up to 1990, fell to a nadir at 1993, and began to rise thereafter. A small birth cohort effect was evident, with women born before 1950 at increased risk of primary cesarean; no cohort effect was seen for repeat cesarean deliveries. Adjustment for maternal BMI had a small effect on these findings. Period effects in primary cesarean were explained by a combination of trends in obesity and chronic hypertension, as well as demographic shifts over time. Maternal age and period appear to have important contributions to the temporal increase in the cesarean rates, although the effect of parity on these associations remains undetermined.

  18. The impact of CRISPR repeat sequence on structures of a Cas6 protein-RNA complex

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Ruiying; Zheng, Han; Preamplume, Gan; Shao, Yaming; Li, Hong [FSU

    2012-03-15

    The repeat-associated mysterious proteins (RAMPs) comprise the most abundant family of proteins involved in prokaryotic immunity against invading genetic elements conferred by the clustered regularly interspaced short palindromic repeat (CRISPR) system. Cas6 is one of the first characterized RAMP proteins and is a key enzyme required for CRISPR RNA maturation. Despite a strong structural homology with other RAMP proteins that bind hairpin RNA, Cas6 distinctly recognizes single-stranded RNA. Previous structural and biochemical studies show that Cas6 captures the 5' end while cleaving the 3' end of the CRISPR RNA. Here, we describe three structures and complementary biochemical analysis of a noncatalytic Cas6 homolog from Pyrococcus horikoshii bound to CRISPR repeat RNA of different sequences. Our study confirms the specificity of the Cas6 protein for single-stranded RNA and further reveals the importance of the bases at Positions 5-7 in Cas6-RNA interactions. Substitutions of these bases result in structural changes in the protein-RNA complex including its oligomerization state.

  19. The design and structural characterization of a synthetic pentatricopeptide repeat protein.

    Science.gov (United States)

    Gully, Benjamin S; Shah, Kunal R; Lee, Mihwa; Shearston, Kate; Smith, Nicole M; Sadowska, Agata; Blythe, Amanda J; Bernath-Levin, Kalia; Stanley, Will A; Small, Ian D; Bond, Charles S

    2015-02-01

    Proteins of the pentatricopeptide repeat (PPR) superfamily are characterized by tandem arrays of a degenerate 35-amino-acid α-hairpin motif. PPR proteins are typically single-stranded RNA-binding proteins with essential roles in organelle biogenesis, RNA editing and mRNA maturation. A modular, predictable code for sequence-specific binding of RNA by PPR proteins has recently been revealed, which opens the door to the de novo design of bespoke proteins with specific RNA targets, with widespread biotechnological potential. Here, the design and production of a synthetic PPR protein based on a consensus sequence and the determination of its crystal structure to 2.2 Å resolution are described. The crystal structure displays helical disorder, resulting in electron density representing an infinite superhelical PPR protein. A structural comparison with related tetratricopeptide repeat (TPR) proteins, and with native PPR proteins, reveals key roles for conserved residues in directing the structure and function of PPR proteins. The designed proteins have high solubility and thermal stability, and can form long tracts of PPR repeats. Thus, consensus-sequence synthetic PPR proteins could provide a suitable backbone for the design of bespoke RNA-binding proteins with the potential for high specificity.

  20. Distribution and characterization of staphylococcal interspersed repeat units (SIRUs) and potential use for strain differentiation

    DEFF Research Database (Denmark)

    Hardy, K.J.; Ussery, David; Oppenheim, B.A.;

    2004-01-01

    in copy numbers were observed in all loci, within both the sequenced genomes and the UK epidemic methicillin-resistant S. aureus (EMRSA) isolates. Clonally related UK EMRSA isolates were clustered using SIRUs, which provided a greater degree of discrimination than multi-locus sequence typing, indicating......Variable-number tandem repeats (VNTRs) have been shown to be a powerful tool in the determination of evolutionary relationships and population genetics of bacteria. The sequencing of a number of Staphylococcus aureus genomes has allowed the identification of novel VNTR sequences in S. aureus, which...

  1. [Clustered regularly interspaced short palindromic repeats: structure, function and application--a review].

    Science.gov (United States)

    Cui, Yujun; Li, Yanjun; Yan, Yanfeng; Yang, Ruifu

    2008-11-01

    CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats), the basis of spoligotyping technology, can provide prokaryotes with heritable adaptive immunity against phages' invasion. Studies on CRISPR loci and their associated elements, including various CAS (CRISPR-associated) proteins and leader sequences, are still in its infant period. We introduce the brief history', structure, function, bioinformatics research and application of this amazing immunity system in prokaryotic organism for inspiring more scientists to find their interest in this developing topic.

  2. Chemical synthesis of the tetrasaccharide repeating unit of the O-polysaccharide isolated from Azospirillum brasilense SR80.

    Science.gov (United States)

    Sarkar, Vikramjit; Mukhopadhyay, Balaram

    2015-04-10

    A linear strategy has been developed for the synthesis of the tetrasaccharide repeating unit of the O-polysaccharide from Azospirillum brasilense SR80. Stepwise glycosylation of the rationally protected thioglycoside donors activated by NIS in the presence of La(OTf)3 furnished the target tetrasaccharide. The glycosylation reactions resulted in the formation of the desired linkage with absolute stereoselectivity and afforded the required derivatives in good to excellent yields. The phthalimido group has been used as the precursor of the desired acetamido group to meet the requirement of 1,2-trans glycosidic linkage.

  3. Structural Analyses of the Ankyrin Repeat Domain of TRPV6 and Related TRPV Ion Channels

    Energy Technology Data Exchange (ETDEWEB)

    Phelps, C.B.; Huang, R.J.; Lishko, P.V.; Wang, R.R.; Gaudet, R. (Harvard)

    2008-06-03

    Transient receptor potential (TRP) proteins are cation channels composed of a transmembrane domain flanked by large N- and C-terminal cytoplasmic domains. All members of the vanilloid family of TRP channels (TRPV) possess an N-terminal ankyrin repeat domain (ARD). The ARD of mammalian TRPV6, an important regulator of calcium uptake and homeostasis, is essential for channel assembly and regulation. The 1.7 A crystal structure of the TRPV6-ARD reveals conserved structural elements unique to the ARDs of TRPV proteins. First, a large twist between the fourth and fifth repeats is induced by residues conserved in all TRPV ARDs. Second, the third finger loop is the most variable region in sequence, length and conformation. In TRPV6, a number of putative regulatory phosphorylation sites map to the base of this third finger. Size exclusion chromatography and crystal packing indicate that the TRPV6-ARD does not assemble as a tetramer and is monomeric in solution. Adenosine triphosphate-agarose and calmodulin-agarose pull-down assays show that the TRPV6-ARD does not interact with either ligand, indicating a different functional role for the TRPV6-ARD than in the paralogous thermosensitive TRPV1 channel. Similar biochemical findings are also presented for the highly homologous mammalian TRPV5-ARD. The implications of the structural and biochemical data on the role of the ankyrin repeats in different TRPV channels are discussed.

  4. Exploring bacterial community structure and function associated with atrazine biodegradation in repeatedly treated soils.

    Science.gov (United States)

    Fang, Hua; Lian, Jianjun; Wang, Huifang; Cai, Lin; Yu, Yunlong

    2015-04-09

    Substantial application of the herbicide atrazine in agriculture leads to persistent contamination, which may damage the succeeding crops and pose potential threats to soil ecology and environmental health. Here, the degradation characteristics of atrazine and dynamic change of soil bacterial community structure and function as well as their relations were studied during three repeated treatments at the recommended, double, and five-fold doses. The results showed that the degradation half-life of atrazine obviously decreased with increased treatment frequency. Soil microbial functional diversity displayed a variation trend of suppression-recovery-stimulation, which was associated with increased degradation rate of atrazine. 16S amplicon sequencing was conducted to explore bacterial community structure and correlate the genus to potential atrazine degradation. A total of seven potentially atrazine-degrading bacterial genera were found including Nocardioides, Arthrobacter, Bradyrhizobium, Burkholderia, Methylobacterium, Mycobacterium, and Clostridium. These bacterial genera showed almost complete atrazine degradation pathways including dechlorination, dealkylation, hydroxylation, and ring cleavage. Furthermore, the relative abundance of four of them (i.e., Nocardioides, Arthrobacter, Methylobacterium, and Bradyrhizobium) increased with treatment frequency and atrazine concentration, suggesting that they may participate in atrazine degradation during repeated treatments. Our findings reveal the potential relationship between atrazine degradation and soil bacterial community structure in repeatedly treated soils. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Effects of repeated use and resterilization on structural and functional integrity of microwave ablation antennas.

    Science.gov (United States)

    Finck, Cyrielle A; Zur Linden, Alex R; Singh, Ameet; Foster, Robert A; Nykamp, Stephanie G; Sears, William C

    2017-04-01

    OBJECTIVE To determine effects of repeated use and resterilization on structural and functional integrity of microwave ablation (MWA) antennas. SAMPLE 17 cooled-shaft MWA antennas (3 groups of 5 antennas/group and 2 control antennas). PROCEDURES 1, 2, and 3 ablations in the livers of bovine cadavers were performed at the maximum recommended settings. Antennas were cleaned and sterilized in hydrogen peroxide plasma, and the process was repeated (reprocessing cycle; n = 6). Control antennas were only sterilized (6 times). Aerobic and anaerobic bacterial cultures were performed, and antennas were microscopically assessed for damage. RESULTS 6 cycles were completed. Thirteen of 15 MWA antennas remained functional for up to 4 cycles, 10 were functional after 5 cycles, and only 7 were functional after 6 cycles. Progressive tearing of the silicone coating of the antennas was observed, with a negative effect of the number of cycles for silicone tearing. Size of the ablation zone decreased mildly over time after cycles 5 and 6; however, this was not considered clinically relevant. No significant changes in the shape of ablation zones were detected. All cultures yielded negative results, except for an isolated case, which was considered a contaminant. CONCLUSIONS AND CLINICAL RELEVANCE Structural and functional integrity of the microwave antennas remained acceptable during repeated use and reprocessing for up to 4 cycles. However, there was a decrease in functional integrity at cycles 5 and 6. We suggest that these microwave antennas be subjected to > 3 reprocessing cycles. Antennas should be carefully examined before reuse.

  6. Long-term effects of repeated superovulation on ovarian structure and function in rhesus monkeys.

    Science.gov (United States)

    Dong, Guoying; Guo, Yueshuai; Cao, Huarong; Zhou, Tao; Zhou, Zuomin; Sha, Jiahao; Guo, Xuejiang; Zhu, Hui

    2014-11-01

    To assess the long-term effects of repeated controlled ovarian hyperstimulation (COH) on ovarian structure and function. Experimental study. Laboratory. Adult female rhesus macaques. A repeated COH rhesus macaque model (superovulation group) with spontaneously ovulating macaques used as controls (normal group) and samples of serum and ovarian tissue collected over a 5-year period. Steroid hormone levels, and structural, functional, and protein changes in ovaries. The follicular histology, proportion of follicles at each developmental stage, and expression levels of oocyte-specific genes showed no statistically significant differences between the two groups. However, the superovulation group exhibited mitochondrial abnormalities in the granulosa cells and a low expression of genes involved in steroid hormone synthesis compared with the normal group. A comparison of protein expression in the ovaries of both groups using tandem mass tag labeling with mass spectrometry revealed that most of the differentially-expressed proteins were down-regulated in the superovulation group. These proteins were mainly localized in the mitochondria and cytosol, and changes in protein levels in the superovulation group mainly inhibited cell proliferation and differentiation but promoted apoptosis. Our study indicates that repeated COH could change the expression of many proteins in the ovaries even after several years, potentially affecting the development and function of ovarian cells. Copyright © 2014 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  7. Increasing the repeating units of ethylene glycol-based dimethacrylates directed toward reduced oxidative stress and co-stimulatory factors expression in human monocytic cells.

    Science.gov (United States)

    Tamura, Atsushi; Fukumoto, Izumi; Yui, Nobuhiko; Matsumura, Mitsuaki; Miura, Hiroyuki

    2015-03-01

    The ethylene glycol-based dimethacrylates are commonly used in biomaterials and dental restorative materials as a cross-linking agent. In this study, toxic effect of triethylene glycol dimethacrylate (TEGDMA) and poly(ethylene glycol) dimethacrylates (PEG-DMAs) with various ethylene glycol repeating units was investigated in terms of cytotoxicity, oxidative stress, and the expression of co-stimulatory factors in human leukemia cell line (THP-1 cells) to verify the effect of ethylene glycol repeating units. Note that the 1-octanol/water partition coefficient of PEG-based dimethacrylates decreased with increasing the ethylene glycol repeating units, indicating that the hydrophilicity of PEG-DMAs increased with ethylene glycol repeating units. The toxic effect of PEG-DMAs such as cytotoxicity, oxidative stress, and the expression of CD86 in treated THP-1 cells are reduced with increasing the ethylene glycol repeating units in PEG-DMAs. However, the expression of CD54 in treated THP-1 cells was not influenced with the ethylene glycol repeating units and the maximal expression level of CD54 was observed at the concentration range of 2-4 mM for all samples. Accordingly, hydrophilic character of PEG-DMAs with long ethylene glycol chains definitely alleviates the some toxic aspect of PEG-based DMAs. This finding would provide important insight into the design of new biomaterials and dental materials with superior biocompatibility. © 2014 Wiley Periodicals, Inc.

  8. Repeatability of ellipsometric data in cholera toxin G M1-ELISA structures

    Science.gov (United States)

    Castro, Leon G.; Thompson, Daniel W.; Tiwald, Thomas; Berberov, Emil M.; Woollam, John A.

    2007-04-01

    The need for repeated measurements in a wide range of biological testing due to statistical variations is well known. In this paper, we discuss a specific example in which the measurement probe is a spectroscopic ellipsometer. Repeatable results are needed in a wide range of applications such as drug testing, immunoassays and other tests for disease, and fundamental biomaterial research. The present paper seeks to help reduce the non-meaningful causes of lack of repeatability by identifying a large number of externally controllable factors. Another goal of this work was to quantify the effects of many of these factors on ellipsometric measurements. By exploiting the sensitivity of spectroscopic ellipsometry to ultrathin layers, improved ways to detect and quantitatively differentiate biological events can be explored. This initial work was motivated from an interest to distinguish one disease from another or discern effects of one drug from another using the high surface sensitivity of spectroscopic ellipsometry. In this paper, we investigate the example biological system of cholera toxin (CT) in an ELISA structure with monosialoganglioside (G M1).

  9. Deletion of intragenic tandem repeats in unit C of FLO1 of Saccharomyces cerevisiae increases the conformational stability of flocculin under acidic and alkaline conditions.

    Directory of Open Access Journals (Sweden)

    Ee Li

    Full Text Available Flocculation is an attractive property for Saccaromyces cerevisiae, which plays important roles in fermentation industry and environmental remediation. The process of flocculation is mediated by a family of cell surface flocculins. As one member of flocculins, Flo1 is characterized by four families of repeats (designated as repeat units A, B, C and D in the central domain. It is generally accepted that variation of repeat unit A in length in Flo1 influences the degree of flocculation or specificity for sugar recognization. However, no reports were observed for other repeat units. Here, we compared the flocculation ability and its sensitivity to environmental factors between yeast strain YSF1 carrying the intact FLO1 gene and yeast strains carrying the derived forms of FLO1 with partial or complete deletion of repeats in unit C. No obvious differences in flocculation ability and specificity of carbohydrate recognition were observed among these yeast strains, which indicates the truncated flocculins can stride across the cell wall and cluster the N-terminal domain on the surface of yeast cells as the intact Flo1 thereby improving intercellular binding. However, yeast strains with the truncated flocculins required more mannose to inhibit completely the flocculation, displayed broad tolerance of flocculation to pH fluctuation, and the fewer the repeats in unit C, the stronger adaptability of flocculation to pH change, which was not relevant to the position of deletion. This suggests that more stable active conformation is obtained for flocculin by deletion the repeat unit C in the central domain of Flo1, which was validated further by the higher hydrophobicity on the surface of cells of YSF1c with complete deletion of unit C under neutral and alkaline conditions and the stabilization of GFP conformation by fusion with flocculin with complete deletion of unit C in the central domain.

  10. Murine protein H is comprised of 20 repeating units, 61 amino acids in length

    DEFF Research Database (Denmark)

    Kristensen, Torsten; Tack, B F

    1986-01-01

    A cDNA library constructed from size-selected (greater than 28 S) poly(A)+ RNA isolated from the livers of C57B10. WR mice was screened by using a 249-base-pair (bp) cDNA fragment encoding 83 amino acid residues of human protein H as a probe. Of 120,000 transformants screened, 30 hybridized......, 448 bp of 3'-untranslated sequence, and a polyadenylylated tail of undetermined length. Murine pre-protein H was deduced to consist of an 18-amino acid signal peptide and 1216 residues of H-protein sequence. Murine H was composed of 20 repetitive units, each about 61 amino acid residues in length...

  11. Chain folding controlled by an isomeric repeat unit: helix formation versus random aggregation in acetylene-bridged carbazole-bipyridine co-oligomers.

    Science.gov (United States)

    Divya, Kizhmuri P; Sreejith, Sivaramapanicker; Suresh, Cherumuttathu H; Philips, Divya S; Ajayaghosh, Ayyappanpillai

    2013-07-01

    An unprecedented, positional effect of the isomeric repeat unit on chain folding in donor–acceptor-linked oligomers, which contain alternating bipyridine and carbazole moieties that are connected through an acetylinic linkage, is reported. 4,4′-Linked oligomer 1 adopts an intrachain helical conformation (CD-active) in CHCl3/MeCN (20:80 v/v), whereas oligomer 2, which contains an isomeric 6,6′-linkage, forms interchain randomly coiled aggregates (CD-inactive). The substitution position plays a significant role in controlling the variations in electronic effects and dipole moments around the bipyridyl moiety, which are responsible for this observed phenomenon. Two model compounds of oligomers 1 and 2 (3 and 4, respectively) were prepared and their properties were compared. A systematic investigation of the photophysical and CD properties of these structures, as well as theoretical studies, support our conclusions.

  12. Murine protein H is comprised of 20 repeating units, 61 amino acids in length

    DEFF Research Database (Denmark)

    Kristensen, Torsten; Tack, B F

    1986-01-01

    A cDNA library constructed from size-selected (greater than 28 S) poly(A)+ RNA isolated from the livers of C57B10. WR mice was screened by using a 249-base-pair (bp) cDNA fragment encoding 83 amino acid residues of human protein H as a probe. Of 120,000 transformants screened, 30 hybridized...... with this cDNA probe. Ten positives were colony-purified, and the largest plasmid cDNA insert, MH8 (4.4 kb), was sequenced by the dideoxy chain termination method. MH8 contained the complete coding sequence for the precursor of murine complement protein factor H (3702 bp), 100 bp of 5'-untranslated sequence......, 448 bp of 3'-untranslated sequence, and a polyadenylylated tail of undetermined length. Murine pre-protein H was deduced to consist of an 18-amino acid signal peptide and 1216 residues of H-protein sequence. Murine H was composed of 20 repetitive units, each about 61 amino acid residues in length...

  13. Plasmodium alveolins possess distinct but structurally and functionally related multi-repeat domains.

    Science.gov (United States)

    Al-Khattaf, Fatimah S; Tremp, Annie Z; Dessens, Johannes T

    2015-02-01

    The invasive and motile life stages of malaria parasites (merozoite, ookinete and sporozoite) possess a distinctive cortical structure termed the pellicle. The pellicle is characterised by a double-layered 'inner membrane complex' (IMC) located underneath the plasma membrane, which is supported by a cytoskeletal structure termed the subpellicular network (SPN). The SPN consists of intermediate filaments, whose major constituents include a family of proteins called alveolins. Here, we re-appraise the alveolins in the genus Plasmodium with respect to their repertoire, structure and interrelatedness. Amongst 13 family members identified, we distinguish two domain types that, albeit distinct at the primary structure level, are structurally related and contain tandem repeats with a consensus 12-amino acid periodicity. Analysis in Plasmodium berghei of the most divergent alveolin, PbIMC1d, reveals a zoite-specific expression in ookinetes and a subcellular localisation in the pellicle, consistent with its predicted role as a SPN component. Knockout of PbIMC1d gives rise to a wild-type phenotype with respect to ookinete morphogenesis, tensile strength, gliding motility and infectivity, presenting the first example of apparent functional redundancy amongst alveolin family members.

  14. The crystal structure of a partial mouse Notch-1 ankyrin domain: Repeats 4 through 7 preserve an ankyrin fold

    Energy Technology Data Exchange (ETDEWEB)

    Lubman, Olga Y.; Kopan, Raphael; Waksman, Gabriel; Korolev, Sergey (Birbeck); (St. Louis-MED); (WU-MED)

    2010-07-20

    Folding and stability of proteins containing ankyrin repeats (ARs) is of great interest because they mediate numerous protein-protein interactions involved in a wide range of regulatory cellular processes. Notch, an ankyrin domain containing protein, signals by converting a transcriptional repression complex into an activation complex. The Notch ANK domain is essential for Notch function and contains seven ARs. Here, we present the 2.2 {angstrom} crystal structure of ARs 4-7 from mouse Notch 1 (m1ANK). These C-terminal repeats were resistant to degradation during crystallization, and their secondary and tertiary structures are maintained in the absence of repeats 1-3. The crystallized fragment adopts a typical ankyrin fold including the poorly conserved seventh AR, as seen in the Drosophila Notch ANK domain (dANK). The structural preservation and stability of the C-terminal repeats shed a new light onto the mechanism of hetero-oligomeric assembly during Notch-mediated transcriptional activation.

  15. Molecular mechanisms for maintenance of G-rich short tandem repeats capable of adopting G4 DNA structures

    Energy Technology Data Exchange (ETDEWEB)

    Nakagama, Hitoshi [Biochemistry Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 (Japan)]. E-mail: hnakagam@gan2.res.ncc.go.jp; Higuchi, Kumiko [Biochemistry Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 (Japan); Tanaka, Etsuko [Biochemistry Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 (Japan); Tsuchiya, Naoto [Biochemistry Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 (Japan); Nakashima, Katsuhiko [Biochemistry Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 (Japan); Katahira, Masato [Biochemistry Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 (Japan); Fukuda, Hirokazu [Biochemistry Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045 (Japan)

    2006-06-25

    Mammalian genomes contain several types of repetitive sequences. Some of these sequences are implicated in various specific cellular events, including meiotic recombination, chromosomal breaks and transcriptional regulation, and also in several human disorders. In this review, we document the formation of DNA secondary structures by the G-rich repetitive sequences that have been found in several minisatellites, telomeres and in various triplet repeats, and report their effects on in vitro DNA synthesis. d(GGCAG) repeats in the mouse minisatellite Pc-1 were demonstrated to form an intra-molecular folded-back quadruplex structure (also called a G4' structure) by NMR and CD spectrum analyses. d(TTAGGG) telomere repeats and d(CGG) triplet repeats were also shown to form G4' and other unspecified higher order structures, respectively. In vitro DNA synthesis was substantially arrested within the repeats, and this could be responsible for the preferential mutability of the G-rich repetitive sequences. Electrophoretic mobility shift assays using NIH3T3 cell extracts revealed heterogeneous nuclear ribonucleoprotein (hnRNP) A1 and A3, which were tightly and specifically bound to d(GGCAG) and d(TTAGGG) repeats with K {sub d} values in the order of nM. HnRNP A1 unfolded the G4' structure formed in the d(GGCAG) {sub n} and d(TTAGGG) {sub n} repeat regions, and also resolved the higher order structure formed by d(CGG) triplet repeats. Furthermore, DNA synthesis arrest at the secondary structures of d(GGCAG) repeats, telomeres and d(CGG) triplet repeats was efficiently repressed by the addition of hnRNP A1. High expression of hnRNPs may contribute to the maintenance of G-rich repetitive sequences, including telomere repeats, and may also participate in ensuring the stability of the genome in cells with enhanced proliferation. Transcriptional regulation of genes, such as c-myc and insulin, by G4 sequences found in the promoter regions could be an intriguing field of

  16. Evolutionary fate of memory-one strategies in repeated prisoner's dilemma game in structured populations

    Science.gov (United States)

    Liu, Xu-Sheng; Wu, Zhi-Xi; Chen, Michael Z. Q.; Guan, Jian-Yue

    2017-07-01

    We study evolutionary spatial prisoner's dilemma game involving a one-step memory mechanism of the individuals whenever making strategy updating. In particular, during the process of strategy updating, each individual keeps in mind all the outcome of the action pairs adopted by himself and each of his neighbors in the last interaction, and according to which the individuals decide what actions they will take in the next round. Computer simulation results imply that win-stay-lose-shift like strategy win out of the memory-one strategy set in the stationary state. This result is robust in a large range of the payoff parameter, and does not depend on the initial state of the system. Furthermore, theoretical analysis with mean field and quasi-static approximation predict the same result. Thus, our studies suggest that win-stay-lose-shift like strategy is a stable dominant strategy in repeated prisoner's dilemma game in homogeneous structured populations.

  17. Creation and structure determination of an artificial protein with three complete sequence repeats

    Energy Technology Data Exchange (ETDEWEB)

    Adachi, Motoyasu, E-mail: adachi.motoyasu@jaea.go.jp; Shimizu, Rumi; Kuroki, Ryota [Japan Atomic Energy Agency, Shirakatashirane 2-4, Nakagun Tokaimura, Ibaraki 319-1195 (Japan); Blaber, Michael [Japan Atomic Energy Agency, Shirakatashirane 2-4, Nakagun Tokaimura, Ibaraki 319-1195 (Japan); Florida State University, Tallahassee, FL 32306-4300 (United States)

    2013-11-01

    An artificial protein with three complete sequence repeats was created and the structure was determined by X-ray crystallography. The structure showed threefold symmetry even though there is an amino- and carboxy-terminal. The artificial protein with threefold symmetry may be useful as a scaffold to capture small materials with C3 symmetry. Symfoil-4P is a de novo protein exhibiting the threefold symmetrical β-trefoil fold designed based on the human acidic fibroblast growth factor. First three asparagine–glycine sequences of Symfoil-4P are replaced with glutamine–glycine (Symfoil-QG) or serine–glycine (Symfoil-SG) sequences protecting from deamidation, and His-Symfoil-II was prepared by introducing a protease digestion site into Symfoil-QG so that Symfoil-II has three complete repeats after removal of the N-terminal histidine tag. The Symfoil-QG and SG and His-Symfoil-II proteins were expressed in Eschericha coli as soluble protein, and purified by nickel affinity chromatography. Symfoil-II was further purified by anion-exchange chromatography after removing the HisTag by proteolysis. Both Symfoil-QG and Symfoil-II were crystallized in 0.1 M Tris-HCl buffer (pH 7.0) containing 1.8 M ammonium sulfate as precipitant at 293 K; several crystal forms were observed for Symfoil-QG and II. The maximum diffraction of Symfoil-QG and II crystals were 1.5 and 1.1 Å resolution, respectively. The Symfoil-II without histidine tag diffracted better than Symfoil-QG with N-terminal histidine tag. Although the crystal packing of Symfoil-II is slightly different from Symfoil-QG and other crystals of Symfoil derivatives having the N-terminal histidine tag, the refined crystal structure of Symfoil-II showed pseudo-threefold symmetry as expected from other Symfoils. Since the removal of the unstructured N-terminal histidine tag did not affect the threefold structure of Symfoil, the improvement of diffraction quality of Symfoil-II may be caused by molecular characteristics of

  18. Direct repeat unit (dru) typing and antimicrobial resistance of methicillin-resistant Staphylococcus pseudintermedius isolated from dogs in Atlantic Canada.

    Science.gov (United States)

    Saab, Matthew E; Weese, J Scott; McClure, J T

    2017-07-01

    There are few reports investigating the characterization of methicillin-resistant Staphylococcus pseudintermedius (MRSP) in dogs in Canada and none from Atlantic Canada. The objectives of this study were to strain type MRSP isolates cultured at a regional diagnostic laboratory using direct repeat unit (dru) typing and to describe their antimicrobial resistance profiles. Ninety-four isolates recovered from dogs between 2010 and 2012 had dru typing, cluster analysis, and antimicrobial susceptibility testing done. The majority of isolates belonged to type dt11a (30.9%), dt10h (24.5%), dt9a (18.1%), and dt11af (10.6%) with the remaining 15.9% of isolates distributed among 13 dru types. The predominant dru types identified were similar in Ontario; however, cluster 9a appears to be less common in Atlantic Canada. A significant difference in the distribution of clusters among Atlantic provinces was detected (P = 0.01). Resistance to ≥ 2 non-β-lactam antimicrobials was observed in 71.4% of the isolates. The MRSP isolates from this study were notably less resistant than those reported in the literature. A more comprehensive study of the MRSP dru types could help further elucidate the distribution of this pathogen in Canada.

  19. Disruption of Higher Order DNA Structures in Friedreich's Ataxia (GAA)(n) Repeats by PNA or LNA Targeting

    DEFF Research Database (Denmark)

    Bergquist, Helen; Rocha, Cristina S. J.; Alvarez-Asencio, Ruben

    2016-01-01

    Expansion of (GAA)n repeats in the first intron of the Frataxin gene is associated with reduced mRNA and protein levels and the development of Friedreich’s ataxia. (GAA)n expansions form non-canonical structures, including intramolecular triplex (H-DNA), and R-loops and are associated with epigen......Expansion of (GAA)n repeats in the first intron of the Frataxin gene is associated with reduced mRNA and protein levels and the development of Friedreich’s ataxia. (GAA)n expansions form non-canonical structures, including intramolecular triplex (H-DNA), and R-loops and are associated...... with epigenetic modifications. With the aim of interfering with higher order H-DNA (like) DNA structures within pathological (GAA)n expansions, we examined sequence-specific interaction of peptide nucleic acid (PNA) with (GAA)n repeats of different lengths (short: n=9, medium: n=75 or long: n=115) by chemical...... probing of triple helical and single stranded regions. We found that a triplex structure (H-DNA) forms at GAA repeats of different lengths; however, single stranded regions were not detected within the medium size pathological repeat, suggesting the presence of a more complex structure. Furthermore, (GAA...

  20. Repeatability of the Dust and Gas Morphological Structures in the Coma of Comet

    Science.gov (United States)

    Lejoly, Cassandra; Samarasinha, N. H.; Ojha, L.; Schleicher, D. G.

    2013-10-01

    Comet 1P/Halley is the most famous comet in history and has been observed for over two millennia, making it one of the most extensively studied comets. The morphology in the coma of comet 1P/Halley originates due to the activity at the nucleus and could be used as a probe of the nuclear rotation and the activity. We will present the results from a study summarizing the evolution of coma morphology of comet 1P/Halley observed from ground between October 1985 and June 1986. The results to be presented include analysis of dust features as well as gas (CN) features in the coma and comparisons will be made between their spatial and temporal evolution. About 80 CN images and 300 continuum images from the Small Bodies Node of the NASA Planetary Data System were analyzed using image enhancement techniques that were not available n the 1980s. This enables us to see coma structure never observed before in comet 1P/Halley. Because of the comet's proximity to Earth, most of our best signal-to-noise images were taken in the March-April interval of 1986. Despite the limited coverage of preceding and following months, there is a sufficient number of images to monitor morphological evolution over many months. The initial synodic periods as a function of time used to phase the images together were extrapolated from the lightcurves of the active coma (Schleicher et al. 1990, AJ, 100, 896-912). We will present the periods of repeatability of individual coma features measured using the position angle at different spatial distances from the nucleus in adjacent cycles. Separate features appear to have slightly different periods of repeatability, perhaps depending on the corresponding source regions on the nucleus and/or projection effects. The periods of repeatability of coma morphologies will be presented as a function of time from the perihelion. These results will ultimately be used in detailed modeling of the coma morphologies of comet 1P/Halley over the 1985-1986 apparition in

  1. Sequence-structure-function relations of the mosquito leucine-rich repeat immune proteins

    Directory of Open Access Journals (Sweden)

    Povelones Michael

    2010-09-01

    Full Text Available Abstract Background The discovery and characterisation of factors governing innate immune responses in insects has driven the elucidation of many immune system components in mammals and other organisms. Focusing on the immune system responses of the malaria mosquito, Anopheles gambiae, has uncovered an array of components and mechanisms involved in defence against pathogen infections. Two of these immune factors are LRIM1 and APL1C, which are leucine-rich repeat (LRR containing proteins that activate complement-like defence responses against malaria parasites. In addition to their LRR domains, these leucine-rich repeat immune (LRIM proteins share several structural features including signal peptides, patterns of cysteine residues, and coiled-coil domains. Results The identification and characterisation of genes related to LRIM1 and APL1C revealed putatively novel innate immune factors and furthered the understanding of their likely molecular functions. Genomic scans using the shared features of LRIM1 and APL1C identified more than 20 LRIM-like genes exhibiting all or most of their sequence features in each of three disease-vector mosquitoes with sequenced genomes: An. gambiae, Aedes aegypti, and Culex quinquefasciatus. Comparative sequence analyses revealed that this family of mosquito LRIM-like genes is characterised by a variable number of 6 to 14 LRRs of different lengths. The "Long" LRIM subfamily, with 10 or more LRRs, and the "Short" LRIMs, with 6 or 7 LRRs, also share the signal peptide, cysteine residue patterning, and coiled-coil sequence features of LRIM1 and APL1C. The "TM" LRIMs have a predicted C-terminal transmembrane region, and the "Coil-less" LRIMs exhibit the characteristic LRIM sequence signatures but lack the C-terminal coiled-coil domains. Conclusions The evolutionary plasticity of the LRIM LRR domains may provide templates for diverse recognition properties, while their coiled-coil domains could be involved in the formation

  2. In situ optical sequencing and structure analysis of a trinucleotide repeat genome region by localization microscopy after specific COMBO-FISH nano-probing

    Science.gov (United States)

    Stuhlmüller, M.; Schwarz-Finsterle, J.; Fey, E.; Lux, J.; Bach, M.; Cremer, C.; Hinderhofer, K.; Hausmann, M.; Hildenbrand, G.

    2015-10-01

    Trinucleotide repeat expansions (like (CGG)n) of chromatin in the genome of cell nuclei can cause neurological disorders such as for example the Fragile-X syndrome. Until now the mechanisms are not clearly understood as to how these expansions develop during cell proliferation. Therefore in situ investigations of chromatin structures on the nanoscale are required to better understand supra-molecular mechanisms on the single cell level. By super-resolution localization microscopy (Spectral Position Determination Microscopy; SPDM) in combination with nano-probing using COMBO-FISH (COMBinatorial Oligonucleotide FISH), novel insights into the nano-architecture of the genome will become possible. The native spatial structure of trinucleotide repeat expansion genome regions was analysed and optical sequencing of repetitive units was performed within 3D-conserved nuclei using SPDM after COMBO-FISH. We analysed a (CGG)n-expansion region inside the 5' untranslated region of the FMR1 gene. The number of CGG repeats for a full mutation causing the Fragile-X syndrome was found and also verified by Southern blot. The FMR1 promotor region was similarly condensed like a centromeric region whereas the arrangement of the probes labelling the expansion region seemed to indicate a loop-like nano-structure. These results for the first time demonstrate that in situ chromatin structure measurements on the nanoscale are feasible. Due to further methodological progress it will become possible to estimate the state of trinucleotide repeat mutations in detail and to determine the associated chromatin strand structural changes on the single cell level. In general, the application of the described approach to any genome region will lead to new insights into genome nano-architecture and open new avenues for understanding mechanisms and their relevance in the development of heredity diseases.

  3. Expansion of protein domain repeats.

    Directory of Open Access Journals (Sweden)

    Asa K Björklund

    2006-08-01

    Full Text Available Many proteins, especially in eukaryotes, contain tandem repeats of several domains from the same family. These repeats have a variety of binding properties and are involved in protein-protein interactions as well as binding to other ligands such as DNA and RNA. The rapid expansion of protein domain repeats is assumed to have evolved through internal tandem duplications. However, the exact mechanisms behind these tandem duplications are not well-understood. Here, we have studied the evolution, function, protein structure, gene structure, and phylogenetic distribution of domain repeats. For this purpose we have assigned Pfam-A domain families to 24 proteomes with more sensitive domain assignments in the repeat regions. These assignments confirmed previous findings that eukaryotes, and in particular vertebrates, contain a much higher fraction of proteins with repeats compared with prokaryotes. The internal sequence similarity in each protein revealed that the domain repeats are often expanded through duplications of several domains at a time, while the duplication of one domain is less common. Many of the repeats appear to have been duplicated in the middle of the repeat region. This is in strong contrast to the evolution of other proteins that mainly works through additions of single domains at either terminus. Further, we found that some domain families show distinct duplication patterns, e.g., nebulin domains have mainly been expanded with a unit of seven domains at a time, while duplications of other domain families involve varying numbers of domains. Finally, no common mechanism for the expansion of all repeats could be detected. We found that the duplication patterns show no dependence on the size of the domains. Further, repeat expansion in some families can possibly be explained by shuffling of exons. However, exon shuffling could not have created all repeats.

  4. Effect of repeated retrogradation on structural characteristics and in vitro digestibility of waxy potato starch.

    Science.gov (United States)

    Xie, Yao-Yu; Hu, Xiao-Pei; Jin, Zheng-Yu; Xu, Xue-Ming; Chen, Han-Qing

    2014-11-15

    The effects of repeated retrogradation (RR) treatment on the structural characteristics and in vitro digestibility of waxy potato starch were investigated. The cycling times of RR ranging from 1 to 5 were designated as RR-1, RR-2, RR-3, RR-4, and RR-5, respectively. A maximum SDS content (40.41%) was obtained by RR-2 treatment with the time interval of 48h. RR-2-treated starch product exhibited a narrower melting temperature range, a higher onset temperature and a lower melting enthalpy compared with RR-1 treatment. Compared with native starch, X-ray diffraction patterns of treated starches were altered from B-type to C-type. The variation in relative crystallinity of RR-treated starch products was consistent with that in melting enthalpy. Moreover, compared with RR-1-treated starch, a large number of cavities were observed on the surface of RR-2-treated starch product with a time interval of 48h, whereas more smooth regions were found on the surface of RR-5-treated starch product. This study suggested that structural changes of waxy potato starch treated with different cycling times of RR significantly affected the digestibility.

  5. Effect of repeated cycled crystallization on digestibility and molecular structure of glutinous Bora rice starch.

    Science.gov (United States)

    Borah, Pallab Kumar; Deka, Sankar Chandra; Duary, Raj Kumar

    2017-05-15

    The effects of repeated cycled crystallization on the digestibility and molecular structure of glutinous Bora rice starch were investigated. Temperature cycle 4/45°C; cycle duration 5d; time interval of cycles 24h; and starch to water ratio 1:2 were found to be optimum for SDS (slow digestible starch) product development. The SDS content increased from 18.01±2.11% to 82.81±2.34%. An increase in the resistance to digestion, crystallinity, molecular weight, polydispersity and molecular order was observed in the optimal SDS product. Notably, the FT-IR peak at 947cm(-1) and XRD peaks at 2θ≈13° and 20° in the optimal SDS product indicated the formation of V-type complexes even without the presence of co-polymers. Birefringence studies showed a loss of typical Maltese cross in the SDS product and revealed a reorientation of crystalline structures within starch granules, suggestive of imperfect crystallite development.

  6. The Repeat Pattern Toolkit (RPT): Analyzing the structure and evolution of the C. elegans genome

    Energy Technology Data Exchange (ETDEWEB)

    Agarwal, P.; States, D.J. [Washington Univ., St. Louis, MO (United States)

    1994-12-31

    Over 3.6 million bases of DNA sequence from chromosome III of the C. elegans have been determined. The availability of this extended region of contiguous sequence has allowed us to analyze the nature and prevalence of repetitive sequences in the genome of a eukaryotic organism with a high gene density. We have assembled a Repeat Pattern Toolkit (RPT) to analyze the patterns of repeats occurring in DNA. The tools include identifying significant local alignments (utilizing both two-way and three-way alignments), dividing the set of alignments into connected components (signifying repeat families), computing evolutionary distance between repeat family members, constructing minimum spanning trees from the connected components, and visualizing the evolution of the repeat families. Over 7000 families of repetitive sequences were identified. The size of the families ranged from isolated pairs to over 1600 segments of similar sequence. Approximately 12.3% of the analyzed sequence participates in a repeat element.

  7. Implementation of a Consensus Set of Hypervariable Mycobacterial Interspersed Repetitive-Unit-Variable-Number Tandem-Repeat Loci in Mycobacterium tuberculosis Molecular Epidemiology.

    Science.gov (United States)

    Trovato, Alberto; Tafaj, Silva; Battaglia, Simone; Alagna, Riccardo; Bardhi, Donika; Kapisyzi, Perlat; Bala, Silvana; Haldeda, Migena; Borroni, Emanuele; Hafizi, Hasan; Cirillo, Daniela Maria

    2016-02-01

    This study shows that the addition of a consensus 4-locus set of hypervariable mycobacterial interspersed repetitive-unit-variable-number tandem repeat (MIRU-VNTR) loci to the spoligotyping-24-locus MIRU-VNTR typing strategy is a well-standardized approach that can contribute to an improvement of the true cluster definition while retaining high typeability in non-Beijing strains.

  8. Convergent synthesis of a tetrasaccharide repeating unit of the O-specific polysaccharide from the cell wall lipopolysaccharide of Azospirillum brasilense strain Sp7

    Directory of Open Access Journals (Sweden)

    Pintu Kumar Mandal

    2014-01-01

    Full Text Available A straightforward convergent synthesis has been carried out for the tetrasaccharide repeating unit of the O-specific cell wall lipopolysaccharide of the strain Sp7 of Azospirillum brasilense. The target tetrasaccharide has been synthesized from suitably protected monosaccharide intermediates in 42% overall yield in seven steps by using a [2 + 2] block glycosylation approach.

  9. Accessing Structure of Megacontrol Type RTU Units

    Directory of Open Access Journals (Sweden)

    A.Pavel

    2008-05-01

    Full Text Available The cases presented in this paper are the results of a practical situation that compare the situation in which the RS485 network could be created, to the situation in which communication with RTU (remote terminal units has to use more than one point to point RS232 connection.

  10. Disruption of Higher Order DNA Structures in Friedreich's Ataxia (GAA)(n) Repeats by PNA or LNA Targeting

    DEFF Research Database (Denmark)

    Bergquist, Helen; Rocha, Cristina S. J.; Alvarez-Asencio, Ruben;

    2016-01-01

    Expansion of (GAA)n repeats in the first intron of the Frataxin gene is associated with reduced mRNA and protein levels and the development of Friedreich’s ataxia. (GAA)n expansions form non-canonical structures, including intramolecular triplex (H-DNA), and R-loops and are associated with epigen......Expansion of (GAA)n repeats in the first intron of the Frataxin gene is associated with reduced mRNA and protein levels and the development of Friedreich’s ataxia. (GAA)n expansions form non-canonical structures, including intramolecular triplex (H-DNA), and R-loops and are associated...

  11. Children's Conceptions of Bullying and Repeated Conventional Transgressions: Moral, Conventional, Structuring and Personal-Choice Reasoning

    Science.gov (United States)

    Thornberg, Robert; Thornberg, Ulrika Birberg; Alamaa, Rebecca; Daud, Noor

    2016-01-01

    This study examined 307 elementary school children's judgements and reasoning about bullying and other repeated transgressions when school rules regulating these transgressions have been removed in hypothetical school situations. As expected, children judged bullying (repeated moral transgressions) as wrong independently of rules and as more wrong…

  12. Liver cirrhosis is a risk factor of repeat acute hemorrhagic rectal ulcer in intensive care unit patients

    Directory of Open Access Journals (Sweden)

    Pi-Kai Chang

    2014-01-01

    Full Text Available Background: Acute hemorrhagic rectal ulcer (AHRU can be found in patients with severe comorbid illness, who are bedridden for a long time. Per anal suturing is a quick and feasible treatment. However, recurrent bleeding occurs frequently after suture ligation of a bleeder and can be life-threatening. However, the risk factor for recurrent bleeding is not well known. Our study tries to clarify the risk factor of repeat AHRU in Intensive Care Unit (ICU patients. Materials and Methods: From January 2004 to December 2009, the medical records of 32 patients, who were admitted to the ICU of the Tri-Service General Hospital, a tertiary referral center in Taiwan, and who underwent per anal suturing of acute hemorrhagic rectal ulcer were retrospectively reviewed. Results: Of the 96 patients who received emergency treatment for acute massive hematochezia, 32 patients were diagnosed with AHRU. Eight (25% patients had recurrent bleeding following suture ligation of AHRU and underwent a reoperation; no patient had recurrent bleeding after the second operation. The duration from the first hematochezia attack to surgery (P = 0.04, liver cirrhosis (P = 0.002, and coagulopathy (P = 0.01 were the risk factors of recurrent bleeding after suture ligation of a bleeder. Multivariate logistic regression analysis indicated that liver cirrhosis (OR = 37.77, P = 0.014 was an independent risk factor for recurrent bleeding. Conclusion: AHRU could be a major cause of acute massive hematochezia in patients with severe illness. Our data showed that per anal suturing could quickly and effectively control bleeding. We found that liver cirrhosis was an independent risk factor for recurrent bleeding. Therefore, treatment of a liver cirrhosis patient with AHUR should be more aggressive, such as, early detection and proper suture ligation.

  13. Genetic Diversity and Structure of Lolium Species Surveyed on Nuclear Simple Sequence Repeat and Cytoplasmic Markers

    Directory of Open Access Journals (Sweden)

    Hongwei Cai

    2017-04-01

    Full Text Available To assess the genetic diversity and population structure of Lolium species, we used 32 nuclear simple sequence repeat (SSR markers and 7 cytoplasmic gene markers to analyze a total of 357 individuals from 162 accessions of 9 Lolium species. This survey revealed a high level of polymorphism, with an average number of alleles per locus of 23.59 and 5.29 and an average PIC-value of 0.83 and 0.54 for nuclear SSR markers and cytoplasmic gene markers, respectively. Analysis of molecular variance (AMOVA revealed that 16.27 and 16.53% of the total variation was due to differences among species, with the remaining 56.35 and 83.47% due to differences within species and 27.39 and 0% due to differences within individuals in 32 nuclear SSR markers set and 6 chloroplast gene markers set, respectively. The 32 nuclear SSR markers detected three subpopulations among 357 individuals, whereas the 6 chloroplast gene markers revealed three subpopulations among 160 accessions in the STRUCTURE analysis. In the clustering analysis, the three inbred species clustered into a single group, whereas the outbreeding species were clearly divided, especially according to nuclear SSR markers. In addition, almost all Lolium multiflorum populations were clustered into group C4, which could be further divided into three subgroups, whereas Lolium perenne populations primarily clustered into two groups (C2 and C3, with a few lines that instead grouped with L. multiflorum (C4 or Lolium rigidum (C6. Together, these results will useful for the use of Lolium germplasm for improvement and increase the effectiveness of ryegrass breeding.

  14. Genetic structure of the Azores Islands: a study using 15 autosomal short tandem repeat loci.

    Science.gov (United States)

    Santos, Cristina; Alvarez, Luis; Aluja, Maria Pilar; Bruges-Armas, Jacome; Lima, Manuela

    2009-12-01

    The Azores archipelago (Portugal), located in the Atlantic Ocean, 1,500 km from the European mainland, is formed by nine islands of volcanic origin. The relative position of these islands allows the definition of three geographical groups: Eastern, Central and Western. Previous studies of the Azores using Short Tandem Repeats (STRs) have highlighted differences in the frequencies of several loci, when compared to Mainland Portugal or Madleira Island. Furthermore, linkage disequilibrium (LD), described for Azorean samples has been tentatively explained as reflecting the presence of genetic sub-structuring in the archipelago. To provide information concerning the genetic profile of the Azores Islands and to evaluate the presence of substructuring we have determined the allelic frequencies of 15 autosomal STR loci, using the AmpFlSTR Identifiler Kit, in representative samples from the Azorean Islands. Either considering the Azores as a whole, or analysing by island all the loci were in conformity with Hardy-Weinberg equilibrium. Average gene diversity ranged from 0.7669 in Corvo to 0.7972 in Terceira Island. Allelic independence between loci, tested for the global sample, detected significant LD (after correction for multiple tests) for pairs D21S11/D7S820 and D3S1358/D5S818. The exact test of population differentiation, combining the information of the 15 markers analysed, revealed significant differences between the three groups of islands, and between islands. Inter-island analysis reinforces the previous data that suggested the existence of sub-structuring in the Azores archipelago. Moreover, the data generated by this study can be used in a future forensic genetic database of the Azores after the appropriate enlacement of sample size by island, preventing, in that way, misinterpretations caused by population substructuring and small sample sizes.

  15. Short consensus repeat domains extend the E-selectin structure in order to grab cells out of flow

    KAUST Repository

    Aleisa, Fajr

    2017-01-08

    Selectins are key adhesion molecules responsible for initiating a multistep process that leads a cell out of the blood circulation and into a tissue or organ. They are composed of an N-terminal extracellular C-type lectin like domain, followed by an Endothelial Growth Factor like domain (EGF), a defined number of short consensus repeats SCR (also called “sushi” domains), a transmembrane domain and a C-terminal cytoplasmic tail. The adhesion of cells (expressing ligands) to the endothelium (expressing the selection i.e., E-selectin) occurs through the interaction between the lectin domain of selectins and sLeX presenting ligands. Structural/function studies to date have mainly focused on investigating the influence of the lectin domain of E-selectin on its ability to bind its ligands while other domains received less atention. We prepared a number of different recombinant E-selectin proteins with changes in the SCR units. Specifically we generated wild-type E-selectin proteins as monomeric or dimeric structures, mutant proteins with varied numbers of SCRs as well as proteins where strategic residues were mutated to change the conformation of the selectin. Using a novel real time immunoprecipitation surface plasmon resonance (SPR)-based in vitro binding study developed in our lab, the interaction of recombinant E-selectin proteins with immunoprecipitated endogenous ligands (i.e. CD44) captured on a CM-5 chip was assessed. These studies provided quantitative binding kinetics with on and off rates of selectin-ligand interactions and suggested that robust binding is dependent on the presence of the SCRs and oligomerization. These results provide significant implications on the functional mechanism of E-selectin binding to its ligands.

  16. Artificial leucine rich repeats as new scaffolds for protein design.

    Science.gov (United States)

    Baabur-Cohen, Hemda; Dayalan, Subashini; Shumacher, Inbal; Cohen-Luria, Rivka; Ashkenasy, Gonen

    2011-04-15

    The leucine rich repeat (LRR) motif that participates in many biomolecular recognition events in cells was suggested as a general scaffold for producing artificial receptors. We describe here the design and first total chemical synthesis of small LRR proteins, and their structural analysis. When evaluating the tertiary structure as a function of different number of repeating units (1-3), we were able to find that the 3-repeats sequence, containing 90 amino acids, folds into the expected structure.

  17. Diversity, population structure, and evolution of local peach cultivars in China identified by simple sequence repeats.

    Science.gov (United States)

    Shen, Z J; Ma, R J; Cai, Z X; Yu, M L; Zhang, Z

    2015-01-15

    The fruit peach originated in China and has a history of domestication of more than 4000 years. Numerous local cultivars were selected during the long course of cultivation, and a great morphological diversity exists. To study the diversity and genetic background of local peach cultivars in China, a set of 158 accessions from different ecological regions, together with 27 modern varieties and 10 wild accessions, were evaluated using 49 simple sequence repeats (SSRs) covering the peach genome. Broad diversity was also observed in local cultivars at the SSR level. A total of 648 alleles were amplified with an average of 13.22 observed alleles per locus. The number of genotypes detected ranged from 9 (UDP96015) to 58 (BPPCT008) with an average of 27.00 genotypes per marker. Eight subpopulations divided by STRUCTURE basically coincided with the dendrogram of genetic relationships and could be explained by the traditional groups. The 8 subpopulations were juicy honey peach, southwestern peach I, wild peach, Buddha peach + southwestern peach II, northern peach, southern crisp peach, ornamental peach, and Prunus davidiana + P. kansuensis. Most modern varieties carried the genetic backgrounds of juicy honey peach and southwestern peach I, while others carried diverse genetic backgrounds, indicating that local cultivars were partly used in modern breeding programs. Based on the traditional evolution pathway, a modified pathway for the development of local peach cultivars in China was proposed using the genetic background of subpopulations that were identified by SSRs. Current status and prospects of utilization of Chinese local peach cultivars were also discussed according to the SSR information.

  18. Structural racism and myocardial infarction in the United States

    OpenAIRE

    Lukachko, Alicia; Mark L Hatzenbuehler; Katherine M Keyes

    2014-01-01

    There is a growing research literature suggesting that racism is an important risk factor undermining the health of Blacks in the United States. Racism can take many forms, ranging from interpersonal interactions to institutional/structural conditions and practices. Existing research, however, tends to focus on individual forms of racial discrimination using self-report measures. Far less attention has been paid to whether structural racism may disadvantage the health of Blacks in the United ...

  19. Structural stability estimation of whirling unit

    Institute of Scientific and Technical Information of China (English)

    Son-Jae HWAN; Han-Chang WOO; Lee-Sang RYONG; Lee-Young MOON

    2009-01-01

    Whirling is a cutting process in which a series of cutting edges on whirling ring remove material by turning over a rotating workpiece. In this study static and dynamic stability of whirling unit was estimated by using ADAMS and NASTRAN softwares. Each maximum force acting on the bearing attached to the spindle assembly and the cutting tool attached to the whirling ring with the rotating speed of 6 000 r/min was 235 N and 902 N respectively. The maximum stress of 0.74 Mpa on the base frame is far smaller than the yield strength of 282 Mpa. The calculated natural frequency of 148 Hz of the system is far from the frequency of the driving speed of 6 000 r/min. The experimentally obtained maximum cutting force of 792 N is smaller than that of calculated value. And the experimentally obtained natural frequency of 118 Hz is beyond the driving speed of 6 000 r/min. From above results it can be judged that the whirling system is statically and dynamically stable.

  20. Reduction in the structural instability of cloned eukaryotic tandem-repeat DNA by low-temperature culturing of host bacteria.

    Science.gov (United States)

    Thapana, Watcharaporn; Sujiwattanarat, Penporn; Srikulnath, Kornsorn; Hirai, Hirohisa; Koga, Akihiko

    2014-10-27

    Summary For accurate analyses of eukaryotic tandem-repeat DNA, it is often required to clone a genomic DNA fragment into a bacterial plasmid. It is, however, a serious problem that tandem-repeat DNA is frequently subjected to structural changes during maintenance or amplification in the host bacteria. Here, we show an example of a clear difference in the instability of tandem-repeat DNA between different culturing temperatures. A fragment of monkey centromeric DNA carried by pUC19 was considerably degraded by culturing bacteria at 37 °C, but the damage was reduced at 25 °C. Thus, culturing temperature is a significant factor for avoiding degradation, in addition to the genotype of the host bacteria.

  1. Comparative Geometrical Analysis of Leucine-Rich Repeat Structures in the Nod-Like and Toll-Like Receptors in Vertebrate Innate Immunity

    Directory of Open Access Journals (Sweden)

    Norio Matsushima

    2015-08-01

    Full Text Available The NOD-like receptors (NLRs and Toll-like receptors (TLRs are pattern recognition receptors that are involved in the innate, pathogen pattern recognition system. The TLR and NLR receptors contain leucine-rich repeats (LRRs that are responsible for ligand interactions. In LRRs short β-strands stack parallel and then the LRRs form a super helical arrangement of repeating structural units (called a coil of solenoids. The structures of the LRR domains of NLRC4, NLRP1, and NLRX1 in NLRs and of TLR1-5, TLR6, TLR8, TLR9 in TLRs have been determined. Here we report nine geometrical parameters that characterize the LRR domains; these include four helical parameters from HELFIT analysis. These nine parameters characterize well the LRR structures in NLRs and TLRs; the LRRs of NLR adopts a right-handed helix. In contrast, the TLR LRRs adopt either a left-handed helix or are nearly flat; RP105 and CD14 also adopt a left-handed helix. This geometrical analysis subdivides TLRs into four groups consisting of TLR3/TLR8/TLR9, TLR1/TLR2/TRR6, TLR4, and TLR5; these correspond to the phylogenetic tree based on amino acid sequences. In the TLRs an ascending lateral surface that consists of loops connecting the β-strand at the C-terminal side is involved in protein, protein/ligand interactions, but not the descending lateral surface on the opposite side.

  2. Crystal structures of the human G3BP1 NTF2-like domain visualize FxFG Nup Repeat Specificity

    DEFF Research Database (Denmark)

    Vognsen, Tina Reinholdt; Möller, Ingvar Rúnar; Kristensen, Ole

    2013-01-01

    Ras GTPase Activating Protein SH3 Domain Binding Protein (G3BP) is a potential anti-cancer drug target implicated in several cellular functions. We have used protein crystallography to solve crystal structures of the human G3BP1 NTF2-like domain both alone and in complex with an FxFG Nup repeat...... crystal form might indicate a novel ligand binding site that, however, remains to be validated. The crystal structures give insight into the nuclear transportation mechanisms of G3BP and provide a basis for future structure based drug design....

  3. Fine structures and states of water in poly(vinyl alcohol) hydrogels prepared by repeated freezing and thawing

    OpenAIRE

    1997-01-01

    Investigations have been made into the relationship between structure and states of water in unfrozen poly (vinyl alcohol) (PVA) hydrogels prepared by repeated freezing and thawing of aqueous solution with various PVA concentrations. The states of water were investigated by using a pulsed nuclear magnetic resonance spectroscopy. Every unfrozen PVA hydrogel gave only one spin-lattice relaxation time (T-1) value. T-1 of all unfrozen hydrogels were smaller than that of free water and decreased w...

  4. Cerastoderma glaucum 5S ribosomal DNA: characterization of the repeat unit, divergence with respect to Cerastoderma edule, and PCR-RFLPs for the identification of both cockles.

    Science.gov (United States)

    Freire, Ruth; Insua, Ana; Méndez, Josefina

    2005-06-01

    The 5S rDNA repeat unit of the cockle Cerastoderma glaucum from the Mediterranean and Baltic coasts was PCR amplified and sequenced. The length of the units was 539-568 bp, of which 120 bp were assigned to the 5S rRNA gene and 419-448 bp to the spacer region, and the G/C content was 46%-49%, 54%, and 44%-47%, respectively. Two types of units (A and B), differing in the spacer, were distinguished based on the percentage of differences and clustering in phylogenetic trees. A PCR assay with specific primers for each unit type indicated that the occurrence of both units is not restricted to the sequenced individuals. The 5S rDNA units of C. glaucum were compared with new and previously reported sequences of Cerastoderma edule. The degree of variation observed in C. edule was lower than that in C. glaucum and evidence for the existence of units A and B in C. edule was not found. The two cockles have the same coding region but displayed numerous fixed differences in the spacer region and group separately in the phylogenetic trees. Digestion of the 5S rDNA PCR product with the restriction enzymes HaeIII and EcoRV revealed two RFLPs useful for cockle identification.

  5. How acidic are monomeric structural units of heparin?

    Science.gov (United States)

    Remko, Milan; Broer, Ria; Van Duijnen, Piet Th.

    2013-12-01

    Density functional theory methods with the B3LYP functional have been used to letter the acidity of carboxyl, O-sulfo and N-sulfo groups in six basic monomeric structural units of heparin (1-OMe ΔUA-2S, 1-OMe GlcN-S6S, 1,4-DiOMe GlcA, 1,4-DiOMe GlcN-S3S6S, 1,4-DiOMe IdoA-2S, and 1,4-DiOMe GlcN-S6S). The predicted gas-phase acidity of the acidic functional groups in the monomeric structural units of heparin is: O-sulfo > N-sulfo > carboxyl. The computed pKa values provide the same order of acidity as was observed in water solution. This implies that hydration does not change ordering of acidity of major acidic groups of monomeric structural units of heparin.

  6. Structure determines medication errors in nursing units: a mechanistic approach.

    Science.gov (United States)

    Hung, Chang-Chiao; Lee, Bih-O; Tsai, Shu-Ling; Tseng, Yun Shan; Chang, Chia-Hao

    2015-03-01

    Medication errors have long been considered critical in global health care systems. However, few studies have been conducted to explore the effects of nursing unit structure on medication errors. The purpose of this study, therefore, was to determine the effects of structural factors on medication errors in nursing units. A total of 977 staff nurses and 62 head nurses participated in this cross-sectional design study. The findings show that professional autonomy (β = .53, t = 6.03, p nursing experts (β = .52, t = 5.99, p medication error rates. This study shows that the structural factors influence medication administration and the mechanistic approach is specifically in relation of low medication error rates. The author suggests that head nurses should consider strategies that require adjustments to unit control mechanisms.

  7. A genetic and structural study of genome rearrangements mediated by high copy repeat Ty1 elements.

    Directory of Open Access Journals (Sweden)

    Jason E Chan

    2011-05-01

    Full Text Available Ty elements are high copy number, dispersed repeated sequences in the Saccharomyces cerevisiae genome known to mediate gross chromosomal rearrangements (GCRs. Here we found that introduction of Ty912, a previously identified Ty1 element, onto the non-essential terminal region of the left arm of chromosome V led to a 380-fold increase in the rate of accumulating GCRs in a wild-type strain. A survey of 48 different mutations identified those that either increased or decreased the rate of Ty-mediated GCRs and demonstrated that suppression of Ty-mediated GCRs differs from that of both low copy repeat sequence- and single copy sequence-mediated GCRs. The majority of the Ty912-mediated GCRs observed were monocentric nonreciprocal translocations mediated by RAD52-dependent homologous recombination (HR between Ty912 and a Ty element on another chromosome arm. The remaining Ty912-mediated GCRs appeared to involve Ty912-mediated formation of unstable dicentric translocation chromosomes that were resolved by one or more Ty-mediated breakage-fusion-bridge cycles. Overall, the results demonstrate that the Ty912-mediated GCR assay is an excellent model for understanding mechanisms and pathways that suppress genome rearrangements mediated by high copy number repeat sequences, as well as the mechanisms by which such rearrangements occur.

  8. Repeated Demographic-Structural Crises Propel the Spread of Large-scale Agrarian States Throughout the Old World

    Directory of Open Access Journals (Sweden)

    James Bennett

    2016-06-01

    Full Text Available I investigate the geographical consequences of demographic-structural dynamics using a spatially resolved agent-based model of agrarian empires in several Old World regions between 1500 BCE and 1500 CE. I estimate and bound key model parameters from two historical datasets. Although several very large-scale polities (e.g., Roman, Persian, Tang empires do not arise and certain geographical expansions occur at different times, overall the model suggests that factional civil wars, the result of repeated internal demographic-structural crises, can substantially account for the spread of large-scale agriculture throughout the Old World after the Bronze Age.

  9. Structure and organization of the mitochondrial DNA control region with tandemly repeated sequence in the Amazon ornamental fish.

    Science.gov (United States)

    Terencio, Maria Leandra; Schneider, Carlos Henrique; Gross, Maria Claudia; Feldberg, Eliana; Porto, Jorge Ivan Rebelo

    2013-02-01

    Tandemly repeated sequences are a common feature of vertebrate mitochondrial DNA control regions. However, questions still remain about their mode of evolution and function. To better understand patterns of variation in length and to explore the existence of previously described domain, we have characterized the control region structure of the Amazonian ornamental fish Nannostomus eques and Nannostomus unifasciatus. The control region ranged from 1121 to 1142 bp in length and could be separated into three domains: the domain associated with the extended terminal associated sequences, the central conserved domain, and the conserved sequence blocks domain. In the first domain, we encountered a sequence repeated 10 times in tandem (variable number tandem repeat (VNTR)) that could adopt an "inverted repetitions" type structural conformation. The results suggest that the VNTR pattern encountered in both N. eques and N. unifasciatus is consistent with the prerequisites of the illegitimate elongation model in which the unequal pairing of the chains near the 5'-end of the control region favors the formation of repetitions.

  10. Structural Evaluation of the Second Oldest Glued-Laminated Structure in the United States

    Science.gov (United States)

    Douglas R. Rammer; Jorge de Melo Moura

    2013-01-01

    The second glued-laminated structure built in the United States was constructed at the USDA Forest Products Laboratory (FPL) in 1934 to demonstrate the performance of wooden arch buildings. After decades of use the structure was decommissioned in 2010. Shortly after construction, researchers structurally evaluated the glued-laminated arch structure for uniform loading...

  11. Types of structural unemployment in the United Kingdom.

    Science.gov (United States)

    Hart, P E

    1990-01-01

    The author assesses the importance of each classification of "structural unemployment, namely technological, mismatch of skills, geographical mismatch, demographic shifts, institutional rigidities, 'unemployability', and capital-restructuring unemployment." in the United Kingdom. He also reviews recent evidence on regional wage differential adjustments and their impact on the disequilibrium within the British labor market.

  12. Biology 23. Unit One -- The Cell: Structure and Physiology.

    Science.gov (United States)

    Nederland Independent School District, TX.

    GRADES OR AGES: Not given. SUBJECT MATTER: Biology, the structure and physiology of the cell. ORGANIZATION AND PHYSICAL APPEARANCE: There are four sections: a) objectives for the unit, b) bibliography, c) activities, and d) evaluation. The guide is directed to the student rather than the teacher. The guide is mimeographed and stapled, with no…

  13. In silico structural and functional analysis of fragments of the ankyrin repeat protein p18(INK4c).

    Science.gov (United States)

    Sklenovsý, P; Otyepka, M

    2010-02-01

    Ankyrin repeat proteins (ARPs) are ubiquitous proteins that play critical regulatory roles in organisms and consist of repeating motifs (ankyrin repeats) stacked in non-globular, almost linear, "quasi one-dimensional" configurations. They also have highly unusual mechanical properties, notably ARPs can behave as nano-springs. Both their essential cellular functions and distinctive nano-mechanical properties have aroused interest in ARPs for potential applications in medicine and nanotechnology. Further, the modular architecture of ARPs, which lack the long-range contacts that typically stabilize globular proteins, provides a new paradigm for understanding protein stability and folding mechanisms of proteins. In the present study, the stability of ARP p18INK4c (p18) and fifty p18 fragments was investigated by all- atomic molecular dynamics (MD) simulations in explicit water on a ~3.3 micro- seconds timescale. The fragment simulations indicate that p18 alpha-helices are significantly stabilized by tertiary interactions, because in the absence of their native context they readily melt. All single p18 ARs and their structural elements are also unstable outside their native context. The minimal stable motifs are pairs of ARs, implying that inter-repeat contacts are essential for AR stability. Further, pairs of internal ARs are less stable than pairs that include a native capping AR. The MD simulations also provide indications of the functional roles of p18 turns and loops; the turns appear to be essential for the stability of the protein, while the loops both help to stabilize the p18 structure and are involved in recognition processes. Temperature-induced unfolding analysis shows that the p18 melts from the N-terminus to the C- terminus.

  14. Structural racism and myocardial infarction in the United States.

    Science.gov (United States)

    Lukachko, Alicia; Hatzenbuehler, Mark L; Keyes, Katherine M

    2014-02-01

    There is a growing research literature suggesting that racism is an important risk factor undermining the health of Blacks in the United States. Racism can take many forms, ranging from interpersonal interactions to institutional/structural conditions and practices. Existing research, however, tends to focus on individual forms of racial discrimination using self-report measures. Far less attention has been paid to whether structural racism may disadvantage the health of Blacks in the United States. The current study addresses gaps in the existing research by using novel measures of structural racism and by explicitly testing the hypothesis that structural racism is a risk factor for myocardial infarction among Blacks in the United States. State-level indicators of structural racism included four domains: (1) political participation; (2) employment and job status; (3) educational attainment; and (4) judicial treatment. State-level racial disparities across these domains were proposed to represent the systematic exclusion of Blacks from resources and mobility in society. Data on past-year myocardial infarction were obtained from the National Epidemiologic Survey on Alcohol and Related Conditions (non-Hispanic Black: N = 8245; non-Hispanic White: N = 24,507), a nationally representative survey of the U.S. civilian, non-institutionalized population aged 18 and older. Models were adjusted for individual-level confounders (age, sex, education, household income, medical insurance) as well as for state-level disparities in poverty. Results indicated that Blacks living in states with high levels of structural racism were generally more likely to report past-year myocardial infarction than Blacks living in low-structural racism states. Conversely, Whites living in high structural racism states experienced null or lower odds of myocardial infarction compared to Whites living in low-structural racism states. These results raise the provocative possibility that structural

  15. Synthesis of the tetrasaccharide repeating unit of the O-glycan from the polar flagellum flagellin of Azospirillum brasilense Sp7.

    Science.gov (United States)

    Pal, Kumar Bhaskar; Mukhopadhyay, Balaram

    2014-12-01

    Chemical synthesis of the tetrasaccharide repeating unit of the O-glycan from the polar flagellum flagellin of Azospirillum brasilense Sp7 in the form of its p-methoxyphenyl glycoside is reported. The required glycosidic linkages have been accomplished by activation of thioglycosides with N-iodosuccinimide in the presence of H2SO4-silica. H2SO4-silica was found to be an effective alternative to the classical acid promoters like TfOH or TMSOTf and it can lead to the formation of both 1,2-cis and 1,2-trans glycosidic linkages depending on the protecting group manipulation and control of the reaction condition.

  16. Structural and Biochemical Consequences of Disease-Causing Mutations in the Ankyrin Repeat Domain of the Human TRPV4 Channel

    Energy Technology Data Exchange (ETDEWEB)

    Inada, Hitoshi; Procko, Erik; Sotomayor, Marcos; Gaudet, Rachelle (Harvard-Med); (Harvard)

    2012-10-23

    The TRPV4 calcium-permeable cation channel plays important physiological roles in osmosensation, mechanosensation, cell barrier formation, and bone homeostasis. Recent studies reported that mutations in TRPV4, including some in its ankyrin repeat domain (ARD), are associated with human inherited diseases, including neuropathies and skeletal dysplasias, probably because of the increased constitutive activity of the channel. TRPV4 activity is regulated by the binding of calmodulin and small molecules such as ATP to the ARD at its cytoplasmic N-terminus. We determined structures of ATP-free and -bound forms of human TRPV4-ARD and compared them with available TRPV-ARD structures. The third inter-repeat loop region (Finger 3 loop) is flexible and may act as a switch to regulate channel activity. Comparisons of TRPV-ARD structures also suggest an evolutionary link between ARD structure and ATP binding ability. Thermal stability analyses and molecular dynamics simulations suggest that ATP increases stability in TRPV-ARDs that can bind ATP. Biochemical analyses of a large panel of TRPV4-ARD mutations associated with human inherited diseases showed that some impaired thermal stability while others weakened ATP binding ability, suggesting molecular mechanisms for the diseases.

  17. Organellar genome, nuclear ribosomal DNA repeat unit, and microsatellites isolated from a small-scale of 454 GS FLX sequencing on two mosses.

    Science.gov (United States)

    Liu, Yang; Forrest, Laura L; Bainard, Jillian D; Budke, Jessica M; Goffinet, Bernard

    2013-03-01

    Recent innovations in high-throughput DNA sequencing methodology (next generation sequencing technologies [NGS]) allow for the generation of large amounts of high quality data that may be particularly critical for resolving ambiguous relationships such as those resulting from rapid radiations. Application of NGS technology to bryology is limited to assembling entire nuclear or organellar genomes of selected exemplars of major lineages (e.g., classes). Here we outline how organellar genomes and the entire nuclear ribosomal DNA repeat can be obtained from minimal amounts of moss tissue via small-scale 454 GS FLX sequencing. We sampled two Funariaceae species, Funaria hygrometrica and Entosthodon obtusus, and assembled nearly complete organellar genomes and the whole nuclear ribosomal DNA repeat unit (18S-ITS1-5.8S-ITS2-26S-IGS1-5S-IGS2) for both taxa. Sequence data from these species were compared to sequences from another Funariaceae species, Physcomitrella patens, revealing low overall degrees of divergence of the organellar genomes and nrDNA genes with substitutions spread rather evenly across their length, and high divergence within the external spacers of the nrDNA repeat. Furthermore, we detected numerous microsatellites among the 454 assemblies. This study demonstrates that NGS methodology can be applied to mosses to target large genomic regions and identify microsatellites.

  18. Assessment of teamwork during structured interdisciplinary rounds on medical units.

    Science.gov (United States)

    O'Leary, Kevin J; Boudreau, Yvonne N; Creden, Amanda J; Slade, Maureen E; Williams, Mark V

    2012-01-01

    Interdisciplinary rounds (IDR) provide a means to assemble hospital team members and improve collaboration. Little is known about teamwork during IDR. To evaluate and characterize teamwork during IDR. Cross-sectional observational study. Six medical units which had implemented structured interdisciplinary rounds (SIDR). We adapted the Observational Teamwork Assessment for Surgery (OTAS) tool, a behaviorally anchored rating scale shown to be reliable and valid in surgical settings. OTAS provides scores ranging from 0 to 6 (0 = problematic behavior; 6 = exemplary behavior) across 5 domains (communication, coordination, cooperation/backup behavior, leadership, and monitoring/situational awareness) and for prespecified subteams. Two researchers conducted direct observations using the adapted OTAS tool. We conducted 7-8 independent observations for each unit (total = 44) and 20 joint observations. Inter-rater reliability was excellent at the unit level (Spearman's rho = 0.75), and good across domains (rho = 0.53-0.68) and subteams (rho = 0.53-0.76) with the exception of the physician subteam, for which it was poor (rho = 0.35). Though teamwork scores were generally high, we found differences across units, with a median (interquartile range [IQR]) 4.5 (3.9-4.9) for the lowest and 5.4 (5.3-5.5) for the highest performing unit (P teamwork during SIDR across units, domains, and most subteams. Variation in performance suggests a need to improve consistency of teamwork and emphasizes the importance of leadership. Copyright © 2012 Society of Hospital Medicine.

  19. Topological Quantization in Units of the Fine Structure Constant

    Energy Technology Data Exchange (ETDEWEB)

    Maciejko, Joseph; /Stanford U., Phys. Dept. /Stanford U., Materials Sci. Dept. /SLAC; Qi, Xiao-Liang; /Station Q, UCSB /Stanford U., Phys. Dept. /Stanford U., Materials Sci. Dept. /SLAC; Drew, H.Dennis; /Maryland U.; Zhang, Shou-Cheng; /Stanford U., Phys. Dept. /Stanford U., Materials Sci. Dept. /SLAC

    2011-11-11

    Fundamental topological phenomena in condensed matter physics are associated with a quantized electromagnetic response in units of fundamental constants. Recently, it has been predicted theoretically that the time-reversal invariant topological insulator in three dimensions exhibits a topological magnetoelectric effect quantized in units of the fine structure constant {alpha} = e{sup 2}/{h_bar}c. In this Letter, we propose an optical experiment to directly measure this topological quantization phenomenon, independent of material details. Our proposal also provides a way to measure the half-quantized Hall conductances on the two surfaces of the topological insulator independently of each other.

  20. Crystal structure of the dimeric protein core of decorin, the archetypal small leucine-rich repeat proteoglycan.

    Science.gov (United States)

    Scott, Paul G; McEwan, Paul A; Dodd, Carole M; Bergmann, Ernst M; Bishop, Paul N; Bella, Jordi

    2004-11-02

    Decorin is a ubiquitous extracellular matrix proteoglycan with a variety of important biological functions that are mediated by its interactions with extracellular matrix proteins, cytokines, and cell surface receptors. Decorin is the prototype of the family of small leucine-rich repeat proteoglycans and proteins (SLRPs), characterized by a protein core composed of leucine-rich repeats (LRRs), flanked by two cysteine-rich regions. We report here the crystal structure of the dimeric protein core of decorin, the best characterized member of the SLRP family. Each monomer adopts the curved solenoid fold characteristic of LRR domains, with a parallel beta-sheet on the inside interwoven with loops containing short segments of beta-strands, 3(10) helices, and polyproline II helices on the outside. Two main features are unique to this structure. First, decorin dimerizes through the concave surfaces of the LRR domains, which have been implicated previously in protein-ligand interactions. The amount of surface buried in this dimer rivals the buried surfaces of some of the highest-affinity macromolecular complexes reported to date. Second, the C-terminal region adopts an unusual capping motif that involves a laterally extended LRR and a disulfide bond. This motif seems to be unique to SLRPs and has not been observed in any other LRR protein structure to date. Possible implications of these features for decorin ligand binding and SLRP function are discussed.

  1. Structure-Correlation NMR Spectroscopy for Macromolecules Using Repeated Bidirectional Photoisomerization of Azobenzene.

    Science.gov (United States)

    Nagashima, Toshio; Ueda, Keisuke; Nishimura, Chiaki; Yamazaki, Toshio

    2015-11-17

    Control over macromolecular structure offers bright potentials for manipulation of macromolecular functions. We here present structure-correlation NMR spectroscopy to analyze the correlation between polymorphic macromolecular structures driven by photoisomerization of azobenzene. The structural conversion of azobenzene was induced within the mixing time of a NOESY experiment using a colored light source, and the reverse structural conversion was induced during the relaxation delay using a light source of another color. The correlation spectrum between trans- and cis-azobenzene was then obtained. To maximize the efficiency of the bidirectional photoisomerization of azobenzene-containing macromolecules, we developed a novel light-irradiation NMR sample tube and method for irradiating target molecules in an NMR radio frequency (rf) coil. When this sample tube was used for photoisomerization of an azobenzene derivative at a concentration of 0.2 mM, data collection with reasonable sensitivity applicable to macromolecules was achieved. We performed isomerization of an azobenzene-cross-linked peptide within the mixing time of a NOESY experiment that produced cross-peaks between helix and random-coil forms of the peptide. Thus, these results indicate that macromolecular structure manipulation can be incorporated into an NMR pulse sequence using an azobenzene derivative and irradiation with light of two types of wavelengths, providing a new method for structural analysis of metastable states of macromolecules.

  2. Optimum Structural Design of a Chain-Driving Pumping Unit

    Institute of Scientific and Technical Information of China (English)

    Zhang Ailin; Liu Yang

    1994-01-01

    @@ Operating Principle and Essential Parameters In this paper the pumping unit of type QLCJ14-6 is studied. Through the belt driving unit, the motor drives the driving sprocket in which the rotation rate has been reduced by the reduction gearbox.The locus chain moves between the driving sprocket and upper sprocket which are vertically set. There's a special chain element in the locus chain, which drives the reciprocating holster with the main shaft linchpin and slide block. The reciprocating holster could only move up and down when the locus chain moves in a circle. In this way the up and down stroke of the sucker rod and the machine is realized.The lower end of the reciprocating holster is connected with the equilibrium system to make the structure balance. The balancing cylinder is replaced by the balancing block to make the structure simplified.

  3. Process and structure: resource management and the development of sub-unit organisational structure.

    Science.gov (United States)

    Packwood, T; Keen, J; Buxton, M

    1992-03-01

    Resource Management (RM) requires hospital units to manage their work in new ways, and the new management processes affect, and are affected by, organisation structure. This paper is concerned with these effects, reporting on the basis of a three-year evaluation of the national RM experiment that was commissioned by the DH. After briefly indicating some of the major characteristics of the RM process, the two main types of unit structures existing in the pilot sites at the beginning of the experiment, unit disciplinary structure and clinical directorates, are analysed. At the end of the experiment, while clinical directorates had become more popular, another variant, clinical grouping, had replaced the unit disciplinary structure. Both types of structure represent a movement towards sub-unit organisation, bringing the work and interests of the service providers and unit managers closer together. Their properties are likewise analysed and their implications, particularly in terms of training and organisational development (OD), are then considered. The paper concludes by considering the causes for these structural changes, which, in the immediate time-scale, appear to owe as much to the NHS Review as to RM.

  4. Resistance and resilience of removal efficiency and bacterial community structure of gas biofilters exposed to repeated shock loads.

    Science.gov (United States)

    Cabrol, Léa; Malhautier, Luc; Poly, Franck; Roux, Xavier Le; Lepeuple, Anne-Sophie; Fanlo, Jean-Louis

    2012-11-01

    Since full-scale biofilters are often operated under fluctuating conditions, it is critical to understand their response to transient states. Four pilot-scale biofilters treating a composting gas mixture and undergoing repeated substrate pulses of increasing intensity were studied. A systematic approach was proposed to quantify the resistance and resilience capacity of their removal efficiency, which enabled to distinguish between recalcitrant (ammonia, DMDS, ketones) and easily degradable (esters and aldehyde) compounds. The threshold of disturbing shock intensity and the influence of disturbance history depended on the contaminant considered. The spatial and temporal distribution of the bacterial community structure in response to the perturbation regime was analysed by Denaturing Gradient Gel Electrophoresis (DGGE). Even if the substrate-pulses acted as a driving force for some community characteristics (community stratification), the structure-function relationships were trickier to evidence: the distributions of resistance and composition were only partially coupled, with contradictory results depending on the contaminant considered.

  5. Crystal Structure of DNA-PKcs Reveals a Large Open-Ring Cradle Comprised of HEAT Repeats

    Science.gov (United States)

    Sibanda, Bancinyane L.; Chirgadze, Dimitri Y.; Blundell, Tom L.

    2009-01-01

    Broken chromosomes arising from DNA double strand breaks result from endogenous events such as the production of reactive oxygen species during cellular metabolism, as well as from exogenous sources such as ionizing radiation1, 2, 3. Left unrepaired or incorrectly repaired they can lead to genomic changes that may result in cell death or cancer. DNA-dependent protein kinase (DNA-PK), a holo-enzyme that comprises DNA-dependent protein kinase catalytic subunit (DNA-PKcs)4, 5 and the heterodimer Ku70/Ku80, plays a major role in non-homologous end joining (NHEJ), the main pathway in mammals used to repair double strand breaks6, 7, 8. DNA-PKcs is a serine/threonine protein kinase comprising a single polypeptide chain of 4128 amino acids and belonging to the phosphotidyl inositol 3-kinase (PI3-K)- related protein family9. DNA-PKcs is involved in the sensing and transmission of DNA damage signals to proteins such as p53, setting off events that lead to cell cycle arrest10, 11. It phosphorylates a wide range of substrates in vitro, including Ku70/Ku80, which is translocated along DNA12. Here we present the crystal structure of human DNA-PKcs at 6.6Å resolution, in which the overall fold is for the first time clearly visible. The many α-helical HEAT repeats (helix-turn-helix motifs) facilitate bending and allow the polypeptide chain to fold into a hollow circular structure. The C-terminal kinase domain is located on top of this structure and a small HEAT repeat domain that likely binds DNA is inside. The structure provides a flexible cradle to promote DNA double-strand-break repair. PMID:20023628

  6. Structural model for the interaction of a designed Ankyrin Repeat Protein with the human epidermal growth factor receptor 2.

    Directory of Open Access Journals (Sweden)

    V Chandana Epa

    Full Text Available Designed Ankyrin Repeat Proteins are a class of novel binding proteins that can be selected and evolved to bind to targets with high affinity and specificity. We are interested in the DARPin H10-2-G3, which has been evolved to bind with very high affinity to the human epidermal growth factor receptor 2 (HER2. HER2 is found to be over-expressed in 30% of breast cancers, and is the target for the FDA-approved therapeutic monoclonal antibodies trastuzumab and pertuzumab and small molecule tyrosine kinase inhibitors. Here, we use computational macromolecular docking, coupled with several interface metrics such as shape complementarity, interaction energy, and electrostatic complementarity, to model the structure of the complex between the DARPin H10-2-G3 and HER2. We analyzed the interface between the two proteins and then validated the structural model by showing that selected HER2 point mutations at the putative interface with H10-2-G3 reduce the affinity of binding up to 100-fold without affecting the binding of trastuzumab. Comparisons made with a subsequently solved X-ray crystal structure of the complex yielded a backbone atom root mean square deviation of 0.84-1.14 Ångstroms. The study presented here demonstrates the capability of the computational techniques of structural bioinformatics in generating useful structural models of protein-protein interactions.

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

    Science.gov (United States)

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

    2017-05-01

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

  8. Investigating the Structural Impact of the Glutamine Repeat in Huntingtin Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Perevozchikova, Tatiana [ORNL; Stanley, Christopher B [ORNL; McWilliams-Koeppen, Helen P [ORNL; Rowe, Erica L [ORNL; Berthelier-Jung, Valerie M [ORNL

    2014-01-01

    Acquiring detailed structural information about the various aggregation states of the huntingtin-exon1 protein (Htt-exon1) is crucial not only for identifying the true nature of the neurotoxic species responsible for Huntington s disease (HD) but also for designing effective therapeutics. Using time-resolved small-angle neutron scattering (TR-SANS), we followed the conformational changes that occurred during fibrillization of the pathologic form of Htt-exon1 (NtQ42P10) and compared the results with those obtained for the wild-type (NtQ22P10). Our results show that the aggregation pathway of NtQ22P10 is very different from that of NtQ42P10, as the initial steps require a monomer to 7-mer transition stage. In contrast, the earliest species identified for NtQ42P10 are monomer and dimer. The divergent pathways ultimately result in NtQ22P10 fibrils that possess a pack- ing arrangement consistent with the common amyloid sterical zipper model, whereas NtQ42P10 fibrils present a better fit to the Perutz b-helix structural model. The structural details obtained by TR-SANS should help to delineate the key mechanisms that underpin Htt-exon1 aggregation leading to HD.

  9. Concerted evolution of the tandemly repeated genes encoding primate U2 small nuclear RNA (the RNU2 locus) does not prevent rapid diversification of the (CT){sub n} {center_dot} (GA){sub n} microsatellite embedded within the U2 repeat unit

    Energy Technology Data Exchange (ETDEWEB)

    Liao, D.; Weiner, A.M. [Yale Univ., New Haven, CT (United States)

    1995-12-10

    The RNU2 locus encoding human U2 small nuclear RNA (snRNA) is organized as a nearly perfect tandem array containing 5 to 22 copies of a 5.8-kb repeat unit. Just downstream of the U2 snRNA gene in each 5.8-kb repeat unit lies a large (CT){sub n}{center_dot}(GA){sub n} dinucleotide repeat (n {approx} 70). This form of genomic organization, in which one repeat is embedded within another, provides an unusual opportunity to study the balance of forces maintaining the homogeneity of both kinds of repeats. Using a combination of field inversion gel electrophoresis and polymerase chain reaction, we have been able to study the CT microsatellites within individual U2 tandem arrays. We find that the CT microsatellites within an RNU2 allele exhibit significant length polymorphism, despite the remarkable homogeneity of the surrounding U2 repeat units. Length polymorphism is due primarily to loss or gain of CT dinucleotide repeats, but other types of deletions, insertions, and substitutions are also frequent. Polymorphism is greatly reduced in regions where pure (CT){sub n} tracts are interrupted by occasional G residues, suggesting that irregularities stabilize both the length and the sequence of the dinucleotide repeat. We further show that the RNU2 loci of other catarrhine primates (gorilla, chimpanzee, ogangutan, and baboon) contain orthologous CT microsatellites; these also exhibit length polymorphism, but are highly divergent from each other. Thus, although the CT microsatellite is evolving far more rapidly than the rest of the U2 repeat unit, it has persisted through multiple speciation events spanning >35 Myr. The persistence of the CT microsatellite, despite polymorphism and rapid evolution, suggests that it might play a functional role in concerted evolution of the RNU2 loci, perhaps as an initiation site for recombination and/or gene conversion. 70 refs., 5 figs.

  10. Bacterial community structure and dissolved organic matter in repeatedly flooded subsurface karst water pools.

    Science.gov (United States)

    Shabarova, Tanja; Villiger, Jörg; Morenkov, Oleg; Niggemann, Jutta; Dittmar, Thorsten; Pernthaler, Jakob

    2014-07-01

    Bacterial diversity, community assembly, and the composition of the dissolved organic matter (DOM) were studied in three temporary subsurface karst pools with different flooding regimes. We tested the hypothesis that microorganisms introduced to the pools during floods faced environmental filtering toward a 'typical' karst water community, and we investigated whether DOM composition was related to floodings and the residence time of water in stagnant pools. As predicted, longer water residence consistently led to a decline of bacterial diversity. The microbial assemblages in the influx water harbored more 'exotic' lineages with large distances to known genotypes, yet these initial communities already appeared to be shaped by selective processes. β-Proteobacterial operational taxonomic units (OTUs) closely related to microbes from subsurface or surface aquatic environments were mainly responsible for the clustering of samples according to water residence time in the pools. By contrast, several Cytophagaceae and Flavobacteriaceae OTUs were related to different floodings, which were also the main determinants of DOM composition. A subset of compounds distinguishable by molecular mass and O/C content were characteristic for individual floods. Moreover, there was a transformation of DOM in stagnant pools toward smaller and more aromatic compounds, potentially also reflecting microbial utilization. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

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

    Science.gov (United States)

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

    2016-08-01

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

  12. Revisiting the TALE repeat.

    Science.gov (United States)

    Deng, Dong; Yan, Chuangye; Wu, Jianping; Pan, Xiaojing; Yan, Nieng

    2014-04-01

    Transcription activator-like (TAL) effectors specifically bind to double stranded (ds) DNA through a central domain of tandem repeats. Each TAL effector (TALE) repeat comprises 33-35 amino acids and recognizes one specific DNA base through a highly variable residue at a fixed position in the repeat. Structural studies have revealed the molecular basis of DNA recognition by TALE repeats. Examination of the overall structure reveals that the basic building block of TALE protein, namely a helical hairpin, is one-helix shifted from the previously defined TALE motif. Here we wish to suggest a structure-based re-demarcation of the TALE repeat which starts with the residues that bind to the DNA backbone phosphate and concludes with the base-recognition hyper-variable residue. This new numbering system is consistent with the α-solenoid superfamily to which TALE belongs, and reflects the structural integrity of TAL effectors. In addition, it confers integral number of TALE repeats that matches the number of bound DNA bases. We then present fifteen crystal structures of engineered dHax3 variants in complex with target DNA molecules, which elucidate the structural basis for the recognition of bases adenine (A) and guanine (G) by reported or uncharacterized TALE codes. Finally, we analyzed the sequence-structure correlation of the amino acid residues within a TALE repeat. The structural analyses reported here may advance the mechanistic understanding of TALE proteins and facilitate the design of TALEN with improved affinity and specificity.

  13. Exposure to Hycanthone alters chromatin structure around specific gene functions and specific repeats in Schistosoma mansoni

    Directory of Open Access Journals (Sweden)

    David eRoquis

    2014-07-01

    Full Text Available Schistosoma mansoni is a parasitic plathyhelminth responsible for intestinal schistosomiasis (or bilharziasis, a disease affecting 67 million people worldwide and causing an important economic burden. The schistosomicides hycanthone, and its later proxy oxamniquine, were widely used for treatments in endemic areas during the 20th century. Recently, the mechanism of action, as well as the genetic origin of a stably and Mendelian inherited resistance for both drugs was elucidated in two strains. However, several observations suggested early on that alternative mechanisms might exist, by which resistance could be induced for these two drugs in sensitive lines of schistosomes. This induced resistance appeared rapidly, within the first generation, but was metastable (not stably inherited. Epigenetic inheritance could explain such a phenomenon and we therefore re-analyzed the historical data with our current knowledge of epigenetics. In addition, we performed new experiments such as ChIP-seq on hycanthone treated worms. We found distinct chromatin structure changes between sensitive worms and induced resistant worms from the same strain. No specific pathway was discovered, but genes in which chromatin structure modification were observed are mostly associated with transport and catabolism, which makes sense in the context of the elimination of the drug. Specific differences were observed in the repetitive compartment of the genome. We finally describe what types of experiments are needed to understand the complexity of heritability that can be based on genetic and/or epigenetic mechanisms for drug resistance in schistosomes.

  14. Genotyping of Brucella melitensis strains from dromedary camels (Camelus dromedarius) from the United Arab Emirates with multiple-locus variable-number tandem repeat analysis.

    Science.gov (United States)

    Gyuranecz, Miklós; Wernery, Ulli; Kreizinger, Zsuzsa; Juhász, Judit; Felde, Orsolya; Nagy, Péter

    2016-04-15

    Camel brucellosis is a widespread zoonotic disease in camel-rearing countries caused by Brucella melitensis and Brucella abortus. The aim of this study was the first genetic analysis of B. melitensis strains isolated from dromedary camels (Camelus dromedarius) using multiple-locus variable-number tandem repeat analysis (MLVA). MLVA 16 and its MLVA 8 and MLVA11 subsets were used to determine the genotypes of 15 B. melitensis isolates from dromedary camels (11 strains) and other host species (4 strains) from the United Arab Emirates and the results were then compared to B. melitensis MLVA genotypes from other parts of the world. Five, including two novel genotypes were identified with MLVA 8. MLVA 16 further discriminated these five genotypes to ten variants. The eleven camel isolates clustered into four main genetic groups within the East-Mediterranean and African clades and this clustering correlated with the geographic origin of the hosts (United Arab Emirates, Kingdom of Saudi Arabia and Sudan) and the date of their isolation. The camel strains were also genetically related to strains isolated from wild and domestic ruminants from their close habitat or from other parts of the world. Although limited number of strains were analysed, based on our data imported animals from foreign countries, local small ruminants and wildlife species are hypothesized to be the main sources of camel brucellosis in the United Arab Emirates. MLVA was successfully applied to determine the epidemiological links between the different camel B. melitensis infections in the United Arab Emirates and it can be a beneficial tool in future disease control programs.

  15. Structure-function Aspects of Extracellular Leucine-rich Repeat-containing Cell Surface Receptors in Plants

    Institute of Scientific and Technical Information of China (English)

    Zhao Zhang; Bart PHJ Thomma

    2013-01-01

    Plants exploit several types of cell surface receptors for perception of extracellular signals, of which the extracellular leucine-rich repeat (eLRR)-containing receptors form the major class. Although the function of most plant eLRR receptors remains unclear, an increasing number of these receptors are shown to play roles in innate immunity and a wide variety of developmental processes. Recent efforts using domain swaps, gene shuffling analyses, site-directed mutagenesis, interaction studies, and crystallographic analyses resulted in the current knowledge on ligand binding and the mechanism of activation of plant eLRR receptors. This review provides an overview of eLRR receptor research, specifically summarizing the recent understanding of interactions among plant eLRR receptors, their co-receptors and corresponding ligands. The functions of distinct eLRR receptor domains, and their role in structure, ligand perception and multimeric complex formation are discussed.

  16. S1 satellite DNA repetitive units display identical structure and overall variability in all Anatolian brown frog taxa.

    Science.gov (United States)

    Picariello, Orfeo; Feliciello, Isidoro; Chinali, Gianni

    2016-02-01

    S1 satellite DNA from Palearctic brown frogs has a species-specific structure in all European species. We characterized S1 satellite DNA from the Anatolian brown frogs Rana macrocnemis, R. camerani, and R. holtzi in order to define their taxonomic rank and the structure of this satellite in this frog lineage. Southern blots of genomic DNA digested with KpnI, EcoRV, NdeI, NheI, or StuI produced the same pattern of satellite DNA bands. Moreover, quantitative dot blots showed that this satellite DNA accounts for 0.1 % of the genome in all taxa. Analysis of the overall genomic variability of the S1a repeat sequence in specimens from various populations demonstrated that this repetitive unit also has the same size (476 bp), the same most common sequence (MCS) and the same overall variability in all three taxa, and also in R. macrocnemis tavasensis. The S1a repetitive unit presents three deletions of 9, 8 and 1 bp compared to the 494-bp S1a repeat from European frogs. The S1a MCS has three variable positions (sequence WWTK in positions 183-186), due to the presence of two repeat subpopulations with motifs AATG and WWTT in all taxa. Unlike previously analyzed mitochondrial and nuclear sequences that show considerable variations among these taxa, no difference could be detected in the structure and variability of the S1 satellite repetitive units. This suggests that these taxa should belong to a single species. Our results indicate that this satellite DNA variety probably formed when the Anatolian lineage radiated from common ancestor about 4 mya, and since then has maintained its structure in all four taxa examined.

  17. Poly(2-thiophen-3-yl-malonic acid), a polythiophene with two carboxylic acids per repeating unit.

    Science.gov (United States)

    Bertran, Oscar; Armelin, Elaine; Estrany, Francesc; Gomes, Alex; Torras, Juan; Alemán, Carlos

    2010-05-20

    A new substituted polythiophene derivative bearing malonic acid, poly(2-thiophen-3-yl-malonic acid), has been prepared and characterized using a strategy that combines both experimental and theoretical methodologies. The chemical structure of this material has been investigated using FTIR and (1)H NMR, and its molecular conformation has been determined using quantum mechanical calculations. Interestingly, the arrangement of the inter-ring dihedral angles was found to depend on the ionization degree of the material, that is, on the pH, which has been found completely soluble in aqueous base solution. Thus, the preferred anti-gauche conformation changes to syn-gauche when the negatively charged carboxylate groups transforms into neutral carboxylic acid. UV-vis experiments and quantum mechanical calculations on model systems with a head-to-tail regiochemistry showed that the lowest pi-pi* transition energy is 2.25 and 2.39 eV for the negatively charged and the neutral polymer, respectively. These values are slightly larger than those previously reported for other polythiophenes with bulky polar side groups. The polymer presents a good thermal stability with a decomposition temperature above 215 degrees C and an electrical conductivity of 10(-5) S/cm, which is characteristic of semiconductor materials. Scanning electron microscopy micrographs showed that, after doping, the surface of this material displays regular distribution pores with irregular sizes. This surface suggests that poly(2-thiophen-3-yl-malonic acid) is a candidate for potential applications such as selective membranes for electrodialysis, wastewater treatment, or ion-selective membranes for biomedical uses.

  18. Long inverted repeat transiently stalls DNA replication by forming hairpin structures on both leading and lagging strands.

    Science.gov (United States)

    Lai, Pey Jiun; Lim, Chew Theng; Le, Hang Phuong; Katayama, Tsutomu; Leach, David R F; Furukohri, Asako; Maki, Hisaji

    2016-02-01

    Long inverted repeats (LIRs), often found in eukaryotic genomes, are unstable in Escherichia coli where they are recognized by the SbcCD (the bacterial Mre11/Rad50 homologue), an endonuclease/exonuclease capable of cleaving hairpin DNA. It has long been postulated that LIRs form hairpin structures exclusively on the lagging-strand template during DNA replication, and SbcCD cleaves these hairpin-containing lagging strands to generate DNA double-strand breaks. Using a reconstituted oriC plasmid DNA replication system, we have examined how a replication fork behaves when it meets a LIR on DNA. We have shown that leading-strand synthesis stalls transiently within the upstream half of the LIR. Pausing of lagging-strand synthesis at the LIR was not clearly observed, but the pattern of priming sites for Okazaki fragment synthesis was altered within the downstream half of the LIR. We have found that the LIR on a replicating plasmid was cleaved by SbcCD with almost equal frequency on both the leading- and lagging-strand templates. These data strongly suggest that the LIR is readily converted to a cruciform DNA, before the arrival of the fork, creating SbcCD-sensitive hairpin structures on both leading and lagging strands. We propose a model for the replication-dependent extrusion of LIRs to form cruciform structures that transiently impede replication fork movement.

  19. Crystal structures of ryanodine receptor SPRY1 and tandem-repeat domains reveal a critical FKBP12 binding determinant.

    Science.gov (United States)

    Yuchi, Zhiguang; Yuen, Siobhan M Wong King; Lau, Kelvin; Underhill, Ainsley Q; Cornea, Razvan L; Fessenden, James D; Van Petegem, Filip

    2015-08-06

    Ryanodine receptors (RyRs) form calcium release channels located in the membranes of the sarcoplasmic and endoplasmic reticulum. RyRs play a major role in excitation-contraction coupling and other Ca(2+)-dependent signalling events, and consist of several globular domains that together form a large assembly. Here we describe the crystal structures of the SPRY1 and tandem-repeat domains at 1.2-1.5 Å resolution, which reveal several structural elements not detected in recent cryo-EM reconstructions of RyRs. The cryo-EM studies disagree on the position of SPRY domains, which had been proposed based on homology modelling. Computational docking of the crystal structures, combined with FRET studies, show that the SPRY1 domain is located next to FK506-binding protein (FKBP). Molecular dynamics flexible fitting and mutagenesis experiments suggest a hydrophobic cluster within SPRY1 that is crucial for FKBP binding. A RyR1 disease mutation, N760D, appears to directly impact FKBP binding through interfering with SPRY1 folding.

  20. Monitoring fluvial erosion of the Oso landslide, Washington, using repeat Structure-from-Motion photogrammetry

    Science.gov (United States)

    Anderson, S. W.; Magirl, C. S.; Keith, M. K.

    2015-12-01

    On March 22, 2014, the Oso landslide, located in northwestern Washington State, catastrophically mobilized about 8 million m3 of mixed glacial sediment, creating a valley-wide blockage that impounded the North Fork Stillaguamish River to a height of 8 m. The river overtopped the landslide blockage within several days and incised a new channel through predominately fine-grained, cohesive glaciolacustrine sediment in the center of the deposit. Our research focuses on the evolution of this new channel. Using a consumer-grade digital camera mounted on a fixed wing-aircraft, we used structure-from-motion (SfM) photogrammetry to produce 25 cm digital elevation models (DEMs) of the channel at one-month intervals between November 2014 and July 2015. A large RTK GPS validation dataset and inter-survey comparisons documents sub-decimeter vertical and horizontal accuracies. In combination with aerial lidar surveys acquired in March and April 2014, this dataset provides a uniquely resolved look at the erosion of a landslide dam. The newly-formed channel incised rapidly, lowering to within a meter of its pre-slide elevation by May 2014 despite modest flows. During high flows of the 2014-2015 winter flood season, erosion was dominated by channel widening of tens of meters with an overall stable planform. Incision fully returned the channel to pre-slide elevations by December 2014. A total of 510,000 +/- 50,000 m3 of material was eroded between March 2014 and July 2015, split evenly between the initial period of incision and the later period of widening. Sediment yield and channel morphology showed asymptotic trends towards stability. Measurements of deposit bulk density and grain size allowed conversion of volumetric sediment yields to mass yields by size classes. Over the 16 months after the slide, the river eroded about 0.82 +/- 0.1 Mt of sediment, of which 0.78 Mt was finer than 2mm. This yield agrees within 15% of an independent estimate based on concurrent sediment gaging

  1. Distinct Secondary Structures of the Leucine-Rich Repeat Proteoglycans Decorin and Biglycan: Glycosylation-Dependent Conformational Stability

    Science.gov (United States)

    Krishnan, Priya; Hocking, Anne M.; Scholtz, J. Martin; Pace, C. Nick; Holik, Kimberly K.; McQuillan, David J.

    1998-01-01

    Biglycan and decorin, closely related small leucine-rich repeat proteoglycans, have been overexpressed in eukaryotic cers and two major glycoforms isolated under native conditions: a proteoglycan substituted with glycosaminoglycan chains; and a core protein form secreted devoid of glycosaminoglycans. A comparative biophysical study of these glycoforms has revealed that the overall secondary structures of biglycan and decorin are different. Far-UV Circular Dichroism (CD) spectroscopy of decorin and biglycan proteoglycans indicates that, although they are predominantly Beta-sheet, biglycan has a significantly higher content of alpha-helical structure. Decorin proteoglycan and core protein are very similar, whereas the biglycan core protein exhibits closer similarity to the decorin glycoforms than to. the biglycan proteoglycan form. However, enzymatic removal of the chondroitin sulfate chains from biglycan proteoglycan does not induce a shift to the core protein structure, suggesting that the fmal form is influenced by polysaccharide addition only during biosynthesis. Fluorescence emission spectroscopy demonstrated that the single tryptophan residue, which is at a conserved position at the C-terminal domain of both biglycan and decorin, is found in similar microenvironments. This indicates that at least in this specific domain, the different glycoforms do exhibit apparent conservation of structure. Exposure of decorin and biglycan to 10 M urea resulted in an increase in fluorescent intensity, which indicates that the emission from tryptophan in the native state is quenched. Comparison of urea-induced protein unfolding curves provided further evidence that decorin and biglycan assume different structures in solution. Decorin proteoglycan and core protein unfold in a manner similar to a classic two-state model, in which there is a steep transition to an unfolded state between 1-2 M urea. The biglycan core protein also shows a similar steep transition. However, biglycan

  2. Studies of the Temperature Characteristics of Solid at the Microlevel by the Method of Structural Units

    Directory of Open Access Journals (Sweden)

    A.A. Mochalov

    2014-11-01

    Full Text Available The mathematical model of the heat transfer process based on the structural unit method is proposed. Calculation results of the model equations of thermodynamic characteristics of structural unit for solids are represented.

  3. Unit cell geometry of multiaxial preforms for structural composites

    Science.gov (United States)

    Ko, Frank; Lei, Charles; Rahman, Anisur; Du, G. W.; Cai, Yun-Jia

    1993-01-01

    The objective of this study is to investigate the yarn geometry of multiaxial preforms. The importance of multiaxial preforms for structural composites is well recognized by the industry but, to exploit their full potential, engineering design rules must be established. This study is a step in that direction. In this work the preform geometry for knitted and braided preforms was studied by making a range of well designed samples and studying them by photo microscopy. The structural geometry of the preforms is related to the processing parameters. Based on solid modeling and B-spline methodology a software package is developed. This computer code enables real time structural representations of complex fiber architecture based on the rule of preform manufacturing. The code has the capability of zooming and section plotting. These capabilities provide a powerful means to study the effect of processing variables on the preform geometry. the code also can be extended to an auto mesh generator for downstream structural analysis using finite element method. This report is organized into six sections. In the first section the scope and background of this work is elaborated. In section two the unit cell geometries of braided and multi-axial warp knitted preforms is discussed. The theoretical frame work of yarn path modeling and solid modeling is presented in section three. The thin section microscopy carried out to observe the structural geometry of the preforms is the subject in section four. The structural geometry is related to the processing parameters in section five. Section six documents the implementation of the modeling techniques into the computer code MP-CAD. A user manual for the software is also presented here. The source codes and published papers are listed in the Appendices.

  4. Amino Acid Molecular Units: Building Primary and Secondary Protein Structures

    Directory of Open Access Journals (Sweden)

    Aparecido R. Silva

    2008-05-01

    Full Text Available In order to guarantee the learning quality and suitable knowledge  use  about structural biology, it is fundamental to  exist, since the beginning of  students’ formation, the possibility of clear visualization of biomolecule structures. Nevertheless, the didactic books can only bring  schematic  drawings; even more elaborated figures and graphic computation  do not permit the necessary interaction.  The representation of three-dimensional molecular structures with ludic models, built with representative units, have supplied to the students and teachers a successfully experience to  visualize such structures and correlate them to the real molecules.  The design and applicability of the representative units were discussed with researchers and teachers before mould implementation.  In this stage  it  will be presented the  developed  kit  containing the  representative  plastic parts of the main amino acids.  The kit can demonstrate the interaction among the amino acids  functional groups  (represented by colors, shapes,  sizes and  the peptidic bonds between them  facilitating the assembly and visuali zation of the primary and secondary protein structure.  The models were designed for  Ca,  amino,  carboxyl groups  and  hydrogen. The  lateral chains have  well defined models that represent their geometrical shape.  The completed kit set  will be presented in this meeting (patent requested.  In the last phase of the project will be realized  an effective evaluation  of the kit  as a facilitative didactic tool of the teaching/learning process in the Structural Molecular Biology area.

  5. A little adjustment of synthetic strategy led to a new highly repeated heteropolyblue: Structure, characterizations and photocatalytic properties

    Science.gov (United States)

    Chen, Wu-Hua; Zhang, Zhu-Sen; Zhao, Jin-Hua; Qiu, Ze-Hai; Yuan, Qiu-Lan; Huang, Tian-Fu; Lin, Xue-Yu; Hu, Zhi-Biao

    2017-06-01

    Hydrothermal synthesis is known as the most efficient method to prepare novel structural polyoxometalate (POM)-based materials, but controlled synthesis of a structure-directing POM is always challenging task. The experimental repeatability is usually one of the key topics. To explore a reliable hydrothermal synthesis approach for new POMs will be a meaningful work. Our previous work, which we have hydrothermally synthesized the first Cr-complexes-capped Keggin-type POM, [Hdma]3[H2phen]{[Cr(phen)]2[MoV8MoVI4O36(PO4)]}·nH2O (n ≈ 2) (Chen et al., polyhedron, 2015, 85, 117), afford us some commendable synthetic experiences, arouse us some introspections as well for its tricky preparation conditions and low experimental repeatability. Based on the aforementioned work, a new high-repetition-rate and more steady heteropolyblue, [H3O]0.5(Hdma)2.5(dma)0.25{[Cr(phen)]2[MoV6MoVI6O8(PO4)]}·2H2O (1) (dma = dimethylamine (C2H7N), phen = 1,10-phenanthroline (C12H8N2)), has been successfully obtained by virtue of reasonably adjusting synthetic strategy. The adjustment of synthetic strategy includes controlling ratio of reactants and aging time, reasonably using redoxes and stepwise self-assembly plans. Compound 1 is the second POM with Keggin-type polyanion capped by Cr-complexes. Experiments demonstrate that compound 1 has good catalytic activity in the both degradation reactions of rhodamine B (RHB) and methyl orange (MO) under ultraviolet (UV)-light and oxidant H2O2 conditions. Detailed structural characterizations include single-crystal X-ray diffraction (XRD) analyses, energy-dispersive X-ray spectrometry (EDS) analyses, elemental analyses, cerate oxidimetry, powder XRD, fourier transform infrared (FT-IR) spectroscopy, ultraviolet-visible-near-infrared (UV-Vis-NIR) solid diffuse reflection spectrum and X-ray photoelectron spectroscopy (XPS) analyses. The electrochemical property (cyclic voltammetry (CV)) of compound 1 has also been studied.

  6. Nuclear Magnetic Resonance Structure of a Novel Globular Domain in RBM10 Containing OCRE, the Octamer Repeat Sequence Motif.

    Science.gov (United States)

    Martin, Bryan T; Serrano, Pedro; Geralt, Michael; Wüthrich, Kurt

    2016-01-01

    The OCtamer REpeat (OCRE) has been annotated as a 42-residue sequence motif with 12 tyrosine residues in the spliceosome trans-regulatory elements RBM5 and RBM10 (RBM [RNA-binding motif]), which are known to regulate alternative splicing of Fas and Bcl-x pre-mRNA transcripts. Nuclear magnetic resonance structure determination showed that the RBM10 OCRE sequence motif is part of a 55-residue globular domain containing 16 aromatic amino acids, which consists of an anti-parallel arrangement of six β strands, with the first five strands containing complete or incomplete Tyr triplets. This OCRE globular domain is a distinctive component of RBM10 and is more widely conserved in RBM10s across the animal kingdom than the ubiquitous RNA recognition components. It is also found in the functionally related RBM5. Thus, it appears that the three-dimensional structure of the globular OCRE domain, rather than the 42-residue OCRE sequence motif alone, confers specificity on RBM10 intermolecular interactions in the spliceosome.

  7. An ancient satellite DNA has maintained repetitive units of the original structure in most species of the living fossil plant genus Zamia.

    Science.gov (United States)

    Cafasso, Donata; Chinali, Gianni

    2014-03-01

    ZpS1 satellite DNA is specific to the genus Zamia and presents repetitive units organized as long arrays and also as very short arrays dispersed in the genome. We have characterized the structure of the ZpS1 repeats in 12 species representative of the whole geographic distribution of the genus. In most species, the clone most common sequences (cMCS) were so similar that a general most common sequence (GMCS) of the ZpS1 repetitive unit in the genus could be obtained. The few partial variations from the GMCS found in cMCS of some species correspond to variable positions present in most other species, as indicated by the clone consensus sequences (cCS). Two species have an additional species-specific variety of ZpS1 satellite. The dispersed repeats were found to contain more mutations than repeats from long arrays. Our results indicate that all or most species of Zamia inherited the ZpS1 satellite from a common ancestor in Miocene and have maintained repetitive units of the original structure till present. The features of ZpS1 satellite in the genus Zamia are poorly compatible with the model of concerted evolution, but they are perfectly consistent with a new model of satellite evolution based on experimental evidences indicating that a specific amplification-substitution repair mechanism maintains the homogeneity and stability of the repeats structure in each satellite DNA originally present in a species as long as the species exists.

  8. Context-Dependent Sensitivity to Mutations Disrupting the Structural Integrity of Individual EGF Repeats in the Mouse Notch Ligand DLL1.

    Science.gov (United States)

    Schuster-Gossler, Karin; Cordes, Ralf; Müller, Julia; Geffers, Insa; Delany-Heiken, Patricia; Taft, Manuel; Preller, Matthias; Gossler, Achim

    2016-03-01

    The highly conserved Notch-signaling pathway mediates cell-to-cell communication and is pivotal for multiple developmental processes and tissue homeostasis in adult organisms. Notch receptors and their ligands are transmembrane proteins with multiple epidermal-growth-factor-like (EGF) repeats in their extracellular domains. In vitro the EGF repeats of mammalian ligands that are essential for Notch activation have been defined. However, in vivo the significance of the structural integrity of each EGF repeat in the ligand ectodomain for ligand function is still unclear. Here, we analyzed the mouse Notch ligand DLL1. We expressed DLL1 proteins with mutations disrupting disulfide bridges in each individual EGF repeat from single-copy transgenes in the HPRT locus of embryonic stem cells. In Notch transactivation assays all mutations impinged on DLL1 function and affected both NOTCH1 and NOTCH2 receptors similarly. An allelic series in mice that carried the same point mutations in endogenous Dll1, generated using a mini-gene strategy, showed that early developmental processes depending on DLL1-mediated NOTCH activation were differently sensitive to mutation of individual EGF repeats in DLL1. Notably, some mutations affected only somite patterning and resulted in vertebral column defects resembling spondylocostal dysostosis. In conclusion, the structural integrity of each individual EGF repeat in the extracellular domain of DLL1 is necessary for full DLL1 activity, and certain mutations in Dll1 might contribute to spondylocostal dysostosis in humans.

  9. Malfunction analysis of OPGW of stainless steel-unit structure

    Institute of Scientific and Technical Information of China (English)

    李星梅; 张素芳; 王旭锋; 乞建勋

    2008-01-01

    Composite fiber optic overhead ground wire (OPGW) is increasingly applied in China’s overhead transmission lines. The stainless steel structure is adopted by most OPGWs as it is very small and easy to match the existing ground wire. The malfunction of OPGW in Beijing-Shanghai Optical Communication Project was analyzed through the chemical composition method and spectrum semi-quantitative method. The analysis indicates that the cable fault was due to the failure of seepage and irregular holes in the steel pipe of the optical unit. The rain water and the watery air entered into the optical units, and the water in turn became ice when temperature dropped. The occurrence of ice led to the acceleration of attenuation of the fiber. The results show that the rupture of stainless steel tube is mainly due to the instability of welding technique. The malfunction of OPGW is due to the local defects of welding seam because of local stress concentration in the manufacturing process.

  10. Tree diversity, composition, forest structure and aboveground biomass dynamics after single and repeated fire in a Bornean rain forest.

    Science.gov (United States)

    Slik, J W Ferry; Bernard, Caroline S; Van Beek, Marloes; Breman, Floris C; Eichhorn, Karl A O

    2008-12-01

    Forest fires remain a devastating phenomenon in the tropics that not only affect forest structure and biodiversity, but also contribute significantly to atmospheric CO2. Fire used to be extremely rare in tropical forests, leaving ample time for forests to regenerate to pre-fire conditions. In recent decades, however, tropical forest fires occur more frequently and at larger spatial scales than they used to. We studied forest structure, tree species diversity, tree species composition, and aboveground biomass during the first 7 years since fire in unburned, once burned and twice burned forest of eastern Borneo to determine the rate of recovery of these forests. We paid special attention to changes in the tree species composition during burned forest regeneration because we expect the long-term recovery of aboveground biomass and ecosystem functions in burned forests to largely depend on the successful regeneration of the pre-fire, heavy-wood, species composition. We found that forest structure (canopy openness, leaf area index, herb cover, and stem density) is strongly affected by fire but shows quick recovery. However, species composition shows no or limited recovery and aboveground biomass, which is greatly reduced by fire, continues to be low or decline up to 7 years after fire. Consequently, large amounts of the C released to the atmosphere by fire will not be recaptured by the burned forest ecosystem in the near future. We also observed that repeated fire, with an inter-fire interval of 15 years, does not necessarily lead to a huge deterioration in the regeneration potential of tropical forest. We conclude that burned forests are valuable and should be conserved and that long-term monitoring programs in secondary forests are necessary to determine their recovery rates, especially in relation to aboveground biomass accumulation.

  11. Streptococcus salivarius Fimbriae Are Composed of a Glycoprotein Containing a Repeated Motif Assembled into a Filamentous Nondissociable Structure

    Science.gov (United States)

    Lévesque, Céline; Vadeboncoeur, Christian; Chandad, Fatiha; Frenette, Michel

    2001-01-01

    Streptococcus salivarius, a gram-positive bacterium found in the human oral cavity, expresses flexible peritrichous fimbriae. In this paper, we report purification and partial characterization of S. salivarius fimbriae. Fimbriae were extracted by shearing the cell surface of hyperfimbriated mutant A37 (a spontaneous mutant of S. salivarius ATCC 25975) with glass beads. Preliminary experiments showed that S. salivarius fimbriae did not dissociate when they were incubated at 100°C in the presence of sodium dodecyl sulfate. This characteristic was used to separate them from other cell surface components by successive gel filtration chromatography procedures. Fimbriae with molecular masses ranging from 20 × 106 to 40 × 106 Da were purified. Examination of purified fimbriae by electron microscopy revealed the presence of filamentous structures up to 1 μm long and 3 to 4 nm in diameter. Biochemical studies of purified fimbriae and an amino acid sequence analysis of a fimbrial internal peptide revealed that S. salivarius fimbriae were composed of a glycoprotein assembled into a filamentous structure resistant to dissociation. The internal amino acid sequence was composed of a repeated motif of two amino acids alternating with two modified residues: A/X/T-E-Q-M/φ, where X represents a modified amino acid residue and φ represents a blank cycle. Immunolocalization experiments also revealed that the fimbriae were associated with a wheat germ agglutinin-reactive carbohydrate. Immunolabeling experiments with antifimbria polyclonal antibodies showed that antigenically related fimbria-like structures were expressed in two other human oral streptococcal species, Streptococcus mitis and Streptococcus constellatus. PMID:11292790

  12. The Vertebrate Brain, Evidence of Its Modular Organization and Operating System: Insights into the Brain's Basic Units of Structure, Function, and Operation and How They Influence Neuronal Signaling and Behavior.

    Science.gov (United States)

    Baslow, Morris H

    2011-01-01

    The human brain is a complex organ made up of neurons and several other cell types, and whose role is processing information for use in eliciting behaviors. However, the composition of its repeating cellular units for both structure and function are unresolved. Based on recent descriptions of the brain's physiological "operating system", a function of the tri-cellular metabolism of N-acetylaspartate (NAA) and N-acetylaspartylglutamate (NAAG) for supply of energy, and on the nature of "neuronal words and languages" for intercellular communication, insights into the brain's modular structural and functional units have been gained. In this article, it is proposed that the basic structural unit in brain is defined by its physiological operating system, and that it consists of a single neuron, and one or more astrocytes, oligodendrocytes, and vascular system endothelial cells. It is also proposed that the basic functional unit in the brain is defined by how neurons communicate, and consists of two neurons and their interconnecting dendritic-synaptic-dendritic field. Since a functional unit is composed of two neurons, it requires two structural units to form a functional unit. Thus, the brain can be envisioned as being made up of the three-dimensional stacking and intertwining of myriad structural units which results not only in its gross structure, but also in producing a uniform distribution of binary functional units. Since the physiological NAA-NAAG operating system for supply of energy is repeated in every structural unit, it is positioned to control global brain function.

  13. Variability of United States isolates of Macrophomina phaseolina based on simple sequence repeats and cross genus transferability to related genera within botryosphaeriaceae.

    Science.gov (United States)

    Baird, Richard E; Wadl, Phillip A; Allen, Thomas; McNeill, David; Wang, Xinwang; Moulton, John K; Rinehart, Timothy A; Abbas, Hamed K; Shier, Thomas; Trigiano, Robert N

    2010-09-01

    Twelve simple sequence repeat (SSRs) loci were used to evaluate genetic diversity of 109 isolates of Macrophomina phaseolina collected from different geographical regions and host species throughout the United States (US). Genetic diversity was assessed using Nei's minimum genetic distance, and the usefulness of each locus was determined by calculating the polymorphism information content (PIC). A total of 98 alleles were detected and of these 31 were unique to individual genotypes. Eight of twelve loci were highly informative with PIC values greater than 0.50. The majority of pairwise comparisons of genetic distance were greater than 0.60 indicating moderate to high genetic diversity. Dendrograms based on the genetic dissimilarities were created for the 109 isolates of which 79 were from soybean. Some clustering by host and geography was noted, but, the dendrograms generally grouped isolates independent of host or geography. Additionally, sequencing of the internal transcribed spacer region (ITS) for 10 isolates revealed that all of these isolates were 99% similar. Three SSR loci from M. phaseolina were cross amplified in other genera in the Botryosphaeriaceae. This was the first study of genotyping and assessing genetic diversity of M. phaseolina isolates collected from a widespread host and geographic range across the US with SSRs. With an additional 34 loci publically available for M. phaseolina, the results indicate that previously developed SSRs from one species can be used in future population, ecological, and genetic studies of M. phaseolina and other genera within the Botryosphaeriaceae.

  14. Crystal structure of the Xpo1p nuclear export complex bound to the SxFG/PxFG repeats of the nucleoporin Nup42p.

    Science.gov (United States)

    Koyama, Masako; Hirano, Hidemi; Shirai, Natsuki; Matsuura, Yoshiyuki

    2017-08-08

    Xpo1p (yeast CRM1) is the major nuclear export receptor that carries a plethora of proteins and ribonucleoproteins from the nucleus to cytoplasm. The passage of the Xpo1p nuclear export complex through nuclear pore complexes (NPCs) is facilitated by interactions with nucleoporins (Nups) containing extensive repeats of phenylalanine-glycine (so-called FG repeats), although the precise role of each Nup in the nuclear export reaction remains incompletely understood. Here we report structural and biochemical characterization of the interactions between the Xpo1p nuclear export complex and the FG repeats of Nup42p, a nucleoporin localized at the cytoplasmic face of yeast NPCs and has characteristic SxFG/PxFG sequence repeat motif. The crystal structure of Xpo1p-PKI-Nup42p-Gsp1p-GTP complex identified three binding sites for the SxFG/PxFG repeats on HEAT repeats 14-20 of Xpo1p. Mutational analyses of Nup42p showed that the conserved serines and prolines in the SxFG/PxFG repeats contribute to Xpo1p-Nup42p binding. Our structural and biochemical data suggest that SxFG/PxFG-Nups such as Nup42p and Nup159p at the cytoplasmic face of NPCs provide high-affinity docking sites for the Xpo1p nuclear export complex in the terminal stage of NPC passage and that subsequent disassembly of the nuclear export complex facilitates recycling of free Xpo1p back to the nucleus. © 2017 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.

  15. Exons I and VII of the gene (Ker10) encoding human keratin 10 undergo structural rearrangements within repeats.

    Science.gov (United States)

    Tkachenko, A V; Buchman, V L; Bliskovsky, V V; Shvets YuP; Kisselev, L L

    1992-07-15

    A genomic fragment containing the K51 gene previously isolated from a rat genomic library by hybridization with the v-mos probe in nonstringent conditions [Chumakov et al., Dokl. Akad. Nauk SSSR 290 (1986) 1252-1254], resembles a human keratin type-I-encoding gene [Shvets et al., Mol. Biol. 24 (1990) 663-677]. This genomic clone, K51, has been used as a probe to search for related human genes. A recombinant clone, HK51, with a 1.5-kb insert, was isolated from a human embryonic skin cDNA library, and its nucleotide (nt) sequence was determined. Analysis has shown that the cloned cDNA encodes human keratin 10 (Ker10). All presently known nt sequences of the human Ker10-encoding gene (Ker10) are not identical. Differences are concentrated in the 5'-end of the first exon and in the middle of the seventh exon within repeats. In spite of structural rearrangements in two of eight exons, the reading frame and position of the stop codon are preserved. The genetic rearrangements cause changes in hydrophobicity profiles of the N and C termini of Ker10. It was also noticed that insertion of one nt leads to the formation of an unusual 3'-end of the transcript.

  16. Evaluation of Population Structure, Genetic Diversity and Origin of Northeast Asia Weedy Rice Based on Simple Sequence Repeat Markers

    Directory of Open Access Journals (Sweden)

    Li Mao-bai

    2015-07-01

    Full Text Available Weedy rice exerts a severe impact on rice production by competing for sunlight, water and nutrients. This study assayed the population structure, genetic diversity and origin of Northeast Asia weedy rice by using 48 simple sequence repeat markers. The results showed that weedy rice in Northeast Asia had a high genetic diversity, with Shannon's diversity index (I of 0.748 and the heterozygosity (He of 0.434. In each regional population, I value varied widely. The widest range of I (0.228–0.489 was observed in the weedy rice of Eastern China, which was larger than that of Northeast China and Korea (0.168–0.270. The F-statistics of regional populations (Fis, Fit and Fst also showed higher values in the weedy rice of Eastern China than those of Northeast China and Korea. All weedy rice accessions were grouped into two clusters in the unweighted pair group method with arithmetic mean cluster analysis dendrogram, namely Eastern China branch and Northeastern China plus Korea branch. There was significant differentiation in genetic characteristics in weedy rice of northeastern and eastern Asia, especially in Eastern China.

  17. Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 2. Teaching Units that Utilize an Interactive Web-Accessible Subset of the Cambridge Structural Database

    Science.gov (United States)

    Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

    2010-01-01

    A series of online interactive teaching units have been developed that illustrate the use of experimentally measured three-dimensional (3D) structures to teach fundamental chemistry concepts. The units integrate a 500-structure subset of the Cambridge Structural Database specially chosen for their pedagogical value. The units span a number of key…

  18. Clustering of Tuberculosis Cases Based on Variable-Number Tandem-Repeat Typing in Relation to the Population Structure of Mycobacterium tuberculosis in the Netherlands

    NARCIS (Netherlands)

    Sloot, R.; Borgdorff, M.W.; Beer, J.L. de; Ingen, J. van; Supply, P.; Soolingen, D. van

    2013-01-01

    The population structure of 3,776 Mycobacterium tuberculosis isolates was determined using variable-number tandem-repeat (VNTR) typing. The degree of clonality was so high that a more relaxed definition of clustering cannot be applied. Among recent immigrants with non-Euro-American isolates, transmi

  19. The Effect of Repeated Listenings on Ability to Recognize the Structural Elements of Music and the Influence of this Ability on Affective Shift. Final Report.

    Science.gov (United States)

    Bartlett, Dale L.

    This study, conducted over a period of three weeks at the University of Kansas, attempted to determine whether knowledge of musical structure would effect greater understanding and, eventually, enjoyment of music. Experimental and control groups comprising freshmen who were not enrolled in a music course listened repeatedly to excerpts of…

  20. Accelerating VASP electronic structure calculations using graphic processing units

    KAUST Repository

    Hacene, Mohamed

    2012-08-20

    We present a way to improve the performance of the electronic structure Vienna Ab initio Simulation Package (VASP) program. We show that high-performance computers equipped with graphics processing units (GPUs) as accelerators may reduce drastically the computation time when offloading these sections to the graphic chips. The procedure consists of (i) profiling the performance of the code to isolate the time-consuming parts, (ii) rewriting these so that the algorithms become better-suited for the chosen graphic accelerator, and (iii) optimizing memory traffic between the host computer and the GPU accelerator. We chose to accelerate VASP with NVIDIA GPU using CUDA. We compare the GPU and original versions of VASP by evaluating the Davidson and RMM-DIIS algorithms on chemical systems of up to 1100 atoms. In these tests, the total time is reduced by a factor between 3 and 8 when running on n (CPU core + GPU) compared to n CPU cores only, without any accuracy loss. © 2012 Wiley Periodicals, Inc.

  1. Structure, organization, and sequence of alpha satellite DNA from human chromosome 17: evidence for evolution by unequal crossing-over and an ancestral pentamer repeat shared with the human X chromosome.

    Science.gov (United States)

    Waye, J S; Willard, H F

    1986-09-01

    The centromeric regions of all human chromosomes are characterized by distinct subsets of a diverse tandemly repeated DNA family, alpha satellite. On human chromosome 17, the predominant form of alpha satellite is a 2.7-kilobase-pair higher-order repeat unit consisting of 16 alphoid monomers. We present the complete nucleotide sequence of the 16-monomer repeat, which is present in 500 to 1,000 copies per chromosome 17, as well as that of a less abundant 15-monomer repeat, also from chromosome 17. These repeat units were approximately 98% identical in sequence, differing by the exclusion of precisely 1 monomer from the 15-monomer repeat. Homologous unequal crossing-over is suggested as a probable mechanism by which the different repeat lengths on chromosome 17 were generated, and the putative site of such a recombination event is identified. The monomer organization of the chromosome 17 higher-order repeat unit is based, in part, on tandemly repeated pentamers. A similar pentameric suborganization has been previously demonstrated for alpha satellite of the human X chromosome. Despite the organizational similarities, substantial sequence divergence distinguishes these subsets. Hybridization experiments indicate that the chromosome 17 and X subsets are more similar to each other than to the subsets found on several other human chromosomes. We suggest that the chromosome 17 and X alpha satellite subsets may be related components of a larger alphoid subfamily which have evolved from a common ancestral repeat into the contemporary chromosome-specific subsets.

  2. A structural model for binding of the serine-rich repeat adhesin GspB to host carbohydrate receptors.

    Directory of Open Access Journals (Sweden)

    Tasia M Pyburn

    2011-07-01

    Full Text Available GspB is a serine-rich repeat (SRR adhesin of Streptococcus gordonii that mediates binding of this organism to human platelets via its interaction with sialyl-T antigen on the receptor GPIbα. This interaction appears to be a major virulence determinant in the pathogenesis of infective endocarditis. To address the mechanism by which GspB recognizes its carbohydrate ligand, we determined the high-resolution x-ray crystal structure of the GspB binding region (GspB(BR, both alone and in complex with a disaccharide precursor to sialyl-T antigen. Analysis of the GspB(BR structure revealed that it is comprised of three independently folded subdomains or modules: 1 an Ig-fold resembling a CnaA domain from prokaryotic pathogens; 2 a second Ig-fold resembling the binding region of mammalian Siglecs; 3 a subdomain of unique fold. The disaccharide was found to bind in a pocket within the Siglec subdomain, but at a site distinct from that observed in mammalian Siglecs. Confirming the biological relevance of this binding pocket, we produced three isogenic variants of S. gordonii, each containing a single point mutation of a residue lining this binding pocket. These variants have reduced binding to carbohydrates of GPIbα. Further examination of purified GspB(BR-R484E showed reduced binding to sialyl-T antigen while S. gordonii harboring this mutation did not efficiently bind platelets and showed a significant reduction in virulence, as measured by an animal model of endocarditis. Analysis of other SRR proteins revealed that the predicted binding regions of these adhesins also had a modular organization, with those known to bind carbohydrate receptors having modules homologous to the Siglec and Unique subdomains of GspB(BR. This suggests that the binding specificity of the SRR family of adhesins is determined by the type and organization of discrete modules within the binding domains, which may affect the tropism of organisms for different tissues.

  3. A Structural Model for Binding of the Serine-Rich Repeat Adhesin GspB to Host Carbohydrate Receptors

    Energy Technology Data Exchange (ETDEWEB)

    Pyburn, Tasia M.; Bensing, Barbara A.; Xiong, Yan Q.; Melancon, Bruce J.; Tomasiak, Thomas M.; Ward, Nicholas J.; Yankovskaya, Victoria; Oliver, Kevin M.; Cecchini, Gary; Sulikowski, Gary A.; Tyska, Matthew J.; Sullam, Paul M.; Iverson, T.M. (VA); (UCLA); (Vanderbilt); (UCSF)

    2014-10-02

    GspB is a serine-rich repeat (SRR) adhesin of Streptococcus gordonii that mediates binding of this organism to human platelets via its interaction with sialyl-T antigen on the receptor GPIb{alpha}. This interaction appears to be a major virulence determinant in the pathogenesis of infective endocarditis. To address the mechanism by which GspB recognizes its carbohydrate ligand, we determined the high-resolution x-ray crystal structure of the GspB binding region (GspB{sub BR}), both alone and in complex with a disaccharide precursor to sialyl-T antigen. Analysis of the GspB{sub BR} structure revealed that it is comprised of three independently folded subdomains or modules: (1) an Ig-fold resembling a CnaA domain from prokaryotic pathogens; (2) a second Ig-fold resembling the binding region of mammalian Siglecs; (3) a subdomain of unique fold. The disaccharide was found to bind in a pocket within the Siglec subdomain, but at a site distinct from that observed in mammalian Siglecs. Confirming the biological relevance of this binding pocket, we produced three isogenic variants of S. gordonii, each containing a single point mutation of a residue lining this binding pocket. These variants have reduced binding to carbohydrates of GPIb{alpha}. Further examination of purified GspB{sub BR}-R484E showed reduced binding to sialyl-T antigen while S. gordonii harboring this mutation did not efficiently bind platelets and showed a significant reduction in virulence, as measured by an animal model of endocarditis. Analysis of other SRR proteins revealed that the predicted binding regions of these adhesins also had a modular organization, with those known to bind carbohydrate receptors having modules homologous to the Siglec and Unique subdomains of GspBBR. This suggests that the binding specificity of the SRR family of adhesins is determined by the type and organization of discrete modules within the binding domains, which may affect the tropism of organisms for different tissues.

  4. Exploring the repeat protein universe through computational protein design.

    Science.gov (United States)

    Brunette, T J; Parmeggiani, Fabio; Huang, Po-Ssu; Bhabha, Gira; Ekiert, Damian C; Tsutakawa, Susan E; Hura, Greg L; Tainer, John A; Baker, David

    2015-12-24

    A central question in protein evolution is the extent to which naturally occurring proteins sample the space of folded structures accessible to the polypeptide chain. Repeat proteins composed of multiple tandem copies of a modular structure unit are widespread in nature and have critical roles in molecular recognition, signalling, and other essential biological processes. Naturally occurring repeat proteins have been re-engineered for molecular recognition and modular scaffolding applications. Here we use computational protein design to investigate the space of folded structures that can be generated by tandem repeating a simple helix-loop-helix-loop structural motif. Eighty-three designs with sequences unrelated to known repeat proteins were experimentally characterized. Of these, 53 are monomeric and stable at 95 °C, and 43 have solution X-ray scattering spectra consistent with the design models. Crystal structures of 15 designs spanning a broad range of curvatures are in close agreement with the design models with root mean square deviations ranging from 0.7 to 2.5 Å. Our results show that existing repeat proteins occupy only a small fraction of the possible repeat protein sequence and structure space and that it is possible to design novel repeat proteins with precisely specified geometries, opening up a wide array of new possibilities for biomolecular engineering.

  5. The 1.7 Å resolution structure of At2g44920, a pentapeptide-repeat protein in the thylakoid lumen of Arabidopsis thaliana

    Energy Technology Data Exchange (ETDEWEB)

    Ni, Shuisong; McGookey, Michael E.; Tinch, Stuart L.; Jones, Alisha N.; Jayaraman, Seetharaman; Tong, Liang; Kennedy, Michael A. (Miami U); (Columbia)

    2012-01-09

    At2g44920 belongs to a diverse family (Pfam PF00805) of pentapeptide-repeat proteins (PRPs) that are present in all known organisms except yeast. PRPs contain at least eight tandem-repeating sequences of five amino acids with an approximate consensus sequence (STAV)(D/N)(L/F)(S/T/R)(X). Recent crystal structures show that PRPs adopt a highly regular four-sided right-handed {beta}-helical structure consisting mainly of type II and type IV {beta}-turns, sometimes referred to as a repeated five-residue (or Rfr) fold. Among sequenced genomes, PRP genes are most abundant in cyanobacteria, leading to speculation that PRPs play an important role in the unique lifestyle of photosynthetic cyanobacteria. Despite the recent structural characterization of several cyanobacterial PRPs, most of their functions remain unknown. Plants, whose chloroplasts are of cyanobacterial origin, have only four PRP genes in their genomes. At2g44920 is one of three PRPs located in the thylakoid lumen. Here, the crystal structure of a double methionine mutant of residues 81-224 of At2g44920, the naturally processed fragment of one of its full-length isoforms, is reported at 1.7 {angstrom} resolution. The structure of At2g44920 consists of the characteristic Rfr fold with five uninterrupted coils made up of 25 pentapeptide repeats and {alpha}-helical elements capping both termini. A disulfide bridge links the two {alpha}-helices with a conserved loop between the helical elements at its C-terminus. This structure represents the first structure of a PRP protein whose subcellular location has been experimentally confirmed to be the thylakoid lumen in a plant species.

  6. TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences

    Directory of Open Access Journals (Sweden)

    Söding Johannes

    2007-01-01

    Full Text Available Abstract Background Solenoid repeat proteins of the Tetratrico Peptide Repeat (TPR family are involved as scaffolds in a broad range of protein-protein interactions. Several resources are available for the prediction of TPRs, however, they often fail to detect divergent repeat units. Results We have developed TPRpred, a profile-based method which uses a P-value-dependent score offset to include divergent repeat units and which exploits the tendency of repeats to occur in tandem. TPRpred detects not only TPR-like repeats, but also the related Pentatrico Peptide Repeats (PPRs and SEL1-like repeats. The corresponding profiles were generated through iterative searches, by varying the threshold parameters for inclusion of repeat units into the profiles, and the best profiles were selected based on their performance on proteins of known structure. We benchmarked the performance of TPRpred in detecting TPR-containing proteins and in delineating the individual repeats therein, against currently available resources. Conclusion TPRpred performs significantly better in detecting divergent repeats in TPR-containing proteins, and finds more individual repeats than the existing methods. The web server is available at http://tprpred.tuebingen.mpg.de, and the C++ and Perl sources of TPRpred along with the profiles can be downloaded from ftp://ftp.tuebingen.mpg.de/ebio/protevo/TPRpred/.

  7. Effects of Repeated Growing Season Prescribed Fire on the Structure and Composition of Pine–Hardwood Forests in the Southeastern Piedmont, USA

    Directory of Open Access Journals (Sweden)

    Matthew J. Reilly

    2016-12-01

    Full Text Available We examined the effects of repeated growing season prescribed fire on the structure and composition of mixed pine–hardwood forests in the southeastern Piedmont region, Georgia, USA. Plots were burned two to four times over an eight-year period with low intensity surface fires during one of four six-week long periods from early April to mid-September. Density of saplings (0.25–11.6 cm diameter at breast height was significantly reduced after one or two fires during the first four-year period. Sapling density declined with additional burning over the next four years, but density of mesic hardwoods including sweetgum (Liquidambar styraciflua and red maple (Acer rubrum remained relatively high (~865 stems ha−1. Repeated burning had little effect on density or basal area of trees (≥11.7 cm dbh and changes in overstory structure were limited to small increases in the quadratic mean diameter of all trees and pines. We found little evidence to suggest differential effects on structure or composition due to timing of burn within the growing season. Although repeated growing season burning alters midstory structure and composition, burning alone is unlikely to result in immediate shifts in overstory composition or structure in mixed pine–hardwood forests of the southeastern Piedmont region.

  8. Deployment Repeatability

    Science.gov (United States)

    2016-04-01

    controlled to great precision, but in a Cubesat , there may be no attitude determination at all. Such a Cubesat might treat sun angle and tumbling rates as...could be sensitive to small differences in motor controller timing. In these cases, the analyst might choose to model the entire deployment path, with...knowledge of the material damage model or motor controller timing precision. On the other hand, if many repeated and environmentally representative

  9. A formalism for scattering of complex composite structures. I. Applications to branched structures of asymmetric sub-units.

    Science.gov (United States)

    Svaneborg, Carsten; Pedersen, Jan Skov

    2012-03-14

    We present a formalism for the scattering of an arbitrary linear or acyclic branched structure build by joining mutually non-interacting arbitrary functional sub-units. The formalism consists of three equations expressing the structural scattering in terms of three equations expressing the sub-unit scattering. The structural scattering expressions allow composite structures to be used as sub-units within the formalism itself. This allows the scattering expressions for complex hierarchical structures to be derived with great ease. The formalism is generic in the sense that the scattering due to structural connectivity is completely decoupled from internal structure of the sub-units. This allows sub-units to be replaced by more complex structures. We illustrate the physical interpretation of the formalism diagrammatically. By applying a self-consistency requirement, we derive the pair distributions of an ideal flexible polymer sub-unit. We illustrate the formalism by deriving generic scattering expressions for branched structures such as stars, pom-poms, bottle-brushes, and dendrimers build out of asymmetric two-functional sub-units.

  10. An all-atom model of the chromatin fiber containing linker histones reveals a versatile structure tuned by the nucleosomal repeat length.

    Directory of Open Access Journals (Sweden)

    Hua Wong

    Full Text Available In the nucleus of eukaryotic cells, histone proteins organize the linear genome into a functional and hierarchical architecture. In this paper, we use the crystal structures of the nucleosome core particle, B-DNA and the globular domain of H5 linker histone to build the first all-atom model of compact chromatin fibers. In this 3D jigsaw puzzle, DNA bending is achieved by solving an inverse kinematics problem. Our model is based on recent electron microscopy measurements of reconstituted fiber dimensions. Strikingly, we find that the chromatin fiber containing linker histones is a polymorphic structure. We show that different fiber conformations are obtained by tuning the linker histone orientation at the nucleosomes entry/exit according to the nucleosomal repeat length. We propose that the observed in vivo quantization of nucleosomal repeat length could reflect nature's ability to use the DNA molecule's helical geometry in order to give chromatin versatile topological and mechanical properties.

  11. Structural Insights Reveal the Dynamics of the Repeating r(CAG) Transcript Found in Huntington's Disease (HD) and Spinocerebellar Ataxias (SCAs).

    Science.gov (United States)

    Tawani, Arpita; Kumar, Amit

    2015-01-01

    In humans, neurodegenerative disorders such as Huntington's disease (HD) and many spinocerebellar ataxias (SCAs) have been found to be associated with CAG trinucleotide repeat expansion. An important RNA-mediated mechanism that causes these diseases involves the binding of the splicing regulator protein MBNL1 (Muscleblind-like 1 protein) to expanded r(CAG) repeats. Moreover, mutant huntingtin protein translated from expanded r(CAG) also yields toxic effects. To discern the role of mutant RNA in these diseases, it is essential to gather information about its structure. Detailed insight into the different structures and conformations adopted by these mutant transcripts is vital for developing therapeutics targeting them. Here, we report the crystal structure of an RNA model with a r(CAG) motif, which is complemented by an NMR-based solution structure obtained from restrained Molecular Dynamics (rMD) simulation studies. Crystal structure data of the RNA model resolved at 2.3 Å reveals non-canonical pairing of adenine in 5´-CAG/3´-GAC motif samples in different syn and anti conformations. The overall RNA structure has helical parameters intermediate to the A- and B-forms of nucleic acids due to the global widening of major grooves and base-pair preferences near internal AA loops. The comprehension of structural behaviour by studying the spectral features and the dynamics also supports the flexible nature of the r(CAG) motif.

  12. Structural Insights Reveal the Dynamics of the Repeating r(CAG Transcript Found in Huntington's Disease (HD and Spinocerebellar Ataxias (SCAs.

    Directory of Open Access Journals (Sweden)

    Arpita Tawani

    Full Text Available In humans, neurodegenerative disorders such as Huntington's disease (HD and many spinocerebellar ataxias (SCAs have been found to be associated with CAG trinucleotide repeat expansion. An important RNA-mediated mechanism that causes these diseases involves the binding of the splicing regulator protein MBNL1 (Muscleblind-like 1 protein to expanded r(CAG repeats. Moreover, mutant huntingtin protein translated from expanded r(CAG also yields toxic effects. To discern the role of mutant RNA in these diseases, it is essential to gather information about its structure. Detailed insight into the different structures and conformations adopted by these mutant transcripts is vital for developing therapeutics targeting them. Here, we report the crystal structure of an RNA model with a r(CAG motif, which is complemented by an NMR-based solution structure obtained from restrained Molecular Dynamics (rMD simulation studies. Crystal structure data of the RNA model resolved at 2.3 Å reveals non-canonical pairing of adenine in 5´-CAG/3´-GAC motif samples in different syn and anti conformations. The overall RNA structure has helical parameters intermediate to the A- and B-forms of nucleic acids due to the global widening of major grooves and base-pair preferences near internal AA loops. The comprehension of structural behaviour by studying the spectral features and the dynamics also supports the flexible nature of the r(CAG motif.

  13. The Pentapeptide Repeat Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Vetting,M.; Hegde, S.; Fajardo, J.; Fiser, A.; Roderick, S.; Takiff, H.; Blanchard, J.

    2006-01-01

    The Pentapeptide Repeat Protein (PRP) family has over 500 members in the prokaryotic and eukaryotic kingdoms. These proteins are composed of, or contain domains composed of, tandemly repeated amino acid sequences with a consensus sequence of [S, T,A, V][D, N][L, F]-[S, T,R][G]. The biochemical function of the vast majority of PRP family members is unknown. The three-dimensional structure of the first member of the PRP family was determined for the fluoroquinolone resistance protein (MfpA) from Mycobacterium tuberculosis. The structure revealed that the pentapeptide repeats encode the folding of a novel right-handed quadrilateral {beta}-helix. MfpA binds to DNA gyrase and inhibits its activity. The rod-shaped, dimeric protein exhibits remarkable size, shape and electrostatic similarity to DNA.

  14. Debris Control at Hydraulic Structures in Selected Areas of the United States and Europe

    Science.gov (United States)

    2007-11-02

    Selected Areas of the United States and Europe by N. Wallerstein , C. R. Thome, University of Nottingham S. R. Abt, Colorado State University Approved...December 1997 Debris Control at Hydraulic Structures in Selected Areas of the United States and Europe by N. Wallerstein , C. R. Thome Department... Wallerstein , N. Debris control at hydraulic structures in selected areas of the United States and Europe / by N. Wallerstein , C.R. Thome, S.R. Abt

  15. Units of analysis and kinetic structure of behavioral repertoires.

    Science.gov (United States)

    Thompson, T; Lubinski, D

    1986-09-01

    It is suggested that molar streams of behavior are constructed of various arrangements of three elementary constituents (elicited, evoked, and emitted response classes). An eight-cell taxonomy is elaborated as a framework for analyzing and synthesizing complex behavioral repertoires based on these functional units. It is proposed that the local force binding functional units into a smoothly articulated kinetic sequence arises from temporally arranged relative response probability relationships. Behavioral integration is thought to reflect the joint influence of the organism's hierarchy of relative response probabilities, fluctuating biological states, and the arrangement of environmental and behavioral events in time.

  16. Complex repeat structures and novel features in the mitochondrial genomes of the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana.

    Science.gov (United States)

    Oudot-Le Secq, Marie-Pierre; Green, Beverley R

    2011-05-01

    The mitochondrial genome of the raphid pennate diatom Phaeodactylum tricornutum has several novel features compared with the mitochondrial genomes of the centric diatom Thalassiosira pseudonana and the araphid pennate diatom Synedra acus. It is almost double the size (77,356 bp) due to a 35,454 bp sequence block consisting of an elaborate combination of direct repeats, making it the largest stramenopile (heterokont) mitochondrial genome known. In addition, the cox1 gene has a +1 translational frameshift involving Pro codons CCC and CCT, the first translational frameshift to be detected in an algal mitochondrial genome. The nad9 and rps14 genes are fused by the insertion of an in-frame sequence and cotranscribed. The nad11 gene is split into two parts corresponding to the FeS and molybdate-binding domains, but both parts are still on the mitochondrial genome, in contrast to the brown algae where the second domain appears to have been transferred to the nucleus. In contrast to P. tricornutum, the repeat region of T. pseudonana consists of a much smaller 4790 bp string of almost identical double-hairpin elements, evidence of slipped-strand mispairing and active gene conversion. The diatom mitochondrial genomes have undergone considerable gene rearrangement since the three lineages of diatoms diverged, but all three have kept their repeat regions segregated from their relatively compact coding regions.

  17. Decentralized University Budgeting, United with a More Flexible Tuition Structure

    Science.gov (United States)

    Fethke, Gary

    2014-01-01

    With tuition revenues replacing state appropriations as the primary source of public university funding, it becomes difficult for universities to use historically based budget allocations and inflexible tuition structures to subsidize high-cost programs. It is argued here that combining targeted subsidies with a flexible tuition structure and…

  18. Large-scale analysis of structural, sequence and thermodynamic characteristics of A-to-I RNA editing sites in human Alu repeats

    Directory of Open Access Journals (Sweden)

    Eisenberg Eli

    2010-07-01

    Full Text Available Abstract Background Alu repeats in the human transcriptome undergo massive adenosine to inosine RNA editing. This process is selective, as editing efficiency varies greatly among different adenosines. Several studies have identified weak sequence motifs characterizing the editing sites, but these alone do not account for the large diversity observed. Results Here we build a dataset of 29,971 editing sites and use it to characterize editing preferences. We focus on structural aspects, studying the double-stranded RNA structure of the Alu repeats, and show the editing frequency of a given site to depend strongly on the micro-structure it resides in. Surprisingly, we find that interior loops, and especially the nucleotides at their edges, are more likely to be edited than helices. In addition, the sequence motifs characterizing editing sites vary with the micro-structure. Finally, we show that thermodynamic stability of the site is important for its editing. Conclusions Analysis of a large dataset of editing events reveals more information on sequence and structural motifs characterizing the A-to-I editing process

  19. Electronic structure calculations of ESR parameters of melanin units.

    Science.gov (United States)

    Batagin-Neto, Augusto; Bronze-Uhle, Erika Soares; Graeff, Carlos Frederico de Oliveira

    2015-03-21

    Melanins represent an important class of natural pigments present in plants and animals that are currently considered to be promising materials for applications in optic and electronic devices. Despite their interesting properties, some of the basic features of melanins are not satisfactorily understood, including the origin of their intrinsic paramagnetism. A number of experiments have been performed to investigate the electron spin resonance (ESR) response of melanin derivatives, but until now, there has been no consensus regarding the real structure of the paramagnetic centers involved. In this work, we have employed electronic structure calculations to evaluate the ESR parameters of distinct melanin monomers and dimers in order to identify the possible structures associated with unpaired spins in this biopolymer. The g-factors and hyperfine constants of the cationic, anionic and radicalar structures were investigated. The results confirm the existence of at least two distinct paramagnetic centers in melanin structure, identifying the chemical species associated with them and their roles in electrical conductivity.

  20. Protein sectors: evolutionary units of three-dimensional structure

    Science.gov (United States)

    Halabi, Najeeb; Rivoire, Olivier; Leibler, Stanislas; Ranganathan, Rama

    2011-01-01

    Proteins display a hierarchy of structural features at primary, secondary, tertiary, and higher-order levels, an organization that guides our current understanding of their biological properties and evolutionary origins. Here, we reveal a structural organization distinct from this traditional hierarchy by statistical analysis of correlated evolution between amino acids. Applied to the S1A serine proteases, the analysis indicates a decomposition of the protein into three quasi-independent groups of correlated amino acids that we term “protein sectors”. Each sector is physically connected in the tertiary structure, has a distinct functional role, and constitutes an independent mode of sequence divergence in the protein family. Functionally relevant sectors are evident in other protein families as well, suggesting that they may be general features of proteins. We propose that sectors represent a structural organization of proteins that reflects their evolutionary histories. PMID:19703402

  1. Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.

    Science.gov (United States)

    Rehm, Charlotte; Wurmthaler, Lena A; Li, Yuanhao; Frickey, Tancred; Hartig, Jörg S

    2015-01-01

    In prokaryotes simple sequence repeats (SSRs) with unit sizes of 1-5 nucleotides (nt) are causative for phase and antigenic variation. Although an increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs of 6-9 nt are rare. In particular G-rich repeat sequences with the propensity to fold into G-quadruplex (G4) structures have received little attention. In silico analysis of prokaryotic genomes show putative G4 forming sequences to be abundant. This report focuses on a surprisingly enriched G-rich repeat of the type GGGNATC in Xanthomonas and cyanobacteria such as Nostoc. We studied in detail the genomes of Xanthomonas campestris pv. campestris ATCC 33913 (Xcc), Xanthomonas axonopodis pv. citri str. 306 (Xac), and Nostoc sp. strain PCC7120 (Ana). In all three organisms repeats are spread all over the genome with an over-representation in non-coding regions. Extensive variation of the number of repetitive units was observed with repeat numbers ranging from two up to 26 units. However a clear preference for four units was detected. The strong bias for four units coincides with the requirement of four consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus repeat sequences was found in biophysical studies utilizing CD spectroscopy. The G-rich repeats are preferably located between aligned open reading frames (ORFs) and are under-represented in coding regions or between divergent ORFs. The G-rich repeats are preferentially located within a distance of 50 bp upstream of an ORF on the anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis of whole transcriptome sequence data showed that the majority of repeat sequences are transcribed. The genetic loci in the vicinity of repeat regions show increased genomic stability. In conclusion, we introduce and characterize a special class of highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria.

  2. Source parameters of a M4.8 and its accompanying repeating earthquakes off Kamaishi, NE Japan: Implications for the hierarchical structure of asperities and earthquake cycle

    Science.gov (United States)

    Uchida, N.; Matsuzawa, T.; Ellsworth, W.L.; Imanishi, K.; Okada, T.; Hasegawa, A.

    2007-01-01

    We determine the source parameters of a M4.9 ?? 0.1 'characteristic earthquake' sequence and its accompanying microearthquakes at ???50 km depth on the subduction plate boundary offshore of Kamaishi, NE Japan. The microearthquakes tend to occur more frequently in the latter half of the recurrence intervals of the M4.9 ?? 0.1 events. Our results show that the microearthquakes are repeating events and they are located not only around but also within the slip area for the 2001 M4.8 event. From the hierarchical structure of slip areas and smaller stress drops for the microearthquakes compared to the M4.8 event, we infer the small repeating earthquakes rupture relatively weak patches in and around the slip area for the M4.8 event and their activity reflects a stress concentration process and/or change in frictional property (healing) at the area. We also infer the patches for the M4.9 ?? 0.1 and other repeating earthquakes undergo aseismic slip during their interseismic period. Copyright 2007 by the American Geophysical Union.

  3. Numerological Phraseological Units in Multi-structural Languages

    Directory of Open Access Journals (Sweden)

    Rauan Dossymbekova

    2016-11-01

    Full Text Available This paper is devoted to the comparative-semantic analysis of numerological phraseological units (PU in the unrelated languages, namely, Kazakh and English. The identification of the similarities and differences of fixed collocations of multiple languages is a spread type of comparative analysis in phraseology. The possibility of verbalization of the natural environment and man-made environment of ethnic group becomes apparent in comparative studies and description of any lexical-semantic groups of two or more languages. In our work we consider lexical-semantic group of numbers category in Kazakh and English. Numerals are actively involved in the formation of PU, thereby forming a large reservoir of numerological PU and deserve a special consideration. The work is ethnolinguistic and linguoculturological description of the main vernacular numerals, included in the set phrases of the languages. Main methods of the research are: method of semantic analysis, descriptive method, comparative analysis, method of sampling.

  4. The effect of family structure on parents' child care time in the United States and the United Kingdom

    OpenAIRE

    Kalenkoski, Charlene Marie; Ribar, David C.; Stratton, Leslie Sundt

    2006-01-01

    We use time-diary data from the 2003 and 2004 American Time Use Surveys and the 2000 United Kingdom Time Use Study to estimate the effect of family structure on the time mothers and fathers spend on primary and passive child care and on market work, using a system of correlated Tobit equations and family structure equations. Estimates from these models indicate that single parents in both countries spend more time in child care than married or cohabiting parents. There are differences, howeve...

  5. A new method to determine the structure of the metal environment in metalloproteins: investigation of the prion protein octapeptide repeat Cu(2+) complex.

    Science.gov (United States)

    Mentler, Matthias; Weiss, Andreas; Grantner, Klaus; del Pino, Pablo; Deluca, Dominga; Fiori, Stella; Renner, Christian; Klaucke, Wolfram Meyer; Moroder, Luis; Bertsch, Uwe; Kretzschmar, Hans A; Tavan, Paul; Parak, Fritz G

    2005-03-01

    Since high-intensity synchrotron radiation is available, "extended X-ray absorption fine structure" spectroscopy (EXAFS) is used for detailed structural analysis of metal ion environments in proteins. However, the information acquired is often insufficient to obtain an unambiguous picture. ENDOR spectroscopy allows the determination of hydrogen positions around a metal ion. However, again the structural information is limited. In the present study, a method is proposed which combines computations with spectroscopic data from EXAFS, EPR, electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM). From EXAFS a first picture of the nearest coordination shell is derived which has to be compatible with EPR data. Computations are used to select sterically possible structures, from which in turn structures with correct H and N positions are selected by ENDOR and ESEEM measurements. Finally, EXAFS spectra are re-calculated and compared with the experimental data. This procedure was successfully applied for structure determination of the Cu(2+) complex of the octapeptide repeat of the human prion protein. The structure of this octarepeat complex is rather similar to a pentapeptide complex which was determined by X-ray structure analysis. However, the tryptophan residue has a different orientation: the axial water is on the other side of the Cu.

  6. Dynamic Effects of Embedded Macro-Fiber Composite Actuators on Ultra-Light Flexible Structures of Repeated Pattern- a Homogenization Approach

    Directory of Open Access Journals (Sweden)

    A. Salehian

    2012-01-01

    Full Text Available Motivated by deployable satellite technology, this article presents a homogenization model of an inflatable, rigidized lattice structure with distributed macro-fiber composite (MFC actuation. The model is based upon a general expression for the strain and kinetic energy of a fundamental repeated element of the structure. These expressions are reduced in order and expressed in terms of the strain and displacement components of an equivalent one-dimensional vibration model. The resulting model is used to analyze changes in the structural natural frequencies introduced by the local effects of the added macro-fiber composite actuators for several configurations. A finite element solution is used as a comparison for the homogenization model, and the two are shown to be in good agreement, although the latter requires significantly less computational effort.

  7. Thickness of the middle Fort Union hydrogeologic unit in the Williston structural basin

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — These data represent the thickness, in feet, of the middle Fort Union hydrogeologic unit in the Williston structural basin. The data are presented as ASCII text...

  8. Thickness of the Upper Hell Creek hydrogeologic unit in the Williston structural basin

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — These data represent the thickness, in feet, of the Upper Hell Creek hydrogeologic unit in the Williston structural basin. The data are presented as ASCII text...

  9. The Interaction of the Logistics System with the Structural Units of the Company

    Directory of Open Access Journals (Sweden)

    Aleksey Shapovalov

    2012-12-01

    Full Text Available The article detects major flows that occur in business activities of any business entity. The examined flows describe the interaction of the logistic system with the structural units of the company.

  10. Structure and Membrane Binding Properties of the Endosomal Tetratricopeptide Repeat (TPR) Domain-containing Sorting Nexins SNX20 and SNX21.

    Science.gov (United States)

    Clairfeuille, Thomas; Norwood, Suzanne J; Qi, Xiaying; Teasdale, Rohan D; Collins, Brett M

    2015-06-01

    Sorting nexins (SNX) orchestrate membrane trafficking and signaling events required for the proper distribution of proteins within the endosomal network. Their phox homology (PX) domain acts as a phosphoinositide (PI) recognition module that targets them to specific endocytic membrane domains. The modularity of SNX proteins confers a wide variety of functions from signaling to membrane deformation and cargo binding, and many SNXs are crucial modulators of endosome dynamics and are involved in a myriad of physiological and pathological processes such as neurodegenerative diseases, cancer, and inflammation. Here, we have studied the poorly characterized SNX20 and its paralogue SNX21, which contain an N-terminal PX domain and a C-terminal PX-associated B (PXB) domain of unknown function. The two proteins share similar PI-binding properties and are recruited to early endosomal compartments by their PX domain. The crystal structure of the SNX21 PXB domain reveals a tetratricopeptide repeat (TPR)-fold, a module that typically binds short peptide motifs, with three TPR α-helical repeats. However, the C-terminal capping helix adopts a highly unusual and potentially self-inhibitory topology. SAXS solution structures of SNX20 and SNX21 show that these proteins adopt a compact globular architecture, and membrane interaction analyses indicate the presence of overlapping PI-binding sites that may regulate their intracellular localization. This study provides the first structural analysis of this poorly characterized subfamily of SNX proteins, highlighting a likely role as endosome-associated scaffolds.

  11. Rational design of alpha-helical tandem repeat proteins with closed architectures

    Science.gov (United States)

    Doyle, Lindsey; Hallinan, Jazmine; Bolduc, Jill; Parmeggiani, Fabio; Baker, David; Stoddard, Barry L.; Bradley, Philip

    2015-01-01

    Tandem repeat proteins, which are formed by repetition of modular units of protein sequence and structure, play important biological roles as macromolecular binding and scaffolding domains, enzymes, and building blocks for the assembly of fibrous materials1,2. The modular nature of repeat proteins enables the rapid construction and diversification of extended binding surfaces by duplication and recombination of simple building blocks3,4. The overall architecture of tandem repeat protein structures – which is dictated by the internal geometry and local packing of the repeat building blocks – is highly diverse, ranging from extended, super-helical folds that bind peptide, DNA, and RNA partners5–9, to closed and compact conformations with internal cavities suitable for small molecule binding and catalysis10. Here we report the development and validation of computational methods for de novo design of tandem repeat protein architectures driven purely by geometric criteria defining the inter-repeat geometry, without reference to the sequences and structures of existing repeat protein families. We have applied these methods to design a series of closed alpha-solenoid11 repeat structures (alpha-toroids) in which the inter-repeat packing geometry is constrained so as to juxtapose the N- and C-termini; several of these designed structures have been validated by X-ray crystallography. Unlike previous approaches to tandem repeat protein engineering12–20, our design procedure does not rely on template sequence or structural information taken from natural repeat proteins and hence can produce structures unlike those seen in nature. As an example, we have successfully designed and validated closed alpha-solenoid repeats with a left-handed helical architecture that – to our knowledge – is not yet present in the protein structure database21. PMID:26675735

  12. Rational design of α-helical tandem repeat proteins with closed architectures.

    Science.gov (United States)

    Doyle, Lindsey; Hallinan, Jazmine; Bolduc, Jill; Parmeggiani, Fabio; Baker, David; Stoddard, Barry L; Bradley, Philip

    2015-12-24

    Tandem repeat proteins, which are formed by repetition of modular units of protein sequence and structure, play important biological roles as macromolecular binding and scaffolding domains, enzymes, and building blocks for the assembly of fibrous materials. The modular nature of repeat proteins enables the rapid construction and diversification of extended binding surfaces by duplication and recombination of simple building blocks. The overall architecture of tandem repeat protein structures--which is dictated by the internal geometry and local packing of the repeat building blocks--is highly diverse, ranging from extended, super-helical folds that bind peptide, DNA, and RNA partners, to closed and compact conformations with internal cavities suitable for small molecule binding and catalysis. Here we report the development and validation of computational methods for de novo design of tandem repeat protein architectures driven purely by geometric criteria defining the inter-repeat geometry, without reference to the sequences and structures of existing repeat protein families. We have applied these methods to design a series of closed α-solenoid repeat structures (α-toroids) in which the inter-repeat packing geometry is constrained so as to juxtapose the amino (N) and carboxy (C) termini; several of these designed structures have been validated by X-ray crystallography. Unlike previous approaches to tandem repeat protein engineering, our design procedure does not rely on template sequence or structural information taken from natural repeat proteins and hence can produce structures unlike those seen in nature. As an example, we have successfully designed and validated closed α-solenoid repeats with a left-handed helical architecture that--to our knowledge--is not yet present in the protein structure database.

  13. Thermal performance of direct illumination high-power LED backlight units with different assembling structures

    Science.gov (United States)

    Wang, Yiwei; Cen, Jiwen; Cao, Wenjiong; Jiang, Fangming

    2016-10-01

    This work presents a detailed study about the heat dissipation performance of direct illumination high-power light emitting diode (LED) backlight units with two different assembling structures, one of which is traditional and the other is new. The traditional structure, referred to by structure-1, consists of multiple LEDs being directly welded to the printed circuit board (PCB), where the PCB is used as a physical support, an electrical connector and also as a heat dissipation medium. The new structure, referred to by structure-2, places the LEDs directly on the cooling boss; in this case the PCB plays mainly the role of an electrical connector. Thermal characteristics related to the two backlight units are analyzed in terms of thermal resistance network, numerically simulated and experimentally tested. The obtained results by different methods accord with each other reasonably well and all indicate that both structures can meet the requirements of heat dissipation for backlight units at an ambient temperature of 30 °C. Among the two structures, the LED junction temperature of structure-1 backlight unit is 7-8 °C higher and the temperature distribution in the back plane of the backlight unit is also more uniform.

  14. A Study for the Characteristic Changes Under the Repeated Thermal Exposure in the Process of Repairing Aircraft Sandwich Structures

    Science.gov (United States)

    Kim, Yun Hae; Han, Joong Won; Kim, Don Won; Choi, Byung Keun; Murakami, R.

    Delamination can be observed in the sound areas during and/or after a couple times exposure to the elevated curing temperature due to the repeated repair condition. This study was conducted for checking the degree of degradation of properties of the cured parts and delamination between skin prepreg and honeycomb core. Specimens with glass honeycomb sandwich construction and glass/epoxy prepreg were prepared. The specimens were cured 1 to 5 times at 260°F in an autoclave and each additionally exposed 50, 100 and 150 hours in the 260°F oven. Each specimen was tested for tensile strength, compressive strength, flatwise tensile strength and interlaminar shear strength. To monitor the characteristics of the resin itself, the cured resin was tested using DMA and DSC. As a results, the decrease of Tg value were observed in the specific specimen which is exposed over 50 hrs at 260°F. This means the change or degradative of resin properties is also related to the decrease of flatwise tensile properties. Accordingly, minimal exposure on the curing temperature is recommended for parts in order to prevent the delation and maintain the better condition.

  15. Reaction of sulfur-containing structural units of transition metals

    Institute of Scientific and Technical Information of China (English)

    陈忠宁; 康北笙; 童叶翔; 张华新; 苏成勇; 林璋; 洪茂椿; 郁开北

    1997-01-01

    Two tri-n-butylphosphme-participated ( PBu3n) nickel (Ⅱ) complexes of 2-mercaptophenol(H2mp),i.e,Ni2Ru(mp)3(Hmp)(PBu3n)3 3 exhibiting a curved heterotrinuclear metal skeleton and its mononuclear "synthon",[HNEt3] [Ni(mp) (Hmp) (PBu3n)] 1 were synthesized and characterized by X-crystallography and 1H NMR,FAB-MS and cyclic valtammogram measurements.The nickel(Ⅱ) center in 1 has a square-planar geometry For 3,the ruthenium(Ⅲ) atom is in a distorted octahedral environment and the two mckel(Ⅱ) atoms exhibit square-planar and rare triangle-planar geometries,respectively.The Ni (1)-Ru-Ni(2 ) arrangement is severely asymmetric with the distances 0.254 and 0.394 nm,respectively,for Ni(1)-Ru and Ni(2)-Ru.The structural regularities of relevant complexes are summarized in relation to the structural as well as spectra data.

  16. Structure of bacteriophage [phi]29 head fibers has a supercoiled triple repeating helix-turn-helix motif

    Energy Technology Data Exchange (ETDEWEB)

    Xiang, Ye; Rossmann, Michael G. (Purdue)

    2011-12-22

    The tailed bacteriophage {phi}29 capsid is decorated with 55 fibers attached to quasi-3-fold symmetry positions. Each fiber is a homotrimer of gene product 8.5 (gp8.5) and consists of two major structural parts, a pseudohexagonal base and a protruding fibrous portion that is about 110 {angstrom} in length. The crystal structure of the C-terminal fibrous portion (residues 112-280) has been determined to a resolution of 1.6 {angstrom}. The structure is about 150 {angstrom} long and shows three distinct structural domains designated as head, neck, and stem. The stem region is a unique three-stranded helix-turn-helix supercoil that has not previously been described. When fitted into a cryoelectron microscope reconstruction of the virus, the head structure corresponded to a disconnected density at the distal end of the fiber and the neck structure was located in weak density connecting it to the fiber. Thin section studies of Bacillus subtilis cells infected with fibered or fiberless {phi}29 suggest that the fibers might enhance the attachment of the virions onto the host cell wall.

  17. Structure of bacteriophage phi29 head fibers has a supercoiled triple repeating helix-turn-helix motif.

    Science.gov (United States)

    Xiang, Ye; Rossmann, Michael G

    2011-03-22

    The tailed bacteriophage 29 capsid is decorated with 55 fibers attached to quasi-3-fold symmetry positions. Each fiber is a homotrimer of gene product 8.5 (gp8.5) and consists of two major structural parts, a pseudohexagonal base and a protruding fibrous portion that is about 110 Å in length. The crystal structure of the C-terminal fibrous portion (residues 112-280) has been determined to a resolution of 1.6 Å. The structure is about 150 Å long and shows three distinct structural domains designated as head, neck, and stem. The stem region is a unique three-stranded helix-turn-helix supercoil that has not previously been described. When fitted into a cryoelectron microscope reconstruction of the virus, the head structure corresponded to a disconnected density at the distal end of the fiber and the neck structure was located in weak density connecting it to the fiber. Thin section studies of Bacillus subtilis cells infected with fibered or fiberless 29 suggest that the fibers might enhance the attachment of the virions onto the host cell wall.

  18. The structural basis of actinomycin D-binding induces nucleotide flipping out, a sharp bend and a left-handed twist in CGG triplet repeats.

    Science.gov (United States)

    Lo, Yu-Sheng; Tseng, Wen-Hsuan; Chuang, Chien-Ying; Hou, Ming-Hon

    2013-04-01

    The potent anticancer drug actinomycin D (ActD) functions by intercalating into DNA at GpC sites, thereby interrupting essential biological processes including replication and transcription. Certain neurological diseases are correlated with the expansion of (CGG)n trinucleotide sequences, which contain many contiguous GpC sites separated by a single G:G mispair. To characterize the binding of ActD to CGG triplet repeat sequences, the structural basis for the strong binding of ActD to neighbouring GpC sites flanking a G:G mismatch has been determined based on the crystal structure of ActD bound to ATGCGGCAT, which contains a CGG triplet sequence. The binding of ActD molecules to GCGGC causes many unexpected conformational changes including nucleotide flipping out, a sharp bend and a left-handed twist in the DNA helix via a two site-binding model. Heat denaturation, circular dichroism and surface plasmon resonance analyses showed that adjacent GpC sequences flanking a G:G mismatch are preferred ActD-binding sites. In addition, ActD was shown to bind the hairpin conformation of (CGG)16 in a pairwise combination and with greater stability than that of other DNA intercalators. Our results provide evidence of a possible biological consequence of ActD binding to CGG triplet repeat sequences.

  19. The crystal structure of HIV CRF07 B′/C gp41 reveals a hyper-mutant site in the middle of HR2 heptad repeat

    Energy Technology Data Exchange (ETDEWEB)

    Du, Jiansen; Xue, Hailing; Ma, Jing; Liu, Fang [State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071 (China); Zhou, Jianhua [Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001 (China); Shao, Yiming [State Key Laboratory for Infectious Disease Prevention and Control, and National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206 (China); Qiao, Wentao, E-mail: wentaoqiao@nankai.edu.cn [State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071 (China); Liu, Xinqi, E-mail: liu2008@nankai.edu.cn [State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071 (China)

    2013-11-15

    HIV CRF07 B′/C is a strain circulating mainly in northwest region of China. The gp41 region of CRF07 is derived from a clade C virus. In order to compare the difference of CRF07 gp41 with that of typical clade B virus, we solved the crystal structure of the core region of CRF07 gp41. Compared with clade B gp41, CRF07 gp41 evolved more basic and hydrophilic residues on its helix bundle surface. Based on sequence alignment, a hyper-mutant cluster located in the middle of HR2 heptads repeat was identified. The mutational study of these residues revealed that this site is important in HIV mediated cell–cell fusion and plays critical roles in conformational changes during viral invasion. - Highlights: • We solved the crystal structure of HIV CRF07 gp41 core region. • A hyper-mutant cluster in the middle of HR2 heptads repeat was identified. • The hyper-mutant site is important in HIV-cell fusion. • The model will help to understand the HIV fusion process.

  20. Evaluation of genetic diversity and population structure in a commercially important freshwater fish Prochilodus costatus (Characiformes, Prochilodontidae) using complex hypervariable repeats.

    Science.gov (United States)

    Barroca, T M; Santos, G B; Duarte, N V R; Kalapothakis, E

    2012-12-17

    We used complex hypervariable repeats to evaluate the genetic diversity and structure of Prochilodus costatus (Characiformes), an ecologically and economically important species endemic to the São Francisco River basin. Hydroelectric dams along the river have led to population fragmentation, which can limit gene flow. Restocking from hatcheries has been used to repopulate declining populations. To determine how fragmentation and hatchery supplementation affect P. costatus population structure, we studied populations from three sites up and downstream of the Gafanhoto Dam (Pará River, State of Minas Gerais). High levels of genetic diversity were found within populations (0.926 to 0.873); the three populations showed significant differentiation (F(ST) = 0.16), suggesting that populations from the three sites were affected by fragmentation of the river and by hatchery contributions. These results will be useful for developing a management and conservation plan for fish species in this area.

  1. Parallel Block Structured Adaptive Mesh Refinement on Graphics Processing Units

    Energy Technology Data Exchange (ETDEWEB)

    Beckingsale, D. A. [Atomic Weapons Establishment (AWE), Aldermaston (United Kingdom); Gaudin, W. P. [Atomic Weapons Establishment (AWE), Aldermaston (United Kingdom); Hornung, R. D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Gunney, B. T. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Gamblin, T. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Herdman, J. A. [Atomic Weapons Establishment (AWE), Aldermaston (United Kingdom); Jarvis, S. A. [Atomic Weapons Establishment (AWE), Aldermaston (United Kingdom)

    2014-11-17

    Block-structured adaptive mesh refinement is a technique that can be used when solving partial differential equations to reduce the number of zones necessary to achieve the required accuracy in areas of interest. These areas (shock fronts, material interfaces, etc.) are recursively covered with finer mesh patches that are grouped into a hierarchy of refinement levels. Despite the potential for large savings in computational requirements and memory usage without a corresponding reduction in accuracy, AMR adds overhead in managing the mesh hierarchy, adding complex communication and data movement requirements to a simulation. In this paper, we describe the design and implementation of a native GPU-based AMR library, including: the classes used to manage data on a mesh patch, the routines used for transferring data between GPUs on different nodes, and the data-parallel operators developed to coarsen and refine mesh data. We validate the performance and accuracy of our implementation using three test problems and two architectures: an eight-node cluster, and over four thousand nodes of Oak Ridge National Laboratory’s Titan supercomputer. Our GPU-based AMR hydrodynamics code performs up to 4.87× faster than the CPU-based implementation, and has been scaled to over four thousand GPUs using a combination of MPI and CUDA.

  2. Intensive English Programs in the United States: An Overview of Structure and Mentoring

    Science.gov (United States)

    Thompson, Amy S.

    2013-01-01

    Although English as a second language (ESL) programs are common in the United States, there is surprisingly little research documenting the existing structures and mentoring strategies they use. This lack of research could be partly due to ESL programs' widely varying internal structures (Larson, 1990) and the fact that they are often marginalized…

  3. The structure formed by inverted repeats in p53 response elements determines the transactivation activity of p53 protein.

    Science.gov (United States)

    Brázda, Václav; Čechová, Jana; Battistin, Michele; Coufal, Jan; Jagelská, Eva B; Raimondi, Ivan; Inga, Alberto

    2017-01-29

    The TP53 gene is the most frequently mutated gene in human cancer and p53 protein plays a crucial role in gene expression and cancer protection. Its role is manifested by interactions with other proteins and DNA. p53 is a transcription factor that binds to DNA response elements (REs). Due to the palindromic nature of the consensus binding site, several p53-REs have the potential to form cruciform structures. However, the influence of cruciform formation on the activity of p53-REs has not been evaluated. Therefore, we prepared sets of p53-REs with identical theoretical binding affinity in their linear state, but different probabilities to form extra helical structures, for in vitro and in vivo analyses. Then we evaluated the presence of cruciform structures when inserted into plasmid DNA and employed a yeast-based assay to measure transactivation potential of these p53-REs cloned at a chromosomal locus in isogenic strains. We show that transactivation in vivo correlated more with relative propensity of an RE to form cruciforms than to its predicted in vitro DNA binding affinity for wild type p53. Structural features of p53-REs could therefore be an important determinant of p53 transactivation function.

  4. Tree diversity, composition, forest structure and aboveground biomass dynamics after single and repeated fire in a Bornean rain forest

    NARCIS (Netherlands)

    Slik, J.W.F.; Bernard, C.S.; Beek, van M.; Breman, F.C.; Eichhorn, K.A.O.

    2008-01-01

    Forest fires remain a devastating phenomenon in the tropics that not only affect forest structure and biodiversity, but also contribute significantly to atmospheric CO2. Fire used to be extremely rare in tropical forests, leaving ample time for forests to regenerate to pre-fire conditions. In recent

  5. Teaching with Crystal Structures: Helping Students Recognize and Classify the Smallest Repeating Particle in a Given Substance

    Science.gov (United States)

    Smithenry, Dennis W.

    2009-01-01

    Classifying a particle requires an understanding of the type of bonding that exists within and among the particles, which requires an understanding of atomic structure and electron configurations, which requires an understanding of the elements of periodic properties, and so on. Rather than getting tangled up in all of these concepts at the start…

  6. High light-extraction-efficiency OLED based on photonic crystal slab structures with taper unit cells

    Institute of Scientific and Technical Information of China (English)

    YAN Rong-jin; WANG Qing-kang

    2006-01-01

    To improve the light-extraction-efficiency of OLED,we introduced PCS (Photonic Crystal Slab) structures into the interface of ITO layer and glass substrate.PCS structures with Taper unit cells are proved to be effective in reducing the energy of guided wave trapped in high refractive index material,and an increase of light-extraction-efficiency to 95.26% is gained.This enhancement is much greater than the traditional PCS with cylinder unit cells (60%-70%).Physical mechanisms of light-extraction-efficiency enhancement in these structures are further discussed.

  7. Structure of the organic crystallite unit in coal as determined by X-ray diffraction

    Institute of Scientific and Technical Information of China (English)

    Song Dangyu; Yang Cunbei; Zhang Xiaokui; Su Xianbo; Zhang Xiaodong

    2011-01-01

    X-ray diffraction (XRD) was used to study the structure of the organic crystallite unit (La,Lc,d002) in coals collected from Henan and Shanxi Provinces,XRD patterns of coal were collected in a step-scan mode (0.1 °/step) over an angular range of 2-90° (2θ),allowing 8 s at each step.The structure of the crystallite unit was determined from the Scherrer equation and peak parameters deduced from whole pattern fitting.The results show that the structure of the crystallite unit in coal is mainly controlled by the coal rank.As the coal rank increases the average diameter of a coal crystallite unit (La) increases,the interlayer spacing (d002) decreases slightly,and the average height of a coal crystallite unit (Lc) increases at first but then decreases.A new diffraction peak from the crystallite unit in coal was found at a low scattering angle in the XRD pattern (2-10°).This suggests a structure with an inter-layer spacing from 1.9 to 2.8 nm exists in coal crystallites.

  8. Genetic variation and population structure of Sudanese populations as indicated by 15 Identifiler sequence-tagged repeat (STR loci

    Directory of Open Access Journals (Sweden)

    Babiker Hiba MA

    2011-05-01

    Full Text Available Abstract Background There is substantial ethnic, cultural and linguistic diversity among the people living in east Africa, Sudan and the Nile Valley. The region around the Nile Valley has a long history of succession of different groups, coupled with demographic and migration events, potentially leading to genetic structure among humans in the region. Result We report the genotypes of the 15 Identifiler microsatellite markers for 498 individuals from 18 Sudanese populations representing different ethnic and linguistic groups. The combined power of exclusion (PE was 0.9999981, and the combined match probability was 1 in 7.4 × 1017. The genotype data from the Sudanese populations was combined with previously published genotype data from Egypt, Somalia and the Karamoja population from Uganda. The Somali population was found to be genetically distinct from the other northeast African populations. Individuals from northern Sudan clustered together with those from Egypt, and individuals from southern Sudan clustered with those from the Karamoja population. The similarity of the Nubian and Egyptian populations suggest that migration, potentially bidirectional, occurred along the Nile river Valley, which is consistent with the historical evidence for long-term interactions between Egypt and Nubia. Conclusion We show that despite the levels of population structure in Sudan, standard forensic summary statistics are robust tools for personal identification and parentage analysis in Sudan. Although some patterns of population structure can be revealed with 15 microsatellites, a much larger set of genetic markers is needed to detect fine-scale population structure in east Africa and the Nile Valley.

  9. Cre/loxP-mediated excision of a neomycin resistance expression unit from an integrated retroviral vector increases long terminal repeat-driven transcription in human hematopoietic cells.

    Science.gov (United States)

    Fernex, C; Dubreuil, P; Mannoni, P; Bagnis, C

    1997-01-01

    Recombinant retroviruses are currently the most attractive vehicles for gene transfer into hematopoietic cells. Retroviral vectors often contain an easily selectable marker gene in addition to the gene of interest. However, the presence and selection for expression of the selectable gene often result in a significant reduction of the expression of the gene of interest in the transduced cells. In order to circumvent this problem, we have developed a Cre/loxP recombination system for specific excision of the selectable expression unit from integrated retroviruses. A retroviral vector, containing both a neomycin resistance expression unit flanked by loxP sites and granulocyte-macrophage colony-stimulating factor cDNA, was used to transduce the human hematopoietic K-562 cell line. Four transduced cell clones were then superinfected with a retrovirus containing a Cre recombinase expression unit. Molecular analyses of 30 doubly transduced subclones showed a strict correlation between cre expression and loxP-flanked selectable cassette excision, thus implying that Cre recombinase activity is very efficient in a retroviral context. Moreover, the excision of the selectable cassette results in a significant increase of granulocyte-macrophage colony-stimulating factor transcription driven by the retroviral promoter. PMID:9311833

  10. The population structure of Trypanosoma cruzi: expanded analysis of 54 strains using eight polymorphic CA-repeat microsatellites

    Directory of Open Access Journals (Sweden)

    Riva P Oliveira

    1999-09-01

    Full Text Available Recently we cloned and sequenced the first eight Trypanosoma cruzi polymorphic microsatellite loci and studied 31 clones and strains to obtain valuable information about the population structure of the parasite. We have now studied 23 further strains, increasing from 11 to 31 the number of strains obtained from patients with chronic Chagas disease. This expanded set of 54 strains and clones analyzed with the eight microsatellites markers confirmed the previously observed diploidy, clonal population organization and very high polymorphism of T. cruzi. Moreover, this new study disclosed two new features of the population genetic structure of T. cruzi. The first was the discovery that, similarly to what we had previously shown for strains isolated from insect vectors, mammals and humans with acute disease, isolates from patients in the chronic phase of Chagas disease could also be multiclonal, albeit at a reduced proportion. Second, when we used parsimony to display the genetic relationship among the clonal lineages in an unrooted Wagner network we observed, like before, a good correlation of the tree topography with the classification in three clusters on the basis of single locus analysis of the ribosomal RNA genes. However, a significant new finding was that now the strains belonging to cluster 2 split in two distant sub-clusters. This observation suggests that the evolutionary history of T. cruzi may be more complex than we previously thought.

  11. Dynamics and internal structure of an Alaskan debris-covered glacier from repeat airborne photogrammetry and surface geophysics

    Science.gov (United States)

    Holt, John; Levy, Joseph; Petersen, Eric; Larsen, Chris; Fahnestock, Mark

    2016-04-01

    Debris-covered glaciers and rock glaciers encompass a range of compositions and activity, and can be useful paleoclimate indicators. They also respond differently to ongoing climate change than glaciers without a protective cover. Their flow dynamics are not well understood, and their unique surface morphologies, including lobate fronts and arcuate ridges, likely result from viscous flow influenced by a combination of composition, structure, and climatic factors. However, basic connections between flow kinematics and surface morphology have not yet been established, limiting our ability to understand these features. In order to begin to address this problem we have undertaken airborne and surface studies of multiple debris-covered glaciers in Alaska and the western U.S. Sourdough Rock Glacier in the St. Elias Mountains, Alaska, is completely debris-covered and exhibits numerous transverse compressional ridges. Its trunk also exhibits highly regular bumps and swales with a wavelength of ~175 m and amplitudes up to 12 m. In the middle trunk, lineations (boulder trains and furrows) bend around a point roughly 200m from the eastern edge. We acquired five high-resolution airborne surveys of Sourdough Rock Glacier between late 2013 and late 2015 using lidar and photogrammetry to assess annual and seasonal change at the sub-meter level. Differencing the DTMs provides vertical change while feature tracking in orthophotos provide horizontal velocities that indicate meters of annual motion. The flow field is highly correlated with surface features; in particular, compressional ridges in the lower lobe. Stranded, formerly active lobes are also apparent. Surface geophysical studies were undertaken to constrain internal structure and composition using a combination of ground-penetrating radar (GPR) at 50 and 100 MHz in six transects, and time-domain electromagnetic (TDEM) measurements at 47 locations, primarily in an along-flow transect and two cross-flow transects. We infer

  12. Structural and Functional Characterization of an Archaeal Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated Complex for Antiviral Defense (CASCADE)

    DEFF Research Database (Denmark)

    Lintner, Nathanael G; Kerou, Melina; Brumfield, Susan K

    2011-01-01

    In response to viral infection, many prokaryotes incorporate fragments of virus-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). The loci are then transcribed, and the processed CRISPR transcripts are used to target invading viral DNA and RNA....... The Escherichia coli "CRISPR-associated complex for antiviral defense" (CASCADE) is central in targeting invading DNA. Here we report the structural and functional characterization of an archaeal CASCADE (aCASCADE) from Sulfolobus solfataricus. Tagged Csa2 (Cas7) expressed in S. solfataricus co-purifies with Cas5......a-, Cas6-, Csa5-, and Cas6-processed CRISPR-RNA (crRNA). Csa2, the dominant protein in aCASCADE, forms a stable complex with Cas5a. Transmission electron microscopy reveals a helical complex of variable length, perhaps due to substoichiometric amounts of other CASCADE components. A recombinant Csa2...

  13. The structure of a single unit of ribosomal RNA gene (rDNA) including intergenic subrepeats in the Australian bulldog ant Myrmecia croslandi (Hymenoptera: Formicidae).

    Science.gov (United States)

    Ohnishi, Hitoshi; Yamamoto, Masa-Toshi

    2004-02-01

    A complete single unit of a ribosomal RNA gene (rDNA) of M. croslandi was sequenced. The ends of the 18S, 5.8S and 28S rRNA genes were determined by using the sequences of D. melanogaster rDNAs as references. Each of the tandemly repeated rDNA units consists of coding and non-coding regions whose arrangement is the same as that of D. melanogaster rDNA. The intergenic spacer (IGS) contains, as in other species, a region with subrepeats, of which the sequences are different from those previously reported in other insect species. The length of IGSs was estimated to be 7-12 kb by genomic Southern hybridization, showing that an rDNA repeating unit of M. croslandi is 14-19 kb-long. The sequences of the coding regions are highly conserved, whereas IGS and ITS (internal transcribed spacer) sequences are not. We obtained clones with insertions of various sizes of R2 elements, the target sequence of which was found in the 28S rRNA coding region. A short segment in the IGS that follows the 3' end of the 28S rRNA gene was predicted to form a secondary structure with long stems.

  14. Unit roots and structural breakpoints in China's macroeconomic and financial time series

    Institute of Scientific and Technical Information of China (English)

    LIANG Qi; TENG Jianzhou

    2006-01-01

    This paper applies unit-root tests to 10 Chinese macroeconomic and financial time series that allow for the possibility of up to two endogenous structural breaks.We found that 6 of the series,i.e.,GDP,GDP per capita,employment,bank credit,deposit liabilities and investment,can be more accurately characterized as a segmented trend stationarity process around one or two structural breakpoints as opposed to a stochastic unit root process.Our findings have important implications for policy-makers to formulate long-term growth strategy and short-run stabilization policies,as well as causality analysis among the series.

  15. Structural and Functional Characterization of an Archaeal Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated Complex for Antiviral Defense (CASCADE)*

    Science.gov (United States)

    Lintner, Nathanael G.; Kerou, Melina; Brumfield, Susan K.; Graham, Shirley; Liu, Huanting; Naismith, James H.; Sdano, Matthew; Peng, Nan; She, Qunxin; Copié, Valérie; Young, Mark J.; White, Malcolm F.; Lawrence, C. Martin

    2011-01-01

    In response to viral infection, many prokaryotes incorporate fragments of virus-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). The loci are then transcribed, and the processed CRISPR transcripts are used to target invading viral DNA and RNA. The Escherichia coli “CRISPR-associated complex for antiviral defense” (CASCADE) is central in targeting invading DNA. Here we report the structural and functional characterization of an archaeal CASCADE (aCASCADE) from Sulfolobus solfataricus. Tagged Csa2 (Cas7) expressed in S. solfataricus co-purifies with Cas5a-, Cas6-, Csa5-, and Cas6-processed CRISPR-RNA (crRNA). Csa2, the dominant protein in aCASCADE, forms a stable complex with Cas5a. Transmission electron microscopy reveals a helical complex of variable length, perhaps due to substoichiometric amounts of other CASCADE components. A recombinant Csa2-Cas5a complex is sufficient to bind crRNA and complementary ssDNA. The structure of Csa2 reveals a crescent-shaped structure unexpectedly composed of a modified RNA-recognition motif and two additional domains present as insertions in the RNA-recognition motif. Conserved residues indicate potential crRNA- and target DNA-binding sites, and the H160A variant shows significantly reduced affinity for crRNA. We propose a general subunit architecture for CASCADE in other bacteria and Archaea. PMID:21507944

  16. Structural and functional characterization of an archaeal clustered regularly interspaced short palindromic repeat (CRISPR)-associated complex for antiviral defense (CASCADE).

    Science.gov (United States)

    Lintner, Nathanael G; Kerou, Melina; Brumfield, Susan K; Graham, Shirley; Liu, Huanting; Naismith, James H; Sdano, Matthew; Peng, Nan; She, Qunxin; Copié, Valérie; Young, Mark J; White, Malcolm F; Lawrence, C Martin

    2011-06-17

    In response to viral infection, many prokaryotes incorporate fragments of virus-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). The loci are then transcribed, and the processed CRISPR transcripts are used to target invading viral DNA and RNA. The Escherichia coli "CRISPR-associated complex for antiviral defense" (CASCADE) is central in targeting invading DNA. Here we report the structural and functional characterization of an archaeal CASCADE (aCASCADE) from Sulfolobus solfataricus. Tagged Csa2 (Cas7) expressed in S. solfataricus co-purifies with Cas5a-, Cas6-, Csa5-, and Cas6-processed CRISPR-RNA (crRNA). Csa2, the dominant protein in aCASCADE, forms a stable complex with Cas5a. Transmission electron microscopy reveals a helical complex of variable length, perhaps due to substoichiometric amounts of other CASCADE components. A recombinant Csa2-Cas5a complex is sufficient to bind crRNA and complementary ssDNA. The structure of Csa2 reveals a crescent-shaped structure unexpectedly composed of a modified RNA-recognition motif and two additional domains present as insertions in the RNA-recognition motif. Conserved residues indicate potential crRNA- and target DNA-binding sites, and the H160A variant shows significantly reduced affinity for crRNA. We propose a general subunit architecture for CASCADE in other bacteria and Archaea.

  17. Structural and biochemical analysis of nuclease domain of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 3 (Cas3).

    Science.gov (United States)

    Mulepati, Sabin; Bailey, Scott

    2011-09-09

    RNA transcribed from clustered regularly interspaced short palindromic repeats (CRISPRs) protects many prokaryotes from invasion by foreign DNA such as viruses, conjugative plasmids, and transposable elements. Cas3 (CRISPR-associated protein 3) is essential for this CRISPR protection and is thought to mediate cleavage of the foreign DNA through its N-terminal histidine-aspartate (HD) domain. We report here the 1.8 Å crystal structure of the HD domain of Cas3 from Thermus thermophilus HB8. Structural and biochemical studies predict that this enzyme binds two metal ions at its active site. We also demonstrate that the single-stranded DNA endonuclease activity of this T. thermophilus domain is activated not by magnesium but by transition metal ions such as manganese and nickel. Structure-guided mutagenesis confirms the importance of the metal-binding residues for the nuclease activity and identifies other active site residues. Overall, these results provide a framework for understanding the role of Cas3 in the CRISPR system.

  18. [Contributions and results of lipo-structure in repair and rejuvenation of frontal anatomical unit].

    Science.gov (United States)

    Chichery, A; Mojallal, A; Voulliaume, D; Comparin, J-P; Foyatier, J-L

    2009-04-01

    Forehead is the most large anatomical unit of face. It includes forehead and anterior part of temple. Deteriorations of frontal anatomical units are numerous, ageing forehead has atrophy with eyebrow ptosis. In this work, we want to estimate contribution of lipo-structure in repair and rejuvenation of frontal anatomical unit (FAU). We present seven cases of repair of FAU and three cases of rejuvenation of the forehead. Results are satisfactory, particularly about frontal band. Results are questionable about Lipo-structure of temple. Applications of Lipo-structure in plastic and aesthetic surgery of the forehead are huge. Lipo-structure is the reference technique of volumetric filling. It is preferred to other techniques as flaps (pediculed or free) or materials, because it is a safe, easy and efficient technique, which permits large fillings. In aesthetic surgery, Lipo-structure gives volume to eyebrow region and fills root of the nose. It can be used with injections of botulinum toxin A. Lipo-structure of forehead takes part in rejuvenation of eye and nose. In conclusion, lipo-structure is actually the major technique of filling with a large implication in plastic and aesthetic surgery of FAU.

  19. Structural Vulnerability and Health: Latino Migrant Laborers in the United States

    Science.gov (United States)

    Quesada, James; Hart, Laurie K.; Bourgois, Philippe

    2011-01-01

    Latino immigrants in the United States constitute a paradigmatic case of a population group subject to structural violence. Their subordinated location in the global economy and their culturally depreciated status in the United States are exacerbated by legal persecution. Medical Anthropology Volume 30, issues 4 and 5, include a series of ethnographic analyses of the processes that render undocumented Latino immigrants structurally vulnerable to ill-health. We hope to extend the social science concept of ‘structural vulnerability’ to make it a useful tool for health care. Defined as a positionality that imposes physical/emotional suffering on specific population groups and individuals in patterned ways, structural vulnerability is a product of two complementary forces: (1) class-based economic exploitation and cultural, gender/sexual, and racialized discrimination; and (2) processes of symbolic violence and subjectivity formation that have increasingly legitimized punitive neoliberal discourses of individual unworthiness. PMID:21777121

  20. Hemolysin coregulated protein 1 as a molecular gluing unit for the assembly of nanoparticle hybrid structures

    Directory of Open Access Journals (Sweden)

    Tuan Anh Pham

    2016-03-01

    Full Text Available Hybrid nanoparticle (NP structures containing organic building units such as polymers, peptides, DNA and proteins have great potential in biosensor and electronic applications. The nearly free modification of the polymer chain, the variation of the protein and DNA sequence and the implementation of functional moieties provide a great platform to create inorganic structures of different morphology, resulting in different optical and magnetic properties. Nevertheless, the design and modification of a protein structure with functional groups or sequences for the assembly of biohybrid materials is not trivial. This is mainly due to the sensitivity of its secondary, tertiary and quaternary structure to the changes in the interaction (e.g., hydrophobic, hydrophilic, electrostatic, chemical groups between the protein subunits and the inorganic material. Here, we use hemolysin coregulated protein 1 (Hcp1 from Pseudomonas aeruginosa as a building and gluing unit for the formation of biohybrid structures by implementing cysteine anchoring points at defined positions on the protein rim (Hcp1_cys3. We successfully apply the Hcp1_cys3 gluing unit for the assembly of often linear, hybrid structures of plasmonic gold (Au NP, magnetite (Fe3O4 NP, and cobalt ferrite nanoparticles (CoFe2O4 NP. Furthermore, the assembly of Au NPs into linear structures using Hcp1_cys3 is investigated by UV–vis spectroscopy, TEM and cryo-TEM. One key parameter for the formation of Au NP assembly is the specific ionic strength in the mixture. The resulting network-like structure of Au NPs is characterized by Raman spectroscopy, showing surface-enhanced Raman scattering (SERS by a factor of 8·104 and a stable secondary structure of the Hcp1_cys3 unit. In order to prove the catalytic performance of the gold hybrid structures, they are used as a catalyst in the reduction reaction of 4-nitrophenol showing similar catalytic activity as the pure Au NPs. To further extend the

  1. Repeat-until-success quantum repeaters

    Science.gov (United States)

    Bruschi, David Edward; Barlow, Thomas M.; Razavi, Mohsen; Beige, Almut

    2014-09-01

    We propose a repeat-until-success protocol to improve the performance of probabilistic quantum repeaters. Conventionally, these rely on passive static linear-optics elements and photodetectors to perform Bell-state measurements (BSMs) with a maximum success rate of 50%. This is a strong impediment for entanglement swapping between distant quantum memories. Every time a BSM fails, entanglement needs to be redistributed between the corresponding memories in the repeater link. The key ingredients of our scheme are repeatable BSMs. Under ideal conditions, these turn probabilistic quantum repeaters into deterministic ones. Under realistic conditions, our protocol too might fail. However, using additional threshold detectors now allows us to improve the entanglement generation rate by almost orders of magnitude, at a nominal distance of 1000 km, compared to schemes that rely on conventional BSMs. This improvement is sufficient to make the performance of our scheme comparable to the expected performance of some deterministic quantum repeaters.

  2. Can technical, functional and structural characteristics of dental units predict Legionella pneumophila and Pseudomonas aeruginosa contamination?

    Science.gov (United States)

    Aprea, Luigi; Cannova, Lucia; Firenze, Alberto; Bivona, Maria S; Amodio, Emanuele; Romano, Nino

    2010-12-01

    Legionella pneumophila and Pseudomonas aeruginosa are common colonizers of water environments, particularly dental unit waterlines. The aim of this study was to assess whether the technical, functional and structural characteristics of dental units can influence the presence and the levels of opportunistic pathogens. Overall, 42 water samples were collected from dental units in a teaching hospital in Palermo, Italy, including 21 samples from the 21 taps supplied by the municipal water distribution system and 21 samples from oral rinsing cups at 21 dental units. L. pneumophila was present in 16 out of 21 water samples (76.2%) from dental units, and the median concentration was higher in samples from oral rinsing cups than in those from taps (P < 0.001). P. aeruginosa was equally distributed in water samples collected from oral rinsing cups and from taps. Some characteristics of dental units (age, number of chairs per room, number of patients per day and water temperature) were slightly associated with the presence of P. aeruginosa, but not with contamination by L. pneumophila. Our experience suggests that L. pneumophila is frequently detected in dental units, as reported in previous studies, whereas P. aeruginosa is not a frequent contaminant. As a consequence, microbiological control of water quality should be routinely performed, and should include the detection of opportunistic pathogens when bacterial contamination is expected.

  3. Teaching Basic Science Environmentally, The Concept: The cell is basic unit of structure of most organisms.

    Science.gov (United States)

    Busch, Phyllis S.

    1985-01-01

    Suggests simple ways to introduce students to the concept that the cell is the basic unit of structure of most organisms. Mentions materials for microscope study that are readily available and easy to handle, e.g., membranes from between the scales of the onion bulb, thin-leaved plants, pond water, and pollen. (JHZ)

  4. Molecular structure of basic oligomeric building units of heparan-sulfate glycosaminoglycans

    NARCIS (Netherlands)

    Remko, Milan; Van Duijnen, Piet Th.; Broer, Ria

    2010-01-01

    This study reports in detail the results of systematic large-scale theoretical investigations of the acidic dimeric structural units (D-E, E-F, F-G, and G-H) and pentamer D-E-F-G-H (fondaparinux) of the glycosaminoglycan heparin, and their anionic forms. The geometries and energies of these oligomer

  5. Quaternary Structure and Functional Unit of Energy Coupling Factor (ECF)-type Transporters

    NARCIS (Netherlands)

    Beek, Josy ter; Duurkens, Ria H.; Erkens, Guus B.; Slotboom, Dirk Jan

    2011-01-01

    ATP-binding cassette (ABC) transporters mediate transport of diverse substrates across membranes. We have determined the quaternary structure and functional unit of the recently discovered ECF-type (energy coupling factor) of ABC transporters, which is widespread among prokaryotes. ECF transporters

  6. Mechanical Properties and Fatigue Behavior of Unitized Composite Airframe Structures at Elevated Temperature

    Science.gov (United States)

    2016-09-01

    suitability of this composite for use in aerospace components designed to contain high-temperature environments, mechanical tests were performed under... contain high-temperature environments, mechanical tests were performed under temperature conditions simulating the actual operating conditions. In all... MECHANICAL PROPERTIES AND FATIGUE BEHAVIOR OF UNITIZED COMPOSITE AIRFRAME STRUCTURES AT ELEVATED

  7. Regional impacts of technical change: the case of structural particleboard in the United States.

    Science.gov (United States)

    Zhi Xu; David N. Bengston; Hans M. Gregersen; Allen L. Lundgren

    1992-01-01

    Analyzes the regional impacts of research benefits in the United States due to the introduction of structural particleboard. The distribution of consumer benefits, producer benefits, direct employment impacts, and changes in wood requirements are analyzed for the four census regions. The distribution of benefits is found to differ widely between regions, indicating...

  8. Experimental broadband absorption enhancement in silicon nanohole structures with optimized complex unit cells.

    Science.gov (United States)

    Lin, Chenxi; Martínez, Luis Javier; Povinelli, Michelle L

    2013-09-09

    We design silicon membranes with nanohole structures with optimized complex unit cells that maximize broadband absorption. We fabricate the optimized design and measure the optical absorption. We demonstrate an experimental broadband absorption about 3.5 times higher than an equally-thick thin film.

  9. ProtRepeatsDB: a database of amino acid repeats in genomes

    Directory of Open Access Journals (Sweden)

    Chauhan Virander S

    2006-07-01

    Full Text Available Abstract Background Genome wide and cross species comparisons of amino acid repeats is an intriguing problem in biology mainly due to the highly polymorphic nature and diverse functions of amino acid repeats. Innate protein repeats constitute vital functional and structural regions in proteins. Repeats are of great consequence in evolution of proteins, as evident from analysis of repeats in different organisms. In the post genomic era, availability of protein sequences encoded in different genomes provides a unique opportunity to perform large scale comparative studies of amino acid repeats. ProtRepeatsDB http://bioinfo.icgeb.res.in/repeats/ is a relational database of perfect and mismatch repeats, access to which is designed as a resource and collection of tools for detection and cross species comparisons of different types of amino acid repeats. Description ProtRepeatsDB (v1.2 consists of perfect as well as mismatch amino acid repeats in the protein sequences of 141 organisms, the genomes of which are now available. The web interface of ProtRepeatsDB consists of different tools to perform repeat s; based on protein IDs, organism name, repeat sequences, and keywords as in FASTA headers, size, frequency, gene ontology (GO annotation IDs and regular expressions (REGEXP describing repeats. These tools also allow formulation of a variety of simple, complex and logical queries to facilitate mining and large-scale cross-species comparisons of amino acid repeats. In addition to this, the database also contains sequence analysis tools to determine repeats in user input sequences. Conclusion ProtRepeatsDB is a multi-organism database of different types of amino acid repeats present in proteins. It integrates useful tools to perform genome wide queries for rapid screening and identification of amino acid repeats and facilitates comparative and evolutionary studies of the repeats. The database is useful for identification of species or organism specific

  10. Common interruptions in the repeating tripeptide sequence of non-fibrillar collagens: sequence analysis and structural studies on triple-helix peptide models.

    Science.gov (United States)

    Thiagarajan, Geetha; Li, Yingjie; Mohs, Angela; Strafaci, Christopher; Popiel, Magdalena; Baum, Jean; Brodsky, Barbara

    2008-02-22

    Interruptions in the repeating (Gly-X1-X2)(n) amino acid sequence pattern are found in the triple-helix domains of all non-fibrillar collagens, and perturbations to the triple-helix at such sites are likely to play a role in collagen higher-order structure and function. This study defines the sequence features and structural consequences of the most common interruption, where one residue is missing from the tripeptide pattern, Gly-X1-X2-Gly-AA(1)-Gly-X1-X2, designated G1G interruptions. Residues found within G1G interruptions are predominantly hydrophobic (70%), followed by a significant amount of charged residues (16%), and the Gly-X1-X2 triplets flanking the interruption are atypical. Studies on peptide models indicate the degree of destabilization is much greater when Pro is in the interruption, GP, than when hydrophobic residues (GF, GY) are present, and a rigid Gly-Pro-Hyp tripeptide adjacent to the interruption leads to greater destabilization than a flexible Gly-Ala-Ala sequence. Modeling based on NMR data indicates the Phe residue within a GF interruption is located on the outside of the triple helix. The G1G interruptions resemble a previously studied collagen interruption GPOGAAVMGPO, designated G4G-type, in that both are destabilizing, but allow continuation of rod-like triple helices and maintenance of the single residue stagger throughout the imperfection, with a loss of axial register of the superhelix on both sides. Both kinds of interruptions result in a highly localized perturbation in hydrogen bonding and dihedral angles, but the hydrophobic residue of a G4G interruption packs near the central axis of the superhelix, while the hydrophobic residue of a G1G interruption is located on the triple-helix surface. The different structural consequences of G1G and G4G interruptions in the repeating tripeptide sequence pattern suggest a physical basis for their differential susceptibility to matrix metalloproteinases in type X collagen.

  11. Missed Opportunities for Repeat HIV Testing in Pregnancy: Implications for Elimination of Mother-to-Child Transmission in the United States.

    Science.gov (United States)

    Liao, Caiyun; Golden, William Christopher; Anderson, Jean R; Coleman, Jenell S

    2017-01-01

    HIV testing is an effective intervention that is used for reducing perinatal HIV transmission. Centers for Disease Control and Prevention recommends a second HIV test during the third trimester of pregnancy for women in settings with an elevated HIV incidence (≥17 cases per 100,000 person-years). We conducted a retrospective cohort study at a single hospital in Baltimore, Maryland, to determine whether a second HIV test was done and to compare HIV retesting with mandated syphilis retesting. Of women who delivered at this hospital, 98.8% received prenatal care. Descriptive, bivariate, and multivariable analyses were performed. Among 1632 women, mean age was 27.6 years (standard deviation: 6.3), 59.6% were black, and 55.5% were single. HIV retesting was done in 28.4% of women, which was significantly less often compared with the state-mandated syphilis retesting (78.7%, p < 0.001). The odds of having an HIV retest were 15 times higher among women who received prenatal care at a teaching clinic [adjusted odds ratio (aOR): 15.58; 95% confidence interval (CI): 11.12-21.81], and they were lower among women with private insurance (aOR: 0.54, 95% CI: 0.34-0.86). The odds of having a syphilis retest were twice as high among women who received prenatal care at a faculty practice (aOR: 2.17; 95% CI: 1.53-3.09), and they were lower among women with private insurance (aOR: 0.61, 95% CI: 0.43-0.88). Emphasizing an "opt-out" HIV retesting approach through state laws may minimize risk perception, and this is one strategy that can be considered in areas of high HIV incidence to reach the goal of eliminating perinatal HIV transmission in the United States.

  12. An Empirical Comparison of Competing Factor Structures for the Repeatable Battery for the Assessment of Neuropsychological Status: A Project FRONTIER Study†

    Science.gov (United States)

    Torrence, Nicole D.; John, Samantha E.; Gavett, Brandon E.; O'Bryant, Sid E.

    2016-01-01

    The original factor structure of the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) has received little empirical support, but at least eight alternative factor structures have been identified in the literature. The current study used confirmatory factor analysis to compare the original RBANS model with eight alternatives, which were adjusted to include a general factor. Participant data were obtained from Project FRONTIER, an epidemiological study of rural health, and comprised 341 adults (229 women, 112 men) with mean age of 61.2 years (SD = 12.1) and mean education of 12.4 years (SD = 3.3). A bifactor version of the model proposed by Duff and colleagues provided the best fit to the data (CFI = 0.98; root-mean-squared error of approximation = 0.07), but required further modification to produce appropriate factor loadings. The results support the inclusion of a general factor and provide partial replication of the Duff and colleagues RBANS model. PMID:26429558

  13. Analysis of genetic diversity and population structure of oil palm (Elaeis guineensis) from China and Malaysia based on species-specific simple sequence repeat markers.

    Science.gov (United States)

    Zhou, L X; Xiao, Y; Xia, W; Yang, Y D

    2015-12-08

    Genetic diversity and patterns of population structure of the 94 oil palm lines were investigated using species-specific simple sequence repeat (SSR) markers. We designed primers for 63 SSR loci based on their flanking sequences and conducted amplification in 94 oil palm DNA samples. The amplification result showed that a relatively high level of genetic diversity was observed between oil palm individuals according a set of 21 polymorphic microsatellite loci. The observed heterozygosity (Ho) was 0.3683 and 0.4035, with an average of 0.3859. The Ho value was a reliable determinant of the discriminatory power of the SSR primer combinations. The principal component analysis and unweighted pair-group method with arithmetic averaging cluster analysis showed the 94 oil palm lines were grouped into one cluster. These results demonstrated that the oil palm in Hainan Province of China and the germplasm introduced from Malaysia may be from the same source. The SSR protocol was effective and reliable for assessing the genetic diversity of oil palm. Knowledge of the genetic diversity and population structure will be crucial for establishing appropriate management stocks for this species.

  14. Crystal Structure of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Csn2 Protein Revealed Ca[superscript 2+]-dependent Double-stranded DNA Binding Activity

    Energy Technology Data Exchange (ETDEWEB)

    Nam, Ki Hyun; Kurinov, Igor; Ke, Ailong (Cornell); (NWU)

    2012-05-22

    Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein genes (cas genes) are widespread in bacteria and archaea. They form a line of RNA-based immunity to eradicate invading bacteriophages and malicious plasmids. A key molecular event during this process is the acquisition of new spacers into the CRISPR loci to guide the selective degradation of the matching foreign genetic elements. Csn2 is a Nmeni subtype-specific cas gene required for new spacer acquisition. Here we characterize the Enterococcus faecalis Csn2 protein as a double-stranded (ds-) DNA-binding protein and report its 2.7 {angstrom} tetrameric ring structure. The inner circle of the Csn2 tetrameric ring is {approx}26 {angstrom} wide and populated with conserved lysine residues poised for nonspecific interactions with ds-DNA. Each Csn2 protomer contains an {alpha}/{beta} domain and an {alpha}-helical domain; significant hinge motion was observed between these two domains. Ca{sup 2+} was located at strategic positions in the oligomerization interface. We further showed that removal of Ca{sup 2+} ions altered the oligomerization state of Csn2, which in turn severely decreased its affinity for ds-DNA. In summary, our results provided the first insight into the function of the Csn2 protein in CRISPR adaptation by revealing that it is a ds-DNA-binding protein functioning at the quaternary structure level and regulated by Ca{sup 2+} ions.

  15. Analysis of genetic diversity and population structure of peanut cultivars and breeding lines from China, India and the US using simple sequence repeat markers.

    Science.gov (United States)

    Wang, Hui; Khera, Pawan; Huang, Bingyan; Yuan, Mei; Katam, Ramesh; Zhuang, Weijian; Harris-Shultz, Karen; Moore, Kim M; Culbreath, Albert K; Zhang, Xinyou; Varshney, Rajeev K; Xie, Lianhui; Guo, Baozhu

    2016-05-01

    Cultivated peanut is grown worldwide as rich-source of oil and protein. A broad genetic base is needed for cultivar improvement. The objectives of this study were to develop highly informative simple sequence repeat (SSR) markers and to assess the genetic diversity and population structure of peanut cultivars and breeding lines from different breeding programs in China, India and the US. A total of 111 SSR markers were selected for this study, resulting in a total of 472 alleles. The mean values of gene diversity and polymorphic information content (PIC) were 0.480 and 0.429, respectively. Country-wise analysis revealed that alleles per locus in three countries were similar. The mean gene diversity in the US, China and India was 0.363, 0.489 and 0.47 with an average PIC of 0.323, 0.43 and 0.412, respectively. Genetic analysis using the STRUCTURE divided these peanut lines into two populations (P1, P2), which was consistent with the dendrogram based on genetic distance (G1, G2) and the clustering of principal component analysis. The groupings were related to peanut market types and the geographic origin with a few admixtures. The results could be used by breeding programs to assess the genetic diversity of breeding materials to broaden the genetic base and for molecular genetics studies.

  16. Analysis of genetic diversity and population structure of peanut cultivars and breeding lines from China, India and the US using simple sequence repeat markers

    Institute of Scientific and Technical Information of China (English)

    Hui Wang; Xinyou Zhang; Rajeev K. Varshney; Lianhui Xie; Baozhu Guo; Pawan Khera; Bingyan Huang; Mei Yuan; Ramesh Katam; Weijian Zhuang; Karen Harris-Shultz; Kim M. Moore; Albert K. Culbreath

    2016-01-01

    Cultivated peanut is grown worldwide as rich-source of oil and protein. A broad genetic base is needed for cultivar improvement. The objectives of this study were to develop highly informative simple sequence repeat (SSR) markers and to assess the genetic diversity and population structure of peanut cultivars and breeding lines from different breeding programs in China, India and the US. A total of 111 SSR markers were selected for this study, resulting in a total of 472 alleles. The mean values of gene diversity and polymorphic information content (PIC) were 0.480 and 0.429, respectively. Country-wise analysis revealed that alleles per locus in three countries were similar. The mean gene diversity in the US, China and India was 0.363, 0.489 and 0.47 with an average PIC of 0.323, 0.43 and 0.412, respectively. Genetic analysis using the STRUCTURE divided these peanut lines into two populations (P1, P2), which was consistent with the dendro-gram based on genetic distance (G1, G2) and the clustering of principal component analysis. The groupings were related to peanut market types and the geographic origin with a few admixtures. The results could be used by breeding programs to assess the genetic diversity of breeding materials to broaden the genetic base and for molecular genetics studies.

  17. [Conformational polymorphysm of G-rich fragments of DNA Alu-repeats. II. the putative role of G-quadruplex structures in genomic rearrangements].

    Science.gov (United States)

    Varizhuk, A M; Sekridova, A V; Tankevich, M V; Podgorsky, V S; Smirnov, I P; Pozmogova, G E

    2016-11-01

    Three evolutionary conserved sites of Alu repeats (PQS2, PQS3 and PQS4) were shown to form stable inter- and intramolecular G-quadruplexes (GQs) in vitro. Structures and topologies of these GQs were elucidated using spectral methods. Self-association of G-rich Alu fragments was studied. Dimeric GQ formation from two distal identical or different putative quadruplex sites - (PQS2)2, (PQS3)2 or PQS2-PQS3 - within one lengthy DNA strand was demonstrated by a FRET-based method. Oligomer PQS4 (folded into a parallel intramolecular GQ) was shown to form stacks of quadruplexes that are stabilized by stacking interactions of external G-tetrads (this was confirmed by DOSY NMR, AFM microscopy and differential CD spectroscopy). Comparative analysis of the properties of various GQs allowed us to put forward a hypothesis of two general mechanisms of intermolecular GQ-dependant genomic rearrangements: 1) formation of a dimeric GQs; 2) association of pre-folded intramolecular parallel GQs from different strands into GQ-stacks. Thus, the observed co-localization of G-rich motifs of Alu elements with double-strand break hotspots and rearrangement hotspots may be accounted for by the specific secondary structure of these motifs. At the same time, this is likely primarily due to high abundance of such G-rich Alu fragments in the genome.

  18. Crystal structure of clustered regularly interspaced short palindromic repeats (CRISPR)-associated Csn2 protein revealed Ca2+-dependent double-stranded DNA binding activity.

    Science.gov (United States)

    Nam, Ki Hyun; Kurinov, Igor; Ke, Ailong

    2011-09-02

    Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein genes (cas genes) are widespread in bacteria and archaea. They form a line of RNA-based immunity to eradicate invading bacteriophages and malicious plasmids. A key molecular event during this process is the acquisition of new spacers into the CRISPR loci to guide the selective degradation of the matching foreign genetic elements. Csn2 is a Nmeni subtype-specific cas gene required for new spacer acquisition. Here we characterize the Enterococcus faecalis Csn2 protein as a double-stranded (ds-) DNA-binding protein and report its 2.7 Å tetrameric ring structure. The inner circle of the Csn2 tetrameric ring is ∼26 Å wide and populated with conserved lysine residues poised for nonspecific interactions with ds-DNA. Each Csn2 protomer contains an α/β domain and an α-helical domain; significant hinge motion was observed between these two domains. Ca(2+) was located at strategic positions in the oligomerization interface. We further showed that removal of Ca(2+) ions altered the oligomerization state of Csn2, which in turn severely decreased its affinity for ds-DNA. In summary, our results provided the first insight into the function of the Csn2 protein in CRISPR adaptation by revealing that it is a ds-DNA-binding protein functioning at the quaternary structure level and regulated by Ca(2+) ions.

  19. Automated quality checks on repeat prescribing.

    OpenAIRE

    Rogers, Jeremy E; Wroe, Christopher J; Roberts, Angus; Swallow, Angela; Stables, David; Cantrill, Judith A; Rector, Alan L.

    2003-01-01

    BACKGROUND: Good clinical practice in primary care includes periodic review of repeat prescriptions. Markers of prescriptions that may need review have been described, but manually checking all repeat prescriptions against the markers would be impractical. AIM: To investigate the feasibility of computerising the application of repeat prescribing quality checks to electronic patient records in United Kingdom (UK) primary care. DESIGN OF STUDY: Software performance test against benchmark manual...

  20. Trends in resource utilization by children with neurological impairment in the United States inpatient health care system: a repeat cross-sectional study.

    Directory of Open Access Journals (Sweden)

    Jay G Berry

    2012-01-01

    Full Text Available BACKGROUND: Care advances in the United States (US have led to improved survival of children with neurological impairment (NI. Children with NI may account for an increasing proportion of hospital resources. However, this assumption has not been tested at a national level. METHODS AND FINDINGS: We conducted a study of 25,747,016 US hospitalizations of children recorded in the Kids' Inpatient Database (years 1997, 2000, 2003, and 2006. Children with NI were identified with International Classification of Diseases, 9th Revision, Clinical Modification diagnoses resulting in functional and/or intellectual impairment. We assessed trends in inpatient resource utilization for children with NI with a Mantel-Haenszel chi-square test using all 4 y of data combined. Across the 4 y combined, children with NI accounted for 5.2% (1,338,590 of all hospitalizations. Epilepsy (52.2% [n = 538,978] and cerebral palsy (15.9% [n = 164,665] were the most prevalent NI diagnoses. The proportion of hospitalizations attributable to children with NI did not change significantly (p = 0.32 over time. In 2006, children with NI accounted for 5.3% (n = 345,621 of all hospitalizations, 13.9% (n = 3.4 million of bed days, and 21.6% (US$17.7 billion of all hospital charges within all hospitals. Over time, the proportion of hospitalizations attributable to children with NI decreased within non-children's hospitals (3.0% [n = 146,324] in 1997 to 2.5% [n = 113,097] in 2006, p<.001 and increased within children's hospitals (11.7% [n = 179,324] in 1997 to 13.5% [n = 209,708] in 2006, p<0.001. In 2006, children with NI accounted for 24.7% (2.1 million of bed days and 29.0% (US$12.0 billion of hospital charges within children's hospitals. CONCLUSIONS: Children with NI account for a substantial proportion of inpatient resources utilized in the US. Their impact is growing within children's hospitals. We must ensure that the current health care system is staffed, educated, and equipped to

  1. Ising Model Reprogramming of a Repeat Protein's Equilibrium Unfolding Pathway.

    Science.gov (United States)

    Millership, C; Phillips, J J; Main, E R G

    2016-05-08

    Repeat proteins are formed from units of 20-40 aa that stack together into quasi one-dimensional non-globular structures. This modular repetitive construction means that, unlike globular proteins, a repeat protein's equilibrium folding and thus thermodynamic stability can be analysed using linear Ising models. Typically, homozipper Ising models have been used. These treat the repeat protein as a series of identical interacting subunits (the repeated motifs) that couple together to form the folded protein. However, they cannot describe subunits of differing stabilities. Here we show that a more sophisticated heteropolymer Ising model can be constructed and fitted to two new helix deletion series of consensus tetratricopeptide repeat proteins (CTPRs). This analysis, showing an asymmetric spread of stability between helices within CTPR ensembles, coupled with the Ising model's predictive qualities was then used to guide reprogramming of the unfolding pathway of a variant CTPR protein. The designed behaviour was engineered by introducing destabilising mutations that increased the thermodynamic asymmetry within a CTPR ensemble. The asymmetry caused the terminal α-helix to thermodynamically uncouple from the rest of the protein and preferentially unfold. This produced a specific, highly populated stable intermediate with a putative dimerisation interface. As such it is the first step in designing repeat proteins with function regulated by a conformational switch. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  2. Occupational structure and socioeconomic inequality: a comparative study between Brazil and the United States

    Directory of Open Access Journals (Sweden)

    Alexandre Gori Maia

    2015-08-01

    Full Text Available ABSTRACTThis paper explores how occupational structure is associated with economic inequality in Brazil in comparison to the United States. Changes in the Brazilian and American occupational structures between 1983 and 2011 are investigated in order to assess how closely they generate high socioeconomic inequalities. The effects of education, age, gender and race on occupational attainment are taken into account. Highlights of the results include: (1 a higher level of socioeconomic development in the American occupational structure, reflecting huge socioeconomic differences between these countries; (2 a tenuous convergence between the Brazilian and American occupational structures; (3 a significant decrease in the net impacts of education, age, gender and race on occupational attainment (i.e., reduced social stratification in both countries. These results suggest the analytical worth of considering occupational structure as a significant intermediate variable affecting the level of socioeconomic inequality within a country over time, as well as between two countries at a given point in time.

  3. Orthographic units in the absence of visual processing: Evidence from sublexical structure in braille.

    Science.gov (United States)

    Fischer-Baum, Simon; Englebretson, Robert

    2016-08-01

    Reading relies on the recognition of units larger than single letters and smaller than whole words. Previous research has linked sublexical structures in reading to properties of the visual system, specifically on the parallel processing of letters that the visual system enables. But whether the visual system is essential for this to happen, or whether the recognition of sublexical structures may emerge by other means, is an open question. To address this question, we investigate braille, a writing system that relies exclusively on the tactile rather than the visual modality. We provide experimental evidence demonstrating that adult readers of (English) braille are sensitive to sublexical units. Contrary to prior assumptions in the braille research literature, we find strong evidence that braille readers do indeed access sublexical structure, namely the processing of multi-cell contractions as single orthographic units and the recognition of morphemes within morphologically-complex words. Therefore, we conclude that the recognition of sublexical structure is not exclusively tied to the visual system. However, our findings also suggest that there are aspects of morphological processing on which braille and print readers differ, and that these differences may, crucially, be related to reading using the tactile rather than the visual sensory modality.

  4. The secondary structure of the R region of a murine leukemia virus is important for stimulation of long terminal repeat-driven gene expression.

    Science.gov (United States)

    Cupelli, L; Okenquist, S A; Trubetskoy, A; Lenz, J

    1998-10-01

    In addition to their role in reverse transcription, the R-region sequences of some retroviruses affect viral transcription. The first 28 nucleotides of the R region within the long terminal repeat (LTR) of the murine type C retrovirus SL3 were predicted to form a stem-loop structure. We tested whether this structure affected the transcriptional activity of the viral LTR. Mutations that altered either side of the stem and thus disrupted base pairing were generated. These decreased the level of expression of a reporter gene under the control of viral LTR sequences about 5-fold in transient expression assays and 10-fold in cells stably transformed with the LTR-reporter plasmids. We also generated a compensatory mutant in which both the ascending and descending sides of the stem were mutated such that the nucleotide sequence was different but the predicted secondary structure was maintained. Most of the activity of the wild-type SL3 element was restored in this mutant. Thus, the stem-loop structure was important for the maximum activity of the SL3 LTR. Primer extension analysis indicated that the stem-loop structure affected the levels of cytoplasmic RNA. Nuclear run-on assays indicated that deletion of the R region had a small effect on transcriptional initiation and no effect on RNA polymerase processivity. Thus, the main effect of the R-region element was on one or more steps that occurred after the template was transcribed by RNA polymerase. This finding implied that the main function of the R-region element involved RNA processing. R-region sequences of human immunodeficiency virus type 1 or mouse mammary tumor virus could not replace the SL3 element. R-region sequences from an avian reticuloendotheliosis virus partially substituted for the SL3 sequences. R-region sequences from Moloney murine leukemia virus or feline leukemia virus did function in place of the SL3 element. Thus, the R region element appears to be a general feature of the mammalian type C genus of

  5. Genetic diversity and population structure among pea (Pisum sativum L.) cultivars as revealed by simple sequence repeat and novel genic markers.

    Science.gov (United States)

    Jain, Shalu; Kumar, Ajay; Mamidi, Sujan; McPhee, Kevin

    2014-10-01

    Field pea (Pisum sativum L.) is an important cool season legume crop widely grown around the world. This research provides a basis for selection of pea germplasm across geographical regions in current and future breeding and genetic mapping efforts for pea improvement. Eleven novel genic markers were developed from pea expressed sequence tag (EST) sequences having significant similarity with gene calls from Medicago truncatula spanning at least one intron. In this study, 96 cultivars widely grown or used in breeding programs in the USA and Canada were analyzed for genetic diversity using 31 microsatellite or simple sequence repeat (SSR) and 11 novel EST-derived genic markers. The polymorphic information content varied from 0.01-0.56 among SSR markers and 0.04-0.43 among genic markers. The results showed that SSR and EST-derived genic markers displayed one or more highly reproducible, multi-allelic, and easy to score loci ranging from 200 to 700 bp in size. Genetic diversity was assessed through unweighted neighbor-joining method, and 96 varieties were grouped into three main clusters based on the dissimilarity matrix. Four subpopulations were determined through STRUCTURE analysis with no significant geographic separation of the subpopulations. The findings of the present study can be used to select diverse genotypes to be used as parents of crosses aimed for breeding improved pea cultivars.

  6. Water proton configurations in structures I, II, and H clathrate hydrate unit cells.

    Science.gov (United States)

    Takeuchi, Fumihito; Hiratsuka, Masaki; Ohmura, Ryo; Alavi, Saman; Sum, Amadeu K; Yasuoka, Kenji

    2013-03-28

    Position and orientation of water protons need to be specified when the molecular simulation studies are performed for clathrate hydrates. Positions of oxygen atoms in water are experimentally determined by X-ray diffraction analysis of clathrate hydrate structures, but positions of water hydrogen atoms in the lattice are disordered. This study reports a determination of the water proton coordinates in unit cell of structure I (sI), II (sII), and H (sH) clathrate hydrates that satisfy the ice rules, have the lowest potential energy configuration for the protons, and give a net zero dipole moment. Possible proton coordinates in the unit cell were chosen by analyzing the symmetry of protons on the hexagonal or pentagonal faces in the hydrate cages and generating all possible proton distributions which satisfy the ice rules. We found that in the sI and sII unit cells, proton distributions with small net dipole moments have fairly narrow potential energy spreads of about 1 kJ∕mol. The total Coulomb potential on a test unit charge placed in the cage center for the minimum energy∕minimum dipole unit cell configurations was calculated. In the sI small cages, the Coulomb potential energy spread in each class of cage is less than 0.1 kJ∕mol, while the potential energy spread increases to values up to 6 kJ∕mol in sH and 15 kJ∕mol in the sII cages. The guest environments inside the cages can therefore be substantially different in the sII case. Cartesian coordinates for oxygen and hydrogen atoms in the sI, sII, and sH unit cells are reported for reference.

  7. Family structure and breakfast consumption of 11-15 year old boys and girls in Scotland, 1994-2010: a repeated cross-sectional study

    Directory of Open Access Journals (Sweden)

    Levin Kate A

    2012-03-01

    Full Text Available Abstract Background The benefits of breakfast during childhood and adolescence have been reported previously though few studies have considered family structure inequalities in breakfast consumption. The proportion of young people living in non-traditional family types has increased in recent years, strengthening the need to describe and monitor the impact of the changing family unit on adolescent breakfast consumption. This study aimed to describe changes in daily breakfast consumption among adolescents in Scotland between 1994 and 2010, while also considering family structure inequalities, and the degree to which these have changed over time. Methods Data from the 1994, 1998, 2002, 2006 and 2010 Scottish Health Behaviour in School-aged Children (HBSC surveys were analysed using logistic multilevel regression models for binary outcome variable daily breakfast consumption. Results Daily breakfast consumption among adolescents increased between 1994 and 2010, although there were differences by age and sex. In fact those aged over 14.5 years saw decreases in breakfast consumption, and girls saw significantly larger increases than boys. Daily breakfast consumption was more prevalent among adolescents from 'both parent' families, with lowest prevalence among those from single parent families. Trends in daily breakfast consumption between 1994 and 2010 also varied by family structure. While prevalence of daily breakfast consumption increased among those living with 'both parents', the largest proportion of the population, prevalence decreased over time among adolescents of single parent families, and particularly among those living with their father. Conclusions Family structure inequalities in daily breakfast consumption increased between 1994 and 2010, while breakfast consumption across the population as a whole increased. As the proportion of young people living in an alternative family structure continues to grow it is important to understand why

  8. A taxonomy of state public health preparedness units: an empirical examination of organizational structure.

    Science.gov (United States)

    Menachemi, Nir; Yeager, Valerie A; Duncan, W Jack; Katholi, Charles R; Ginter, Peter M

    2012-01-01

    State public health preparedness units (SPHPUs) were developed in response to federal funding to improve response to disasters: a responsibility that had not traditionally been within the purview of public health. The SPHPUs were created within the existing public health organizational structure, and their placement may have implications for how the unit functions, how communication takes place, and ultimately how well the key responsibilities are performed. This study empirically identifies a taxonomy of similarly structured SPHPUs and examines whether this structure is associated with state geographic, demographic, and threat-vulnerability characteristics. Data representing each SPHPU were extracted from publically available sources, including organizational charts and emergency preparedness plans for 2009. A cross-sectional segmentation analysis was conducted of variables representing structural attributes. Fifty state public health departments. Variables representing "span of control" and "hierarchal levels" were extracted from organizational charts. Structural "complexity" and "centralization" were extracted from state emergency preparedness documents and other secondary sources. On average, 6.6 people report to the same manager as the SPHPU director; 2.1 levels separate the SPHPU director from the state health officer; and a mean of 13.5 agencies collaborate with SPHPU during a disaster. Despite considerable variability in how SPHPUs had been structured, results of the cluster and principal component analysis identified 7 similarly structured groups. Neither the taxonomic groups nor the individual variables representing structure were found to be associated with state characteristics, including threat vulnerabilities. Our finding supports the hypothesis that SPHPUs are seemingly inadvertently (eg, not strategically) organized. This taxonomy provides the basis for which future research can examine how SPHPU structure relates to performance measures and

  9. An evaluation of a structured learning program as a component of the clinical practicum in undergraduate nurse education: A repeated measures analysis.

    Science.gov (United States)

    Watt, Elizabeth; Murphy, Maria; MacDonald, Lee; Pascoe, Elizabeth; Storen, Heather; Scanlon, Andrew

    2016-01-01

    There is evidence that nursing students experience stress and anxiety and a reduction in self-efficacy when undertaking clinical placements. Previous reports have identified that a structured three-day program within the Bachelor of Nursing (BN) clinical practicum reduces the students self-report of anxiety and increases self-efficacy. However, it is unreported whether these improved outcomes are sustained for the duration of the clinical placement. The aim of this study was to evaluate the duration of the effect of a three-day structured learning program within the clinical placement on final year Bachelor of Nursing student's report of anxiety and self-efficacy pre- and post-program participation in this intervention and following completion of the clinical practicum. A repeated measures design. University-based Clinical School of Nursing, acute care clinical practicum. Final year Bachelor of Nursing students. The intervention comprised the three-day program on starting the clinical practicum. A questionnaire included the anxiety subscale of The Hospital Anxiety & Depression Scale (The HAD) and the General Self-Efficacy Scale (GSES-12). The questionnaire was completed on day one (time one), upon completion of the three-day program (time two) and upon completion of placement on day 18 (time three). The questionnaire response rate varied over time. There was a statistically significant effect in reducing anxiety over time: F(1.73,74.46)=25.20, plearning program and the benefit of the intervention is sustained for the clinical placement duration. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. The Influenza A Virus Non-structural Protein NS1 Upregulates The Expression of Collagen Triple Helix Repeat Containing 1 Protein.

    Science.gov (United States)

    Zhu, C; Peng, G; Yi, W; Song, H; Liu, F; Liu, X

    2016-12-01

    Influenza A virus (IAV) infection induces a strong immune response and regulates the expression of many host proteins. The collagen triple helix repeat containing 1 (CTHRC1) protein is a secreted protein that exhibits increased expression during the viral infection process. However, the regulatory function of IAV on CTHRC1 expression is obscure. In this study, we investigated the effect of IAV on CTHRC1 expression and its regulatory mechanism. A total of 106 serum specimens from healthy people and 80 serum specimens from patients infected with IAV were collected. The CTHRC1 levels in the sera from the IVA patients and healthy individuals were measured using an enzyme-linked immunosorbent assay (ELISA), and the differences were statistically analysed. A549 cells were infected with the IAV or delNS1 virus. Additionally, A549 cells were cotransfected with a eukaryotic non-structural NS1 protein gene expression plasmid and the CTHRC1 gene promoter reporter plasmid (pCTHRC1-Luc), and, the luciferase activities were assessed. The CTHRC1 mRNA and protein expression were detected using reverse transcription-polymerase chain reaction (RT-PCR) and Western blotting, respectively. The serum CTHRC1 level was significantly higher in the IAV patients than in the healthy individuals. IAV upregulated the CTHRC1 mRNA and protein expression. The non-structural NS1 protein specifically activated CTHRC1 gene promoter activity and upregulated CTHRC1 mRNA and protein expression. The activation function had a dose-dependent effect, indicating that influenza virus upregulated CTHRC1 expression through its NS1 protein.

  11. Accelerating large-scale protein structure alignments with graphics processing units

    Directory of Open Access Journals (Sweden)

    Pang Bin

    2012-02-01

    Full Text Available Abstract Background Large-scale protein structure alignment, an indispensable tool to structural bioinformatics, poses a tremendous challenge on computational resources. To ensure structure alignment accuracy and efficiency, efforts have been made to parallelize traditional alignment algorithms in grid environments. However, these solutions are costly and of limited accessibility. Others trade alignment quality for speedup by using high-level characteristics of structure fragments for structure comparisons. Findings We present ppsAlign, a parallel protein structure Alignment framework designed and optimized to exploit the parallelism of Graphics Processing Units (GPUs. As a general-purpose GPU platform, ppsAlign could take many concurrent methods, such as TM-align and Fr-TM-align, into the parallelized algorithm design. We evaluated ppsAlign on an NVIDIA Tesla C2050 GPU card, and compared it with existing software solutions running on an AMD dual-core CPU. We observed a 36-fold speedup over TM-align, a 65-fold speedup over Fr-TM-align, and a 40-fold speedup over MAMMOTH. Conclusions ppsAlign is a high-performance protein structure alignment tool designed to tackle the computational complexity issues from protein structural data. The solution presented in this paper allows large-scale structure comparisons to be performed using massive parallel computing power of GPU.

  12. Searching for the simplest structural units to describe the three-dimensional structure of proteins

    Science.gov (United States)

    Perczel, András; Csizmadia, Imre G.

    Ab initio computations have been carried out during the past several years on diamides of single amino acids (HCO-NHCHR-CONH2 where R=H (glycine), -CH3 (alanine), -CH(CH3)2 (valine) and -CH2OH (serine)) exploring all possible backbone and side chain conformations. Selected conformations were studied in our laboratory on threonine (R=CH(CH3)OH), cystein (R=CH2-SH) and phenyl-alanine (R=CH2-CH5H6) diamides. Tri-, tetra-, penta-, hexa- and hepta-amide systems of poly-L-alanine (H-(CONH-CHCH3-CONH)n-H 2≤n≤6) were also investigated at selected backbone conformations. All these studies confirmed the results of multidimensional conformation analyses: the jth amino acid residue in a polypeptide has a maximum of nine (9) discrete backbone conformations. These structures correspond to nine conformational centres on the 2D-Ramachandran map. On the basis of this rinding, it can be shown that the folded secondary structure of any protein with known internal coordinates, can be described in terms of these nine discrete conformation types.

  13. The Impact of the Demand for Integration in the Large Multi-Business Unit Firm on the IT Organization Structure

    Science.gov (United States)

    Larson, Eric Christopher

    2012-01-01

    Large, multi-business unit firms are decentralizing their overall corporate structures. At the same time, the structures of their IT organizations are becoming more centralized. This is contrary to current wisdom that the IT organization structure will mimic the structure of the corporation, all else being equal. Because the general business…

  14. Population Structure of Listeria monocytogenes Serotype 4b Isolates from Sporadic Human Listeriosis in the United States, 2003-2008

    Science.gov (United States)

    Listeria monocytogenes can cause severe foodborne disease (listeriosis). Serotype 4b strains have resulted in numerous outbreaks, repeatedly involving three epidemic clones (ECI, ECII, and ECIa). Little is known about population structure of L. monocytogenes serotype 4b from sporadic listeriosis, ev...

  15. Copy number of tandem direct repeats within the inverted repeats of Marek's disease virus DNA.

    Science.gov (United States)

    Kanamori, A; Nakajima, K; Ikuta, K; Ueda, S; Kato, S; Hirai, K

    1986-12-01

    We previously reported that DNA of the oncogenic strain BC-1 of Marek's disease virus serotype 1 (MDV1) contains three units of tandem direct repeats with 132 base pair (bp) repeats within the inverted repeats of the long regions of the MDV1 genome, whereas the attenuated, nononcogenic viral DNA contains multiple units of tandem direct repeats (Maotani et al., 1986). In the present study, the difference in the copy numbers of 132 bp repeats of oncogenic and nononcogenic MDV1 DNAs in other strains of MDV1 was investigated by Southern blot hybridization. The main copy numbers in different oncogenic MDV1 strains differed: those of BC-1, JM and highly oncogenic Md5 were 3, 5 to 12 and 2, respectively. The viral DNA population with two units of repeats was small, but detectable, in cells infected with either the oncogenic BC-1 or JM strain. The MDV1 DNA in various MD cell lines contained either two units or both two and three units of repeats. The significance of the copy number of repeats in oncogenicity of MDV1 is discussed.

  16. Development of a Multiple Loci Variable Number of Tandem Repeats Analysis (MLVA to Unravel the Intra-Pathovar Structure of Pseudomonas syringae pv. actinidiae Populations Worldwide.

    Directory of Open Access Journals (Sweden)

    Serena Ciarroni

    Full Text Available The bacterial canker of kiwifruit by Pseudomonas syringae pv. actinidiae is an emblematic example of a catastrophic disease of fruit crops. In 2008 a new, extremely virulent form of the pathogen emerged and rapidly devastated many Actinidia spp. orchards all over the world. In order to understand differences in populations within this pathovar and to elucidate their diffusion and movements on world scale, it is necessary to be able to quickly and on a routine basis compare new isolates with previous records. In this report a worldwide collection of 142 strains was analyzed by MLVA, chosen as investigative technique for its efficacy, reproducibility, simplicity and low cost. A panel of 13 Variable Number of Tandem Repeats (VNTR loci was identified and used to describe the pathogen population. The MLVA clustering is highly congruent with the population structure as previously established by other molecular approaches including whole genome sequencing and correlates with geographic origin, time of isolation and virulence. For convenience, we divided the VNTR loci in two panels. Panel 1 assay, using six loci, recognizes 23 different haplotypes, clustered into ten complexes with highest congruence with previous classifications. Panel 2, with seven VNTR loci, provides discriminatory power. Using the total set of 13 VNTR loci, 58 haplotypes can be distinguished. The recent hypervirulent type shows very limited diversity and includes, beside the strains from Europe, New Zealand and Chile, a few strains from Shaanxi, China. A broad genetic variability is observed in China, but different types are also retrievable in Japan and Korea. The low virulent strains cluster together and are very different from the other MLVA genotypes. Data were used to generate a public database in MLVAbank. MLVA represents a very promising first-line assay for large-scale routine genotyping, prior to whole genome sequencing of only the most relevant samples.

  17. Development of a Multiple Loci Variable Number of Tandem Repeats Analysis (MLVA) to Unravel the Intra-Pathovar Structure of Pseudomonas syringae pv. actinidiae Populations Worldwide.

    Science.gov (United States)

    Ciarroni, Serena; Gallipoli, Lorenzo; Taratufolo, Maria C; Butler, Margi I; Poulter, Russell T M; Pourcel, Christine; Vergnaud, Gilles; Balestra, Giorgio M; Mazzaglia, Angelo

    2015-01-01

    The bacterial canker of kiwifruit by Pseudomonas syringae pv. actinidiae is an emblematic example of a catastrophic disease of fruit crops. In 2008 a new, extremely virulent form of the pathogen emerged and rapidly devastated many Actinidia spp. orchards all over the world. In order to understand differences in populations within this pathovar and to elucidate their diffusion and movements on world scale, it is necessary to be able to quickly and on a routine basis compare new isolates with previous records. In this report a worldwide collection of 142 strains was analyzed by MLVA, chosen as investigative technique for its efficacy, reproducibility, simplicity and low cost. A panel of 13 Variable Number of Tandem Repeats (VNTR) loci was identified and used to describe the pathogen population. The MLVA clustering is highly congruent with the population structure as previously established by other molecular approaches including whole genome sequencing and correlates with geographic origin, time of isolation and virulence. For convenience, we divided the VNTR loci in two panels. Panel 1 assay, using six loci, recognizes 23 different haplotypes, clustered into ten complexes with highest congruence with previous classifications. Panel 2, with seven VNTR loci, provides discriminatory power. Using the total set of 13 VNTR loci, 58 haplotypes can be distinguished. The recent hypervirulent type shows very limited diversity and includes, beside the strains from Europe, New Zealand and Chile, a few strains from Shaanxi, China. A broad genetic variability is observed in China, but different types are also retrievable in Japan and Korea. The low virulent strains cluster together and are very different from the other MLVA genotypes. Data were used to generate a public database in MLVAbank. MLVA represents a very promising first-line assay for large-scale routine genotyping, prior to whole genome sequencing of only the most relevant samples.

  18. Crystal structure and size-dependent neutralization properties of HK20, a human monoclonal antibody binding to the highly conserved heptad repeat 1 of gp41.

    Directory of Open Access Journals (Sweden)

    Charles Sabin

    Full Text Available The human monoclonal antibody (mAb HK20 neutralizes a broad spectrum of primary HIV-1 isolates by targeting the highly conserved heptad repeat 1 (HR1 of gp41, which is transiently exposed during HIV-1 entry. Here we present the crystal structure of the HK20 Fab in complex with a gp41 mimetic 5-Helix at 2.3 Å resolution. HK20 employs its heavy chain CDR H2 and H3 loops to bind into a conserved hydrophobic HR1 pocket that is occupied by HR2 residues in the gp41 post fusion conformation. Compared to the previously described HR1-specific mAb D5, HK20 approaches its epitope with a different angle which might favor epitope access and thus contribute to its higher neutralization breadth and potency. Comparison of the neutralization activities of HK20 IgG, Fab and scFv employing both single cycle and multiple cycle neutralization assays revealed much higher potencies for the smaller Fab and scFv over IgG, implying that the target site is difficult to access for complete antibodies. Nevertheless, two thirds of sera from HIV-1 infected individuals contain significant titers of HK20-inhibiting antibodies. The breadth of neutralization of primary isolates across all clades, the higher potencies for C-clade viruses and the targeting of a distinct site as compared to the fusion inhibitor T-20 demonstrate the potential of HK20 scFv as a therapeutic tool.

  19. Some remarks on the influence of temperature-variations, non-linearities, repeatability and ageing on modal-analysis for structural health monitoring of real bridges

    Directory of Open Access Journals (Sweden)

    Maas Stefan

    2015-01-01

    Full Text Available Structural Health Monitoring (SHM intends to identify damage by changes of characteristics as for instance the modal parameters. The eigenfrequencies, mode-shapes and damping-values are either directly used as damage indicators or the changes of derived parameters are analysed, such as e.g. flexibilities or updated finite element models. One common way is a continuous monitoring under environmental excitation forces, such as wind or traffic, i.e. the so-called output-only modal analysis. Alternatively, a forced measured external excitation in distinct time-intervals may be used for input-output modal analysis. Both methods are limited by the precision or the repeatability under real-life conditions at site. The paper will summarize several field tests of artificially step-by-step damaged bridges prior to their final demolishment and it will show the changes of eigenfrequencies due to induced artificial damage. Additionally, some results of a monitoring campaign of a healthy bridge in Luxembourg are presented. Reinforced concrete shows non-linear behaviour in the sense that modal parameters depend on the excitation force amplitude, i.e. higher forces lead often to lower eigenfrequencies than smaller forces. Furthermore, the temperature of real bridges is neither constant in space nor in time, while for instance the stiffness of asphalt is strongly dependant on it. Finally, ageing as such can also change a bridge’s stiffness and its modal parameters, e.g. because creep and shrinkage of concrete or ageing of elastomeric bearing pads influence their modulus of elasticity. These effects cannot be considered as damage, though they influence the measurement of modal parameters and hinder damage detection.

  20. Repeat concussions in the national football league.

    Science.gov (United States)

    Casson, Ira R; Viano, David C; Powell, John W; Pellman, Elliot J

    2011-01-01

    Repeat concussion is an important issue in the National Football League (NFL). An initial description of repeat injuries was published for 6 years (1996-2001). The characteristics and frequency of repeat concussion in the NFL have not changed in the subsequent 6 years (2002-2007). Case control. From 1996 to 2007, concussions were reported using a standardized form documenting signs and symptoms, loss of consciousness and medical action taken. Data on repeat concussions were analyzed for the 12 years and compared between the 2 periods. In 2002-2007, 152 players had repeat concussions (vs 160 in 1996-2001); 44 had 3+ head injuries (vs 52). The positions most often associated with repeat concussion in 2002-2007 were the defensive secondary, kick unit, running back, and linebacker. The odds for repeat concussion were elevated for wide receivers, tight ends, and linebackers but lower than in the earlier period. During 2002-2007, over half of players with repeat concussion were removed from play, and fewer immediately returned (vs 1996-2001). The average duration between concussions was 1.25 years for 2002-2007 and 1.65 years for the 12-year period. Over 12 years, 7.6% of all repeat concussions occurred within 2 weeks of the prior concussion. The defensive secondary, kick unit, running back, and linebacker have the highest incidence of repeat concussion. During 2002-2007, more than half of players with repeat concussion were removed from play, and only a fraction immediately returned. Although concussion was managed more conservatively by team physicians in the recent 6 years, repeat concussions occurred at similar rates during both periods.

  1. Structural characterization and condition for measurement statistics preservation of a unital quantum operation

    Science.gov (United States)

    Lee, Kai-Yan; Fung, Chi-Hang Fred; Chau, H. F.

    2013-05-01

    We investigate the necessary and sufficient condition for a convex cone of positive semidefinite operators to be fixed by a unital quantum operation ϕ acting on finite-dimensional quantum states. By reducing this problem to the problem of simultaneous diagonalization of the Kraus operators associated with ϕ, we can completely characterize the kinds of quantum states that are fixed by ϕ. Our work has several applications. It gives a simple proof of the structural characterization of a unital quantum operation that acts on finite-dimensional quantum states—a result not explicitly mentioned in earlier studies. It also provides a necessary and sufficient condition for determining what kind of measurement statistics is preserved by a unital quantum operation. Finally, our result clarifies and extends the work of Størmer by giving a proof of a reduction theorem on the unassisted and entanglement-assisted classical capacities, coherent information, and minimal output Renyi entropy of a unital channel acting on a finite-dimensional quantum state.

  2. [Representational structure of intensive care for professionals working in mobile intensive care units].

    Science.gov (United States)

    do Nascimento, Keyla Cristiane; Gomes, Antônio Marcos Tosoli; Erdmann, Alacoque Lorenzini

    2013-02-01

    This qualitative study was performed based on the Social Representations Theory, using a structured approach. The objective was to analyze the social representations of intensive care for professionals who work in mobile intensive care units, given the determination of the central nucleus and the peripheral system. This study included the participation of 73 health care professionals from an Emergency Mobile Care Service. Data collection was performed through free association with the inducing term care for people in a life threatening situation, and analyzed using EVOC software. It is observed that a nucleus is structured in knowledge and responsibility, while contrasting elements present lexicons such as agility, care, stress, and humanization. The representational structure revealed by participants in this study refer particularly to the functionality of intensive care, distinguishing itself by the challenges and encouragements provided to anyone working in this area.

  3. Complex fragmentation and silicification structures in fault zones: quartz mineralization and repeated fragmentation along the Fountain Range Fault (Mt. Isa Inlier, Australia)

    Science.gov (United States)

    Seybold, Lina; Blenkinsop, Tom; Heuss, Soraya; Ord, Alison; Kruhl, Jörn H.

    2015-04-01

    In large-scale fault zones fracture networks are commonly generated by high volumes of pressurized fluids, followed by quartz precipitation. In this way large amounts of quartz are formed as microcrystalline masses and as complex vein systems, with partly highly different textures, as a result of different formation processes. Based on field and microstructural data and the quantification of vein patterns, the spatial and temporal connection between fragmentation, quartz crystallization and fluid and material flow along the Fountain Range Fault at Fountain Springs was investigated. Dextral strike-slip led to up to 25 km horizontal displacement along the fault. Due to various fragmentation and quartz formation processes, a ca. 100 m high, 80 - 100 m wide and km-long quartz ridge with numerous vein systems and variable microfabrics was formed. Locally, lenses of highly altered metamorphic wall-rocks occur in the quartz zone. Where exposed, the contact to wall rocks is sharp. Millimetre- to decimetre-thick quartz veins penetrate the wall-rocks only within metre distance from the contact. Several clearly distinguishable fine-grained reddish, brownish to dark and pigment-rich quartz masses form up to 50 m wide and up to several 100 m long steep lenses that build the major part of the silicified fault zone. A chronology can be established. Some of these lenses are oriented slightly oblique to the general trend of the quartz zone, in agreement with the supposed dextral strike slip along the fault. Numerous generations of typically µm-cm thick quartz veins transect the microcrystalline quartz masses and, locally, form anisotropic networks. In the quartz masses, angular fragments often composed of quartz with, again, internal fragmentation structures, indicate earlier fracturing and silicification events. Within the veins, quartz forms geodes, locally filled with fine-grained reddish quartz and palisade structures with feathery textures and fluid-inclusion zoning

  4. Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.

    Directory of Open Access Journals (Sweden)

    Charlotte Rehm

    Full Text Available In prokaryotes simple sequence repeats (SSRs with unit sizes of 1-5 nucleotides (nt are causative for phase and antigenic variation. Although an increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs of 6-9 nt are rare. In particular G-rich repeat sequences with the propensity to fold into G-quadruplex (G4 structures have received little attention. In silico analysis of prokaryotic genomes show putative G4 forming sequences to be abundant. This report focuses on a surprisingly enriched G-rich repeat of the type GGGNATC in Xanthomonas and cyanobacteria such as Nostoc. We studied in detail the genomes of Xanthomonas campestris pv. campestris ATCC 33913 (Xcc, Xanthomonas axonopodis pv. citri str. 306 (Xac, and Nostoc sp. strain PCC7120 (Ana. In all three organisms repeats are spread all over the genome with an over-representation in non-coding regions. Extensive variation of the number of repetitive units was observed with repeat numbers ranging from two up to 26 units. However a clear preference for four units was detected. The strong bias for four units coincides with the requirement of four consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus repeat sequences was found in biophysical studies utilizing CD spectroscopy. The G-rich repeats are preferably located between aligned open reading frames (ORFs and are under-represented in coding regions or between divergent ORFs. The G-rich repeats are preferentially located within a distance of 50 bp upstream of an ORF on the anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis of whole transcriptome sequence data showed that the majority of repeat sequences are transcribed. The genetic loci in the vicinity of repeat regions show increased genomic stability. In conclusion, we introduce and characterize a special class of highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria.

  5. Understanding the Functional Central Limit Theorems with Some Applications to Unit Root Testing with Structural Change

    Directory of Open Access Journals (Sweden)

    Juan Carlos Aquino

    2013-06-01

    Full Text Available The application of different unit root statistics is by now a standard practice in empirical work. Even when it is a practical issue, these statistics have complex nonstandard distributions depending on functionals of certain stochastic processes, and their derivations represent a barrier even for many theoretical econometricians. These derivations are based on rigorous and fundamental statistical tools which are not (very well known by standard econometricians. This paper aims to fill this gap by explaining in a simple way one of these fundamental tools: namely, the Functional Central Limit Theorem. To this end, this paper analyzes the foundations and applicability of two versions of the Functional Central Limit Theorem within the framework of a unit root with a structural break. Initial attention is focused on the probabilistic structure of the time series to be considered. Thereafter, attention is focused on the asymptotic theory for nonstationary time series proposed by Phillips (1987a, which is applied by Perron (1989 to study the effects of an (assumed exogenous structural break on the power of the augmented Dickey-Fuller test and by Zivot and Andrews (1992 to criticize the exogeneity assumption and propose a method for estimating an endogenous breakpoint. A systematic method for dealing with efficiency issues is introduced by Perron and Rodriguez (2003, which extends the Generalized Least Squares detrending approach due to Elliot et al. (1996. An empirical application is provided.

  6. Modeling the effect of soil structure on water flow and isoproturon dynamics in an agricultural field receiving repeated urban waste compost application.

    Science.gov (United States)

    Filipović, Vilim; Coquet, Yves; Pot, Valérie; Houot, Sabine; Benoit, Pierre

    2014-11-15

    Transport processes in soils are strongly affected by heterogeneity of soil hydraulic properties. Tillage practices and compost amendments can modify soil structure and create heterogeneity at the local scale within agricultural fields. The long-term field experiment QualiAgro (INRA-Veolia partnership 1998-2013) explores the impact of heterogeneity in soil structure created by tillage practices and compost application on transport processes. A modeling study was performed to evaluate how the presence of heterogeneity due to soil tillage and compost application affects water flow and pesticide dynamics in soil during a long-term period. The study was done on a plot receiving a co-compost of green wastes and sewage sludge (SGW) applied once every 2 years since 1998. The plot was cultivated with a biannual rotation of winter wheat-maize (except 1 year of barley) and a four-furrow moldboard plow was used for tillage. In each plot, wick lysimeter outflow and TDR probe data were collected at different depths from 2004, while tensiometer measurements were also conducted during 2007/2008. Isoproturon concentration was measured in lysimeter outflow since 2004. Detailed profile description was used to locate different soil structures in the profile, which was then implemented in the HYDRUS-2D model. Four zones were identified in the plowed layer: compacted clods with no visible macropores (Δ), non-compacted soil with visible macroporosity (Γ), interfurrows created by moldboard plowing containing crop residues and applied compost (IF), and the plow pan (PP) created by plowing repeatedly to the same depth. Isoproturon retention and degradation parameters were estimated from laboratory batch sorption and incubation experiments, respectively, for each structure independently. Water retention parameters were estimated from pressure plate laboratory measurements and hydraulic conductivity parameters were obtained from field tension infiltrometer experiments. Soil hydraulic

  7. Gentamicin binds to the megalin receptor as a competitive inhibitor using the common ligand binding motif of complement type repeats: insight from the nmr structure of the 10th complement type repeat domain alone and in complex with gentamicin

    NARCIS (Netherlands)

    Dagil, R.; O'Shea, C.; Nykjaer, A.; Bonvin, A.M.J.J.; Kragelund, B.B.

    2013-01-01

    Gentamicin is an aminoglycoside widely used in treatments of, in particular, enterococcal, mycobacterial, and severe Gram-negative bacterial infections. Large doses of gentamicin cause nephrotoxicity and ototoxicity, entering the cell via the receptor megalin. Until now, no structural information ha

  8. A Single-Unit Design Structure and Gender Differences in the Swimming World Championships

    OpenAIRE

    2014-01-01

    Four 50 meter male/female finals - the freestyle, butterfly, breaststroke, and backstroke - swum during individual events at the Swimming World Championships (SWCs) can be defined in four clusters. The aim of the present study was to use a single-unit design structure, in which the swimmer was defined at only one scale, to evaluate gender differences in start reaction times among elite swimmers in 50 m events. The top six male and female swimmers in the finals of four swimming stroke final ev...

  9. Quantum repeated games revisited

    CERN Document Server

    Frackiewicz, Piotr

    2011-01-01

    We present a scheme for playing quantum repeated 2x2 games based on the Marinatto and Weber's approach to quantum games. As a potential application, we study twice repeated Prisoner's Dilemma game. We show that results not available in classical game can be obtained when the game is played in the quantum way. Before we present our idea, we comment on the previous scheme of playing quantum repeated games.

  10. Use of the Primitive Unit Cell in Understanding Subtle Features of the Cubic Closest-Packed Structure

    Science.gov (United States)

    Hawkins, John A.; Rittenhouse, Jeffrey L.; Soper, Linda M.; Rittenhouse, Robert C.

    2008-01-01

    One of the most important crystal structures adopted by metals is characterized by the "abcabc"...stacking of close-packed layers. This structure is commonly referred to in textbooks as the cubic close-packed (ccp) or face-centered cubic (fcc) structure, since the entire lattice can be generated by replication of a face-centered cubic unit cell…

  11. 47 CFR 90.247 - Mobile repeater stations.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 5 2010-10-01 2010-10-01 false Mobile repeater stations. 90.247 Section 90.247... MOBILE RADIO SERVICES Non-Voice and Other Specialized Operations § 90.247 Mobile repeater stations. A... repeater to extend the communications range of hand-carried units subject to the following: (a)...

  12. Three Dimensional Structure of the Mars North Polar Basal Unit from MARSIS data

    Science.gov (United States)

    Frigeri, A.; Orosei, R.; Cartacci, M.; Cicchetti, A.; Mitri, G.; Giuppi, S.; Noschese, R.; Picardi, G.; Plaut, J.

    2012-04-01

    Mars Advanced Radar for Subsurface and Ionospheric Sounding (MARSIS) is an orbital subsurface sounder aboard ESA's Mars Express spacecraft . It transmits a low-frequency radar pulse that is capable of penetrating below the surface, and is reflected by subsurface dielectric discontinuities. MARSIS has been used to probe both the south and the north polar caps of Mars, revealing their thickness and structure. We report on the results of a campaign of observations of the north polar ice cap of Mars that took place between May and December 2011 in uniquely favorable conditions and produced data of unprecedented quality. The focus of this work is the so-called Basal Unit, a dark, ice-rich, complexely layered geologic unit lying stratigraphically between the polar layered deposits and the Vastitas Borealis Formation, and extending beneath most of Planum Boreum and Olympia Planitia. The objective of this work is the to study the full three dimensional structure of the Northern Polar Deposit and in particular of the Basal Unit (BU). It was recently found that the BU consists of two markedly different units, called the Rupes Tenuis unit and the Planum Boreum cavi unit. The Rupes Tenuis unit appears to be older, horizontally layered, and lacking erosional contacts. It has been thus interpreted as the result of precipitation and cold-trapping of dust-laden volatiles. The Planum Boreum cavi unit displays cross-bedding, indicating dune accumulation. Bright layers within it are interpreted as being made of ice-cemented dust, while dark layers should consist of weathered basalt fines. It seems likely that, in places, the Planum Boreum cavi unit rests directly on the Vastitas Borealis, without the Rupes Tenuis unit in between. Because the two units in the BU have formed much earlier than the north polar layered deposits, and at some interval from each other, they bear evidence of past climatic conditions that were very different from present, so that they "could potentially be a

  13. Institutional and Organizational Structure of the Federal Procurement System of the United States

    Directory of Open Access Journals (Sweden)

    Vovchenko Natalya Gennadyevna

    2015-09-01

    Full Text Available The paper deals with the role of the Federal procurement system of the United States as a regulatory tool of the U.S. economy. The scope of research is focused on organizational and institutional aspects of forming and developing the U.S. Federal procurement system. The main purpose of the paper is to study up-to-date mechanism of government acquisition in the United States and to consider all its structural elements taken in conjunction with each other, such as the President, the Office of Management and Budget (OMB, the Office of Federal Procurement Policy (OFPP, the General Services Administration (GSA, other executive and regulatory agencies. The methodological background of the research is based on normative, system-wide, statistical and complex approaches to the study of structural elements of the U.S. Federal procurement system. The theoretical and practical material of the present research can be used in teaching and learning activities at economic faculties, for instance, in the course of lectures on government contacting and public procurement management. It also can be used in training and advanced training of specialists who draft public procurement regulations in the Russian Federation. The statutory regulation of the U.S. Federal procurement system constitutes an organizational framework of executive agencies, their functions and responsibilities, specifics of government control over contract performance, competition requirements and contracting methods. The paper considered interrelated components of the U.S. Federal procurement system, which operates in furtherance of efficient utilization of Federal budget.

  14. Effects of Culture, Age, Gender, and Repeated Trials on Rote Song Learning Skills of Children 6-9 Years Old from England, Panama, Poland, Spain, and the United States.

    Science.gov (United States)

    Moore, Randall S.; Brotons, Melissa; Fyk, Janina; Castillo, Argelis

    1997-01-01

    Examines the effect of repeated trials on children aged six to nine from different countries learning a new song. States that: (1) culture influences responses; (2) rote singing improves with age; (3) girls responses are better; and (4) children repeat rhythms more accurately before they can pitch match melodic contours and precise pitches. (CMK)

  15. Influence of laminar flow on preorientation of coal tar pitch structural units: Raman microspectroscopic study

    Science.gov (United States)

    Urban, O.; Jehlička, J.; Pokorný, J.; Rouzaud, J. N.

    2003-08-01

    In order to estimate the role of laminar flow of viscous, aromatic matter of carbonaceous precursor on microtextural preorientation in pregraphitization stage, we performed experiments with coal tar pitch (CTP). The principal hypothesis of preorientation of basic structural units (BSUs) in the case of laminar flow (pressure impregnation of CTP into porous matrix) and secondary release of volatiles during carbonization were studied. Glass microplates, planar porous medium with average distance between single microplates 5 μm were used as suitable porous matrix. Samples of CTP were carbonized up to 2500 °C. Optical microscopy reveals large flow domains in the sample of cokes carbonized between glass microplates. Raman microspectroscopy and high resolution transmission electron microscopy (HRTEM) show that at nanometric scale, the samples do not support the proposed hypotheses. With increasing temperature of pyrolysis, the graphitization of CTP impregnated into porous matrix proceeds to lower degree of structural ordering in comparison with single pyrolyzed CTP. This is explained by the release of volatile matter during carbonization in geometrically restricted spaces. More evident structural changes were discovered with the sample of single coke, where parts of fine grain mosaics, relicts of 'so called QI parts', reveal higher structural organization, in comparison with large and prolonged flow domains, similar to flow domains of cokes from microplates.

  16. Hydrothermal syntheses and characterization of uranyl tungstates with electro-neutral structural units

    Energy Technology Data Exchange (ETDEWEB)

    Balboni, Enrica; Burns, Peter C. [Univ. of Notre Dame, IN (United States). Dept. of Civil and Enviromental Engineering and Earth Sciences; Univ. of Notre Dame, IN (United States). Dept. of Chemistry and Biochemistry

    2015-11-01

    Two uranyl tungstates, (UO{sub 2})(W{sub 2}O{sub 7})(H{sub 2}O){sub 3} (1) and (UO{sub 2}){sub 3}(W{sub 2}O{sub 8})F{sub 2}(H{sub 2}O){sub 3} (2), were synthesized under hydrothermal conditions at 220 C and were structurally, chemically, and spectroscopically characterized. 1 Crystallizes in space group Pbcm, a = 6.673(5) Aa, b = 12.601(11) Aa, c = 11.552 Aa; 2 is in C2/m, a = 13.648(1) Aa, b = 16.852(1) Aa, c = 9.832(1) Aa, β = 125.980(1) {sup circle}. In 1 the U(VI) cations are present as (UO{sub 2}){sup 2+} uranyl ions that are coordinated by five oxygen atoms to give pentagonal bipyramids. These share two edges with two tungstate octahedra and single vertices with four additional octahedra, resulting in a sheet with the iriginite-type anion topology. Only water molecules are located in the interlayer. The structural units of 2 consist of (UO{sub 2}){sup 2+} uranyl oxy-fluoride pentagonal bipyramids present as either [UO{sub 2}F{sub 2}O{sub 3}]{sup -6} or [UO{sub 2}FO{sub 4}]{sup -5}, and strongly distorted tungstate octahedra. The linkage of uranyl pentagonal bipyramids and tungstate octahedra gives a unique sheet anion topology consisting of pentagons, squares and triangles. In 2, the uranyl tungstates sheets are connected into a novel electro-neutral three-dimensional framework through dimers of uranyl pentagonal bipyramids. These dimers connecting the sheets share an edge defined by F anions. 2 is the first example of a uranyl tungstate oxy-fluoride, and 1 and 2 are rare examples of uranyl compounds containing electro-neutral structural units.

  17. Replication domains are self-interacting structural chromatin units of human chromosomes

    Science.gov (United States)

    Arneodo, Alain

    2011-03-01

    In higher eukaryotes, the absence of specific sequence motifs marking the origins of replication has been a serious hindrance to the understanding of the mechanisms that regulate the initiation and the maintenance of the replication program in different cell types. In silico analysis of nucleotide compositional skew has predicted the existence, in the germline, of replication N-domains bordered by putative replication origins and where the skew decreases rather linearly as the signature of a progressive inversion of the average fork polarity. Here, from the demonstration that the average fork polarity can be directly extracted from the derivative of replication timing profiles, we develop a wavelet-based pattern recognition methodology to delineate replication U-domains where the replication timing profile is shaped as a U and its derivative as a N. Replication U-domains are robustly found in seven cell lines as covering a significant portion (40-50%) of the human genome where the replication timing data actually displays some plasticity between cell lines. The early replication initiation zones at U-domains borders are found to be hypersensitive to DNase I cleavage, to be associated with transcriptional activity and to present a significant enrichment in insular-binding proteins CTCF, the hallmark of an open chromatin structure. A comparative analysis of genome-wide chromatin interaction (HiC) data shows that replication-U domains correspond to self-interacting structural high order chromatin units of megabase characteristic size. Taken together, these findings provide evidence that the epigenetic compartmentalization of the human genome into autonomous replication U-domains comes along with an extensive remodelling of the threedimensional chromosome architecture during development or in specific diseases. The observed cell specific conservation of the replication timing between the human and mouse genomes strongly suggests that this chromosome organization into

  18. Structures and properties of porous coordination polymers based on lanthanide carboxylate building units.

    Science.gov (United States)

    Han, Yinfeng; Li, Xiaoyan; Li, Liqing; Ma, Chunlin; Shen, Zhen; Song, You; You, Xiaozeng

    2010-12-06

    A series of 3-D lanthanide porous coordination polymers, [Ln(6)(BDC)(9)(DMF)(6)(H(2)O)(3)·3DMF](n) [Ln = La, 1; Ce, 2; Nd, 3], [Ln(2)(BDC)(3)(DMF)(2)(H(2)O)(2)](n) [Ln = Y, 4; Dy, 5; Eu, 6], [Ln(2)(ADB)(3)(DMSO)(4)·6DMSO·8H(2)O](n) [Ln = Ce, 7; Sm, 8; Eu, 9; Gd, 10], {[Ce(3)(ADB)(3)(HADB)(3)]·30DMSO·29H(2)O}(n) (11), and [Ce(2)(ADB)(3)(H(2)O)(3)](n) (12) (H(2)BDC = benzene-1,4-dicarboxylic acid and H(2)ADB = 4,4'-azodibenzoic acid), have been synthesized and characterized. In 1-3, the adjacent Ln(III) ions are intraconnected to form 1-D metal-carboxylate oxygen chain-shaped building units, [Ln(4)(CO(2))(12)](n), that constructed a 3-D framework with 4 × 7 Å rhombic channels. In 4-6, the dimeric Ln(III) ions are interlinked to yield scaffolds with 3-D interconnecting tunnels. Compounds 7-10 are all 3-D interpenetrating structures with the CaB6-type topology structure. Compound 11 is constructed by ADB spacers and trinulcear Ce nodes with a NaCl-type topology structure and a 1.9-nm open channel system. In 12, the adjacent Ce(III) ions are intraconnected to form 1-D metal-carboxylate oxygen chain-shaped building units, [Ln(4)(CO(2))(12)](n), and give rise to a 3-D framework. Moreover, 6 exhibits characteristic red luminescence properties of Eu(III) complexes. The magnetic susceptibilities, over a temperature range of 1.8-300 K, of 3, 6, and 7 have also been investigated; the results show paramagnetic properties.

  19. Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli

    Directory of Open Access Journals (Sweden)

    Kanehisa Minoru

    2007-02-01

    Full Text Available Abstract Background Operon structures play an important role in transcriptional regulation in prokaryotes. However, there have been fewer studies on complicated operon structures in which the transcriptional units vary with changing environmental conditions. Information about such complicated operons is helpful for predicting and analyzing operon structures, as well as understanding gene functions and transcriptional regulation. Results We systematically analyzed the experimentally verified transcriptional units (TUs in Bacillus subtilis and Escherichia coli obtained from ODB and RegulonDB. To understand the relationships between TUs and operons, we defined a new classification system for adjacent gene pairs, divided into three groups according to the level of gene co-regulation: operon pairs (OP belong to the same TU, sub-operon pairs (SOP that are at the transcriptional boundaries within an operon, and non-operon pairs (NOP belonging to different operons. Consequently, we found that the levels of gene co-regulation was correlated to intergenic distances and gene expression levels. Additional analysis revealed that they were also correlated to the levels of conservation across about 200 prokaryotic genomes. Most interestingly, we found that functional associations in SOPs were more observed in the environmental and genetic information processes. Conclusion Complicated operon strucutures were correlated with genome organization and gene expression profiles. Such intricately regulated operons allow functional differences depending on environmental conditions. These regulatory mechanisms are helpful in accommodating the variety of changes that happen around the cell. In addition, such differences may play an important role in the evolution of gene order across genomes.

  20. Reconfigurable multiport EPON repeater

    Science.gov (United States)

    Oishi, Masayuki; Inohara, Ryo; Agata, Akira; Horiuchi, Yukio

    2009-11-01

    An extended reach EPON repeater is one of the solutions to effectively expand FTTH service areas. In this paper, we propose a reconfigurable multi-port EPON repeater for effective accommodation of multiple ODNs with a single OLT line card. The proposed repeater, which has multi-ports in both OLT and ODN sides, consists of TRs, BTRs with the CDR function and a reconfigurable electrical matrix switch, can accommodate multiple ODNs to a single OLT line card by controlling the connection of the matrix switch. Although conventional EPON repeaters require full OLT line cards to accommodate subscribers from the initial installation stage, the proposed repeater can dramatically reduce the number of required line cards especially when the number of subscribers is less than a half of the maximum registerable users per OLT. Numerical calculation results show that the extended reach EPON system with the proposed EPON repeater can save 17.5% of the initial installation cost compared with a conventional repeater, and can be less expensive than conventional systems up to the maximum subscribers especially when the percentage of ODNs in lightly-populated areas is higher.

  1. HHrep: de novo protein repeat detection and the origin of TIM barrels.

    Science.gov (United States)

    Söding, Johannes; Remmert, Michael; Biegert, Andreas

    2006-07-01

    HHrep is a web server for the de novo identification of repeats in protein sequences, which is based on the pairwise comparison of profile hidden Markov models (HMMs). Its main strength is its sensitivity, allowing it to detect highly divergent repeat units in protein sequences whose repeats could as yet only be detected from their structures. Examples include sequences with beta-propellor fold, ferredoxin-like fold, double psi barrels or (betaalpha)8 (TIM) barrels. We illustrate this with proteins from four superfamilies of TIM barrels by revealing a clear 4- and 8-fold symmetry, which we detect solely from their sequences. This symmetry might be the trace of an ancient origin through duplication of a betaalphabetaalpha or betaalpha unit. HHrep can be accessed at http://hhrep.tuebingen.mpg.de.

  2. Optical Coating Performance and Thermal Structure Design for Heat Reflectors of JWST Electronic Control Unit

    Science.gov (United States)

    Quijada, Manuel A.; Threat, Felix; Garrison, Matt; Perrygo, Chuck; Bousquet, Robert; Rashford, Robert

    2008-01-01

    The James Webb Space Telescope (JWST) consists of an infrared-optimized Optical Telescope Element (OTE) that is cooled down to 40 degrees Kelvin. A second adjacent component to the OTE is the Integrated Science Instrument Module, or ISIM. This module includes the electronic compartment, which provides the mounting surfaces and ambient thermally controlled environment for the instrument control electronics. Dissipating the 200 watts generated from the ISIM structure away from the OTE is of paramount importance so that the spacecraft's own heat does not interfere with the infrared light detected from distant cosmic sources. This technical challenge is overcome by a thermal subsystem unit that provides passive cooling to the ISIM control electronics. The proposed design of this thermal radiator consists of a lightweight structure made out of composite materials and low-emittance metal coatings. In this paper, we will present characterizations of the coating emittance, bidirectional reflectance, and mechanical structure design that will affect the performance of this passive cooling system.

  3. Geographic variation, genetic structure and conservation unit designation in the larch mountain salamander( Plethodon larselli)

    Science.gov (United States)

    Wagner, R.S.; Miller, Mark P.; Crisafulli, Charles; Haig, Susan M.

    2005-01-01

    The Larch Mountain salamander (Plethodon larselli Burns, 1954) is an endemic species in the Pacific northwestern United States facing threats related to habitat destruction. To facilitate development of conservation strategies, we used DNA sequences and RAPDs (random amplified polymorphic DNA) to examine differences among populations of this species. Phylogenetic analyses of cytochrome b revealed a clade of haplotypes from populations north of the Columbia River derived from a clade containing haplotypes from the river's southwestern region. Haplotypes from southeastern populations formed a separate clade. Nucleotide diversity was reduced in northern populations relative to southern populations. These results were corroborated by analyses of RAPD loci, which revealed similar patterns of clustering and diversity. Network analyses suggested that northern populations were colonized following a range expansion mediated by individuals from populations located southwest of the river. Changes in the Columbia River's location during the Pliocene and Pleistocene likely released distributional constraints on this species, permitting their northern range expansion. Based on the barrier presented by the Columbia River's present location and differences in haplotype diversity and population structure observed between northern and southern populations, we suggest that designation of separate management units encompassing each region may assist with mitigating different threats to this species.

  4. Stratigraphic structure of the B1 Tertiary tectonostratigraphic unit in eastern Slovenia

    Directory of Open Access Journals (Sweden)

    Bogomir Jelen

    2002-06-01

    Full Text Available High inconsistency and incoherence in the stratigraphy of the Slovenian upper Paleogene and lower Miocene have remained unsolved in the past 150 years. To solve the problem, we tried to rigorously conduct the authentic Galilei’s scientific method. Steps of logical and empirical verification confirmed the existence of the posited B1 Tertiary tectonostratigraphic unit, and a general chronostratigraphic model of new positional relationships of lithologic units resulted from rather good biochronostratigraphic resolution achieved by nannoplankton and planktonic foraminifera biostratigraphy. The application of principles of newly developed fields in science helped us to avoid errors in transmission of messages (to reduce noise from the source (rock to the concept formation,which had been done previously. This in turn has strongly reduced inconsistency andincoherence (high information entropy = uncertainty. The released amount of information enabled us to answer also questions that reached beyond the original difficulty, e.g.: is the tectonostratigraphic structure of eastern Slovenia a manifestation of plate tectonics processes, and of which ones, are theories of continental escape in the Alps and associated dissection and offset of the formerly uniform Slovenian-Hungarian Paleogene basin tenableor not, are then there in the B1 stratigraphic equivalents of the Hungarian Paleogene basin formations, where are the important Eocene / Oligocene, Paleogene / Neogene, Rupelian / Chattian and Kiscellian / Egerian boundaries in Slovenia, and is there acontinuation of the B1 in Croatia and in the Mid-Hungarian tectonic zone?

  5. Internal structure of Family Health Units: access for people with disabilities.

    Science.gov (United States)

    Martins, Kaisy Pereira; Costa, Tatiana Ferreira da; Medeiros, Thayris Mariano de; Fernandes, Maria das Graças Melo; França, Inácia Sátiro Xavier de; Costa, Kátia Nêyla de Freitas Macêdo

    2016-10-01

    This study aimed at evaluating the internal structure of Family Health Units in relation to the access of people with physical and/or sensory disabilities. It is a descriptive, exploratory, population-based research, held in Family Health Units of the municipality of João Pessoa, Paraíba, Brazil. For the collection of data, a checklist based on Technical Standard 9050 was used. For the analysis, the descriptive and exploratory analysis of the data and the Chi-square test were applied. As a result, of the 90 buildings evaluated, only 47.8% have a wheelchair ramp, of these 30.0% have maximum slope and 32.2% have anti-slip flooring. In 28.9% access happens through a staircase without handrail and in 6.7% through a staircase with handrail, 6.7% of these with anti-slip flooring. And only 17.8% of sliding doors have lowered tracks. We concluded that it must be recognized that public policies and institutions do not correspond to the need of these people, and it is necessary to reformulate this form of care and reorganize health services.

  6. Structure and Function: Planning a New Intensive Care Unit to Optimize Patient Care

    Directory of Open Access Journals (Sweden)

    Jozef Kesecioğlu

    2014-08-01

    Full Text Available To survey the recent medical literature reporting effects of intensive care unit (ICU design on patients’ and family members’ well-being, safety and functionality. Features of ICU design linked to the needs of patients and their family are single-rooms, privacy, quiet surrounding, exposure to daylight, views of nature, prevention of infection, a family area and open visiting hours. Other features such as safety, working procedures, ergonomics and logistics have a direct impact on the patient care and the nursing and medical personnel. An organization structured on the needs of the patient and their family is mandatory in designing a new intensive care. The main aims in the design of a new department should be patient centered care, safety, functionality, innovation and a future-proof concept.

  7. China's laws, rights, and administrative structures in occupational safety and health: a comparison with the United States.

    Science.gov (United States)

    Sun, Yinling; Xu, Lingzhong; Shao, Hua; Wang, He

    2014-11-01

    China has achieved rapid economic development, but faces tremendous challenges in occupational safety and health (OSH). We describe China's laws, rights, and administrative structures in OSH and in workers' compensation. The article compares these with comparable laws, rights, and administrative structures in the United States. We hope this comparison may provide useful lessons for continued OSH development and improvement in China.

  8. Structural, compositional, and sensorial properties of United States commercial ice cream products.

    Science.gov (United States)

    Warren, Maya M; Hartel, Richard W

    2014-10-01

    Commercial vanilla ice cream products from the United States (full fat, low fat, and nonfat) were analyzed for their structural, behavioral (i.e., melt rate and drip-through), compositional, and sensorial attributes. Mean size distributions of ice crystals and air cells, drip-through rates, percent partially coalesced fat, percent overrun and total fat, and density were determined. A trained panel carried out sensory analyses in order to determine correlations between ice cream microstructure attributes and sensory properties using a Spectrum(TM) descriptive analysis. Analyses included melt rate, breakdown, size of ice particulates (iciness), denseness, greasiness, and overall creaminess. To determine relationships and interactions, principle component analysis and multivariate pairwise correlation were performed within and between the instrumental and sensorial data. Greasiness and creaminess negatively correlated with drip-through rate and creaminess correlated with percent total fat and percent fat destabilization. Percent fat did not determine the melt rate on a sensorial level. However, drip-through rate at ambient temperatures was predicted by total fat content of the samples. Based on sensory analysis, high-fat products were noted to be creamier than low and nonfat products. Iciness did not correlate with mean ice crystal size and drip-through rate did not predict sensory melt rate. Furthermore, on a sensorial level, greasiness positively correlated with total percent fat destabilization and mean air cell size positively correlated with denseness. These results indicate that commercial ice cream products vary widely in composition, structure, behavior, and sensory properties. There is a wide range of commercial ice creams in the United States market, ranging from full fat to nonfat. In this research we showed that these ice creams vary greatly in their microstructures, behaviors (the melt/drip-though, collapse, and/or stand up properties of ice cream

  9. Recursive quantum repeater networks

    CERN Document Server

    Van Meter, Rodney; Horsman, Clare

    2011-01-01

    Internet-scale quantum repeater networks will be heterogeneous in physical technology, repeater functionality, and management. The classical control necessary to use the network will therefore face similar issues as Internet data transmission. Many scalability and management problems that arose during the development of the Internet might have been solved in a more uniform fashion, improving flexibility and reducing redundant engineering effort. Quantum repeater network development is currently at the stage where we risk similar duplication when separate systems are combined. We propose a unifying framework that can be used with all existing repeater designs. We introduce the notion of a Quantum Recursive Network Architecture, developed from the emerging classical concept of 'recursive networks', extending recursive mechanisms from a focus on data forwarding to a more general distributed computing request framework. Recursion abstracts independent transit networks as single relay nodes, unifies software layer...

  10. Evaluation of structural deformations of a mechanical connecting unit oxidizer supplies by thermo-mechanical simulation

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sang Woo [Dept. of Mechanical Engineering, Institute of Machine Convergence Technology, Hankyong National University, Anseong (Korea, Republic of)

    2016-10-15

    A Mechanical connecting unit (MCU) used in ground facilities for a Liquid propellant rocket (LPR) acts as a bridge between the onboard system and the ground oxidizer filling system. It should be resistant to structural deformations in order to guarantee successful supply of a cryogenic oxidizer and high pressure gases without reduction of sealing capability. The MCU consists of many components and linkages and operates under harsh conditions induced by a cryogenic oxidizer, high pressure gases and other mechanical forces. Thus, the evaluation of structural deformation of the MCU considering complex conditions is expensive and time consuming. The present study efficiently evaluates the structural deformations of the key components of the MCU by Thermo-mechanical simulation (TMS) based on the superposition principle. Deformations due to the mechanical loadings including weights, pressures, and spring forces are firstly evaluated by using a non-linear flexible body simulation module (FFlex) of Multi-body dynamics (MBD) software, RecurDyn. Then, thermal deformations for the deformed geometries obtained by RecurDyn were subsequently calculated. It was conducted by using a Finite element (FE) analysis software, ANSYS. The total deformations for the onboard plate and multi-channel plate in the connecting section due to the mechanical and thermal loadings were successfully evaluated. Moreover, the outer gaps at six points between two plates were calculated and verified by comparison to the measured data. Their values and tendencies showed a good agreement. The author concluded that the TMS using MBD software considering flexible bodies and an FE simulator can efficiently evaluate structural deformations of the MCU operating under the complex load and boundary conditions.

  11. Ultrahigh energy density Li-ion batteries based on cathodes of 1D metals with –Li–N–B–N– repeating units in α-Li{sub x}BN{sub 2} (1 ⩽ x ⩽ 3)

    Energy Technology Data Exchange (ETDEWEB)

    Németh, Károly, E-mail: nemeth@agni.phys.iit.edu [Physics Department, Illinois Institute of Technology, Chicago, Illinois 60616 (United States)

    2014-08-07

    Ultrahigh energy density batteries based on α-Li{sub x}BN{sub 2} (1 ⩽ x ⩽ 3) positive electrode materials are predicted using density functional theory calculations. The utilization of the reversible LiBN{sub 2} + 2 Li{sup +} + 2 e{sup −} ⇌ Li{sub 3}BN{sub 2} electrochemical cell reaction leads to a voltage of 3.62 V (vs Li/Li{sup +}), theoretical energy densities of 3251 Wh/kg and 5927 Wh/l, with capacities of 899 mAh/g and 1638 mAh/cm{sup 3}, while the cell volume of α-Li{sub 3}BN{sub 2} shrinks only 2.8% per two-electron transfer on charge. These values are far superior to the best existing or theoretically designed intercalation or conversion-based positive electrode materials. For comparison, the theoretical energy density of a Li–O{sub 2}/peroxide battery is 3450 Wh/kg (including the weight of O{sub 2}), that of a Li–S battery is 2600 Wh/kg, that of Li{sub 3}Cr(BO{sub 3})(PO{sub 4}) (one of the best designer intercalation materials) is 1700 Wh/kg, while already commercialized LiCoO{sub 2} allows for 568 Wh/kg. α-Li{sub 3}BN{sub 2} is also known as a good Li-ion conductor with experimentally observed 3 mS/cm ionic conductivity and 78 kJ/mol (≈0.8 eV) activation energy of conduction. The attractive features of α-Li{sub x}BN{sub 2} (1 ⩽ x ⩽ 3) are based on a crystal lattice of 1D conjugated polymers with –Li–N–B–N– repeating units. When some of the Li is deintercalated from α-Li{sub 3}BN{sub 2} the crystal becomes a metallic electron conductor, based on the underlying 1D conjugated π electron system. Thus, α-Li{sub x}BN{sub 2} (1 ⩽ x ⩽ 3) represents a new type of 1D conjugated polymers with significant potential for energy storage and other applications.

  12. Revisiting the Unit Root Hypothesis and Structural Break: Asia and Emerging Economies Foreign Exchange Markets

    Directory of Open Access Journals (Sweden)

    Christopher Gan

    2004-01-01

    Full Text Available This study examines the stationary of ten Asian and for emerging Foreign Exchange (FX rates during the 1990s. The paper employs the Augmented Dickey-Fuller (ADF unit root test to the following FX rates: Hong Kong Dollar (HKD Japanese Yen (JPY, South Korean won (KRW new Taiwan dollar (TWN, Chinese Renminbl (CHR, Indonesia Rupiah (IDR, Malaysian Ringgit (MYR, Singapore Dollar (SGD, Thai Bhat (THB, Philippines Peso (PHP, Argentine Peso (AGP, the Brazilian Real (BRR, Mexican Peso (MXP and Russian Rouble (RUR. Structural break is taken into account for series found to be non-stationary using the[1] test. The results show that exchange rate series were found to be non-stationary except for the Chinese Renminbi, Mexican and Argentina pesos. Furthermore, the robustness test indicates that the ADF test is robust across different data frequencies for most series we examined finally; we find the choice of structural break data is crucial in testing that stationary for most series examined.

  13. Four-dimensional structural and Doppler optical coherence tomography imaging on graphics processing units.

    Science.gov (United States)

    Sylwestrzak, Marcin; Szlag, Daniel; Szkulmowski, Maciej; Gorczynska, Iwona; Bukowska, Danuta; Wojtkowski, Maciej; Targowski, Piotr

    2012-10-01

    The authors present the application of graphics processing unit (GPU) programming for real-time three-dimensional (3-D) Fourier domain optical coherence tomography (FdOCT) imaging with implementation of flow visualization algorithms. One of the limitations of FdOCT is data processing time, which is generally longer than data acquisition time. Utilizing additional algorithms, such as Doppler analysis, further increases computation time. The general purpose computing on GPU (GPGPU) has been used successfully for structural OCT imaging, but real-time 3-D imaging of flows has so far not been presented. We have developed software for structural and Doppler OCT processing capable of visualization of two-dimensional (2-D) data (2000 A-scans, 2048 pixels per spectrum) with an image refresh rate higher than 120 Hz. The 3-D imaging of 100×100 A-scans data is performed at a rate of about 9 volumes per second. We describe the software architecture, organization of threads, and optimization. Screen shots recorded during real-time imaging of a flow phantom and the human eye are presented.

  14. Apparent glacially induced structural controls on limestone conduit development in Ohio Caverns, United States

    Directory of Open Access Journals (Sweden)

    Adrienne M. Watts

    2016-01-01

    Full Text Available Rock discontinuities such as bedding planes and joints are important controls on the form that caves take. We examined structural controls on the development of Ohio Caverns. The cave formed in Devonian limestone underlying a small bedrock knob (Mt. Tabor within the Interior Lowland province, United States. The area has been overridden by continental glaciation multiple times. The bedrock is pervasively fractured, with many curved and wavy near-vertical fractures showing many different orientations. In the case of Ohio Caverns, it appears that the controlling fractures in map view may not be joints sensu stricto, but rather some combination of tensile and shear (mode-1 and mode-2 fractures, probably forming in the regime transition between tensile and shear fracturing. This is easy to envision in a situation with ice advancing over this topographic high, and would result in the curved fractures that are observed in many places in the cave. It can also explain the numerous fracture directions. However, not all fractures are conduit-significant. The cave initiated on or near a single bedding plane, and the cave passages exhibit strong keyhole or plus-sign cross sections. Passage and fracture orientations are inconsistent with regionally expected directions. It is likely that mechanical, hydraulic, and thermal stresses related to glaciation caused the fracturing in Mt. Tabor. The cave then developed on this template according to local hydrologic conditions. This presents a newly documented structural template sub-type for cave development.

  15. Structure of the Elastin-Contractile Units in the Thoracic Aorta and How Genes That Cause Thoracic Aortic Aneurysms and Dissections Disrupt This Structure.

    Science.gov (United States)

    Karimi, Ashkan; Milewicz, Dianna M

    2016-01-01

    The medial layer of the aorta confers elasticity and strength to the aortic wall and is composed of alternating layers of smooth muscle cells (SMCs) and elastic fibres. The SMC elastin-contractile unit is a structural unit that links the elastin fibres to the SMCs and is characterized by the following: (1) layers of elastin fibres that are surrounded by microfibrils; (2) microfibrils that bind to the integrin receptors in focal adhesions on the cell surface of the SMCs; and (3) SMC contractile filaments that are linked to the focal adhesions on the inner side of the membrane. The genes that are altered to cause thoracic aortic aneurysms and aortic dissections encode proteins involved in the structure or function of the SMC elastin-contractile unit. Included in this gene list are the genes encoding protein that are structural components of elastin fibres and microfibrils, FBN1, MFAP5, ELN, and FBLN4. Also included are genes that encode structural proteins in the SMC contractile unit, including ACTA2, which encodes SMC-specific α-actin and MYH11, which encodes SMC-specific myosin heavy chain, along with MYLK and PRKG1, which encode kinases that control SMC contraction. Finally, mutations in the gene encoding the protein linking integrin receptors to the contractile filaments, FLNA, also predispose to thoracic aortic disease. Thus, these data suggest that functional SMC elastin-contractile units are important for maintaining the structural integrity of the aorta.

  16. Control structures design for fossil power station units; Diseno de estructuras de control para unidades termoelectricas

    Energy Technology Data Exchange (ETDEWEB)

    Palomares Gonzalez, Daniel; Ricano Castillo, Juan Manuel [Instituto de Investigaciones Electricas, Cuernavaca (Mexico)

    1989-12-31

    In this paper are designed an analyzed the control ties of a 300MW fossil unit at different operation levels. The design and analysis were developed on an operation range of 50% to 100% load. The main control ties were studied among which are the feedwater flow, the superheating zone temperatures and the generated output. The technique used for the design is the decomposition in singular values (DSV) of the plant transference matrix. This is a recent technique that permits finding the most important interactions among output-input variables, over a significative frequencies range for the transference matrix of the plant. For this purpose utilizes the control properties of the transference matrix, such as: control effort, output-input interaction and ruggedness with respect to uncertainties. The control structures obtained were tested in a digital model of a fossil plant unit. A comparison study of both structures (original and modified) showed enhancement in the performance of the power plant with modified structure. [Espanol] En este trabajo se disenan y analizan los lazos de control de una unidad termoelectrica de 300 MW, a diferentes niveles de operacion. El diseno y analisis se desarrollo sobre un rango de operacion de 50 a 100 por ciento de carga. Se estudiaron los principales lazos de control entre los que se encuentran el flujo de agua de alimentacion, las temperaturas de la zona de sobrecalentamiento y la potencia generada. La tecnica utilizada para el diseno es la descomposicion en valores singulares (DVS) de la matriz de transferencia de la planta. Esta es una tecnica reciente que permite encontrar las interacciones mas importantes entre variables entrada-salida, sobre un rango de frecuencias significativas para la matriz de transferencia de la planta. Utiliza para ello las propiedades de control de la matriz de transferencia, como son: esfuerzo de control, interaccion entrada-salida y robustez con respecto a incertidumbres. Las estructuras de control

  17. Intermediates in the folding equilibrium of repeat proteins from the TPR family.

    Science.gov (United States)

    González-Charro, Vicente; Rey, Antonio

    2014-09-01

    In recent decades, advances in computational methods and experimental biophysical techniques have improved our understanding of protein folding. Although some of these advances have been remarkable, the structural variability of globular proteins usually encountered makes it difficult to extract general features of their folding processes. To overcome this difficulty, experimental and computational studies of the folding of repeat (or modular) proteins are of interest. Because their native structures can be described as linear arrays of the same, repeated, supersecondary structure unit, it is possible to seek a possibly independent behavior of the different modules without taking into account the intrinsic stability associated with different secondary structure motifs. In this work we have used a Monte Carlo-based simulation to study the folding equilibrium of four repeat proteins belonging to the tetratricopeptide repeat family. Our studies provide new insights into their energy profiles, enabling investigation about the existence of intermediate states and their relative stabilities. We have also performed structural analyses to describe the structure of these intermediates, going through the vast number of conformations obtained from the simulations. In this way, we have tried to identify the regions of each protein in which the modular structure yields a different behavior and, more specifically, regions of the proteins that can stay folded when the rest of the chain has been thermally denatured.

  18. XML Genetic Structure of SSR1 & SSR2 loci from Iranian Mycobacterium Avium Subspecies Paratuberculosis Isolates by a Short Sequence Repeat Analysis Approach

    Directory of Open Access Journals (Sweden)

    Aida Chalesh (MSc

    2016-01-01

    Full Text Available Background and Objective: Paratuberculosis has been repeatedly reported from Iranian ruminant herds. The extrem fastidious nature of Mycobacterium avium subspecies paratuberculsos hinders genomic diversity studies of the pathogen. Short Sequence Repeat analysis is one of the genome-based approches recently developed to overcome this difficulty. In this study we describe the application of SSR genotyping on three Iranian MAP type strains plus the III & V vaccinal strain. Methods: All the bacteria were examined by PCR-F57 and PCR-IS900 experiments in order to authenticate their identity as MAP. SSR genotyping using SSR1 & SSR2 loci was conducted according to the Amonsin method. PCR amplicons were sequenced to guarantee the accuracy of findings. Results: At SSR1 locus two allels were identified, a larger allel of 770 bp and a smaller allel of 763 bp long. At SSR2 only a single allele, 800 bp long, was detected. Two Iranian bovine and ovine MAP isolates along with the vaccinal III & V strain shared a single SSR1/SSR2 pattern while a different SSR1/SSR2 was represented by the third (caprine Iranian MAP isolate. Conclusion: While finding a shared SSR type between the two Iranian MAP isolates and the III & V strain might represent a mutual ancestral background but this has to be assessed through further studies. Detection of two SSR genotypes between three Iranian type strains is likely a reflection of more MAP clones in Iran.

  19. The role of polar, lamdba (Λ)-shaped building units in noncentrosymmetric inorganic structures.

    Science.gov (United States)

    Donakowski, Martin D; Gautier, Romain; Yeon, Jeongho; Moore, Donald T; Nino, Juan C; Halasyamani, P Shiv; Poeppelmeier, Kenneth R

    2012-05-01

    A methodology for the design of polar, inorganic structures is demonstrated here with the packing of lambda (Λ)-shaped basic building units (BBUs). Noncentrosymmetric (NCS) solids with interesting physical properties can be created with BBUs that lack an inversion center and are likely to pack into a polar configuration; previous methods to construct these solids have used NCS octahedra as BBUs. Using this methodology to synthesize NCS solids, one must increase the coordination of the NCS octahedra with maintenance of the noncentrosymmetry of the bulk. The first step in this progression from an NCS octahedron to an inorganic NCS solid is the formation of a bimetallic BBU. This step is exemplified with the compound CuVOF(4)(H(2)O)(7): this compound, presented here, crystallizes in an NCS structure with ordered, isolated [Cu(H(2)O)(5)](2+) cations and [VOF(4)(H(2)O)](2-) anions into Λ-shaped, bimetallic BBUs to form CuVOF(4)(H(2)O)(6)·H(2)O, owing to the Jahn-Teller distortion of Cu(2+). Conversely, the centrosymmetric heterotypes with the same formula MVOF(4)(H(2)O)(7) (M(II) = Co, Ni, and Zn) exhibit ordered, isolated [VOF(4)(H(2)O)](2-) and [M(H(2)O)(6)](2+) ionic species in a hydrogen bond network. CuVOF(4)(H(2)O)(7) exhibits a net polar moment while the heterotypes do not; this demonstrates that Λ-shaped BBUs give a greater probability for and, in this case, lead to NCS structures.

  20. Fault imprint in clay units: magnetic fabric, structural and mineralogical signature

    Science.gov (United States)

    Moreno, Eva; Homberg, Catherine; Schnyder, Johann; Person, Alain; du Peloux1, Arthur; Dick, Pierre

    2014-05-01

    Fault-induced deformations in clay units can be difficult to decipher because strain markers are not always visible at outcrop scale or using geophysical methods. Previous studies have indicated that the anisotropy of magnetic susceptibility (ASM) provides a powerful and rapid technique to investigate tectonic deformation in clay units even when they appear quite homogenous and undeformed at the outcrop scale (Lee et al. 1990, Mattei et al. 1997). We report here a study based on ASM, structural analysis and magnetic and clay mineralogy from two boreholes (TF1 and ASM1)drilled horizontally in the Experimental Station of Tournemire of the Institute for Radiological Protection and Nuclear Safety (IRSN) in Aveyron (France). The boreholes intersect a N-S trending strike-slip fault from west to east. The ASM study indicates the evolution of the magnetic fabric from the undeformed host rock to the fault core. Also, all the fractures cutting the studied interval of the core have been measured as well as the slip vectors which are generally well preserved. In the two boreholes, the undeformed sediments outside the fault zone are characterized by an oblate fabric, a sub-vertical minimum susceptibility axis (k3) perpendicular to the bedding plane and without magnetic lineation. Within the fault zone, a tilt in the bedding plane has been observed in two boreholes TF1 and ASM1. In addition, in the TF1 core, the fault area presents a tectonic fabric characterized by a triaxial AMS ellipsoid. Moreover, the magnetic lineation increases and k3 switches from a vertical to a sub-horizontal plane. This kind of fabric has not been observed in borehole ASM1. The structural analysis of the individual fractures making the fault zone indicates a complex tectonic history with different imprint in the two fault segments cut by the two boreholes. The large majority of fractures correspond to dextral strike-slip faults but normal and reverse movements were observed and are more or less

  1. Repeating the Past

    Science.gov (United States)

    Moore, John W.

    1998-05-01

    As part of the celebration of the Journal 's 75th year, we are scanning each Journal issue from 25, 50, and 74 years ago. Many of the ideas and practices described are so similar to present-day "innovations" that George Santayana's adage (1) "Those who cannot remember the past are condemned to repeat it" comes to mind. But perhaps "condemned" is too strong - sometimes it may be valuable to repeat something that was done long ago. One example comes from the earliest days of the Division of Chemical Education and of the Journal.

  2. Inhibition of the leucine-rich repeat protein LINGO-1 enhances survival, structure, and function of dopaminergic neurons in Parkinson's disease models.

    Science.gov (United States)

    Inoue, Haruhisa; Lin, Ling; Lee, Xinhua; Shao, Zhaohui; Mendes, Shannon; Snodgrass-Belt, Pamela; Sweigard, Harry; Engber, Tom; Pepinsky, Blake; Yang, Lichuan; Beal, M Flint; Mi, Sha; Isacson, Ole

    2007-09-04

    The nervous system-specific leucine-rich repeat Ig-containing protein LINGO-1 is associated with the Nogo-66 receptor complex and is endowed with a canonical EGF receptor (EGFR)-like tyrosine phosphorylation site. Our studies indicate that LINGO-1 expression is elevated in the substantia nigra of Parkinson's disease (PD) patients compared with age-matched controls and in animal models of PD after neurotoxic lesions. LINGO-1 expression is present in midbrain dopaminergic (DA) neurons in the human and rodent brain. Therefore, the role of LINGO-1 in cell damage responses of DA neurons was examined in vitro and in experimental models of PD induced by either oxidative (6-hydroxydopamine) or mitochondrial (N-methyl-4-phenyl-1,2,3,6-tetrahydropyridine) toxicity. In LINGO-1 knockout mice, DA neuron survival was increased and behavioral abnormalities were reduced compared with WT. This neuroprotection was accompanied by increased Akt phosphorylation (p-Akt). Similar neuroprotective in vivo effects on midbrain DA neurons were obtained in WT mice by blocking LINGO-1 activity using LINGO-1-Fc protein. Neuroprotection and enhanced neurite growth were also demonstrated for midbrain DA neurons in vitro. LINGO-1 antagonists (LINGO-1-Fc, dominant negative LINGO-1, and anti-LINGO-1 antibody) improved DA neuron survival in response to MPP+ in part by mechanisms that involve activation of the EGFR/Akt signaling pathway through a direct inhibition of LINGO-1's binding to EGFR. These results show that inhibitory agents of LINGO-1 activity can protect DA neurons against degeneration and indicate a role for the leucine-rich repeat protein LINGO-1 and related classes of proteins in the pathophysiological responses of midbrain DA neurons in PD.

  3. Effects of repeated low-dose exposure of the nerve agent VX on monoamine levels in different brain structures in mice.

    Science.gov (United States)

    Graziani, S; Christin, D; Daulon, S; Breton, P; Perrier, N; Taysse, L

    2014-05-01

    In a previous report, alterations of the serotonin metabolism were previously reported in mice intoxicated with repeated low doses of soman. In order to better understand the effects induced by repeated low-dose exposure to organophosphorus compounds on physiological and behavioural functions, the levels of endogenous monoamines (serotonin and dopamine) in different brain areas in mice intoxicated with sublethal dose of (O-ethyl-S-[2(di-isopropylamino) ethyl] methyl phosphonothioate) (VX) were analysed by HPLC method with electrochemical detection. Animals were injected once a day for three consecutive days with 0.10 LD50 of VX (5 μg/kg, i.p). Neither severe signs of cholinergic toxicity nor pathological changes in brain tissue of exposed animals were observed. Cholinesterase (ChE) activity was only inhibited in plasma (a maximum of 30% inhibition 24 h after the last injection of VX), but remained unchanged in the brain. Serotonin and dopamine (DA) metabolism appeared significantly modified. During the entire period of investigation, at least one of the three parameters investigated (i.e. DA and DOPAC levels and DOPAC/DA ratio) was modified. During the toxic challenge, an increase of the serotonin metabolism was noted in hippocampus (HPC), hypothalamus/thalamus, pons medulla and cerebellum (CER). This increase was maintained 4 weeks after exposure in HPC, pons medulla and CER whereas a decrease in cortex 3 weeks after the toxic challenge was observed. The lack of correlation between brain ChE activity and neurochemical outcomes points out to independent mechanisms. The involvement in possibly long-lasting behavioural disorders is discussed.

  4. Extreme variation in patterns of tandem repeats in mitochondrial control region of yellow-browed tits (Sylviparus modestus, Paridae).

    Science.gov (United States)

    Wang, Xiaoyang; Liu, Nian; Zhang, Hongli; Yang, Xiao-Jun; Huang, Yuan; Lei, Fumin

    2015-08-19

    To investigate the evolutionary pattern and origins of tandem repeats in the mitochondrial control region of the yellow-browed tit (Sylviparus modestus), the control region and another four mitochondrial loci from fifteen individuals were analyzed. A 117-bp tandem repeat unit that repeated once, twice or three times in different individuals was found, and a rarely reported arrangement for this tandem repeats region that a 5' imperfect copy at its downstream and a 3' imperfect copy at its upstream was observed. The haplotype network, phylogenetic trees, and ancestral state reconstruction of the combined dataset of five loci suggested multiple origins of the same repeat number. The turnover model via slipped-strand mispairing was introduced to interpret the results, because mispairing occurred so frequently that multiple origins of certain repeat number were observed. Insertion via recombination should be a better explanation for the origin of this tandem repeat unit, considering characteristics of the combined sequence of the 3' and 5' imperfect copy, including identification of its homolog in other passerines and its predicted secondary structure.

  5. Patterns of population structure for inshore bottlenose dolphins along the eastern United States.

    Science.gov (United States)

    Richards, Vincent P; Greig, Thomas W; Fair, Patricia A; McCulloch, Stephen D; Politz, Christine; Natoli, Ada; Driscoll, Carlos A; Hoelzel, A Rus; David, Victor; Bossart, Gregory D; Lopez, Jose V

    2013-01-01

    Globally distributed, the bottlenose dolphin (Tursiops truncatus) is found in a range of offshore and coastal habitats. Using 15 microsatellite loci and mtDNA control region sequences, we investigated patterns of genetic differentiation among putative populations along the eastern US shoreline (the Indian River Lagoon, Florida, and Charleston Harbor, South Carolina) (microsatellite analyses: n = 125, mtDNA analyses: n = 132). We further utilized the mtDNA to compare these populations with those from the Northwest Atlantic, Gulf of Mexico, and Caribbean. Results showed strong differentiation among inshore, alongshore, and offshore habitats (ФST = 0.744). In addition, Bayesian clustering analyses revealed the presence of 2 genetic clusters (populations) within the 250 km Indian River Lagoon. Habitat heterogeneity is likely an important force diversifying bottlenose dolphin populations through its influence on social behavior and foraging strategy. We propose that the spatial pattern of genetic variation within the lagoon reflects both its steep longitudinal transition of climate and also its historical discontinuity and recent connection as part of Intracoastal Waterway development. These findings have important management implications as they emphasize the role of habitat and the consequence of its modification in shaping bottlenose dolphin population structure and highlight the possibility of multiple management units existing in discrete inshore habitats along the entire eastern US shoreline.

  6. A Single-Unit Design Structure and Gender Differences in the Swimming World Championships

    Science.gov (United States)

    Pushkar, Svetlana; Issurin, Vladimir B.; Verbitsky, Oleg

    2014-01-01

    Four 50 meter male/female finals - the freestyle, butterfly, breaststroke, and backstroke - swum during individual events at the Swimming World Championships (SWCs) can be defined in four clusters. The aim of the present study was to use a single-unit design structure, in which the swimmer was defined at only one scale, to evaluate gender differences in start reaction times among elite swimmers in 50 m events. The top six male and female swimmers in the finals of four swimming stroke final events in six SWCs were analyzed. An unpaired t-test was used. The p-values were evaluated using Neo-Fisherian significance assessments (Hurlbert and Lombardi, 2012). For the freestyle, gender differences in the start reaction times were positively identified for five of the six SWCs. For the backstroke, gender differences in the start reaction times could be dismissed for five of the six SWCs. For both the butterfly and breaststroke, gender differences in the start reaction times yielded inconsistent statistical differences. Pooling all swimmers together (df = 286) showed that an overall gender difference in the start reaction times could be positively identified: p = 0.00004. The contrast between the gender differences in start reaction times between the freestyle and backstroke may be associated with different types of gender adaptations to swimming performances. When the natural groupings of swimming stroke final events were ignored, sacrificial pseudoreplication occurred, which may lead to erroneous statistical differences. PMID:25414754

  7. A Single-Unit Design Structure and Gender Differences in the Swimming World Championships

    Directory of Open Access Journals (Sweden)

    Pushkar Svetlana

    2014-10-01

    Full Text Available Four 50 meter male/female finals - the freestyle, butterfly, breaststroke, and backstroke - swum during individual events at the Swimming World Championships (SWCs can be defined in four clusters. The aim of the present study was to use a single-unit design structure, in which the swimmer was defined at only one scale, to evaluate gender differences in start reaction times among elite swimmers in 50 m events. The top six male and female swimmers in the finals of four swimming stroke final events in six SWCs were analyzed. An unpaired t-test was used. The p-values were evaluated using Neo-Fisherian significance assessments (Hurlbert and Lombardi, 2012. For the freestyle, gender differences in the start reaction times were positively identified for five of the six SWCs. For the backstroke, gender differences in the start reaction times could be dismissed for five of the six SWCs. For both the butterfly and breaststroke, gender differences in the start reaction times yielded inconsistent statistical differences. Pooling all swimmers together (df = 286 showed that an overall gender difference in the start reaction times could be positively identified: p = 0.00004. The contrast between the gender differences in start reaction times between the freestyle and backstroke may be associated with different types of gender adaptations to swimming performances. When the natural groupings of swimming stroke final events were ignored, sacrificial pseudoreplication occurred, which may lead to erroneous statistical differences

  8. Patterns of Population Structure for Inshore Bottlenose Dolphins along the Eastern United States

    Science.gov (United States)

    2013-01-01

    Globally distributed, the bottlenose dolphin (Tursiops truncatus) is found in a range of offshore and coastal habitats. Using 15 microsatellite loci and mtDNA control region sequences, we investigated patterns of genetic differentiation among putative populations along the eastern US shoreline (the Indian River Lagoon, Florida, and Charleston Harbor, South Carolina) (microsatellite analyses: n = 125, mtDNA analyses: n = 132). We further utilized the mtDNA to compare these populations with those from the Northwest Atlantic, Gulf of Mexico, and Caribbean. Results showed strong differentiation among inshore, alongshore, and offshore habitats (ФST = 0.744). In addition, Bayesian clustering analyses revealed the presence of 2 genetic clusters (populations) within the 250 km Indian River Lagoon. Habitat heterogeneity is likely an important force diversifying bottlenose dolphin populations through its influence on social behavior and foraging strategy. We propose that the spatial pattern of genetic variation within the lagoon reflects both its steep longitudinal transition of climate and also its historical discontinuity and recent connection as part of Intracoastal Waterway development. These findings have important management implications as they emphasize the role of habitat and the consequence of its modification in shaping bottlenose dolphin population structure and highlight the possibility of multiple management units existing in discrete inshore habitats along the entire eastern US shoreline. PMID:24129993

  9. The US business cycle: power law scaling for interacting units with complex internal structure

    Science.gov (United States)

    Ormerod, Paul

    2002-11-01

    In the social sciences, there is increasing evidence of the existence of power law distributions. The distribution of recessions in capitalist economies has recently been shown to follow such a distribution. The preferred explanation for this is self-organised criticality. Gene Stanley and colleagues propose an alternative, namely that power law scaling can arise from the interplay between random multiplicative growth and the complex structure of the units composing the system. This paper offers a parsimonious model of the US business cycle based on similar principles. The business cycle, along with long-term growth, is one of the two features which distinguishes capitalism from all previously existing societies. Yet, economics lacks a satisfactory theory of the cycle. The source of cycles is posited in economic theory to be a series of random shocks which are external to the system. In this model, the cycle is an internal feature of the system, arising from the level of industrial concentration of the agents and the interactions between them. The model-in contrast to existing economic theories of the cycle-accounts for the key features of output growth in the US business cycle in the 20th century.

  10. All-optical repeater.

    Science.gov (United States)

    Silberberg, Y

    1986-06-01

    An all-optical device containing saturable gain, saturable loss, and unsaturable loss is shown to transform weak, distorted optical pulses into uniform standard-shape pulses. The proposed device performs thresholding, amplification, and pulse shaping as required from an optical repeater. It is shown that such a device could be realized by existing semiconductor technology.

  11. Bidirectional Manchester repeater

    Science.gov (United States)

    Ferguson, J.

    1980-01-01

    Bidirectional Manchester repeater is inserted at periodic intervals along single bidirectional twisted pair transmission line to detect, amplify, and transmit bidirectional Manchester 11 code signals. Requiring only 18 TTL 7400 series IC's, some line receivers and drivers, and handful of passive components, circuit is simple and relatively inexpensive to build.

  12. An innovative approach of structural instabilities in tetragonal tungsten bronze crystals through the concept of rigid unit modes

    OpenAIRE

    Smirnov, Mikhail; Saint-Grégoire, Pierre

    2013-01-01

    Tetragonal tungsten bronze (TTB) oxides are one of the most important classes of ferroelectrics. Many of these framework structures undergo ferroelastic transformations related to octahedron tilting deformations. Such tilting deformations are closely related to the Rigid Unit Modes (RUMs). This paper discusses the whole set of RUMs in an ideal TTB lattice and possible crystal structures which can emerge owing to the condensation of some of them. Analysis of available experimental data for the...

  13. Synthesis, Crystal Structure and Photophysical Properties of a Novel Molecule Containing a Triarylamine and an Oxadiazole Units

    Institute of Scientific and Technical Information of China (English)

    YU,Hai-Tao(于海涛); ZHANG,Wan-Xuan(张万轩); BAI,Dong-Ren(白东仁); MENG,Ji-Ben(孟继本)

    2002-01-01

    2-{ 3-[2-(4-N, N-Di-p-tolylaminophenyl )ethenyl ] phenyl }-5- (4-bromophenyl)-1,3,4-oxadiazole (1) containing triarylamine and 2,5-diaryl-1,3,4-oxadiazole units was prepared by HornerWitting reactions. The structure of the compound was confirmed by1H NMR, IR, MS and elemental analyses. The crystal structure of 1 was determined by X-ray diffraction analysis.UV absorption spectra and photoluminescent spectra were measured.

  14. PCR bias in amplification of androgen receptor alleles, a trinucleotide repeat marker used in clonality studies.

    OpenAIRE

    Mutter, G L; Boynton, K A

    1995-01-01

    Trinucleotide CAG repeats in the X-linked human androgen receptor gene (HUMARA) have proved a useful means of determining X chromosome haplotypes, and when combined with methylation analysis of nearby cytosine residues permits identification of non-random X inactivation in tumors of women. Co-amplification of two alleles in a heterozygote generates PCR products which differ in the number of CAG units, and thus their melting and secondary structure characteristics. We have shown that under opt...

  15. Two new hexacoordinated coordination polymers of cadmium(II) containing bridging units only: Syntheses, structures and molecular properties

    Indian Academy of Sciences (India)

    DIPU SUTRADHAR; HABIBAR CHOWDHURY; SUSHOVAN KONER; SUBHASIS ROY; BARINDRA KUMAR GHOSH

    2016-09-01

    The syntheses, characterizations and structures of a neutral 2D coordination polymer [Cd(bnzd)(NCS)₂]n (1) and a polycationic 3D coordination polymer isolated as perchlorate salt [Cd(bnzd)₃]n(ClO₄)₂n (2) (bnzd = benzidine) are described. X-ray structural analyses reveal that each hexacoordinated cadmium(II) center in 1 adopts a distorted octahedral geometry with a CdN₄S₂ chromophore bound by two N atoms of two different bnzd units and two N and two S atoms of symmetric doubly bridged end-toend NCS− units extended in a 2D sheet. Six N atoms of six different bridged bnzd units are bonded to each cadmium(II) in 2 in a non-ended fashion affording a 3D network structure. In the crystalline state, each 2D sheet structure in 1 is further stabilized by π· · ·π interaction which in turn affords a 3D network structure through multiple intermolecular N-H· · · S hydrogen bonds. On the other hand, the 3D network structure in 2 is stabilized by weak intermolecular N-H· · ·O hydrogen bonds and C-H· · ·π interactions. Bnzd, 1 and 2 display intraligand 1(π-π*) fluorescence in DMF solution at room temperature.

  16. Influence of surrounding structures upon the aerodynamic and acoustic performance of the outdoor unit of a split air-conditioner

    Science.gov (United States)

    Wu, Chengjun; Liu, Jiang; Pan, Jie

    2014-07-01

    DC-inverter split air-conditioner is widely used in Chinese homes as a result of its high-efficiency and energy-saving. Recently, the researches on its outdoor unit have focused on the influence of surrounding structures upon the aerodynamic and acoustic performance, however they are only limited to the influence of a few parameters on the performance, and practical design of the unit requires more detailed parametric analysis. Three-dimensional computational fluid dynamics(CFD) and computational aerodynamic acoustics(CAA) simulation based on FLUENT solver is used to study the influence of surrounding structures upon the aforementioned properties of the unit. The flow rate and sound pressure level are predicted for different rotating speed, and agree well with the experimental results. The parametric influence of three main surrounding structures(i.e. the heat sink, the bell-mouth type shroud and the outlet grille) upon the aerodynamic performance of the unit is analyzed thoroughly. The results demonstrate that the tip vortex plays a major role in the flow fields near the blade tip and has a great effect on the flow field of the unit. The inlet ring's size and throat's depth of the bell-mouth type shroud, and the through-flow area and configuration of upwind and downwind sections of the outlet grille are the most important factors that affect the aerodynamic performance of the unit. Furthermore, two improved schemes against the existing prototype of the unit are developed, which both can significantly increase the flow rate more than 6 %(i.e. 100 m3·h-1) at given rotating speeds. The inevitable increase of flow noise level when flow rate is increased and the advantage of keeping a lower rotating speed are also discussed. The presented work could be a useful guideline in designing the aerodynamic and acoustic performance of the split air-conditioner in engineering practice.

  17. Population structure of the emerging plant pathogen Phytophthora ramorum on the west coast of the United States

    Science.gov (United States)

    S. Prospero; E.M. Hansen; N.J. Grünwald; J. Britt; L.M. Winton.

    2009-01-01

    Phytophthora ramorum is a devastating pathogen in native forests in California and southwestern Oregon and in nursery crops in California, Oregon and Washington. In this study we analyzed the population structure of P. ramorum in the west coast (CA, OR, and WA) of the United States by screening 579 isolates recovered...

  18. Latar as the Central Point of Houses Group Unit: Identifiability for Spatial Structure in Kasongan, Yogyakarta, Indonesia

    Directory of Open Access Journals (Sweden)

    T. Yoyok Wahyu Subroto

    2012-05-01

    Full Text Available The massive spatial expansion of the city into the rural area in recent decades has caused such problems as related to the spatial exploitation in villages surrounding. This raises a question of whether the open space change into land coverage building may have a spatial structure implication on settlement growth and evolution process in the villages surrounding. This paper reports a case study of Kasongan village in Bantul regency, Yogyakarta, Indonesia in between 1973-2010 in which the problem refers to the discussion of spatial structure is rarely addressed especially in village’s settlement growth and evolution analysis. The bound axis which consists of 4 (four quadrants and one intersection refers to the reference axes in a Cartesian Coordinate System (CCS is used to analyze the setting of the houses group unit around 4 areas/ quadrants. Through such spatial process analysis by means spatial structure approach, the continuity of latar (yard, in the central of houses group unit is detected. There is finding from this research that the latar which exists in ‘the central point’ of houses group unit in Kasongan during 4 decades significantly becomes the prominent factor of the basic spatial structure. It composes the houses group unit in Kasongan.

  19. "The Great Gatsby" and the Twenties: The Notion of Structure as a Unifying Device in an Interdisciplinary Unit.

    Science.gov (United States)

    Peale, Lydia

    An effective, 3-week unit on the 1920's in America, inspired by a reading of "The Great Gatsby," is designed around the idea of structure in history, government, literature, and writing. It has the following aims for students: (1) to understand the history of the 1920s, (2) to see literature as a creative shaping of the experience of the time, (3)…

  20. Carbon Mitigation Impacts of Increased Softwood Lumber and Structural Panel Use for Nonresidential Construction in the United States

    Science.gov (United States)

    Prakash Nepal; Kenneth E. Skog; David B. McKeever; Richard D. Bergman; Karen L. Abt; Robert C. Abt

    2016-01-01

    More wood use in the United States to construct low-rise nonresidential (NR) buildings would increase consumption and production of softwood (SW) lumber, engineered wood products, and structural and nonstructural wood panels. Using a consequential life-cycle analysis, we estimated the change in net CO2 emissions thatwould be caused by increased...

  1. Occupational and Qualification Structures in the Field of Environmental Protection in the Metal and Chemical Industries in the United Kingdom.

    Science.gov (United States)

    European Centre for the Development of Vocational Training, Berlin (Germany).

    A study analyzed the occupational structure and qualifications associated with the field of environmental protection in the metal and chemical industries in the United Kingdom. The analysis included nine case studies based on interviews with firms in the chemicals and metals sectors. Information was gathered within an analytical framework that…

  2. Computational study of the human dystrophin repeats: interaction properties and molecular dynamics.

    Science.gov (United States)

    Legrand, Baptiste; Giudice, Emmanuel; Nicolas, Aurélie; Delalande, Olivier; Le Rumeur, Elisabeth

    2011-01-01

    Dystrophin is a large protein involved in the rare genetic disease Duchenne muscular dystrophy (DMD). It functions as a mechanical linker between the cytoskeleton and the sarcolemma, and is able to resist shear stresses during muscle activity. In all, 75% of the dystrophin molecule consists of a large central rod domain made up of 24 repeat units that share high structural homology with spectrin-like repeats. However, in the absence of any high-resolution structure of these repeats, the molecular basis of dystrophin central domain's functions has not yet been deciphered. In this context, we have performed a computational study of the whole dystrophin central rod domain based on the rational homology modeling of successive and overlapping tandem repeats and the analysis of their surface properties. Each tandem repeat has very specific surface properties that make it unique. However, the repeats share enough electrostatic-surface similarities to be grouped into four separate clusters. Molecular dynamics simulations of four representative tandem repeats reveal specific flexibility or bending properties depending on the repeat sequence. We thus suggest that the dystrophin central rod domain is constituted of seven biologically relevant sub-domains. Our results provide evidence for the role of the dystrophin central rod domain as a scaffold platform with a wide range of surface features and biophysical properties allowing it to interact with its various known partners such as proteins and membrane lipids. This new integrative view is strongly supported by the previous experimental works that investigated the isolated domains and the observed heterogeneity of the severity of dystrophin related pathologies, especially Becker muscular dystrophy.

  3. Computational study of the human dystrophin repeats: interaction properties and molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Baptiste Legrand

    Full Text Available Dystrophin is a large protein involved in the rare genetic disease Duchenne muscular dystrophy (DMD. It functions as a mechanical linker between the cytoskeleton and the sarcolemma, and is able to resist shear stresses during muscle activity. In all, 75% of the dystrophin molecule consists of a large central rod domain made up of 24 repeat units that share high structural homology with spectrin-like repeats. However, in the absence of any high-resolution structure of these repeats, the molecular basis of dystrophin central domain's functions has not yet been deciphered. In this context, we have performed a computational study of the whole dystrophin central rod domain based on the rational homology modeling of successive and overlapping tandem repeats and the analysis of their surface properties. Each tandem repeat has very specific surface properties that make it unique. However, the repeats share enough electrostatic-surface similarities to be grouped into four separate clusters. Molecular dynamics simulations of four representative tandem repeats reveal specific flexibility or bending properties depending on the repeat sequence. We thus suggest that the dystrophin central rod domain is constituted of seven biologically relevant sub-domains. Our results provide evidence for the role of the dystrophin central rod domain as a scaffold platform with a wide range of surface features and biophysical properties allowing it to interact with its various known partners such as proteins and membrane lipids. This new integrative view is strongly supported by the previous experimental works that investigated the isolated domains and the observed heterogeneity of the severity of dystrophin related pathologies, especially Becker muscular dystrophy.

  4. Investigation of the population structure of Mycobacterium abscessus complex strains using 17-locus variable number tandem repeat typing and the further distinction of Mycobacterium massiliense hsp65 genotypes.

    Science.gov (United States)

    Yoshida, Shiomi; Arikawa, Kentaro; Tsuyuguchi, Kazunari; Kurashima, Atsuyuki; Harada, Toshiyuki; Nagai, Hideaki; Suzuki, Katsuhiro; Iwamoto, Tomotada; Hayashi, Seiji

    2015-03-01

    Mycobacterium abscessus complex is a significant pathogen in patients with non-cystic fibrosis (non-CF). Nevertheless, there is little description of the genetic diversity of this species. The aims of this study were to investigate the distribution of M. abscessus complex isolated from respiratory specimens by variable number tandem repeat (VNTR) typing. The results of 104 clinical isolates from 104 non-CF patients were compared using PFGE, hsp65 genotypes and clarithromycin susceptibility. The allelic diversity (Hunter-Gaston Discriminatory Index) of the 17 loci examined by VNTR typing was high (0.977). We determined that C28 sequevar erm(41) genotypes and clarithromycin-acquired resistance isolates were scattered in the minimum spanning tree. Intriguingly, VNTR typing and PFGE were highly congruent and revealed that there were clear examples of grouping of isolates from different individuals amongst both M. abscessus and M. massiliense, and showed five clusters of distinct identical isolates. Within these clusters, M. massiliense hsp65 type I formed three different clusters. Although the distribution of M. massiliense hsp65 type II-1 was low (9.3 %), M. massiliense hsp65 type II-1 isolates separated from clusters contained hsp65 type I isolates. Thus, M. massiliense hsp65 genotypes could be discriminated by analysing VNTRs with sufficient genetic distance for intra-species-level discrimination.

  5. Dynamic combinatorial libraries of artificial repeat proteins.

    Science.gov (United States)

    Eisenberg, Margarita; Shumacher, Inbal; Cohen-Luria, Rivka; Ashkenasy, Gonen

    2013-06-15

    Repeat proteins are found in almost all cellular systems, where they are involved in diverse molecular recognition processes. Recent studies have suggested that de novo designed repeat proteins may serve as universal binders, and might potentially be used as practical alternative to antibodies. We describe here a novel chemical methodology for producing small libraries of repeat proteins, and screening in parallel the ligand binding of library members. The first stage of this research involved the total synthesis of a consensus-based three-repeat tetratricopeptide (TPR) protein (~14 kDa), via sequential attachment of the respective peptides. Despite the effectiveness of the synthesis and ligation steps, this method was found to be too demanding for the production of proteins containing variable number of repeats. Additionally, the analysis of binding of the individual proteins was time consuming. Therefore, we designed and prepared novel dynamic combinatorial libraries (DCLs), and show that their equilibration can facilitate the formation of TPR proteins containing up to eight repeating units. Interestingly, equilibration of the library building blocks in the presence of the biologically relevant ligands, Hsp90 and Hsp70, induced their oligomerization into forming more of the proteins with large recognition surfaces. We suggest that this work presents a novel simple and rapid tool for the simultaneous screening of protein mixtures with variable binding surfaces, and for identifying new binders for ligands of interest.

  6. Acute Cardiovascular Care Association Position Paper on Intensive Cardiovascular Care Units: An update on their definition, structure, organisation and function.

    Science.gov (United States)

    Bonnefoy-Cudraz, Eric; Bueno, Hector; Casella, Gianni; De Maria, Elia; Fitzsimons, Donna; Halvorsen, Sigrun; Hassager, Christian; Iakobishvili, Zaza; Magdy, Ahmed; Marandi, Toomas; Mimoso, Jorge; Parkhomenko, Alexander; Price, Susana; Rokyta, Richard; Roubille, Francois; Serpytis, Pranas; Shimony, Avi; Stepinska, Janina; Tint, Diana; Trendafilova, Elina; Tubaro, Marco; Vrints, Christiaan; Walker, David; Zahger, Doron; Zima, Endre; Zukermann, Robert; Lettino, Maddalena

    2017-08-01

    Acute cardiovascular care has progressed considerably since the last position paper was published 10 years ago. It is now a well-defined, complex field with demanding multidisciplinary teamworking. The Acute Cardiovascular Care Association has provided this update of the 2005 position paper on acute cardiovascular care organisation, using a multinational working group. The patient population has changed, and intensive cardiovascular care units now manage a large range of conditions from those simply requiring specialised monitoring, to critical cardiovascular diseases with associated multi-organ failure. To describe better intensive cardiovascular care units case mix, acuity of care has been divided into three levels, and then defining intensive cardiovascular care unit functional organisation. For each level of intensive cardiovascular care unit, this document presents the aims of the units, the recommended management structure, the optimal number of staff, the need for specially trained cardiologists and cardiovascular nurses, the desired equipment and architecture, and the interaction with other departments in the hospital and other intensive cardiovascular care units in the region/area. This update emphasises cardiologist training, referring to the recently updated Acute Cardiovascular Care Association core curriculum on acute cardiovascular care. The training of nurses in acute cardiovascular care is additionally addressed. Intensive cardiovascular care unit expertise is not limited to within the unit's geographical boundaries, extending to different specialties and subspecialties of cardiology and other specialties in order to optimally manage the wide scope of acute cardiovascular conditions in frequently highly complex patients. This position paper therefore addresses the need for the inclusion of acute cardiac care and intensive cardiovascular care units within a hospital network, linking university medical centres, large community hospitals, and smaller

  7. Structure and Origins of Trends in Hydrological Measures over the western United States

    Energy Technology Data Exchange (ETDEWEB)

    Das, T; Hidalgo, H G; Dettinger, M D; Cayan, D R; Pierce, D W; Bonfils, C; Barnett, T P; Bala, G; Mirin, A

    2008-08-22

    This study examines, at 1/8 degree spatial resolution, the geographic structure of observed trends in key hydrologically relevant variables across the western United States (U.S.) over the period 1950-1999, and investigates whether these trends are statistically significantly different from trends associated with natural climate variations. A number of variables were analyzed, including late winter and spring temperature, winter-total snowy days as a fraction of winter-total wet days, 1st April Snow Water Equivalent (SWE) as a fraction of October through March precipitation total (P{sub ONDJFM}), and seasonal (January-February-March; JFM) accumulated runoff as a fraction of water year accumulated runoff. The observed changes were compared to natural internal climate variability simulated by an 850-year control run of the CCSM3-FV climate model, statistically downscaled to a 1/8 degree grid using the method of Constructed Analogues. Both observed and downscaled temperature and precipitation data were then used to drive the Variable Infiltration Capacity (VIC) hydrological model to obtain the hydrological variables analyzed in this study. Large trends (magnitudes found less than 5% of the time in the long control run) are common in the observations, and occupy substantial part of the area (37-42%) over the mountainous western U.S. These trends are strongly related to the large scale warming that appears over 89% of the domain. The strongest changes in the hydrologic variables, unlikely to be associated with natural variability alone, have occurred at medium elevations (750 m to 2500 m for JFM runoff fractions and 500 m-3000 m for SWE/PONDJFM) where warming has pushed temperatures from slightly below to slightly above freezing. Further analysis using the data on selected catchments across the simulation domain indicated that hydroclimatic variables must have changed significantly (at 95% confidence level) over at least 45% of the total catchment area to achieve a

  8. Structure and integrity of fish assemblages in streams associated to conservation units in Central Brazil

    Directory of Open Access Journals (Sweden)

    Thiago Belisário d'Araújo Couto

    Full Text Available This study aims to characterize the spatial and seasonal distribution of the fish assemblage and evaluate the integrity of streams in a sustainable use area that includes integral protection conservation units in Distrito Federal, Central Brazil (Cerrado biome. For the study, 12 stretches of 8 streams were sampled in 2008 (dry season and 2009 (wet season. For that evaluation was estimated the Physical Habitat Index (PHI, vegetation cover (VC, pH, dissolved oxygen, turbidity, and conductivity. We recorded 22 species, about eight undescribed species, by a total of 2,327 individuals. The most representative families in number of species were Characidae (31.8%, Loricariidae (31.8%, and Crenuchidae (13.6%. Knodus moenkhausii was the most abundant species with 1,476 individuals, added to Astyanax sp., Phalloceros harpagos, and Hasemania sp. they represent over 95% of the total abundance. The species Astyanax sp. (occurring in 79.2% of the stretches and K. moenkhausii (50.0% were considered constant in both seasons. The longitudinal gradient (River Continuum exerts a strong influence on the studied assemblage. According to CCA, the variables that structure the fish assemblage are based on aspects related to water volume and habitat complexity. No seasonal variation in richness, diversity, abundance, and mass were detected. A cluster analysis suggests a separation of species composition between the stretches of higher and lower orders, which was not observed for seasonality. The streams were considered well preserved (mean PHI 82.9±7.5%, but in some stretches were observed anthropogenic influence, detected in the water quality and, mainly, on the riparian vegetation integrity. The exotic species Poecilia reticulata was sampled in the two stretches considered most affected by anthropogenic activities by PHI, conductivity, and VC.

  9. A 3D bioprinted complex structure for engineering the muscle-tendon unit.

    Science.gov (United States)

    Merceron, Tyler K; Burt, Morgan; Seol, Young-Joon; Kang, Hyun-Wook; Lee, Sang Jin; Yoo, James J; Atala, Anthony

    2015-06-17

    Three-dimensional integrated organ printing (IOP) technology seeks to fabricate tissue constructs that can mimic the structural and functional properties of native tissues. This technology is particularly useful for complex tissues such as those in the musculoskeletal system, which possess regional differences in cell types and mechanical properties. Here, we present the use of our IOP system for the processing and deposition of four different components for the fabrication of a single integrated muscle-tendon unit (MTU) construct. Thermoplastic polyurethane (PU) was co-printed with C2C12 cell-laden hydrogel-based bioink for elasticity and muscle development on one side, while poly(ϵ-caprolactone) (PCL) was co-printed with NIH/3T3 cell-laden hydrogel-based bioink for stiffness and tendon development on the other. The final construct was elastic on the PU-C2C12 muscle side (E = 0.39 ± 0.05 MPa), stiff on the PCL-NIH/3T3 tendon side (E = 46.67 ± 2.67 MPa) and intermediate in the interface region (E = 1.03 ± 0.14 MPa). These constructs exhibited >80% cell viability at 1 and 7 d after printing, as well as initial tissue development and differentiation. This study demonstrates the versatility of the IOP system to create integrated tissue constructs with region-specific biological and mechanical characteristics for MTU engineering.

  10. Population structure of Hispanics in the United States: the multi-ethnic study of atherosclerosis.

    Science.gov (United States)

    Manichaikul, Ani; Palmas, Walter; Rodriguez, Carlos J; Peralta, Carmen A; Divers, Jasmin; Guo, Xiuqing; Chen, Wei-Min; Wong, Quenna; Williams, Kayleen; Kerr, Kathleen F; Taylor, Kent D; Tsai, Michael Y; Goodarzi, Mark O; Sale, Michèle M; Diez-Roux, Ana V; Rich, Stephen S; Rotter, Jerome I; Mychaleckyj, Josyf C

    2012-01-01

    Using ~60,000 SNPs selected for minimal linkage disequilibrium, we perform population structure analysis of 1,374 unrelated Hispanic individuals from the Multi-Ethnic Study of Atherosclerosis (MESA), with self-identification corresponding to Central America (n = 93), Cuba (n = 50), the Dominican Republic (n = 203), Mexico (n = 708), Puerto Rico (n = 192), and South America (n = 111). By projection of principal components (PCs) of ancestry to samples from the HapMap phase III and the Human Genome Diversity Panel (HGDP), we show the first two PCs quantify the Caucasian, African, and Native American origins, while the third and fourth PCs bring out an axis that aligns with known South-to-North geographic location of HGDP Native American samples and further separates MESA Mexican versus Central/South American samples along the same axis. Using k-means clustering computed from the first four PCs, we define four subgroups of the MESA Hispanic cohort that show close agreement with self-identification, labeling the clusters as primarily Dominican/Cuban, Mexican, Central/South American, and Puerto Rican. To demonstrate our recommendations for genetic analysis in the MESA Hispanic cohort, we present pooled and stratified association analysis of triglycerides for selected SNPs in the LPL and TRIB1 gene regions, previously reported in GWAS of triglycerides in Caucasians but as yet unconfirmed in Hispanic populations. We report statistically significant evidence for genetic association in both genes, and we further demonstrate the importance of considering population substructure and genetic heterogeneity in genetic association studies performed in the United States Hispanic population.

  11. Population structure of Hispanics in the United States: the multi-ethnic study of atherosclerosis.

    Directory of Open Access Journals (Sweden)

    Ani Manichaikul

    Full Text Available Using ~60,000 SNPs selected for minimal linkage disequilibrium, we perform population structure analysis of 1,374 unrelated Hispanic individuals from the Multi-Ethnic Study of Atherosclerosis (MESA, with self-identification corresponding to Central America (n = 93, Cuba (n = 50, the Dominican Republic (n = 203, Mexico (n = 708, Puerto Rico (n = 192, and South America (n = 111. By projection of principal components (PCs of ancestry to samples from the HapMap phase III and the Human Genome Diversity Panel (HGDP, we show the first two PCs quantify the Caucasian, African, and Native American origins, while the third and fourth PCs bring out an axis that aligns with known South-to-North geographic location of HGDP Native American samples and further separates MESA Mexican versus Central/South American samples along the same axis. Using k-means clustering computed from the first four PCs, we define four subgroups of the MESA Hispanic cohort that show close agreement with self-identification, labeling the clusters as primarily Dominican/Cuban, Mexican, Central/South American, and Puerto Rican. To demonstrate our recommendations for genetic analysis in the MESA Hispanic cohort, we present pooled and stratified association analysis of triglycerides for selected SNPs in the LPL and TRIB1 gene regions, previously reported in GWAS of triglycerides in Caucasians but as yet unconfirmed in Hispanic populations. We report statistically significant evidence for genetic association in both genes, and we further demonstrate the importance of considering population substructure and genetic heterogeneity in genetic association studies performed in the United States Hispanic population.

  12. Unemployment in Western Europe and the United States: A Problem of Demand, Structure, or Measurement?

    Science.gov (United States)

    Haveman, Robert H.

    1978-01-01

    The main thesis of this paper is that measured unemployment bears a different relationship to real excess labor supply in the 1970s than it did in the 1960s. This thesis is used to explain the increase in measured unemployment in the Netherlands, Sweden, the United Kingdom, and the United States. (Author/EB)

  13. A comparative analysis of business structures suitable for farmer-owned wind power projects in the United States

    Energy Technology Data Exchange (ETDEWEB)

    Bolinger, Mark [Lawrence Berkeley National Laboratory, MS 90-4000, One Cyclotron Road, Berkeley, CA 94720 (United States)]. E-mail: mabolinger@lbl.gov; Wiser, Ryan [Lawrence Berkeley National Laboratory, MS 90-4000, One Cyclotron Road, Berkeley, CA 94720 (United States)

    2006-09-15

    For years, farmers in the United States have looked with envy on their European counterparts' ability to profitably farm the wind through ownership of distributed, utility-scale wind projects. Only within the past few years, however, has farmer- or community-owned wind power development become a reality in the United States. The primary hurdle to this type of development in the United States has been devising and implementing suitable business and legal structures that enable such projects to take advantage of tax-based federal incentives for wind power. This article discusses the limitations of such incentives in supporting farmer- or community-owned wind projects, describes four ownership structures that potentially overcome such limitations, and finally conducts comparative financial analysis on those four structures, using as an example a hypothetical 1.5 MW farmer-owned project located in the state of Oregon. We find that material differences in the competitiveness of each structure do exist, but that choosing the best structure for a given project will largely depend on the conditions at hand; e.g., the ability of the farmer(s) to utilize tax credits, preference for individual versus 'cooperative' ownership, and the state and utility service territory in which the project will be located.

  14. A comparative analysis of business structures suitable forfarmer-owned wind power projects in the United States

    Energy Technology Data Exchange (ETDEWEB)

    Bolinger, Mark; Wiser, Ryan

    2004-11-11

    For years, farmers in the United States have looked with envy on their European counterparts' ability to profitably farm the wind through ownership of distributed, utility-scale wind projects. Only within the past few years, however, has farmer- or community-owned wind power development become a reality in the United States. The primary hurdle to this type of development in the United States has been devising and implementing suitable business and legal structures that enable such projects to take advantage of tax-based federal incentives for wind power. This article discusses the limitations of such incentives in supporting farmer- or community-owned wind projects, describes four ownership structures that potentially overcome such limitations, and finally conducts comparative financial analysis on those four structures, using as an example a hypothetical 1.5 MW farmer-owned project located in the state of Oregon. We find that material differences in the competitiveness of each structure do exist, but that choosing the best structure for a given project will largely depend on the conditions at hand; e.g., the ability of the farmer(s) to utilize tax credits, preference for individual versus ''cooperative'' ownership, and the state and utility service territory in which the project will be located.

  15. Duct Leakage Repeatability Testing

    Energy Technology Data Exchange (ETDEWEB)

    Walker, Iain [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Sherman, Max [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2014-01-01

    Duct leakage often needs to be measured to demonstrate compliance with requirements or to determine energy or Indoor Air Quality (IAQ) impacts. Testing is often done using standards such as ASTM E1554 (ASTM 2013) or California Title 24 (California Energy Commission 2013 & 2013b), but there are several choices of methods available within the accepted standards. Determining which method to use or not use requires an evaluation of those methods in the context of the particular needs. Three factors that are important considerations are the cost of the measurement, the accuracy of the measurement and the repeatability of the measurement. The purpose of this report is to evaluate the repeatability of the three most significant measurement techniques using data from the literature and recently obtained field data. We will also briefly discuss the first two factors. The main question to be answered by this study is to determine if differences in the repeatability of these tests methods is sufficient to indicate that any of these methods is so poor that it should be excluded from consideration as an allowed procedure in codes and standards.

  16. Two-dimensional quantum repeaters

    Science.gov (United States)

    Wallnöfer, J.; Zwerger, M.; Muschik, C.; Sangouard, N.; Dür, W.

    2016-11-01

    The endeavor to develop quantum networks gave rise to a rapidly developing field with far-reaching applications such as secure communication and the realization of distributed computing tasks. This ultimately calls for the creation of flexible multiuser structures that allow for quantum communication between arbitrary pairs of parties in the network and facilitate also multiuser applications. To address this challenge, we propose a two-dimensional quantum repeater architecture to establish long-distance entanglement shared between multiple communication partners in the presence of channel noise and imperfect local control operations. The scheme is based on the creation of self-similar multiqubit entanglement structures at growing scale, where variants of entanglement swapping and multiparty entanglement purification are combined to create high-fidelity entangled states. We show how such networks can be implemented using trapped ions in cavities.

  17. Sequence Analysis of the 5S rRNA Gene Repeat Units in 5 Durum Wheat Species from Xinjiang of China%新疆硬粒小麦5个品种5S rRNA基因重复单元间序列分析

    Institute of Scientific and Technical Information of China (English)

    米日古丽·马木提; 布热比艳木·吾布力卡斯木; 吾买尔江·库尔班; 帕夏伊木·艾麦提; 赵奇

    2015-01-01

    本研究参照GenBank禾本科以及前期新疆7个小麦种5S rDNA NTS序列,通过PCR技术扩增获得新疆5个硬粒小麦品种5S rDNA NTS序列,并通过与5S rRNA序列比对,得到5S rDNA NTS序列结构和边界范围。结果显示:5个硬粒小麦品种均存在两种类型5S rDNA NTS序列且相似程度不同,长NTS序列保守性较高,短NTS片段相对较低;短NTS序列存在两处序列缺失现象,两种类型NTS序列存在不同位置和程度的变异位点和变异频率。利用MEG4.0软件,采用邻接法构建了分子进化树并计算获得了品种间遗传距离。对来自不同品种克隆单元基的序列进行比对,得知对于几个组直向是存在的。直系群体的5S rDNA序列有益于硬粒小麦进一步的系统发育分析。%According to GenBank in barley grasses 5S rDNA sequences and previously published 5S rDNA NTS sequences of seven Xinjiang wheat species, 5S rDNA sequences of five durum wheat varieties from Xinjiang were obtained by Polymerase Chain Reaction, the 5S rDNA structure and NTS boundaries were obtained by further alignments with barley grasses 5S rRNA sequence. Sequence analysis revealed that two types of 5S rDNA NTS sequences were presented in five wheat varieties and the nontranscribed spacer of long repeat classes was less variable than that of short repeat classes. Deletion was presented in two parts of 5S rDNA nontranscribed spacer (NTS) length of short repeat class. The different degrees of variable sites and mutation frequency exists in two types of 5S rDNA NTS sequences. Molecular phylogenetic tree was constructed and genetic distance between varieties was calculated by using the MEGA4.0 software and the neighbor-joining method. Sequence comparisons of individual clones (units) isolated from different species have allowed us to confirm that orthology exists for several groups. This demonstration of orthologous groups suggests that the 5S rDNA sequence may be useful for

  18. The political economy of women’s professional basketball in the United States: A structure-conduct-performance approach

    Directory of Open Access Journals (Sweden)

    Ariel ANTHONY

    2012-11-01

    Full Text Available This study examines the political economy of women’s professional basketball in the United States, including both the American Basketball League (ABL and the Women’s National Basketball Association (WNBA. To do so, we employ the structure-conductperformance paradigm (hereafter SCP from industrial organization. In addition to the importance of television revenues and corporate sponsorships to the success of the leagues, we find evidence of economies of scope, bilateral monopoly issues, and reverse causality in the SCP paradigm as applied to women’s professional basketball in the United States.

  19. Structure of the Elastin-Contractile Units in the Thoracic Aorta and How Genes that Cause Thoracic Aortic Aneurysms and Dissections Disrupt this Structure

    OpenAIRE

    Karimi, Ashkan; Milewicz, Dianna M.

    2015-01-01

    The medial layer of the aorta confers elasticity and strength to the aortic wall and is composed of alternating layers of smooth muscle cells (SMCs) and elastic fibers. The SMC elastin-contractile unit is a structural unit that links the elastin fibers to the SMCs and is characterized by the following: 1. Layers of elastin fibers that are surrounded by microfibrils. 2. Microfibrils that bind to the integrin receptors in focal adhesions on the cell surface of the SMCs. 3. SMC contractile filam...

  20. NMR studies of the R2 repeat and related peptide fragments of the DNA binding domain of c-Myb. New light on the structure and folding of R2.

    Science.gov (United States)

    Ségalas, I.; Desjardins, S.; Oulyadi, H.; Prigent, Y.; Tribouillard, S.; Bernardi, E.; Schoofs, A. R.; Davoust1, D.; Toma, F.

    1999-10-01

    The solution structure of the R2 repeat of the DNA binding domain of the protooncogene c-Myb contains a N-terminal structural motif comprising two antiparallel helices. The motif is stabilized by interactions involving conserved residues. The recognition region in C-terminal position is flexible. This structure differs from that of R2 of another c-Myb protein. La structure en solution de la répétition R2 du domaine de liaison à l'ADN du protooncogène c-Myb possède un motif à deux hélices antiparallèles dans la moitié N-terminale, stabilisé par des interactions entre résidus conservés. La région de reconnaissance à l'ADN en position C-terminale est flexible. Cette structure diffère de celle montrée pour la répétition R2 d'une autre protéine c-Myb.

  1. Thickness of the Upper Hell Creek hydrogeologic unit in the Powder River structural basin

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — These data represent the thickness, in feet, of the Upper Hell Creek hydrogeologic unit in the Powder River basin. The data are presented as ASCII text files that...

  2. Altitude of the top of the middle Fort Union hydrogeologic unit in the Williston structural basin

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — These data represent the altitude, in feet above North American Vertical Datum of 1988 (NAVD88), of the middle Fort Union hydrogeologic unit in the Williston...

  3. Altitude of the top of the Upper Hell Creek hydrogeologic unit in the Williston structural basin

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — These data represent the altitude, in feet above North American Vertical Datum of 1988 (NAVD88), of the Upper Hell Creek hydrogeologic unit in the Williston...

  4. Thickness of the middle Fort Union hydrogeologic unit in the Powder River structural basin

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — These data represent the thickness, in feet, of the middle Fort Union hydrogeologic unit in the Powder River basin. The data are presented as ASCII text files that...

  5. Forest structure and aboveground biomass in the southwestern United States from MODIS and MISR

    Science.gov (United States)

    Red band bidirectional reflectance factor data from the NASA MODerate resolution Imaging Spectroradiometer (MODIS) acquired over the southwestern United States were interpreted through a simple geometric–optical (GO) canopy reflectance model to provide maps of fractional crown cover (dimensionless),...

  6. Altitude of the top of the basal confining unit in the Powder River structural basin

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — These data represent the altitude, in feet above North American Vertical Datum of 1988 (NAVD88), of the basal confining unit in the Powder River basin. The data are...

  7. Fine-resolution repeat topographic surveying of dryland landscapes using UAS-based structure-from-motion photogrammetry: Assessing accuracy and precision against traditional ground-based erosion measurements

    Science.gov (United States)

    Gillian, Jeffrey K.; Karl, Jason W.; Elaksher, Ahmed; Duniway, Michael C.

    2017-01-01

    Structure-from-motion (SfM) photogrammetry from unmanned aerial system (UAS) imagery is an emerging tool for repeat topographic surveying of dryland erosion. These methods are particularly appealing due to the ability to cover large landscapes compared to field methods and at reduced costs and finer spatial resolution compared to airborne laser scanning. Accuracy and precision of high-resolution digital terrain models (DTMs) derived from UAS imagery have been explored in many studies, typically by comparing image coordinates to surveyed check points or LiDAR datasets. In addition to traditional check points, this study compared 5 cm resolution DTMs derived from fixed-wing UAS imagery with a traditional ground-based method of measuring soil surface change called erosion bridges. We assessed accuracy by comparing the elevation values between DTMs and erosion bridges along thirty topographic transects each 6.1 m long. Comparisons occurred at two points in time (June 2014, February 2015) which enabled us to assess vertical accuracy with 3314 data points and vertical precision (i.e., repeatability) with 1657 data points. We found strong vertical agreement (accuracy) between the methods (RMSE 2.9 and 3.2 cm in June 2014 and February 2015, respectively) and high vertical precision for the DTMs (RMSE 2.8 cm). Our results from comparing SfM-generated DTMs to check points, and strong agreement with erosion bridge measurements suggests repeat UAS imagery and SfM processing could replace erosion bridges for a more synoptic landscape assessment of shifting soil surfaces for some studies. However, while collecting the UAS imagery and generating the SfM DTMs for this study was faster than collecting erosion bridge measurements, technical challenges related to the need for ground control networks and image processing requirements must be addressed before this technique could be applied effectively to large landscapes.

  8. Stratigraphic structure of the B1 Tertiary tectonostratigraphic unit in eastern Slovenia

    OpenAIRE

    Bogomir Jelen; Helena Rifelj

    2002-01-01

    High inconsistency and incoherence in the stratigraphy of the Slovenian upper Paleogene and lower Miocene have remained unsolved in the past 150 years. To solve the problem, we tried to rigorously conduct the authentic Galilei’s scientific method. Steps of logical and empirical verification confirmed the existence of the posited B1 Tertiary tectonostratigraphic unit, and a general chronostratigraphic model of new positional relationships of lithologic units resulted from rather good biochrono...

  9. Repeatability of Cryogenic Multilayer Insulation

    Science.gov (United States)

    Johnson, W. L.; Vanderlaan, M.; Wood, J. J.; Rhys, N. O.; Guo, W.; Van Sciver, S.; Chato, D. J.

    2017-01-01

    Due to the variety of requirements across aerospace platforms, and one off projects, the repeatability of cryogenic multilayer insulation has never been fully established. The objective of this test program is to provide a more basic understanding of the thermal performance repeatability of MLI systems that are applicable to large scale tanks. There are several different types of repeatability that can be accounted for: these include repeatability between multiple identical blankets, repeatability of installation of the same blanket, and repeatability of a test apparatus. The focus of the work in this report is on the first two types of repeatability. Statistically, repeatability can mean many different things. In simplest form, it refers to the range of performance that a population exhibits and the average of the population. However, as more and more identical components are made (i.e. the population of concern grows), the simple range morphs into a standard deviation from an average performance. Initial repeatability testing on MLI blankets has been completed at Florida State University. Repeatability of five GRC provided coupons with 25 layers was shown to be +/- 8.4 whereas repeatability of repeatedly installing a single coupon was shown to be +/- 8.0. A second group of 10 coupons have been fabricated by Yetispace and tested by Florida State University, through the first 4 tests, the repeatability has been shown to be +/- 16. Based on detailed statistical analysis, the data has been shown to be statistically significant.

  10. A tandem repeats database for bacterial genomes: application to the genotyping of Yersinia pestis and Bacillus anthracis

    Directory of Open Access Journals (Sweden)

    Denoeud France

    2001-03-01

    Full Text Available Abstract Background Some pathogenic bacteria are genetically very homogeneous, making strain discrimination difficult. In the last few years, tandem repeats have been increasingly recognized as markers of choice for genotyping a number of pathogens. The rapid evolution of these structures appears to contribute to the phenotypic flexibility of pathogens. The availability of whole-genome sequences has opened the way to the systematic evaluation of tandem repeats diversity and application to epidemiological studies. Results This report presents a database (http://minisatellites.u-psud.fr of tandem repeats from publicly available bacterial genomes which facilitates the identification and selection of tandem repeats. We illustrate the use of this database by the characterization of minisatellites from two important human pathogens, Yersinia pestis and Bacillus anthracis. In order to avoid simple sequence contingency loci which may be of limited value as epidemiological markers, and to provide genotyping tools amenable to ordinary agarose gel electrophoresis, only tandem repeats with repeat units at least 9 bp long were evaluated. Yersinia pestis contains 64 such minisatellites in which the unit is repeated at least 7 times. An additional collection of 12 loci with at least 6 units, and a high internal conservation were also evaluated. Forty-nine are polymorphic among five Yersinia strains (twenty-five among three Y. pestis strains. Bacillus anthracis contains 30 comparable structures in which the unit is repeated at least 10 times. Half of these tandem repeats show polymorphism among the strains tested. Conclusions Analysis of the currently available bacterial genome sequences classifies Bacillus anthracis and Yersinia pestis as having an average (approximately 30 per Mb density of tandem repeat arrays longer than 100 bp when compared to the other bacterial genomes analysed to date. In both cases, testing a fraction of these sequences for

  11. Numerical study of self-adaptive vibration suppression for flexible structure using interior inlay viscous fluid unit method

    Science.gov (United States)

    Zhang, Xiongwen; Li, Jun; Xu, Hui; Li, Guojun

    2006-11-01

    This paper investigates the usage of an interior inlay viscous fluid unit as a new vibration suppression method for flexible structures via numerical simulations. The first and second modes of vibration for a beam have been calculated using the commercial computational fluid dynamic package Fluent6.1, together with the liquid surface distribution and the fluid force. The calculated results show that the inlay fluid unit has suppressive effects on flexible structures. The liquid converges self-adaptively to locations of larger vibrations. The fluid force varies with the beam vibration at a phase difference of more than 180°. Thus the fluid force suppresses the beam vibration at most of the time.

  12. Huntington's disease as caused by 34 CAG repeats.

    Science.gov (United States)

    Andrich, Jürgen; Arning, Larissa; Wieczorek, Stefan; Kraus, Peter H; Gold, Ralf; Saft, Carsten

    2008-04-30

    Huntington's disease (HD) is an autosomal dominantly inherited neurodegenerative disorder caused by an abnormal expansion of a polymorphic stretch of CAG repeats in the coding 5' part of the HD gene on chromosome 4p. Expansions of CAG blocks beyond 35 repeats are associated with the clinical presentation of HD. There is an intermediate range of rare alleles between 27 and 35 CAG repeats with a higher risk for further expansion in subsequent generations. Here, we report a 75-year-old male with clinical features of HD and 34 CAG repeat units.

  13. Mathematical analysis and STEM observations of arrangement of structural units in 〈001〉 symmetrical tilt grain boundaries.

    Science.gov (United States)

    Inoue, Kazutoshi; Saito, Mitsuhiro; Chen, Chunlin; Kotani, Motoko; Ikuhara, Yuichi

    2016-12-01

    A collaborative work between mathematics and atom-resolved scanning transmission electron microscopy (STEM) has been conducted. The grain boundary in a bicrystal of a simple rock-salt oxide can show a complicated arrangement of structural units, which can be well predicted by an algorithm utilizing the Farey sequence. The estimated arrangements had a nice agreement with those observed by STEM in atomic-scale up to several tens of nanometers.

  14. A quantative evaluation of the reformulated 1996 path-goal theory of work unit leadership via structural equation modelling

    OpenAIRE

    Howieson, William B

    2008-01-01

    In 1996, Professor Robert J House published a reformulated Path-Goal Theory of Work Unit Leadership, based on his earlier 1971 and 1974 theories. Path-goal leadership attempts to explain the impact that leader behaviour has on subordinate motivation, satisfaction and performance. The aim of this context-specific study is to evaluate this reformulated ‘1996 Theory’ via Structural Equation Modelling with engineers from the Royal Air Force as the primary data source. This th...

  15. Synthesis,Crystal Structure and Photophysical properties of a Novel Molecule Containing a Triarylamine and an Oxadiazole Units

    Institute of Scientific and Technical Information of China (English)

    于海涛; 张万轩; 白东仁; 孟继本

    2002-01-01

    2-{3-[2-(4-N,N-Di-p-tolylaminophenyl)ethenyl]phenyl}-5-(4-bromophenyl)-1,3,4-oxadiazole(1) containing triarylamine and 2,5-diaryl-1,3,4-oxadiazole units was prepared by hornerWitting reactions.The structure of the compound was confirmed by 1H NMR,IR ,MS and elemental analyses.The crystal structure of 1 was determined by X-ray diffraction analysis.UV absorpiton spectra and photoluminescent spectra were measured.

  16. A piezoelectric spectro-electrochemical study on the structural interconversion for poly(o-phenylenediamine) between its ladder structure with phenazine units and polyaniline-like chains

    Institute of Scientific and Technical Information of China (English)

    TU Xinman; XIE Qingji; WANG Meiling; ZHANG Youyu; YAO Shouzhuo

    2005-01-01

    The combination of reflectance UV-Vis spec-troelectrochemistry with electrochemical quartz crystalmicrobalance (EQCM) and separate reflectance FTIR char-acterization were used to investigate the structural intercon-version for poly(o-phenylenediamine) (PoPD) between its ladder structure with phenazine units and polyaniline-like linear chains. The poly(o-phenylenediamine) films potentio-statically (0.8 V vs. SCE) grew on Au electrodes from 0.20 mol·L-1 H2SO4(PoPD1)or 0.40mol·L-1 NaOH(PoPD2)aqueous solution containing 0.20 mol·L-1 Na2SO4+0.10mol·L-1o-phenylenediamine. By considering the mass of deposited PoPD2 film obtained from the EQCM data and the charge consumed under the current peak at ca. 0.6 V vs. SCE for oxidation of -NH2 groups in as-prepared PoPD2 during potential cycling in 0.10mol·L-1 aqueous H2SO4,the nolar percentage of the polyaniline-like chains was estimated to be 19% (relative to total phenylenediamine units), being in agreement with the result obtained from a formaldehyde combination experiment through the aminocarbonyl reaction. After 40-cycle potential sweeps between 0.2 and 0.8 V vs. SCE the polyaniline-like chains in PoPD2 could be completely converted via intramolecular cyclization into the ladder structure with phenazine units. However, PoPD1 was found to be perfectly composed of the ladder structure with phenazine units, and after 40-cycle potential sweeps between -0.4 and 0.1 V vs. SCE only 2.5% in molar percentage of PoPD's ladder structure could be converted into polyaniline-like chains, suggesting that the ladder structure with phenazine units is thermodynamically more stable due to its possessing higher conjugation.

  17. The Structure of Professional Profiles for Tourism in the United Kingdom.

    Science.gov (United States)

    Cooper, Chris; And Others

    The tourism and leisure industries are among the fastest growing in the United Kingdom, generating jobs and spending and stimulating economic development. The hotel and catering sector is by far the best documented of the tourism industry and is the major employer. It is also an underqualified sector, despite a range of courses from craft to…

  18. The Structure of Professional Profiles for Tourism in the United Kingdom.

    Science.gov (United States)

    Cooper, Chris; And Others

    The tourism and leisure industries are among the fastest growing in the United Kingdom, generating jobs and spending and stimulating economic development. The hotel and catering sector is by far the best documented of the tourism industry and is the major employer. It is also an underqualified sector, despite a range of courses from craft to…

  19. The United Nations University: The Concept, History, Structure, Financing, Objectives, Centres and Programmes. Guest Editorial.

    Science.gov (United States)

    Reddy, J.

    2000-01-01

    The United Nations University (UNU) is an international academic organization which brings together leading international scholars to tackle world problems. This article describes for South African scholars, institutions, governments, and their agencies the importance of the work being undertaken by the UNU and encourages their participation. (EV)

  20. Quadratic maximization on the unit simplex: structure, stability, genericity and application in biology

    NARCIS (Netherlands)

    Still, Georg J.; Ahmed, F.

    The paper deals with the simple but important problem of maximizing a (nonconvex) quadratic function on the unit simplex. This program is directly related to the concept of evolutionarily stable strategies (ESS) in biology. We discuss this relation and study optimality conditions, stability and

  1. Triple-helix propensity of hydroxyproline and fluoroproline: comparison of host-guest and repeating tripeptide collagen models.

    Science.gov (United States)

    Persikov, Anton V; Ramshaw, John A M; Kirkpatrick, Alan; Brodsky, Barbara

    2003-09-24

    Peptide models have proved important in defining the structural features of the collagen triple-helix. Some models are based on multiple repeats of a given tripeptide unit, while a host-guest design includes an individual tripeptide unit substituted within a constant repeating Pro-Hyp-Gly framework. In the present study, proline, hydroxyproline, and fluoroproline residues are incorporated in X- or Y-positions of a guest triplet in the host-guest peptide design. All host-guest peptides, including Hyp-Pro-Gly, formed stable triple-helices, even though a triple-helix cannot be formed by (Hyp-Pro-Gly)10. The order of stability Pro-Hyp-Gly > Pro-Pro-Gly > Hyp-Pro-Gly remains the same in all models, while the Pro-Flp-Gly is very stabilizing in a repeating context but destabilizing in a host-guest context. The range of thermal stabilities and calorimetric enthalpies is very small among the five host-guest peptides, consistent with the concept that the effect of one Xaa-Yaa-Gly tripeptide unit in the host-guest system would be less than the much larger variations when there are 10 repeating units. However, a simple additive model based on host-guest peptides predicts a greater stability than experimentally observed. The difference in stability contributions of the same tripeptide unit in host-guest versus repeating tripeptide systems illustrates the impact of sequence environment on stability, and factors that play a role include ring puckering as a consequence of electron inductive effects, residual monomer structure, and native state hydration networks.

  2. Survey of simple sequence repeats in woodland strawberry (Fragaria vesca).

    Science.gov (United States)

    Guan, L; Huang, J F; Feng, G Q; Wang, X W; Wang, Y; Chen, B Y; Qiao, Y S

    2013-07-30

    The use of simple sequence repeats (SSRs), or microsatellites, as genetic markers has become popular due to their abundance and variation in length among individuals. In this study, we investigated linkage groups (LGs) in the woodland strawberry (Fragaria vesca) and demonstrated variation in the abundances, densities, and relative densities of mononucleotide, dinucleotide, and trinucleotide repeats. Mononucleotide, dinucleotide, and trinucleotide repeats were more common than longer repeats in all LGs examined. Perfect SSRs were the predominant SSR type found and their abundance was extremely stable among LGs and chloroplasts. Abundances of mononucleotide, dinucleotide, and trinucleotide repeats were positively correlated with LG size, whereas those of tetranucleotide and hexanucleotide SSRs were not. Generally, in each LG, the abundance, relative abundance, relative density, and the proportion of each unique SSR all declined rapidly as the repeated unit increased. Furthermore, the lengths and frequencies of SSRs varied among different LGs.

  3. The structure, mechanism and application of clustered regularly interspaced short palindromic repeats system%成簇规律间隔短回文重复系统的结构、作用机制及应用

    Institute of Scientific and Technical Information of China (English)

    陈瑾; 王素英; 董世瑞

    2016-01-01

    成簇的规律间隔短回文重复( CRISPR)是一类广泛分布于细菌和古细菌基因组中的DNA重复结构。重复结构与前导序列、一系列相关蛋白一起,为原核生物提供抵御噬菌体和质粒等外源基因的获得性免疫能力。综述了CRISPR系统的结构、作用机制及应用,介绍了最新的研究成果,并对其发展前景进行了展望。%Clustered regularly interspaced short palindromic repeats ( CRISPR) is a kind of repetitive DNA structure, which is widely distributed in bacterial and archaeal genomes. The structure with leader sequence and a series of associated proteins together provide acquired immunity against phage and plasmid genes for prokaryotes. In this paper, the structure, mechanism and application of CRISPR system are summarized, the latest research progress is introduced, and the prospect of its development is prospected.

  4. Native tandem and ion mobility mass spectrometry highlight structural and modular similarities in clustered-regularly-interspaced shot-palindromic-repeats (CRISPR)-associated protein complexes from Escherichia coli and Pseudomonas aeruginosa.

    Science.gov (United States)

    van Duijn, Esther; Barbu, Ioana M; Barendregt, Arjan; Jore, Matthijs M; Wiedenheft, Blake; Lundgren, Magnus; Westra, Edze R; Brouns, Stan J J; Doudna, Jennifer A; van der Oost, John; Heck, Albert J R

    2012-11-01

    The CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) immune system of bacteria and archaea provides acquired resistance against viruses and plasmids, by a strategy analogous to RNA-interference. Key components of the defense system are ribonucleoprotein complexes, the composition of which appears highly variable in different CRISPR/Cas subtypes. Previous studies combined mass spectrometry, electron microscopy, and small angle x-ray scattering to demonstrate that the E. coli Cascade complex (405 kDa) and the P. aeruginosa Csy-complex (350 kDa) are similar in that they share a central spiral-shaped hexameric structure, flanked by associating proteins and one CRISPR RNA. Recently, a cryo-electron microscopy structure of Cascade revealed that the CRISPR RNA molecule resides in a groove of the hexameric backbone. For both complexes we here describe the use of native mass spectrometry in combination with ion mobility mass spectrometry to assign a stable core surrounded by more loosely associated modules. Via computational modeling subcomplex structures were proposed that relate to the experimental IMMS data. Despite the absence of obvious sequence homology between several subunits, detailed analysis of sub-complexes strongly suggests analogy between subunits of the two complexes. Probing the specific association of E. coli Cascade/crRNA to its complementary DNA target reveals a conformational change. All together these findings provide relevant new information about the potential assembly process of the two CRISPR-associated complexes.

  5. Early evidence for complex social structure in Proboscidea from a late Miocene trackway site in the United Arab Emirates

    Science.gov (United States)

    Bibi, Faysal; Kraatz, Brian; Craig, Nathan; Beech, Mark; Schuster, Mathieu; Hill, Andrew

    2012-01-01

    Many living vertebrates exhibit complex social structures, evidence for the antiquity of which is limited to rare and exceptional fossil finds. Living elephants possess a characteristic social structure that is sex-segregated and multi-tiered, centred around a matriarchal family and solitary or loosely associated groups of adult males. Although the fossil record of Proboscidea is extensive, the origin and evolution of social structure in this clade is virtually unknown. Here, we present imagery and analyses of an extensive late Miocene fossil trackway site from the United Arab Emirates. The site of Mleisa 1 preserves exceptionally long trackways of a herd of at least 13 individuals of varying size transected by that of a single large individual, indicating the presence of both herding and solitary social modes. Trackway stride lengths and resulting body mass estimates indicate that the solitary individual was also the largest and therefore most likely a male. Sexual determination for the herd is equivocal, but the body size profile and number of individuals are commensurate with those of a modern elephant family unit. The Mleisa 1 trackways provide direct evidence for the antiquity of characteristic and complex social structure in Proboscidea. PMID:22357934

  6. Early evidence for complex social structure in Proboscidea from a late Miocene trackway site in the United Arab Emirates.

    Science.gov (United States)

    Bibi, Faysal; Kraatz, Brian; Craig, Nathan; Beech, Mark; Schuster, Mathieu; Hill, Andrew

    2012-08-23

    Many living vertebrates exhibit complex social structures, evidence for the antiquity of which is limited to rare and exceptional fossil finds. Living elephants possess a characteristic social structure that is sex-segregated and multi-tiered, centred around a matriarchal family and solitary or loosely associated groups of adult males. Although the fossil record of Proboscidea is extensive, the origin and evolution of social structure in this clade is virtually unknown. Here, we present imagery and analyses of an extensive late Miocene fossil trackway site from the United Arab Emirates. The site of Mleisa 1 preserves exceptionally long trackways of a herd of at least 13 individuals of varying size transected by that of a single large individual, indicating the presence of both herding and solitary social modes. Trackway stride lengths and resulting body mass estimates indicate that the solitary individual was also the largest and therefore most likely a male. Sexual determination for the herd is equivocal, but the body size profile and number of individuals are commensurate with those of a modern elephant family unit. The Mleisa 1 trackways provide direct evidence for the antiquity of characteristic and complex social structure in Proboscidea.

  7. The reaction of the building structure with window unit to the explosiveimpact on the basis of dynamic equation solution

    Directory of Open Access Journals (Sweden)

    Doronin Fedor Leonidovich

    2014-01-01

    Full Text Available When designing residential buildings, additional measures for increasing the strength at dynamic effects indoors are not foreseen. The walls of the structure fixed in the framework are not designed for shock wave caused by explosion of utility gas. When designing a building, the task of the special dynamic load is often reduced to the calculation of the safe shock pressure, exceeding of which leads to the destruction of the structures. The wall with the window area under dynamic effects is a blast relief panel, which reduces the excess pressure inside the room. The proposed method of calculating a design with a window unit allows determining the dynamic reaction of the wall on explosive pulse. The proposed calculation technique of the constructions at shock loads allows tracing the changes of the inertial forces and displacements at any stage of dynamic response. The reaction to dynamic loads can be also set for non-monolithic structures, consisting of different materials with different conditions of fastening. Elastoplastic reaction of a brick wall with glass units was determined using step-by-step method of linear acceleration. The calculation of stress-strain state of brick walls with window panes determined the strength properties of the structures close to the monolithic version. The proposed technique of numerical solution of dynamic equations is applied only in the analysis of elastic systems, in which the dynamic characteristics remain unchanged throughout the reaction process.

  8. "Unitized Structure and Differentiated Staffing in the Elementary School." DSP Progress Report No. 1: Structure and Staffing.

    Science.gov (United States)

    Arends, Richard I.; Essig, Don M.

    This report is the first in a series describing the background, theory, and progress of the Differentiated Staffing Project in the Eugene, Oregon, School District. This particular report reviews the history of the project and outlines the organizational structure that has emerged and developed in the experimental elementary schools. A number of…

  9. One-step synthesis of mesoporous pentasil zeolite with single-unit-cell lamellar structural features

    Science.gov (United States)

    Tsapstsis, Michael; Zhang, Xueyi

    2015-11-17

    A method for making a pentasil zeolite material includes forming an aqueous solution that includes a structure directing agent and a silica precursor; and heating the solution at a sufficient temperature and for sufficient time to form a pentasil zeolite material from the silica precursor, wherein the structure directing agent includes a quaternary phosphonium ion.

  10. Seismic structural fragility investigation for the San Onofre Nuclear Generating Station, Unit 1 (Project I); SONGS-1 AFWS Project

    Energy Technology Data Exchange (ETDEWEB)

    Wesley, D.A.; Hashimoto, P.S.

    1982-04-01

    An evaluation of the seismic capacities of several of the San Onofre Nuclear Generating Station, Unit 1 (SONGS-1) structures was conducted to determine input to the overall probabilistic methodology developed by Lawrence Livermore National Laboratory. Seismic structural fragilities to be used as input consist of median seismic capacities and their variabilities due to randomness and uncertainty. Potential failure modes were identified for each of the SONGS-1 structures included in this study by establishing the seismic load-paths and comparing expected load distributions to available capacities for the elements of each load-path. Particular attention was given to possible weak links and details. The more likely failure modes were screened for more detailed investigation.

  11. Homo- and heterodinuclear coordination polymers based on a tritopic cyclam bis-terpyridine unit: Structure and rheological properties

    Energy Technology Data Exchange (ETDEWEB)

    Qu, Li; Fan, Jiangxia; Ren, Yong; Xiong, Kun [State Key Laboratory Cultivation Base for Nonmetal Composites and Functional Materials, School of Materials Science and Engineering, Southwest University of Science and Technology, Mianyang 621010 (China); Yan, Minhao, E-mail: yanminhao@swust.edu.cn [State Key Laboratory Cultivation Base for Nonmetal Composites and Functional Materials, School of Materials Science and Engineering, Southwest University of Science and Technology, Mianyang 621010 (China); Tuo, Xianguo, E-mail: tuoxg@swust.edu.cn [Laboratory of National Defense for Radioactive Waste and Environmental Security, Southwest University of Science and Technology, Mianyang 621010 (China); Terech, Pierre [SPrAM, UMR CEA/CNRS/UJF-Grenoble 1, INAC, Grenoble F-38054 (France); Royal, Guy [Université Joseph Fourier Grenoble I, Département de Chimie Moléculaire, UMR CNRS-5250, Institut de Chimie Moléculaire de Grenoble, FR CNRS-2607, BP 53, 38041 Grenoble Cedex 9 (France)

    2015-03-01

    An innovative coordination polymer based on a tritopic ligand having the bis-terpyridine cyclam (CHTT) unit is explored. Homo- or heteronuclear 1D coordination polymers can be formed with bivalent metal ions such as Co(II) and Ni(II) in solvent DMF. Creep-recovery curves of the (Co{sup II}){sub 2}CHTT gels formed from 1D coordination polymers were analyzed with the Burgers model and demonstrated an original self-healing property, unusual in the class of molecular gels. The influence of the metal type was studied through the structural features using small-angle neutron scattering (SANS) experiments. In gels, the corresponding network involves genuine fibers (R ≈ 35 Å), bundles of these fibers and also a fraction of finite size aggregates (rods with aspect ratio f ≈ 3–5). We found that the distribution of these latter structural components is sensitive to the metal ions type. Such tritopic 1D coordination polymers exhibit a range of original structural features and a facile control of the developed structures in solutions and gels by tuning their thermodynamic parameters. The versatility associated to the intrinsic dynamic ability of the systems should pave the way to original properties for molecular devices. - Graphical abstract: A tritopic ligand with a bis-terpyridine cyclam (CHTT) unit can form homo- and heterobinuclear coordination polymers with bivalent metal ions in DMF. Gels exhibit a remarkable self-healing property while structures of solutions and gels are studied by small-angle neutron scattering. - Highlights: • Homo- and heteronuclear coordination polymers based on innovative tritopic ligand. • The gels formed from the coordination polymers demonstrated self-healing property. • Influence of the metal type was studied through the structural properties by SANS. • Versatility of the singular system present original properties for molecular device.

  12. The Influence of Structure on the Function of an Administrative Unit: Single Focus Academic Structure or Multiple Focus Academic Structure--Raising Some of the Issues.

    Science.gov (United States)

    Ross, Robert F.; Emmert, Philip

    1990-01-01

    Argues for a multifocused divisional unit versus the traditional single discipline communication department for institutions that are generally small (6 to 10 thousand students) and where enrollments overall have leveled off for both the institution and department. (KEH)

  13. Synthesis, Structure, and Rigid Unit Mode-like Anisotropic Thermal Expansion of BaIr2In9.

    Science.gov (United States)

    Calta, Nicholas P; Han, Fei; Kanatzidis, Mercouri G

    2015-09-08

    This Article reports the synthesis of large single crystals of BaIr2In9 using In flux and their characterization by variable-temperature single-crystal and synchrotron powder X-ray diffraction, resistivity, and magnetization measurements. The title compound adopts the BaFe2Al9-type structure in the space group P6/mmm with room temperature unit cell parameters a = 8.8548(6) Å and c = 4.2696(4) Å. BaIr2In9 exhibits anisotropic thermal expansion behavior with linear expansion along the c axis more than 3 times larger than expansion in the ab plane between 90 and 400 K. This anisotropic expansion originates from a rigid unit mode-like mechanism similar to the mechanism of zero and negative thermal expansion observed in many anomalous thermal expansion materials such as ZrW2O8 and ScF3.

  14. Self Deployable Ultra-Lightweight Modular Unit for Habitat Structural Applications Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Space deployable and rigidizable structures which are ultra-lightweight, and have high rigidity, space durability, and high impact resistance are desirable to...

  15. 3D Printing Complex Unitized Instrument Optical Benches and Metering Structures Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The objective of this project is to determine the engineering techniques required to manufacture complex, thin-shelled instrument structures. These techniques will...

  16. Nucleotide sequence of the BamHI repetitive sequence, including the HindIII fundamental unit, as a possible mobile element from the Japanese monkey Macaca fuscata.

    Science.gov (United States)

    Prassolov, V S; Kuchino, Y; Nemoto, K; Nishimura, S

    1986-01-01

    Clustered repeat units produced by BamHI digestion of genomic DNA from the Japanese monkey Macaca fuscata [JMr(BamHI)] were sequenced by dideoxy DNA sequencing. The nucleotide sequences of several individual repeats showed that the BamHI repeat contains the 170-bp HindIII element as an integral part, and that it has more than 90% homology with the HindIII repeat element [AGMr(HindIII)] found in the genomic DNA of the African green monkey. In the JMr(BamHI) repeat unit, the 170-bp HindIII element is flanked by a 6-bp inverted repeat, which is part of a 22-bp direct repeat. This latter repeat of 22-bp asymmetrically overlaps the border between the internal AGMr(HindIII)-like region and adjacent regions of the JMr(BamHI) repeat. A similar structural feature of the BamHI repeat unit has been found in the genomic DNA of the baboon, but not in that of the African green monkey. These results show clearly that the BamHI repeat of the modern Japanese monkey originated as a result of insertion of an AGMr(HindIII) element into a certain site(s) of the genomic DNA of an ancestor of the modern Japanese monkey before Macaca-Cercocebus divergence.

  17. Studies of an expanded trinucleotide repeat in transgenic mice

    Energy Technology Data Exchange (ETDEWEB)

    Bingham, P.; Wang, S.; Merry, D. [Univ. of Pennsylvania, Philadelphia, PA (United States)

    1994-09-01

    Spinal and bulbar muscular atrophy (SBMA) is a progressive motor neuron disease caused by expansion of a trinucleotide repeat in the androgen receptor gene (AR{sup exp}). AR{sup exp} repeats expand further or contract in approximately 25% of transmissions. Analogous {open_quotes}dynamic mutations{close_quotes} have been reported in other expanded trinucleotide repeat disorders. We have been developing a mouse model of this disease using a transgenic approach. Expression of the SBMA AR was documented in transgenic mice with an inducible promoter. No phenotypic effects of transgene expression were observed. We have extended our previous results on stability of the expanded trinucleotide repeat in transgenic mice in two lines carrying AR{sup exp}. Tail DNA was amplified by PCR using primers spanning the repeat on 60 AR{sup exp} transgenic mice from four different transgenic lines. Migration of the PCR product through an acrylamide gel showed no change of the 45 CAG repeat length in any progeny. Similarly, PCR products from 23 normal repeat transgenics showed no change from the repeat length of the original construct. Unlike the disease allele in humans, the expanded repeat AR cDNA in transgenic mice showed no change in repeat length with transmission. The relative stability of CAG repeats seen in the transgenic mice may indicate either differences in the fidelity of replicative enzymes, or differences in error identification and repair between mice and humans. Integration site or structural properties of the transgene itself might also play a role.

  18. Unit Cell Structure of Crystal Polytypes in InAs and InSb Nanowires

    DEFF Research Database (Denmark)

    Kriegner, Dominik; Panse, Christian; Mandl, Bernhard

    2011-01-01

    , wurtzite, and 4H polytypes for InAs and InSb nanowires, using X-ray diffraction and transmission electron microscopy. The results are compared to density functional theory calculations. Experiment and theory show that the occurrence of hexagonal bilayers tends to stretch the distances of atomic layers...... parallel to the c axis and to reduce the in-plane distances compared to those in zinc blende. The change of the lattice parameters scales linearly with the hexagonality of the polytype, defined as the fraction of bilayers with hexagonal character within one unit cell....

  19. Structure-Based Optimization of a Small Molecule Antagonist of the Interaction Between WD Repeat-Containing Protein 5 (WDR5) and Mixed-Lineage Leukemia 1 (MLL1).

    Science.gov (United States)

    Getlik, Matthäus; Smil, David; Zepeda-Velázquez, Carlos; Bolshan, Yuri; Poda, Gennady; Wu, Hong; Dong, Aiping; Kuznetsova, Ekaterina; Marcellus, Richard; Senisterra, Guillermo; Dombrovski, Ludmila; Hajian, Taraneh; Kiyota, Taira; Schapira, Matthieu; Arrowsmith, Cheryl H; Brown, Peter J; Vedadi, Masoud; Al-Awar, Rima

    2016-03-24

    WD repeat-containing protein 5 (WDR5) is an important component of the multiprotein complex essential for activating mixed-lineage leukemia 1 (MLL1). Rearrangement of the MLL1 gene is associated with onset and progression of acute myeloid and lymphoblastic leukemias, and targeting the WDR5-MLL1 interaction may result in new cancer therapeutics. Our previous work showed that binding of small molecule ligands to WDR5 can modulate its interaction with MLL1, suppressing MLL1 methyltransferase activity. Initial structure-activity relationship studies identified N-(2-(4-methylpiperazin-1-yl)-5-substituted-phenyl) benzamides as potent and selective antagonists of this protein-protein interaction. Guided by crystal structure data and supported by in silico library design, we optimized the scaffold by varying the C-1 benzamide and C-5 substituents. This allowed us to develop the first highly potent (Kdisp < 100 nM) small molecule antagonists of the WDR5-MLL1 interaction and demonstrate that N-(4-(4-methylpiperazin-1-yl)-3'-(morpholinomethyl)-[1,1'-biphenyl]-3-yl)-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide 16d (OICR-9429) is a potent and selective chemical probe suitable to help dissect the biological role of WDR5.

  20. PCR-free digital minisatellite tandem repeat genotyping.

    Science.gov (United States)

    Chen, Yuchao; Seo, Tae Seok

    2011-06-01

    We demonstrated a proof-of-concept for novel minisatellite tandem repeat typing, called PCR-free digital VNTR (variable number tandem repeat) typing, which is composed of three steps: a ligation reaction instead of PCR thermal cycling, magnetic bead-based solid-phase capture for purification, and an elongated sample stacking microcapillary electrophoresis (μCE) for sensitive digital coding of repeat number. We designed a 16-bp fluorescently labeled ligation probe which is complementary to a repeat unit of a biotinylated synthetic template mimicking the human D1S80 VNTR locus and is randomly hybridized with the minisatellite tandem repeats. A quick isothermal ligation reaction was followed to link the adjacent ligation probes on the DNA templates, and then the ligated products were purified by streptavidin-coated magnetic beads. After a denaturing step, a large amount of ligated products whose size difference was equivalent to the repeat unit were released and recovered. Through the elongated sample stacking μCE separation on a microdevice, the fluorescence signal of the ligated products was generated in the electropherogram and the peak number was directly counted which was exactly matched with the repeat number of VNTR locus. We could successfully identify the minisatellite tandem repeat number with only 5 fmol of DNA template in 30 min.

  1. On balanced minimal repeated measurements designs

    Directory of Open Access Journals (Sweden)

    Shakeel Ahmad Mir

    2014-10-01

    Full Text Available Repeated Measurements designs are concerned with scientific experiments in which each experimental unit is assigned more than once to a treatment either different or identical. This class of designs has the property that the unbiased estimators for elementary contrasts among direct and residual effects are obtainable. Afsarinejad (1983 provided a method of constructing balanced Minimal Repeated Measurements designs p < t , when t is an odd or prime power, one or more than one treatment may occur more than once in some sequences and  designs so constructed no longer remain uniform in periods. In this paper an attempt has been made to provide a new method to overcome this drawback. Specifically, two cases have been considered                RM[t,n=t(t-t/(p-1,p], λ2=1 for balanced minimal repeated measurements designs and  RM[t,n=2t(t-t/(p-1,p], λ2=2 for balanced  repeated measurements designs. In addition , a method has been provided for constructing              extra-balanced minimal designs for special case RM[t,n=t2/(p-1,p], λ2=1.

  2. Is single-4-ring the most basic but elusive secondary building unit that transforms to larger structures in zinc phosphate chemistry?

    Science.gov (United States)

    Dar, Aijaz A; Sharma, Sunil K; Murugavel, Ramaswamy

    2015-05-18

    Haloaryl phosphates (X-dippH2, X = Cl, Br, I) react with zinc acetate in the presence of collidine or 2-aminopyridine (2-apy) to yield zinc phosphate clusters [Zn(X-dipp)(collidine)]4 (X = Cl (1), Br (2), I (3)) and [Zn(X-dipp)(2-apy)]4·2MeOH (X = Cl (4), Br (5), I (6)), respectively. Single-crystal X-ray diffraction studies reveal that collidine and 2-apy capped zinc phosphates 1-6 exist as discrete tetrameric zinc phosphate molecules, exhibiting a cubane-shaped D4R core. In contrast, when the same reaction has been carried out in the presence of 4-cyanopyridine (4-CNpy), polymeric zinc phosphates {[Zn4(X-dipp)4(4-CNpy)2(MeOH)2]·2H2O}n (X = Cl (7), Br (8), I (9)) have been isolated. Compounds 7-9 are square-wave-shaped, one-dimensional polymers composed of fused S4R repeating units. The common structural motif found both in D4R cubanes 1-6 and polymers 7-9 is the S4R building block, which presumably undergoes further fusion because of the coordinative unsaturation at zinc and the simultaneous presence of free P═O. The closed shell cubanes 1-6 are obviously formed by a face-to-face dimerization involving two S4R units in which the two P═O groups are in cis-configuration. On the other hand, the one-dimensional (1-D) square-wave polymers 7-9 are formed from a face-to-face association of S4R building units in which the two P═O groups are in a trans-configuration. In order to stabilize these elusive S4R zinc phosphates, the reaction between Cl-dippH2 and zinc acetate was carried out in the presence of excess imidazole as an ancillary ligand (1:1:4), although only an imidazole decorated cubane cluster [Zn(Cl-dipp)(imz)]4.2MeOH (10) was isolated. The chelating N,N'-donor 1,10-phenanthroline ligand was used to eventually isolate cyclic S4R phosphate [Zn(μ2-Cl-dipp)(1,10-phen)(OH2)]2·MeOH·H2O (11). The change of Zn(2+) source to zinc nitrate and the phosphate source to 2,6-dimethylphenyl phosphate (dmppH2) led to the isolation of another polymeric phosphate [Zn

  3. Genus-specific protein binding to the large clusters of DNA repeats (short regularly spaced repeats) present in Sulfolobus genomes

    DEFF Research Database (Denmark)

    Peng, Xu; Brügger, Kim; Shen, Biao

    2003-01-01

    Short regularly spaced repeats (SRSRs) occur in multiple large clusters in archaeal chromosomes and as smaller clusters in some archaeal conjugative plasmids and bacterial chromosomes. The sequence, size, and spacing of the repeats are generally constant within a cluster but vary between clusters...... that are identical in sequence to one of the repeat variants in the S. solfataricus chromosome. Repeats from the pNOB8 cluster were amplified and tested for protein binding with cell extracts from S. solfataricus. A 17.5-kDa SRSR-binding protein was purified from the cell extracts and sequenced. The protein is N...... terminally modified and corresponds to SSO454, an open reading frame of previously unassigned function. It binds specifically to DNA fragments carrying double and single repeat sequences, binding on one side of the repeat structure, and producing an opening of the opposite side of the DNA structure. It also...

  4. Impact of road network on the structure of a multifunctional forest landscape unit in southern Turkey.

    Science.gov (United States)

    Eker, Mehmet; Coban, Huseyin Oguz

    2010-01-01

    Forest roads have many kinds of direct and indirect effects such as physical, ecological, and socio-economic effects in landscape scale. In this study the relationship between forest road network and the structure of a multifunctionally planned forest landscape, in the south of Turkey was examined. The aim of the study was to determine whether or not the correlation between road network and landscape structure across a gradient of road density categorical road/no road approach and landscape pattern data from the managed forest landscapes existed. It was concerned with three type polygons that were forest functioning patches, compartments, and stand patches and were associated with higher road density or existing of road network. To quantify the case, it was analyzed whether the spatial structure of forest patches adjacent to roads differs from the spatial structure of forest patches away from roads. GIS was used to integrate quantitative indices of landscape structure. There was little negatively significant relationship between road density and patch area/size, patch perimeter and shape index of patton index (PI) and no correlation with patch number and Fractal Dimension (FD). The forest road network modified spatial pattern of patch shape through PI values. The road network increased the number of patch and decreased mean patch size. The existence of road network was more effective than topography index appearing of PI and FD in the roaded areas. It was indicated to potential reverse impacts of road network on spatial structure of forest compartments in terms of shape index (FD). Highest proportions of harvestable forest areas fall into roaded areas. The results define that road networks are effective on the spatial structure of forest landscape. The forest road network of study area has all probable ecological impacts of forest roads mentioned in context.

  5. Structure formation of aerated concrete containing waste coal combustion products generated in the thermal vortex power units

    Science.gov (United States)

    Ivanov, A. I.; Stolboushkin, A. Yu; Temlyanstev, M. V.; Syromyasov, V. A.; Fomina, O. A.

    2016-10-01

    The results of fly ash research, generated in the process of waste coal combustion in the thermal vortex power units and used as an aggregate in aerated concrete, are provided. It is established that fly ash can be used in the production of cement or concrete with low loss on ignition (LOI). The permitted value of LOI in fly ash, affecting the structure formation and operational properties of aerated concrete, are defined. During non-autoclaved hardening of aerated concrete with fly ash aggregate and LOI not higher than 2%, the formation of acicular crystals of ettringite, reinforcing interporous partitions, takes place.

  6. On Methods of Establishing Design Diagrams for Structural Integrity of Slender Complex Types of Breakwater Armour Units

    DEFF Research Database (Denmark)

    Burcharth, Hans F.; Howell, Gary J.

    1988-01-01

    was first presented by NRC (Timco 1981 ). Work based on direct strain-gauge measurement of stresses on large concrete model armour units was presented by Nishigori et al. in 1986.So far, none of the mentioned methods have produced general applicable tools for the design of armour layers. This is mainly...... by other researchers, it might be a frame for a uniform presentation of results. Without a uniformity it will take much longer before the oncoming data on structural integrity can be made useful through contributions to the future data bank which will be needed as a design tool....

  7. Structural basis for triplet repeat disorders

    DEFF Research Database (Denmark)

    Baldi, Pierre; Brunak, Søren; Chauvin, Yves

    1999-01-01

    Motivation: Over a dozen major degenerative disorders, including myotonic distrophy, Huntington's disease and fragile X syndrome result from unstable expansions of particular trinucleotides. Remarkably, only some of all the possible triplets, namely CAG/CTG, CGG/CCG and GAA/TTC, have been associa......, which we predict to have very high flexibility, may play a role in the pathogenesis of the neurodegenerative disorder multiple system atrophy (MSA)....

  8. Flight-vehicle structures education in the United States Assessment and recommendations

    Science.gov (United States)

    Noor, Ahmed K.; Dixon, S. C.

    1987-01-01

    An assessment is made of the technical contents of flight-vehicle structures curricula at 41 U.S. universities with accredited aerospace engineering programs. The assessment is based on the technical needs for the new and projected aeronautical and space systems as well as on the likely characteristics of the aerospace engineering work environment. A number of deficiencies and areas of concern are identified and recommendations are presented for enhancing the effectiveness of flight-vehicle structures education. A number of government supported programs that can help aerospace engineering education are listed in the appendix.

  9. DWI Repeaters and Non-Repeaters: A Comparison.

    Science.gov (United States)

    Weeber, Stan

    1981-01-01

    Discussed how driving-while-intoxicated (DWI) repeaters differed signigicantly from nonrepeaters on 4 of 23 variables tested. Repeaters were more likely to have zero or two dependent children, attend church frequently, drink occasionally and have one or more arrests for public intoxication. (Author)

  10. To Repeat or Not to Repeat a Course

    Science.gov (United States)

    Armstrong, Michael J.; Biktimirov, Ernest N.

    2013-01-01

    The difficult transition from high school to university means that many students need to repeat (retake) 1 or more of their university courses. The authors examine the performance of students repeating first-year core courses in an undergraduate business program. They used data from university records for 116 students who took a total of 232…

  11. The Impact of Structural Break(s on the Validity of Purchasing Power Parity in Turkey: Evidence from Zivot-Andrews and Lagrange Multiplier Unit Root Tests

    Directory of Open Access Journals (Sweden)

    Hakan Kum

    2012-01-01

    Full Text Available This study examines the validity of the purchasing power parity (PPP in Turkey for annual data from 1953 to 2009. While results from both the ADF unit root and the DF-GLS unit root test indicate mixed results, PPP holds for Turkey with the presence of structural breaks which are obtained by Zivot and Andrews and Lagrange Multiplier unit root tests.

  12. Optimized three-unit cubesat structure for Delfi-n3Xt

    NARCIS (Netherlands)

    Go, S.Y.; Bouwmeester, J.; Brouwer, G.F.

    2008-01-01

    For the Delfi-n3Xt mission, follow-up to CubeSat Delfi-C3 [1] of Delft University of Technology, several concepts concerning the Structural Subsystem (STS) have been analysed. One of the main objectives is to reduce the time needed for assembly, integration and testing, and to improve handling capab

  13. Genetic structure of the invasive tree Ailanthus altissima in eastern United States cities

    Science.gov (United States)

    Preston R. Aldrich; Joseph S. Briguglio; Shyam N. Kapadia; Minesh U. Morker; Ankit Rawal; Preeti Kalra; Cynthia D. Huebner; Gary K. Greer

    2010-01-01

    Ailanthus altissima is an invasive tree from Asia. It now occurs in most US states, and although primarily an urban weed, it has become a problem in forested areas especially in the eastern states. Little is known about its genetic structure. We explore its naturalized gene pool from 28 populations, mostly of the eastern US where infestations are...

  14. Computing the Density Matrix in Electronic Structure Theory on Graphics Processing Units.

    Science.gov (United States)

    Cawkwell, M J; Sanville, E J; Mniszewski, S M; Niklasson, Anders M N

    2012-11-13

    The self-consistent solution of a Schrödinger-like equation for the density matrix is a critical and computationally demanding step in quantum-based models of interatomic bonding. This step was tackled historically via the diagonalization of the Hamiltonian. We have investigated the performance and accuracy of the second-order spectral projection (SP2) algorithm for the computation of the density matrix via a recursive expansion of the Fermi operator in a series of generalized matrix-matrix multiplications. We demonstrate that owing to its simplicity, the SP2 algorithm [Niklasson, A. M. N. Phys. Rev. B2002, 66, 155115] is exceptionally well suited to implementation on graphics processing units (GPUs). The performance in double and single precision arithmetic of a hybrid GPU/central processing unit (CPU) and full GPU implementation of the SP2 algorithm exceed those of a CPU-only implementation of the SP2 algorithm and traditional matrix diagonalization when the dimensions of the matrices exceed about 2000 × 2000. Padding schemes for arrays allocated in the GPU memory that optimize the performance of the CUBLAS implementations of the level 3 BLAS DGEMM and SGEMM subroutines for generalized matrix-matrix multiplications are described in detail. The analysis of the relative performance of the hybrid CPU/GPU and full GPU implementations indicate that the transfer of arrays between the GPU and CPU constitutes only a small fraction of the total computation time. The errors measured in the self-consistent density matrices computed using the SP2 algorithm are generally smaller than those measured in matrices computed via diagonalization. Furthermore, the errors in the density matrices computed using the SP2 algorithm do not exhibit any dependence of system size, whereas the errors increase linearly with the number of orbitals when diagonalization is employed.

  15. The organizational structure of an intensive care unit influences treatment of hypotension among critically ill patients: A retrospective cohort study.

    Science.gov (United States)

    Boone, M Dustin; Massa, Jennifer; Mueller, Ariel; Jinadasa, Sayuri P; Lee, Joon; Kothari, Rishi; Scott, Daniel J; Callahan, Julie; Celi, Leo Anthony; Hacker, Michele R

    2016-06-01

    Prior studies report that weekend admission to an intensive care unit is associated with increased mortality, potentially attributed to the organizational structure of the unit. This study aims to determine whether treatment of hypotension, a risk factor for mortality, differs according to level of staffing. Using the Multiparameter Intelligent Monitoring in Intensive Care database, we conducted a retrospective study of patients admitted to an intensive care unit at Beth Israel Deaconess Medical Center who experienced one or more episodes of hypotension. Episodes were categorized according to the staffing level, defined as high during weekday daytime (7 am-7 pm) and low during weekends or nighttime (7 pm-7 am). Patients with a hypotensive event on a weekend were less likely to be treated compared with those that occurred during the weekday daytime (P = .02). No association between weekday daytime vs weekday nighttime staffing levels and treatment of hypotension was found (risk ratio, 1.02; 95% confidence interval, 0.98-1.07). Patients with a hypotensive event on a weekend were less likely to be treated than patients with an event during high-staffing periods. No association between weekday nighttime staffing and hypotension treatment was observed. We conclude that treatment of a hypotensive episode relies on more than solely staffing levels. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. A structural econometric model of family valuation and choice of employer-sponsored health insurance in the United States.

    Science.gov (United States)

    Vanness, David J

    2003-09-01

    This paper estimates a fully structural unitary household model of employment and health insurance decisions for dual wage-earner families with children in the United States, using data from the 1987 National Medical Expenditure Survey. Families choose hours of work and the breakdown of compensation between cash wages and health insurance benefits for each wage earner in order to maximize expected utility under uncertain need for medical care. Heterogeneous demand for the employer-sponsored health insurance is thus generated directly from variations in health status and earning potential. The paper concludes by discussing the benefits of using structural models for simulating welfare effects of insurance reform relative to the costly assumptions that must be imposed for identification.

  17. Quantum repeaters based on heralded qubit amplifiers

    CERN Document Server

    Minář, Jiří; Sangouard, Nicolas

    2011-01-01

    We present a quantum repeater scheme based on the recently proposed qubit amplifier [N. Gisin, S. Pironio and N. Sangouard, Phys. Rev. Lett. 105, 070501 (2010)]. It relies on a on-demand entangled-photon pair source which uses on-demand single-photon sources, linear optical elements and atomic ensembles. Interestingly, the imperfections affecting the states created from this source, caused e.g. by detectors with non-unit efficiencies, are systematically purified from an entanglement swapping operation based on a two-photon detection. This allows the distribution of entanglement over very long distances with a high fidelity, i.e. without vacuum components and multiphoton errors. Therefore, the resulting quantum repeater architecture does not necessitate final postselections and thus achieves high entanglement distribution rates. This also provides unique opportunities for device-independent quantum key distribution over long distances with linear optics and atomic ensembles.

  18. Repeatable mechanochemical activation of dynamic covalent bonds in thermoplastic elastomers.

    Science.gov (United States)

    Imato, Keiichi; Kanehara, Takeshi; Nojima, Shiki; Ohishi, Tomoyuki; Higaki, Yuji; Takahara, Atsushi; Otsuka, Hideyuki

    2016-08-18

    Repeated mechanical scission and recombination of dynamic covalent bonds incorporated in segmented polyurethane elastomers are demonstrated by utilizing a diarylbibenzofuranone-based mechanophore and by the design of the segmented polymer structures. The repeated mechanochemical reactions can accompany clear colouration and simultaneous fading.

  19. Synthesis, structure and ring-opening polymerization of macrocyclic arylates containing phthalic unit

    Institute of Scientific and Technical Information of China (English)

    姜洪焱; 陈天禄; 邢彦; 林永华; 徐纪平

    1997-01-01

    A series of maerocyclic arylate diraers have been selectively synthesized by an interfacial polyconden-sation of o-phthaloyldichloride with bisphenols A combination of GPC,FAB-MS,1H and 13C NMR unambiguously confirmed the cyclic nature Although single-crystal X-ray analysis of two such macrocycles reveals no severe strain on the cyclic structures,these macrocycles can undergo facile melt polymerization to give high molecular weight polyary-lates.

  20. Effect of intensive care unit organizational model and structure on outcomes in patients with acute lung injury.

    Science.gov (United States)

    Treggiari, Miriam M; Martin, Diane P; Yanez, N David; Caldwell, Ellen; Hudson, Leonard D; Rubenfeld, Gordon D

    2007-10-01

    Prior studies supported an association between intensive care unit (ICU) organizational model or staffing patterns and outcome in critically ill patients. To examine the association of closed versus open models with patient mortality across adult ICUs in King County (WA). Cohort study of patients with acute lung injury (ALI). ICU structure, organization, and patient care practices were assessed using self-administered mail questionnaires completed by the medical director and nurse manager. We defined closed ICUs as units that required patient transfer to or mandatory patient comanagement by an intensivist and open ICUs as those relying on other organizational models. Outcomes were obtained from the King County Lung Injury Project, a population-based cohort of patients with ALI. The main endpoint was hospital mortality. Of 24 eligible ICUs, 13 ICUs were designated closed and 11 open. Complete survey data were available for 23 (96%) ICUs. Higher physician and nurse availability was reported in closed versus open ICUs. A total of 684 of 1,075 (63%) of patients with ALI were cared for in closed ICUs. After adjusting for potential confounders, patients with ALI cared for in closed ICUs had reduced hospital mortality (adjusted odds ratio, 0.68; 95% confidence interval, 0.53, 0.89; P = 0.004). Consultation by a pulmonologist in open ICUs was not associated with improved mortality (adjusted odds ratio, 0.94; 95% confidence interval, 0.74, 1.20; P = 0.62). These findings were robust for varying assumptions about the study population definition. Patients with ALI cared for in a closed-model ICU have reduced mortality. These data support recommendations to implement structured intensive care in the United States.

  1. Uniting Superhydrophobic, Superoleophobic and Lubricant Infused Slippery Behavior on Copper Oxide Nano-structured Substrates

    Science.gov (United States)

    Ujjain, Sanjeev Kumar; Roy, Pritam Kumar; Kumar, Sumana; Singha, Subhash; Khare, Krishnacharya

    2016-01-01

    Alloys, specifically steel, are considered as the workhorse of our society and are inimitable engineering materials in the field of infrastructure, industry and possesses significant applications in our daily life. However, creating a robust synthetic metallic surface that repels various liquids has remained extremely challenging. The wettability of a solid surface is known to be governed by its geometric nano-/micro structure and the chemical composition. Here, we are demonstrating a facile and economical way to generate copper oxide micro-nano structures with spherical (0D), needle (1D) and hierarchical cauliflower (3D) morphologies on galvanized steel substrates using a simple chemical bath deposition method. These nano/micro textured steel surfaces, on subsequent coating of a low surface energy material display excellent superhydrophobic, superoleophobic and slippery behavior. Polydimethylsiloxane coated textured surfaces illustrate superhydrophobicity with water contact angle about 160°(2) and critical sliding angle ~2°. When functionalized with low-surface energy perfluoroalkylsilane, these surfaces display high repellency for low surface tension oils as well as hydrocarbons. Among them, the hierarchical cauliflower morphology exhibits re-entrant structure thereby showing the best superoleophobicity with contact angle 149° for dodecane. Once infused with a lubricant like silicone oil, they show excellent slippery behavior with low contact angle hysteresis (~ 2°) for water drops. PMID:27752098

  2. Experimental testing of various heat transfer structures in a flat plate thermal energy storage unit

    Science.gov (United States)

    Johnson, Maike; Fiß, Michael; Klemm, Torsten

    2016-05-01

    For solar process heat applications with steam as the working fluid and varying application parameters, a novel latent heat storage concept has been developed using an adaptation of a flat plate heat exchanger as the storage concept. Since the pressure level in these applications usually does not exceed 30 bar, an adaptation with storage material chambers arranged between heat transfer medium chambers is possible. Phase change materials are used as the storage medium, so that the isothermal evaporation of steam during discharging of the storage is paired with the isothermal solidification of the storage material. Heat transfer structures can be inserted into the chambers to adjust the power level for a given application. By combining the required number of flat plate heat exchanger compartments and inserting the appropriate heat transfer structure, the design can easily be adjusted for the required power level and capacity for a specific application. Within this work, the technical feasibility of this concept is proven. The dependence of the operating characteristics on the geometry of the heat exchanger is identified. A focus is on varying the power density by integrating conductive heat structures in the PCM.

  3. Population structure and linkage disequilibrium in elite barley breeding germplasm from the United States

    Institute of Scientific and Technical Information of China (English)

    Hao ZHOU; Gary MUEHLBAUER; Brian STEFFENSON

    2012-01-01

    Cultivated barley is known to have a complex population structure and extensive linkage disequilibrium (LD).To conduct robust association mapping (AM) studies of economically important traits in US barley breeding germplasm,population structure and LD decay were examined in a complete panel of US barley breeding germplasm (3840 lines) genotyped with 3072 single nucleotide polymorphisms (SNPs).Nine subpopulations (sp1-sp9) were identified by the program STRUCTURE and subsequently confirmed by principle component analysis (PCA).Out of the nine subpopulations,seven were very similar to the respective subpopulations identified by Hamblin et al.(2010)which were based on half of the germplasm and half of the SN P markers,but two subpopulations were found to be new.One subpopulation was dominated by six-rowed spring lines from Utah State University (UT) and the other was composed of six-rowed spring lines from multiple breeding programs (USDA-ARS Aberdeen (AB),Busch Agricultural Resources Inc.(BA),UT,and Washington State University (WA)).LD was found to decay across a range from 4.0 to 19.8 cM.This result indicates that the germplasm genotyped with 3072 SNPs would be robust for mapping and possibly identifying the causal polymorphisms contributing to disease resistance and perhaps other traits.

  4. Uniting Superhydrophobic, Superoleophobic and Lubricant Infused Slippery Behavior on Copper Oxide Nano-structured Substrates

    Science.gov (United States)

    Ujjain, Sanjeev Kumar; Roy, Pritam Kumar; Kumar, Sumana; Singha, Subhash; Khare, Krishnacharya

    2016-10-01

    Alloys, specifically steel, are considered as the workhorse of our society and are inimitable engineering materials in the field of infrastructure, industry and possesses significant applications in our daily life. However, creating a robust synthetic metallic surface that repels various liquids has remained extremely challenging. The wettability of a solid surface is known to be governed by its geometric nano-/micro structure and the chemical composition. Here, we are demonstrating a facile and economical way to generate copper oxide micro-nano structures with spherical (0D), needle (1D) and hierarchical cauliflower (3D) morphologies on galvanized steel substrates using a simple chemical bath deposition method. These nano/micro textured steel surfaces, on subsequent coating of a low surface energy material display excellent superhydrophobic, superoleophobic and slippery behavior. Polydimethylsiloxane coated textured surfaces illustrate superhydrophobicity with water contact angle about 160°(2) and critical sliding angle ~2°. When functionalized with low-surface energy perfluoroalkylsilane, these surfaces display high repellency for low surface tension oils as well as hydrocarbons. Among them, the hierarchical cauliflower morphology exhibits re-entrant structure thereby showing the best superoleophobicity with contact angle 149° for dodecane. Once infused with a lubricant like silicone oil, they show excellent slippery behavior with low contact angle hysteresis (~ 2°) for water drops.

  5. Proposal of a flexible structural-organizing model for the Intensive Care Units.

    Science.gov (United States)

    Iapichino, G; Radrizzani, D; Rossi, C; Pezzi, A; Anghileri, A; Boffelli, S; Giardino, M; Mistraletti, G; Bertolini, G

    2007-10-01

    The aim of this study was to verify the capability of the Italian Group for the Evaluation of Intervention in Intensive Care Medicine (Gruppo Italiano Valutazione Interventi in Terapia Intensiva, GiViTI) Intensive Care Units (ICUs) in providing high level care (HLC) and to develop a flexible organiziational model, allowing for different levels of care in each ICU. Once the number of active beds, personnel and technology of each ICU were determined, we computed whether the available bed number and all available resources could provide HLC according to international standards. For ICUs lacking staff or equipment for safe HLC in all declared beds, we calculated the best combination between HLC and observation/monitoring beds with less need for nurses and technology (low level of care, LLC) in order to optimise the utilization of each bed. We also investigated the work organisation of physicians and nurses in these units. There are 2 070 available beds in the 293 GiViTI ICUs. To provide HLC according to international criteria, the beds would decrease to 80.9%, because 144 ICUs do not have nurses or equipment to provide HLC in each bed. In order to maximize the suitable use of available resources, these ICUs would have to reduce the HLC bed number using the regained nurse workload for LLC. Because of this, the total number of HLC beds would further decrease to 65.9% of all declared beds. During Sundays and holidays, the bed/doctor and the bed/nurse ratios increase in most ICUs. To maximize the staff and equipment resources available, the bed numbers of a general ICU providing HLC must vary, even daily, according to the level of care provided. This level is not always high for all patients present. Applying this organizing model to each ICU, we could have enough flexibility to face the different demands for assistance if the ICU is built as a large open space to achieve the best clinical model and use of resources.

  6. Nifty Nines and Repeating Decimals

    Science.gov (United States)

    Brown, Scott A.

    2016-01-01

    The traditional technique for converting repeating decimals to common fractions can be found in nearly every algebra textbook that has been published, as well as in many precalculus texts. However, students generally encounter repeating decimal numerals earlier than high school when they study rational numbers in prealgebra classes. Therefore, how…

  7. Nifty Nines and Repeating Decimals

    Science.gov (United States)

    Brown, Scott A.

    2016-01-01

    The traditional technique for converting repeating decimals to common fractions can be found in nearly every algebra textbook that has been published, as well as in many precalculus texts. However, students generally encounter repeating decimal numerals earlier than high school when they study rational numbers in prealgebra classes. Therefore, how…

  8. All-photonic quantum repeaters

    Science.gov (United States)

    Azuma, Koji; Tamaki, Kiyoshi; Lo, Hoi-Kwong

    2015-01-01

    Quantum communication holds promise for unconditionally secure transmission of secret messages and faithful transfer of unknown quantum states. Photons appear to be the medium of choice for quantum communication. Owing to photon losses, robust quantum communication over long lossy channels requires quantum repeaters. It is widely believed that a necessary and highly demanding requirement for quantum repeaters is the existence of matter quantum memories. Here we show that such a requirement is, in fact, unnecessary by introducing the concept of all-photonic quantum repeaters based on flying qubits. In particular, we present a protocol based on photonic cluster-state machine guns and a loss-tolerant measurement equipped with local high-speed active feedforwards. We show that, with such all-photonic quantum repeaters, the communication efficiency scales polynomially with the channel distance. Our result paves a new route towards quantum repeaters with efficient single-photon sources rather than matter quantum memories. PMID:25873153

  9. Purpose, structure, and function of the United States National Dental Practice-Based Research Network

    Science.gov (United States)

    Gilbert, Gregg H.; Williams, O. Dale; Korelitz, James J.; Fellows, Jeffrey L.; Gordan, Valeria V.; Makhija, Sonia K.; Meyerowitz, Cyril; Oates, Thomas W.; Rindal, D. Brad; Benjamin, Paul L.; Foy, Patrick J.

    2013-01-01

    Objective Following a successful2005–2012 phase with three regional practice-based research networks (PBRNs), a single, unified national network called “The National Dental PBRN” was created in 2012 in the United States to improve oral health by conducting practice-based research and serving dental professionals through education and collegiality. Methods Central administration is based in Alabama. Regional centres are based in Alabama, Florida, Minnesota, Oregon, New York and Texas, with a Coordinating Centre in Maryland. Ideas for studies are prioritized by the Executive Committee, comprised mostly of full-time clinicians. Results To date, 2736 persons have enrolled, from all six network regions; enrollment continues to expand. They represent a broad range of practitioners, practice types, and patient populations. Practitioners are actively improving every step of the research process, from idea generation, to study development, field testing, data collection, and presentation and publication. Conclusions Practitioners from diverse settings are partnering with fellow practitioners and academics to improve clinical practice and meet the needs of clinicians and their patients. Clinical significance This “nation’s network” aims to serve as a precious national resource to improve the scientific basis for clinical decision-making and foster movement of the latest evidence into routine practice. PMID:23597500

  10. Differences in hydraulic pressure producing efficiency of front suspension units for motorcycles due to structural difference

    Energy Technology Data Exchange (ETDEWEB)

    Kajino, Tsutomu; Namazue, Eitaro; Ueno, Yutaka

    1995-12-31

    The front suspension unit for motorcycles is one of the functional parts for which continuous engineering improvement is required for advanced driveability. Especially, the ones for off-road motocross racing are frequently required to have their energy absorbing properties, ability to maintain tire-to-ground contact, driving comfort, etc. to be improved to meet the challenges of the racing courses which include many jumps, to exceed the performance of competitors, and to match the ever-improving performance of the engines and frames. To cope with the situation, the operability, rigidity and hydraulic pressure producing mechanism needs to be upgraded. As part of an improvement program, the authors have developed a air-oil separated front suspension which the authors have called the ``twin chamber`` suspension. In this study, the authors compared the hydraulic pressure producing efficiency of the air-oil separated suspension with that of the conventional single chamber construction. The results of the comparison showed that the twin chamber suspension is less affected by the pressure hysteresis by 8% or more at the piston area and 50% or more at the partition area than the conventional suspension. In addition, for the twin chamber suspension, the rise of pressure becomes smoother to give a quicker response as the velocity increases.

  11. An Expanded CAG Repeat in Huntingtin Causes +1 Frameshifting.

    Science.gov (United States)

    Saffert, Paul; Adamla, Frauke; Schieweck, Rico; Atkins, John F; Ignatova, Zoya

    2016-08-26

    Maintenance of triplet decoding is crucial for the expression of functional protein because deviations either into the -1 or +1 reading frames are often non-functional. We report here that expression of huntingtin (Htt) exon 1 with expanded CAG repeats, implicated in Huntington pathology, undergoes a sporadic +1 frameshift to generate from the CAG repeat a trans-frame AGC repeat-encoded product. This +1 recoding is exclusively detected in pathological Htt variants, i.e. those with expanded repeats with more than 35 consecutive CAG codons. An atypical +1 shift site, UUC C at the 5' end of CAG repeats, which has some resemblance to the influenza A virus shift site, triggers the +1 frameshifting and is enhanced by the increased propensity of the expanded CAG repeats to form a stem-loop structure. The +1 trans-frame-encoded product can directly influence the aggregation of the parental Htt exon 1.

  12. Expansion of tandem repeats in sea anemone Nematostella vectensis proteome: A source for gene novelty?

    Directory of Open Access Journals (Sweden)

    Linial Michal

    2009-12-01

    Full Text Available Abstract Background The complete proteome of the starlet sea anemone, Nematostella vectensis, provides insights into gene invention dating back to the Cnidarian-Bilaterian ancestor. With the addition of the complete proteomes of Hydra magnipapillata and Monosiga brevicollis, the investigation of proteins having unique features in early metazoan life has become practical. We focused on the properties and the evolutionary trends of tandem repeat (TR sequences in Cnidaria proteomes. Results We found that 11-16% of N. vectensis proteins contain tandem repeats. Most TRs cover 150 amino acid segments that are comprised of basic units of 5-20 amino acids. In total, the N. Vectensis proteome has about 3300 unique TR-units, but only a small fraction of them are shared with H. magnipapillata, M. brevicollis, or mammalian proteomes. The overall abundance of these TRs stands out relative to that of 14 proteomes representing the diversity among eukaryotes and within the metazoan world. TR-units are characterized by a unique composition of amino acids, with cysteine and histidine being over-represented. Structurally, most TR-segments are associated with coiled and disordered regions. Interestingly, 80% of the TR-segments can be read in more than one open reading frame. For over 100 of them, translation of the alternative frames would result in long proteins. Most domain families that are characterized as repeats in eukaryotes are found in the TR-proteomes from Nematostella and Hydra. Conclusions While most TR-proteins have originated from prediction tools and are still awaiting experimental validations, supportive evidence exists for hundreds of TR-units in Nematostella. The existence of TR-proteins in early metazoan life may have served as a robust mode for novel genes with previously overlooked structural and functional characteristics.

  13. Efficiency in the United States electric industry: Transaction costs, deregulation, and governance structures

    Science.gov (United States)

    Peterson, Carl

    Transaction costs economics (TCE) posits that firms have an incentive to bypass the market mechanisms in situations where the cost of using the market is prohibitive. Vertical integration, among other governance mechanisms, can be used to minimize the transactions costs associated with the market mechanism. The study analyses different governance mechanisms, which range from complete vertical integration to the use of market mechanisms, for firms in the US electric sector. This sector has undergone tremendous change in the past decade including the introduction of retail competition in some jurisdictions. As a result of the push toward deregulation of the industry, vertically integration, while still significant in the sector, has steadily been replaced by alternative governance structures. Using a sample of 136 investor-owned electric utilities that reported data the US Federal Energy Regulatory Commission between 1996 and 2002, this study estimates firm level efficiency using Data Envelopment Analysis (DEA) and relates these estimates to governance structure and public policies. The analysis finds that vertical integration is positively related to firm efficiency, although in a non-linear fashion suggesting that hybrid governance structures tend to be associated with lower efficiency scores. In addition, while some evidence is found for negative short-term effects on firm efficiency from the choice to deregulate, this result is sensitive to DEA model choice. Further, competition in retail markets is found to be positively related to firm level efficiency, but the retreat from deregulation, which occurred after 2000, is negatively associated with firm-level efficiency. These results are important in the ongoing academic and public policy debates concerning deregulation of the electric section and indicate that vertical economies remain in the industry, but that competition has provided incentives for improving firm level efficiency.

  14. Synthesis of α-D-GlcpNAc-(1→2)-[α-D-ManpNAc-(1→3)-]α-L-Rhap-(1→2)-α-L-Rhap-(1→3)-α-L-Rhap,the repeating unit of O10 antigen from Acinetobacter baumannii

    Institute of Scientific and Technical Information of China (English)

    Jian Jun Zhang; Guang Hui Zong; Xiao Mei Liang; Yun Qi Li; Dao Quan Wang; Fan Zuo Kong

    2008-01-01

    An efficient synthesis of α-D-GlcpNAc-(1→2)-[α-D-ManpNAc-(1→3)-]α-L-Rhap-(1→2)-α-L-Rhap-(1→3)-α-L-Rhap (1),the repeating unit of the O10 antigen from Acinetobacter baumannii was achieved via sequential assembly of the building blocks,pmethoxylphenyl 2,4-di-O-benzoyl-a-L-rhamnopyranoside (2);2-O-allyloxycarbonyl-3,4-di-O-benzoyl-α-L-rhanmopyranosyl trichloroacetimidate (3);4-methoxylphenyl 3-O-allyloxycarbonyl-4-O-benzoyl-α-L-rhamnopyranoside (4);2-azido-3-O-benzoyl-2-deoxy-4,6-O-isopropylidene-α-D-mannopyranosyl trichloroacetimidate (5);2-azido-3,4,6-tri-O-benzoyl-2-deoxy-α,β-D-glucopyrano syl trichloroacetimidate (6).The total yield of 1 from 4 was 4.7%.

  15. Architecture of digital signal’s processing units with the rebuildable structure

    Directory of Open Access Journals (Sweden)

    Sheik-Seikin A. N.

    2011-08-01

    Full Text Available The synthesis technique is developed for the computing system architecture with tunable structure with graph of information connections (GIC affine transformations which assumes additional equipment of initial computing system (CS with the appropriate switching system implementing, depending on character of GIC change, one of the methods of block reorganization providing effective implementation of CS in wide range of GIC parameters change. The received estimations of hardware expenses for various methods of reorganization allow to define efficiency of CS implementation for each specific case.

  16. Window into the Caledonian orogen: Structure of the crust beneath the East Shetland platform, United Kingdom

    Science.gov (United States)

    McBride, J.H.; England, R.W.

    1999-01-01

    Reprocessing and interpretation of commercial and deep seismic reflection data across the East Shetland platform and its North Sea margin provide a new view of crustal subbasement structure beneath a poorly known region of the British Caledonian orogen. The East Shetland platform, east of the Great Glen strike-slip fault system, is one of the few areas of the offshore British Caledonides that remained relatively insulated from the Mesozoic and later rifting that involved much of the area around the British Isles, thus providing an "acoustic window" into the deep structure of the orogen. Interpretation of the reflection data suggests that the crust beneath the platform retains a significant amount of its original Caledonian and older architecture. The upper to middle crust is typically poorly reflective except for individual prominent dipping reflectors with complex orientations that decrease in dip with depth and merge with a lower crustal layer of high reflectivity. The three-dimensional structural orientation of the reflectors beneath the East Shetland platform is at variance with Caledonian reflector trends observed elsewhere in the Caledonian orogen (e.g., north of the Scottish mainland), emphasizing the unique tectonic character of this part of the orogen. Upper to middle crustal reflectors are interpreted as Caledonian or older thrust surfaces that were possibly reactivated by Devonian extension associated with post-Caledonian orogenic collapse. The appearance of two levels of uneven and diffractive (i.e., corrugated) reflectivity in the lower crust, best developed on east-west-oriented profiles, is characteristic of the East Shetland platform. However, a north-south-oriented profile reveals an interpreted south-vergent folded and imbricated thrust structure in the lower crust that appears to be tied to the two levels of corrugated reflectivity on the east-west profiles. A thrust-belt origin for lower crustal reflectivity would explain its corrugated

  17. A dimeric structure of PD-L1: functional units or evolutionary relics?

    OpenAIRE

    Chen, Yong; Liu, Peipei; Gao, Feng; Cheng, Hao; Qi, Jianxun; Gao, George F

    2010-01-01

    PD-L1 is a member of the B7 protein family, most of whose members so far were identified as dimers in a solution and crystalline state, either complexed or uncomplexed with their ligand(s). The binding of PD-L1 with its receptor PD-1 (CD279) delivers an inhibitory signal regulating the T cell function. Simultaneously with the Garboczi group, we successfully solved another structure of human PD-L1 (hPD-L1). Our protein crystallized in the space group of C2221 with two hPD-L1 molecules per asym...

  18. The triple helical structure and stability of collagen model peptide with 4(S)-hydroxyprolyl-Pro-Gly units.

    Science.gov (United States)

    Motooka, Daisuke; Kawahara, Kazuki; Nakamura, Shota; Doi, Masamitsu; Nishi, Yoshinori; Nishiuchi, Yuji; Kang, Young Kee; Nakazawa, Takashi; Uchiyama, Susumu; Yoshida, Takuya; Ohkubo, Tadayasu; Kobayashi, Yuji

    2012-01-01

    Extensive studies on the structure of collagen have revealed that the hydroxylation of Pro residues in a variety of model peptides with the typical (X-Y-Gly)(n) repeats (X and Y: Pro and its analogues) represents one of the major factors influencing the stability of triple helices. While(2S,4R)-hydroxyproline (Hyp) at the position Y stabilizes the triple helix, (2S,4S)-hydroxyproline (hyp) at the X-position destabilizes the helix as demonstrated that the triple helix of (hyp-Pro-Gly)(15) is less stable than that of (Pro-Pro-Gly)(15) and that a shorter peptide (hyp-Pro-Gly)(10) does not form the helix. To clarify the role of the hydroxyl group of Pro residues to play in the stabilization mechanism of the collagen triple helix, we synthesized and crystallized a model peptide (Pro-Hyp-Gly)(4) -(hyp-Pro-Gly)(2) -(Pro-Hyp-Gly)(4) and analyzed its structure by X-ray crystallography and CD spectroscopy. In the crystal, the main-chain of this peptide forms a typical collagen like triple helix. The majority of hyp residues take down pucker with exceptionally shallow angles probably to relieve steric hindrance, but the remainders protrude the hydroxyl group toward solvent with the less favorable up pucker to fit in a triple helix. There is no indication of the existence of an intra-molecular hydrogen bond between the hydroxyl moiety and the carbonyl oxygen of hyp supposed to destabilize the triple helix. We also compared the conformational energies of up and down packers of the pyrrolidine ring in Ac-hyp-NMe(2) by quantum mechanical calculations.

  19. Structural change of the physical economy. Decomposition analysis of physical and hybrid-unit input-output tables

    Energy Technology Data Exchange (ETDEWEB)

    Hoekstra, R.

    2003-10-01

    Economic processes generate a variety of material flows, which cause resource problems through the depletion of natural resources and environmental issues due to the emission of pollutants. This thesis presents an analytical method to study the relationship between the monetary economy and the 'physical economy'. In particular, this method can assess the impact of structural change in the economy on physical throughput. The starting point for the approach is the development of an elaborate version of the physical input-output table (PIOT), which acts as an economic-environmental accounting framework for the physical economy. In the empirical application, hybrid-unit input-output (I/O) tables, which combine physical and monetary information, are constructed for iron and steel, and plastic products for the Netherlands for the years 1990 and 1997. The impact of structural change on material flows is analyzed using Structural Decomposition Analysis (SDA), whic specifies effects such as sectoral shifts, technological change, and alterations in consumer spending and international trade patterns. The study thoroughly reviews the application of SDA to environmental issues, compares the method with other decomposition methods, and develops new mathematical specifications. An SDA is performed using the hybrid-unit input-output tables for the Netherlands. The results are subsequently used in novel forecasting and backcasting scenario analyses for the period 1997-2030. The results show that dematerialization of iron and steel, and plastics, has generally not occurred in the recent past (1990-1997), and will not occur, under a wide variety of scenario assumptions, in the future (1997-2030)

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

    Science.gov (United States)

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

    2012-10-04

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

  1. Oligomeric structure and minimal functional unit of the electrogenic sodium bicarbonate cotransporter NBCe1-A.

    Science.gov (United States)

    Kao, Liyo; Sassani, Pakan; Azimov, Rustam; Pushkin, Alexander; Abuladze, Natalia; Peti-Peterdi, Janos; Liu, Weixin; Newman, Debra; Kurtz, Ira

    2008-09-26

    The electrogenic sodium bicarbonate cotransporter NBCe1-A mediates the basolateral absorption of sodium and bicarbonate in the proximal tubule. In this study the oligomeric state and minimal functional unit of NBCe1-A were investigated. Wild-type (wt) NBCe1-A isolated from mouse kidney or heterologously expressed in HEK293 cells was predominantly in a dimeric state as was shown using fluorescence energy transfer, pulldown, immunoprecipitation, cross-linking experiments, and nondenaturing perfluorooctanoate-PAGE. NBCe1-A monomers were found to be covalently linked by S-S bonds. When each of the 15 native cysteine residues were individually removed on a wt-NBCe1-A backbone, dimerization of the cotransporter was not affected. In experiments involving multiple native cysteine residue removal, both Cys(630) and Cys(642) in extracellular loop 3 were shown to mediate S-S bond formation between NBCe1-A monomers. When native NBCe1-A cysteine residues were individually reintroduced into a cysteineless NBCe1-A mutant backbone, the finding that a Cys(992) construct that lacked S-S bonds functioned normally indicated that stable covalent linkage of NBCe1-A monomers was not a necessary requirement for functional activity of the cotransporter. Studies using concatameric constructs of wt-NBCe1-A, whose activity is resistant to methanesulfonate reagents, and an NBCe1-A(T442C) mutant, whose activity is completely inhibited by methanesulfonate reagents, confirmed that NBCe1-A monomers are functional. Our results demonstrate that wt-NBCe1-A is predominantly a homodimer, dependent on S-S bond formation that is composed of functionally active monomers.

  2. Genetic structure and molecular variability of Cucumber mosaic virus isolates in the United States.

    Directory of Open Access Journals (Sweden)

    Shahideh Nouri

    Full Text Available Cucumber mosaic virus (CMV has a worldwide distribution and the widest host range of any known plant virus. From 2000 to 2012, epidemics of CMV severely affected the production of snap bean (Phaseulos vulgaris L. in the Midwest and Northeastern United States. Virus diversity leading to emergence of new strains is often considered a significant factor in virus epidemics. In addition to epidemics, new disease phenotypes arising from genetic exchanges or mutation can compromise effectiveness of plant disease management strategies. Here, we captured a snapshot of genetic variation of 32 CMV isolates collected from different regions of the U.S including new field as well as historic isolates. Nucleotide diversity (π was low for U.S. CMV isolates. Sequence and phylogenetic analyses revealed that CMV subgroup I is predominant in the US and further showed that the CMV population is a mixture of subgroups IA and IB. Furthermore, phylogenetic analysis suggests likely reassortment between subgroups IA and IB within five CMV isolates. Based on phylogenetic and computational analysis, recombination between subgroups I and II as well as IA and IB in RNA 3 was detected. This is the first report of recombination between CMV subgroups I and II. Neutrality tests illustrated that negative selection was the major force operating upon the CMV genome, although some positively selected sites were detected for all encoded proteins. Together, these data suggest that different regions of the CMV genome are under different evolutionary constraints. These results also delineate composition of the CMV population in the US, and further suggest that recombination and reassortment among strain subgroups does occur but at a low frequency, and point towards CMV genomic regions that differ in types of selection pressure.

  3. Generalizable items and modular structure for computerised physician staffing calculation on intensive care units.

    Science.gov (United States)

    Weiss, Manfred; Marx, Gernot; Iber, Thomas

    2017-08-04

    Intensive care medicine remains one of the most cost-driving areas within hospitals with high personnel costs. Under the scope of limited budgets and reimbursement, realistic needs are essential to justify personnel staffing. Unfortunately, all existing staffing models are top-down calculations with a high variability in results. We present a workload-oriented model, integrating quality of care, efficiency of processes, legal, educational, controlling, local, organisational and economic aspects. In our model, the physician's workload solely related to the intensive care unit depends on three tasks: Patient-oriented tasks, divided in basic tasks (performed in every patient) and additional tasks (necessary in patients with specific diagnostic and therapeutic requirements depending on their specific illness, only), and non patient-oriented tasks. All three tasks have to be taken into account for calculating the required number of physicians. The calculation tool further allows to determine minimal personnel staffing, distribution of calculated personnel demand regarding type of employee due to working hours per year, shift work or standby duty. This model was introduced and described first by the German Board of Anesthesiologists and the German Society of Anesthesiology and Intensive Care Medicine in 2008 and since has been implemented and updated 2012 in Germany. The modular, flexible nature of the Excel-based calculation tool should allow adaption to the respective legal and organizational demands of different countries. After 8 years of experience with this calculation, we report the generalizable key aspects which may help physicians all around the world to justify realistic workload-oriented personnel staffing needs.

  4. Genetic Structure of the Invasive Tree Ailanthus altissima in Eastern United States Cities

    Directory of Open Access Journals (Sweden)

    Preston R. Aldrich

    2010-01-01

    Full Text Available Ailanthus altissima is an invasive tree from Asia. It now occurs in most US states, and although primarily an urban weed, it has become a problem in forested areas especially in the eastern states. Little is known about its genetic structure. We explore its naturalized gene pool from 28 populations, mostly of the eastern US where infestations are especially severe. Five microsatellite markers were used to examine presumed neutral genetic variation. Results show a gene pool that is moderately diverse and sexually active and has significant but small genetic differences among populations and little correspondence between geographic and genetic distance. These findings are consistent with a model of multiple introductions followed by high rates of gene exchange between cities and regions. We propose movement along road and railway systems as the chief mode of range expansion.

  5. Observations on Faults and Associated Permeability Structures in Hydrogeologic Units at the Nevada Test Site

    Energy Technology Data Exchange (ETDEWEB)

    Prothro, Lance B.; Drellack, Sigmund L.; Haugstad, Dawn N.; Huckins-Gang, Heather E.; Townsend, Margaret J.

    2009-03-30

    Observational data on Nevada Test Site (NTS) faults were gathered from a variety of sources, including surface and tunnel exposures, core samples, geophysical logs, and down-hole cameras. These data show that NTS fault characteristics and fault zone permeability structures are similar to those of faults studied in other regions. Faults at the NTS form complex and heterogeneous fault zones with flow properties that vary in both space and time. Flow property variability within fault zones can be broken down into four major components that allow for the development of a simplified, first approximation model of NTS fault zones. This conceptual model can be used as a general guide during development and evaluation of groundwater flow and contaminate transport models at the NTS.

  6. Distribution of transformed organic matter in structural units of loamy sandy soddy-podzolic soil

    Science.gov (United States)

    Kogut, B. M.; Yashin, M. A.; Semenov, V. M.; Avdeeva, T. N.; Markina, L. G.; Lukin, S. M.; Tarasov, S. I.

    2016-01-01

    The effect of land use types and fertilizing systems on the structural and aggregate composition of loamy sandy soddy-podzolic soil and the quantitative parameters of soil organic matter has been studied. The contribution of soil aggregates 2-1 mm in size to the total Corg reserve in the humus horizon is higher than the contributions of other aggregates by 1.3-4.2 times. Reliable correlations have been revealed between the contents of total (Corg), labile (Clab), and active (C0) organic matter in the soil. The proportion of C0 is 44-70% of Clab extractable by neutral sodium pyrophosphate solution. The contributions of each of the 2-1, 0.5-0.25, and humus horizon of loamy sandy soddy-podzolic soil, the active, slow, and passive pools contain 6-11, 34-65, and 26-94% of the total Corg, respectively.

  7. TPR repeats and ELTR pattern: length variation as a function evolution mechanism.

    Science.gov (United States)

    Yang, Ke-Qian

    2007-12-01

    TPR repeat was originally defined as a 34 amino acid structural repeat (TPR-34). Equal length tandem repeats (ELTR) was proposed to represent the ancestral repeat pattern. Length polymorphism of TPR repeats was analyzed using PATTINPROT, two new versions of TPR repeat of 40 and 42 amino acids were identified. These 'long' TPRs endow new functional capacities to the resulting proteins. A strong correlation between varied lengths and new functions supports the hypothesis that length variation is an underlying mechanism for the function evolution of repeat containing proteins.

  8. Structured Ordinary Least Squares: A Sufficient Dimension Reduction approach for regressions with partitioned predictors and heterogeneous units.

    Science.gov (United States)

    Liu, Yang; Chiaromonte, Francesca; Li, Bing

    2017-06-01

    In many scientific and engineering fields, advanced experimental and computing technologies are producing data that are not just high dimensional, but also internally structured. For instance, statistical units may have heterogeneous origins from distinct studies or subpopulations, and features may be naturally partitioned based on experimental platforms generating them, or on information available about their roles in a given phenomenon. In a regression analysis, exploiting this known structure in the predictor dimension reduction stage that precedes modeling can be an effective way to integrate diverse data. To pursue this, we propose a novel Sufficient Dimension Reduction (SDR) approach that we call structured Ordinary Least Squares (sOLS). This combines ideas from existing SDR literature to merge reductions performed within groups of samples and/or predictors. In particular, it leads to a version of OLS for grouped predictors that requires far less computation than recently proposed groupwise SDR procedures, and provides an informal yet effective variable selection tool in these settings. We demonstrate the performance of sOLS by simulation and present a first application to genomic data. The R package "sSDR," publicly available on CRAN, includes all procedures necessary to implement the sOLS approach. © 2016, The International Biometric Society.

  9. Problematics of stress-strain state research in units of metal structures

    Directory of Open Access Journals (Sweden)

    Morozova Dina Vol'demarovna

    2014-05-01

    Full Text Available The article describes the experimental methods of determining stress-strain state of elements and structures with a brief description of the essence of each method. The authors focus mostly on polarization-optical method for determining stresses in the translucent optical sensing models made of epoxy resins. Physical component of the method is described in the article and a simple diagram of a circular polariscope is presented, as well as an example of the resulting interference pattern in illuminated monochromatic light. A polariscope, in its most general definition, consists of two polarizers. The polarizers sandwich a material or object of interest, and allows one to view the changes of the polarity of light passing through the material or object. Since we are unable to perceive the polarity of light with the naked eye, we are forced to use polariscopes to view the changes in polarity caused by the temporary birefringence of our photoelastic materials. A polariscope is constructed of two polarizers, each set perpendicular to the path of light transmitted through the setup. The first polarizer is called the "polarizer", and the second polarizer is called the "analyzer". The method how the polarizer works is quite simple: unpolarized light enters the polariscope through the polarizer, which allows through only the light of its orientation. This light then passes through the material under observation, and experiences some change in polarity. Finally, this light reaches the analyzer, which, like the polarizer, only lets the light of its orientation through.

  10. Structural elucidation and physicochemical properties of mononuclear Uranyl(VI) complexes incorporating dianionic units

    Science.gov (United States)

    Azam, Mohammad; Velmurugan, Gunasekaran; Wabaidur, Saikh Mohammad; Trzesowska-Kruszynska, Agata; Kruszynski, Rafal; Al-Resayes, Saud I.; Al-Othman, Zeid A.; Venuvanalingam, Ponnambalam

    2016-01-01

    Two derivatives of organouranyl mononuclear complexes [UO2(L)THF] (1) and [UO2(L)Alc] (2), where L = (2,2′-(1E,1′E)-(2,2-dimethylpropane-1,3-dyl)bis(azanylylidene, THF = Tetrahydrofuran, Alc = Alcohol), have been prepared. These complexes have been determined by elemental analyses, single crystal X-ray crystallography and various spectroscopic studies. Moreover, the structure of these complexes have also been studied by DFT and time dependent DFT measurements showing that both the complexes have distorted pentagonal bipyramidal environment around uranyl ion. TD-DFT results indicate that the complex 1 displays an intense band at 458.7 nm which is mainly associated to the uranyl centered LMCT, where complex 2 shows a band at 461.8 nm that have significant LMCT character. The bonding has been further analyzed by EDA and NBO. The photocatalytic activity of complexes 1 and 2 for the degradation of rhodamine-B (RhB) and methylene blue (MB) under the irradiation of 500W Xe lamp has been explored, and found more efficient in presence of complex 1 than complex 2 for both dyes. In addition, dye adsorption and photoluminescence properties have also been discussed for both complexes. PMID:27595801

  11. Structural elucidation and physicochemical properties of mononuclear Uranyl(VI) complexes incorporating dianionic units

    Science.gov (United States)

    Azam, Mohammad; Velmurugan, Gunasekaran; Wabaidur, Saikh Mohammad; Trzesowska-Kruszynska, Agata; Kruszynski, Rafal; Al-Resayes, Saud I.; Al-Othman, Zeid A.; Venuvanalingam, Ponnambalam

    2016-09-01

    Two derivatives of organouranyl mononuclear complexes [UO2(L)THF] (1) and [UO2(L)Alc] (2), where L = (2,2‧-(1E,1‧E)-(2,2-dimethylpropane-1,3-dyl)bis(azanylylidene, THF = Tetrahydrofuran, Alc = Alcohol), have been prepared. These complexes have been determined by elemental analyses, single crystal X-ray crystallography and various spectroscopic studies. Moreover, the structure of these complexes have also been studied by DFT and time dependent DFT measurements showing that both the complexes have distorted pentagonal bipyramidal environment around uranyl ion. TD-DFT results indicate that the complex 1 displays an intense band at 458.7 nm which is mainly associated to the uranyl centered LMCT, where complex 2 shows a band at 461.8 nm that have significant LMCT character. The bonding has been further analyzed by EDA and NBO. The photocatalytic activity of complexes 1 and 2 for the degradation of rhodamine-B (RhB) and methylene blue (MB) under the irradiation of 500W Xe lamp has been explored, and found more efficient in presence of complex 1 than complex 2 for both dyes. In addition, dye adsorption and photoluminescence properties have also been discussed for both complexes.

  12. Neoglycoconjugate of Tetrasaccharide Representing One Repeating Unit of the Streptococcus pneumoniae Type 14 Capsular Polysaccharide Induces the Production of Opsonizing IgG1 Antibodies and Possesses the Highest Protective Activity As Compared to Hexa- and Octasaccharide Conjugates

    Directory of Open Access Journals (Sweden)

    Ekaterina A. Kurbatova

    2017-06-01

    Full Text Available Identifying protective synthetic oligosaccharide (OS epitopes of Streptococcus pneumoniae capsular polysaccharides (CPs is an indispensable step in the development of third-generation carbohydrate pneumococcal vaccines. Synthetic tetra-, hexa-, and octasaccharide structurally related to CP of S. pneumoniae type 14 were coupled to bovine serum albumin (BSA, adjuvanted with aluminum hydroxide, and tested for their immunogenicity in mice upon intraperitoneal prime-boost immunizations. Injections of the conjugates induced production of opsonizing anti-OS IgG1 antibodies (Abs. Immunization with the tetra- and octasaccharide conjugates stimulated the highest titers of the specific Abs. Further, the tetrasaccharide ligand demonstrated the highest ability to bind OS and CP Abs. Murine immune sera developed against tetra- and octasaccharide conjugates promoted pathogen opsonization to a higher degree than antisera against conjugated hexasaccharide. For the first time, the protective activities of these glycoconjugates were demonstrated in mouse model of generalized pneumococcal infections. The tetrasaccharide conjugate possessed the highest protective activities. Conversely, the octasaccharide conjugate had lower protective activities and the lowest one showed the hexasaccharide conjugate. Sera against all of the glycoconjugates passively protected naive mice from pneumococcal infections. Given that the BSA-tetrasaccharide induced the most abundant yield of specific Abs and the best protective activity, this OS may be regarded as the most promising candidate for the development of conjugated vaccines against S. pneumoniae type 14 infections.

  13. Prevalence of roll-over protective structure (ROPS)-equipped tractors on Hispanic-operated farms in the United States.

    Science.gov (United States)

    Myers, John R

    2010-04-01

    Roll-over protective structures (ROPS) are known to prevent tractor overturn deaths, but not enough tractors are equipped with them in the United States to reduce the rate of these deaths to levels seen in several European countries. Recent literature has defined the use of ROPS on US farms in general, but little is known about ROPS use on Hispanic farm operations. Data from a national survey for the calendar year 2003 were used to assess the prevalence of ROPS use on Hispanic-operated farms. Farm characteristics previously identified to be associated with low ROPS prevalence rates on other farming operations were examined for these Hispanic farming operations. The overall ROPS prevalence rate on Hispanic farms was 52.2%. Adjusted odds ratios of potential risk factors found that the region where the farm was located and the acreage of the farm appeared to be the most significant indicators of the prevalence of ROPS on Hispanic farms. In addition, the age of the farm operator, the farm status as a full- or part-time operation, and the type of farm operation were also important factors. These findings were similar to those seen for racial minority farms and the general farming population. These results can be used to target ROPS promotion programs for Hispanic farmers across the United States.

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

    Institute of Scientific and Technical Information of China (English)

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

    2007-01-01

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

  15. Team cohesion in intensive care nursing: at the interface of nurse self-concept and unit structure

    DEFF Research Database (Denmark)

    Paunova, Minna; Li-Ying, Jason

    2017-01-01

    Team cohesion is a critical factor in the provision of high-quality care, yet its antecedents remain understudied, particularly in the context of some healthcare professional groups where structural and individual constraints coexist, and demand for high quality performance is prevailing....... In this study, we focus on the nursing group in intensive care units (ICU). Not researched, yet important for employee attitudes towards their workplaces and workgroups, is the interface between the characteristics of individual care providers and those of the teams and organizations in which they are employed...... their teams as cohesive. A multi-source and multi-level study of approximately 140 nurses employed in 20 ICUs across Denmark demonstrates the critical role of self-concept in easing and enhancing the constraints workplaces impose on team cohesion. Furthermore, the study confirms the positive relationship...

  16. Characterization of a CT unit for the detection of low contrast structures

    Science.gov (United States)

    Viry, Anais; Racine, Damien; Ba, Alexandre; Becce, Fabio; Bochud, François O.; Verdun, Francis R.

    2017-03-01

    Major technological advances in CT enable the acquisition of high quality images while minimizing patient exposure. The goal of this study was to objectively compare two generations of iterative reconstruction (IR) algorithms for the detection of low contrast structures. An abdominal phantom (QRM, Germany), containing 8, 6 and 5mm-diameter spheres (with a nominal contrast of 20HU) was scanned using our standard clinical noise index settings on a GE CT: "Discovery 750 HD". Two additional rings (2.5 and 5 cm) were also added to the phantom. Images were reconstructed using FBP, ASIR-50%, and VEO (full statistical Model Based Iterative Reconstruction, MBIR). The reconstructed slice thickness was 2.5 mm except 0.625 mm for VEO reconstructions. NPS was calculated to highlight the potential noise reduction of each IR algorithm. To assess LCD (low Contrast Detectability), a Channelized Hotelling Observer (CHO) with 10 DDoG channels was used with the area under the curve (AUC) as a figure of merit. Spheres contrast was also measured. ASIR-50% allowed a noise reduction by a factor two when compared to FBP without an improvement of the LCD. VEO allowed an additional noise reduction with a thinner slice thickness compared to ASIR-50% but with a major improvement of the LCD especially for the large-sized phantom and small lesions. Contrast decreased up to 10% with the phantom size increase for FBP and ASIR-50% and remained constant with VEO. VEO is particularly interesting for LCD when dealing with large patients and small lesion sizes and when the detection task is difficult.

  17. Analysis of repeated measures data

    CERN Document Server

    Islam, M Ataharul

    2017-01-01

    This book presents a broad range of statistical techniques to address emerging needs in the field of repeated measures. It also provides a comprehensive overview of extensions of generalized linear models for the bivariate exponential family of distributions, which represent a new development in analysing repeated measures data. The demand for statistical models for correlated outcomes has grown rapidly recently, mainly due to presence of two types of underlying associations: associations between outcomes, and associations between explanatory variables and outcomes. The book systematically addresses key problems arising in the modelling of repeated measures data, bearing in mind those factors that play a major role in estimating the underlying relationships between covariates and outcome variables for correlated outcome data. In addition, it presents new approaches to addressing current challenges in the field of repeated measures and models based on conditional and joint probabilities. Markov models of first...

  18. Identification and characterization of tandem repeats in exon III of dopamine receptor D4 (DRD4) genes from different mammalian species

    DEFF Research Database (Denmark)

    Larsen, Svend Arild; Mogensen, Line; Dietz, Rune

    2005-01-01

    tandem repeat, while a tandem repeat consisting of 27-bp modules was identified in a sequence from European badger. Both these tandem repeats were composed of 9-bp basic units, which were closely related with the 9-bp repeat modules identified in the mink and ferret. Tandem repeats could...... repeat being found. In the domestic cow and gray seal we identified tandem repeats composed of 36-bp modules, each consisting of two closely related 18-bp basic units. A tandem repeat consisting of 9-bp modules was identified in sequences from mink and ferret. In the European otter we detected an 18-bp...

  19. Design, Analysis and Fabrication of Secondary Structural Components for the Habitat Demonstration Unit-Deep Space Habitat

    Science.gov (United States)

    Smith, Russell W.; Langford, William M.

    2012-01-01

    In support of NASA s Habitat Demonstration Unit - Deep Space Habitat Prototype, a number of evolved structural sections were designed, fabricated, analyzed and installed in the 5 meter diameter prototype. The hardware consisted of three principal structural sections, and included the development of novel fastener insert concepts. The articles developed consisted of: 1) 1/8th of the primary flooring section, 2) an inner radius floor beam support which interfaced with, and supported (1), 3) two upper hatch section prototypes, and 4) novel insert designs for mechanical fastener attachments. Advanced manufacturing approaches were utilized in the fabrication of the components. The structural components were developed using current commercial aircraft constructions as a baseline (for both the flooring components and their associated mechanical fastener inserts). The structural sections utilized honeycomb sandwich panels. The core section consisted of 1/8th inch cell size Nomex, at 9 lbs/cu ft, and which was 0.66 inches thick. The facesheets had 3 plys each, with a thickness of 0.010 inches per ply, made from woven E-glass with epoxy reinforcement. Analysis activities consisted of both analytical models, as well as initial closed form calculations. Testing was conducted to help verify analysis model inputs, as well as to facilitate correlation between testing and analysis. Test activities consisted of both 4 point bending tests as well as compressive core crush sequences. This paper presents an overview of this activity, and discusses issues encountered during the various phases of the applied research effort, and its relevance to future space based habitats.

  20. GANDivAWeb: A web server for detecting early folding units ("foldons" from protein 3D structures

    Directory of Open Access Journals (Sweden)

    Krishnan Arun

    2008-03-01

    Full Text Available Abstract Background It has long been known that small regions of proteins tend to fold independently and are then stabilized by interactions between these distinct subunits or modules. Such units, also known as autonomous folding units (AFUs or"foldons" play a key role in protein folding. A knowledge of such early folding units has diverse applications in protein engineering as well as in developing an understanding of the protein folding process. Such AFUs can also be used as model systems in order to study the structural organization of proteins. Results In an earlier work, we had utilized a global network partitioning algorithm to identify modules in proteins. We had shown that these modules correlate well with AFUs. In this work, we have developed a webserver, GANDivAWeb, to identify early folding units or "foldons" in networks using the algorithm described earlier. The website has three functionalities: (a It is able to display information on the modularity of a database of 1420 proteins used in the original work, (b It can take as input an uploaded PDB file, identify the modules using the GANDivA algorithm and email the results back to the user and (c It can take as input an uploaded PDB file and a results file (obtained from functionality (b and display the results using the embedded viewer. The results include the module decomposition of the protein, plots of cartoon representations of the protein colored by module identity and connectivity as well as contour plots of the hydrophobicity and relative accessible surface area (RASA distributions. Conclusion We believe that the GANDivAWeb server, will be a useful tool for scientists interested in the phenomena of protein folding as well as in protein engineering. Our tool not only provides a knowledge of the AFUs through a natural graph partitioning approach but is also able to identify residues that are critical during folding. It is our intention to use this tool to study the topological

  1. Landauer's Principle in Repeated Interaction Systems

    Science.gov (United States)

    Hanson, Eric P.; Joye, Alain; Pautrat, Yan; Raquépas, Renaud

    2017-01-01

    We study Landauer's Principle for Repeated Interaction Systems (RIS) consisting of a reference quantum system S in contact with a structured environment E made of a chain of independent quantum probes; S interacts with each probe, for a fixed duration, in sequence. We first adapt Landauer's lower bound, which relates the energy variation of the environment E to a decrease of entropy of the system S during the evolution, to the peculiar discrete time dynamics of RIS. Then we consider RIS with a structured environment E displaying small variations of order {T^{-1}} between the successive probes encountered by S, after {n ˜eq T} interactions, in keeping with adiabatic scaling. We establish a discrete time non-unitary adiabatic theorem to approximate the reduced dynamics of S in this regime, in order to tackle the adiabatic limit of Landauer's bound. We find that saturation of Landauer's bound is related to a detailed balance condition on the repeated interaction system, reflecting the non-equilibrium nature of the repeated interaction system dynamics. This is to be contrasted with the generic saturation of Landauer's bound known to hold for continuous time evolution of an open quantum system interacting with a single thermal reservoir in the adiabatic regime.

  2. Unit-Specific Event-Based and Slot-Based Hybrid Model Framework with Hierarchical Structure for Short-Term Scheduling

    Directory of Open Access Journals (Sweden)

    Yue Wang

    2015-01-01

    Full Text Available Unit-specific event-based continuous-time model has inaccurate calculation problems in involving resource constraints, due to the heterogeneous locations of the event points for different units. In order to address this limitation, a continuous-time unit-specific event-based and slot-based hybrid model framework with hierarchical structure is proposed in this work. A unit-specific event-based model without utility constraints is formulated in upper layer, and a slot-based model is introduced in lower layer. In the hierarchical structure, the two layers jointly address the short-term production scheduling problem of batch plants under utility consideration. The key features of this work include the following: (a eliminating overstrict constraints on utility resources, (b solving multiple counting problems, and (c considering duration time of event points in calculating utility utilization level. The effectiveness and advantages of proposed model are illustrated through two benchmark examples from the literatures.

  3. Population structure of clinical and environmental Vibrio parahaemolyticus from the Pacific Northwest coast of the United States.

    Directory of Open Access Journals (Sweden)

    Jeffrey W Turner

    Full Text Available Vibrio parahaemolyticus is a common marine bacterium and a leading cause of seafood-borne bacterial gastroenteritis worldwide. Although this bacterium has been the subject of much research, the population structure of cold-water populations remains largely undescribed. We present a broad phylogenetic analysis of clinical and environmental V. parahaemolyticus originating largely from the Pacific Northwest coast of the United States. Repetitive extragenic palindromic PCR (REP-PCR separated 167 isolates into 39 groups and subsequent multilocus sequence typing (MLST separated a subset of 77 isolates into 24 sequence types. The Pacific Northwest population exhibited a semi-clonal structure attributed to an environmental clade (ST3, N = 17 isolates clonally related to the pandemic O3:K6 complex and a clinical clade (ST36, N = 20 isolates genetically related to a regionally endemic O4:K12 complex. Further, the identification of at least five additional clinical sequence types (i.e., ST43, 50, 65, 135 and 417 demonstrates that V. parahaemolyticus gastroenteritis in the Pacific Northwest is polyphyletic in nature. Recombination was evident as a significant source of genetic diversity and in particular, the recA and dtdS alleles showed strong support for frequent recombination. Although pandemic-related illnesses were not documented during the study, the environmental occurrence of the pandemic clone may present a significant threat to human health and warrants continued monitoring. It is evident that V. parahaemolyticus population structure in the Pacific Northwest is semi-clonal and it would appear that multiple sequence types are contributing to the burden of disease in this region.

  4. GFP-based fluorescence assay for CAG repeat instability in cultured human cells.

    Directory of Open Access Journals (Sweden)

    Beatriz A Santillan

    Full Text Available Trinucleotide repeats can be highly unstable, mutating far more frequently than point mutations. Repeats typically mutate by addition or loss of units of the repeat. CAG repeat expansions in humans trigger neurological diseases that include myotonic dystrophy, Huntington disease, and several spinocerebellar ataxias. In human cells, diverse mechanisms promote CAG repeat instability, and in mice, the mechanisms of instability are varied and tissue-dependent. Dissection of mechanistic complexity and discovery of potential therapeutics necessitates quantitative and scalable screens for repeat mutation. We describe a GFP-based assay for screening modifiers of CAG repeat instability in human cells. The assay exploits an engineered intronic CAG repeat tract that interferes with expression of an inducible GFP minigene. Like the phenotypes of many trinucleotide repeat disorders, we find that GFP function is impaired by repeat expansion, in a length-dependent manner. The intensity of fluorescence varies inversely with repeat length, allowing estimates of repeat tract changes in live cells. We validate the assay using transcription through the repeat and engineered CAG-specific nucleases, which have previously been reported to induce CAG repeat instability. The assay is relatively fast and should be adaptable to large-scale screens of chemical and shRNA libraries.

  5. Basement structure of the United Arab Emirates derived from an analysis of regional gravity and aeromagnetic database

    Science.gov (United States)

    Ali, M. Y.; Fairhead, J. D.; Green, C. M.; Noufal, A.

    2017-08-01

    Gravity and aeromagnetic data covering the whole territory of the United Arab Emirates (UAE) have been used to evaluate both shallow and deep geological structures, in particular the depth to basement since it is not imaged by seismic data anywhere within the UAE. Thus, the aim has been to map the basement so that its structure can help to assess its control on the distribution of hydrocarbons within the UAE. Power spectrum analysis reveals gravity and magnetic signatures to have some similarities, in having two main density/susceptibility interfaces widely separated in depth such that regional-residual anomaly separation could effectively be undertaken. The upper density/susceptibility interface occurs at a depth of about 1.0 km while the deeper interface varies in depth throughout the UAE. For gravity, this deeper interface is assumed to be due to the combined effect of lateral changes in density structures within the sediments and in depth of basement while for magnetics it is assumed the sediments have negligible susceptibility and the anomalies unrelated to the volcanic/magmatic bodies result from only changes in depth to basement. The power spectrum analysis over the suspect volcanic/magmatic bodies indicates they occur at 5 km depth. The finite tilt-depth and finite local wavenumber methods were used to estimate depth to source and only depths that agree to within 10% of each other were used to generate the depth to basement map. This depth to basement map, to the west of the UAE-Oman Mountains, varies in depth from 5 km to in excess of 15 km depth and is able to structurally account for the location of the shear structures, seen in the residual magnetic data, and the location of the volcanic/magmatic centres relative to a set of elongate N-S to NE-SW trending basement highs. The majority of oilfields in the UAE are located within these basement highs. Therefore, the hydrocarbon distribution in the UAE basin appears to be controlled by the location of the

  6. A proof-of-concept implementation of a unit-based advanced practice registered nurse (APRN) role: structural empowerment, role clarity and team effectiveness.

    Science.gov (United States)

    Feistritzer, Nancye R; Jones, Pam O

    2014-03-01

    The quest for decreased cost of care and improved outcomes has created the need for highly effective clinical roles and teams. This article describes the role of a unit-based advanced practice registered nurse (APRN) within a proof-of-concept implementation of a new care delivery model, the Vanderbilt Anticipatory Care Team. Role clarity is central to both structural empowerment of the APRN and team effectiveness. A modified PeaceHealth Team Development Measure tool measured baseline role clarity as a component of overall team effectiveness. A role description for the unit-based APRN based on a comprehensive assessment of the proof-of-concept unit is provided.

  7. Rising United States Hospital Admissions for Acute Bacterial Skin and Skin Structure Infections: Recent Trends and Economic Impact.

    Directory of Open Access Journals (Sweden)

    Keith S Kaye

    Full Text Available The number of ambulatory patients seeking treatment for skin and skin structure infections (SSSI are increasing. The objective of this study is to determine recent trends in hospital admissions and healthcare resource utilization and identify covariates associated with hospital costs and mortality for hospitalized adult patients with a primary SSSI diagnosis in the United States.We performed a retrospective cross-sectional analysis (years 2005-2011 of data from the US Healthcare Cost and Utilization Project National Inpatient Sample. Recent trends, patient characteristics, and healthcare resource utilization for patients hospitalized with a primary SSSI diagnosis were evaluated. Descriptive and bivariate analyses were conducted to assess patient and hospital characteristics.A total of 1.8% of hospital admissions for the years 2005 through 2011 were for adult patients with a SSSI primary diagnosis. SSSI-related hospital admissions significantly changed during the study period (P < .001 for trend ranging from 1.6% (in 2005 to 2.0% (in 2011. Mean hospital length of stay (LOS decreased from 5.4 days in the year 2005 to 5.0 days in the year 2011 (overall change, P < .001 with no change in hospital costs. Patients with postoperative wound infections had the longest hospital stays (adjusted mean, 5.81 days; 95% confidence interval (CI, 5.80-5.83 and highest total costs (adjusted mean, $9388; 95% CI, $9366-$9410. Year of hospital admission was strongly associated with mortality; infection type, all patient refined diagnosis related group severity of illness level, and LOS were strongly associated with hospital costs.Hospital admissions for adult patients in the United States with a SSSI primary diagnosis continue to increase. Decreasing hospital inpatient LOS and mortality rate may be due to improved early treatment. Future research should focus on identifying alternative treatment processes for patients with SSSI that could shift management from

  8. Selective laser melting: a unit cell approach for the manufacture of porous, titanium, bone in-growth constructs, suitable for orthopedic applications. II. Randomized structures.

    Science.gov (United States)

    Mullen, Lewis; Stamp, Robin C; Fox, Peter; Jones, Eric; Ngo, Chau; Sutcliffe, Christopher J

    2010-01-01

    In this study, the unit cell approach, which has previously been demonstrated as a method of manufacturing porous components suitable for use as orthopedic implants, has been further developed to include randomized structures. These random structures may aid the bone in-growth process because of their similarity in appearance to trabecular bone and are shown to carry legacy properties that can be related back to the original unit cell on which they are ultimately based. In addition to this, it has been shown that randomization improves the mechanical properties of regular unit cell structures, resulting in anticipated improvements to both implant functionality and longevity. The study also evaluates the effect that a post process sinter cycle has on the components, outlines the improved mechanical properties that are attainable, and also the changes in both the macro and microstructure that occur.

  9. Repeated treatments of drooling with botulinum toxin B in neurology

    DEFF Research Database (Denmark)

    Møller, Eigild; Daugaard, Dorthe; Holm, Ole

    2015-01-01

    OBJECTIVES: To investigate efficacy, saliva flow, and composition in repeated BoNT-B treatments of drooling. MATERIALS AND METHODS: Seventeen neurological patients (median 66 years), referred for treatment of drooling participated in this observational study. Median total doses of 4000 units...

  10. Active Listening--Listen, Repeat, Do. Scans Plans Portfolio.

    Science.gov (United States)

    Sample, Barbara

    In this unit, students will use active listening, repeating, or paraphrasing what has been said to confirm understanding and introductory phrases and rising intonation to ask for clarification. They will also follow one, two, or multi-step instructions or give instructions to another person. (Adjunct ERIC Clearinghouse for ESL Literacy Education)…

  11. Limitations on quantum key repeaters.

    Science.gov (United States)

    Bäuml, Stefan; Christandl, Matthias; Horodecki, Karol; Winter, Andreas

    2015-04-23

    A major application of quantum communication is the distribution of entangled particles for use in quantum key distribution. Owing to noise in the communication line, quantum key distribution is, in practice, limited to a distance of a few hundred kilometres, and can only be extended to longer distances by use of a quantum repeater, a device that performs entanglement distillation and quantum teleportation. The existence of noisy entangled states that are undistillable but nevertheless useful for quantum key distribution raises the question of the feasibility of a quantum key repeater, which would work beyond the limits of entanglement distillation, hence possibly tolerating higher noise levels than existing protocols. Here we exhibit fundamental limits on such a device in the form of bounds on the rate at which it may extract secure key. As a consequence, we give examples of states suitable for quantum key distribution but unsuitable for the most general quantum key repeater protocol.

  12. Hysteresis of magnetostructural transitions: Repeatable and non-repeatable processes

    Energy Technology Data Exchange (ETDEWEB)

    Provenzano, Virgil [National Institute of Standards and Technology, Gaithersburg, MD 20899 (United States); Della Torre, Edward; Bennett, Lawrence H. [Department of Electrical and Computer Engineering, The George Washington University, Washington, DC 20052 (United States); ElBidweihy, Hatem, E-mail: Hatem@gwmail.gwu.edu [Department of Electrical and Computer Engineering, The George Washington University, Washington, DC 20052 (United States)

    2014-02-15

    The Gd{sub 5}Ge{sub 2}Si{sub 2} alloy and the off-stoichiometric Ni{sub 50}Mn{sub 35}In{sub 15} Heusler alloy belong to a special class of metallic materials that exhibit first-order magnetostructural transitions near room temperature. The magnetic properties of this class of materials have been extensively studied due to their interesting magnetic behavior and their potential for a number of technological applications such as refrigerants for near-room-temperature magnetic refrigeration. The thermally driven first-order transitions in these materials can be field-induced in the reverse order by applying a strong enough field. The field-induced transitions are typically accompanied by the presence of large magnetic hysteresis, the characteristics of which are a complicated function of temperature, field, and magneto-thermal history. In this study we show that the virgin curve, the major loop, and sequentially measured MH loops are the results of both repeatable and non-repeatable processes, in which the starting magnetostructural state, prior to the cycling of field, plays a major role. Using the Gd{sub 5}Ge{sub 2}Si{sub 2} and Ni{sub 50}Mn{sub 35}In{sub 15} alloys, as model materials, we show that a starting single phase state results in fully repeatable processes and large magnetic hysteresis, whereas a mixed phase starting state results in non-repeatable processes and smaller hysteresis.

  13. Analysis of CR1 Repeats in the Zebra Finch Genome

    Directory of Open Access Journals (Sweden)

    George E. Liu

    2013-06-01

    Full Text Available Most bird species have smaller genomes and fewer repeats than mammals. Chicken Repeat 1 (CR1 repeat is one of the most abundant families of repeats, ranging from ~133,000 to ~187,000 copies accounting for ~50 to ~80% of the interspersed repeats in the zebra finch and chicken genomes, respectively. CR1 repeats are believed to have arisen from the retrotransposition of a small number of master elements, which gave rise to multiple CR1 subfamilies in the chicken. In this study, we performed a global assessment of the divergence distributions, phylogenies, and consensus sequences of CR1 repeats in the zebra finch genome. We identified and validated 34 CR1 subfamilies and further analyzed the correlation between these subfamilies. We also discovered 4 novel lineage-specific CR1 subfamilies in the zebra finch when compared to the chicken genome. We built various evolutionary trees of these subfamilies and concluded that CR1 repeats may play an important role in reshaping the structure of bird genomes.

  14. Evolutionary relationship between 5+5 and 7+7 inverted repeat folds within the amino acid-polyamine-organocation superfamily.

    Science.gov (United States)

    Västermark, Åke; Saier, Milton H

    2014-02-01

    Evidence has been presented that 5+5 TMS and 7+7 TMS inverted repeat fold transporters are members of a single superfamily named the Amino acid-Polyamine-organoCation (APC) superfamily. However, the evolutionary relationship between the 5+5 and the 7+7 topological types has not been established. We have identified a common fold, consisting of a spiny membrane helix/sheet, followed by a U-like structure and a V-like structure that is recurrent between domain duplicated units of 5+5 and 7+7 inverted repeat folds. This fold is found in the following protein structures: AdiC, ApcT, LeuT, Mhp1, BetP, CaiT, and SglT (all 5+5 TMS repeats), as well as UraA and SulP (7+7 TMS repeats). AdiC, LeuT and Mhp1 have two extra TMSs after the second duplicated domain, SglT has four extra C-terminal TMSs, and BetP has two extra TMSs before the first duplicated domain. UraA and SulP on the other hand have two extra TMSs at the N-terminus of each duplicated domain unit. These observations imply that multiple hairpin and domain duplication events occurred during the evolution of the APC superfamily. We suggest that the five TMS architecture was primordial and that families gained two TMSs on either side of this basic structure via dissimilar hairpin duplications either before or after intragenic duplication. Evidence for homology between TMSs 1-2 of AdiC and TMSs 1-2 and 3-4 of UraA suggests that the 7+7 topology arose via an internal duplication of the N-terminal hairpin loop within the five TMS repeat unit followed by duplication of the 7 TMS domain.

  15. The Effectiveness of Cooperative Learning Methods on 7th Level “The Structure of Matter and Properties” Unit

    Directory of Open Access Journals (Sweden)

    Yasemin KOÇ

    2016-04-01

    Full Text Available The aim of this research are to determine the effectiveness of Student Teams-Achievement Division (STAD and Reading-Writing-Application (RWA methods of cooperative learning model on academic achievement at the unit of 7th Level “The Structure of Matter and Properties” and students’ views related to methods. The sample of this research are 102 students from two different secondary school in Ağrı. As data collecting tools, Pre-Knowledge Test (PKT, Academic Achievement Test (AAT and Scale Methods Views (SMV is used. For the analysis of the obtained data, one-way variance analysis (ANOVA was used for pre- test and analysis covariance (ANCOVA for academic achievement test because of significant differences in the groups’ pre- test. Descriptive statistics for students’ views about methods are used. It was found that RWA and STAD have similar effects on students’ academic achievement and students instructed with these techniques are more successful than students instructed with teacher centered instruction.

  16. THE STRUCTURE OF SUBTIDAL MACROALGAL ASSEMBLAGES AT THE TAMOIOS ECOLOGICAL STATION, A THREATENED CONSERVATION UNIT IN RIO DE JANEIRO, BRAZIL

    Directory of Open Access Journals (Sweden)

    Victor de Souza Koutsoukos

    2015-03-01

    Full Text Available The structure of subtidal rocky bottom communities at Tamoios Ecological Station (TES, situated in Ilha Grande Bay, Rio de Janeiro State, as well as in other Brazilian marine protected areas, is insufficiently characterized. The present study describes the macroalgal assemblages of shallow subtidal rocky bottoms on two islands of the TES-Imboassica (IM and Búzios Pequena (BPadopting species and genera as observational units. Two sites were surveyed on each island in summer 2011. Random 30x30 cm quadrats (n=3 were scraped to collect all macroalgae except crustose species. The subtidal assemblages, in which 58 macroalgal species occurred, were characterized by the high frequency and percent cover of Sargassum vulgare C. Agardh (56.8±8.4%. The sites differed significantly in total number of species and Shannon-Weiner diversity index (PERMANOVA, p5% were Sargassum, Laurencia, Wrangelia, Canistrocarpus, Asparagopsis, Hypnea, Ceratodictyon, Gayliella, Spyridia and Chondria.Dissimilarities within and between the islands, as shown by nMDS of the cover data, suggest that different spatial scales should be considered in monitoring the rocky bottom communities of Ilha Grande Bay.

  17. Native tandem and ion mobility mass spectrometry highlight structural and modular similarities in clustered-regularly-interspaced shot-palindromic-repeats (CRISPR)-associated protein complexes from Escherichia coli and Pseudomonas aeruginosa

    NARCIS (Netherlands)

    Duijn, E. van; Barbu, I.M.; Barendregt, A.; Jore, M.M.; Wiedenheft, B.; Lundgren, M.; Westra, E.R.; Brouns, S.J.J.; Doudna, J.A.; van der Oost, J.; Heck, A.J.R.

    2012-01-01

    The CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) immune system of bacteria and archaea provides acquired resistance against viruses and plasmids, by a strategy analogous to RNA-interference. Key components of the defense system are ribonucleoprotein

  18. EAMJ Dec. Repeatability.indd

    African Journals Online (AJOL)

    2008-12-12

    Dec 12, 2008 ... Results:Kappa values for four-week repeatability for the wheeze and asthma questions were 0.61 ... for logistic, cultural and ethical reasons, to use ... individual with baseline forced expiratory volume in .... period is likely to also include the effects of true ... data, the writing of the manuscript or the decision.

  19. Landscape structure in the Pirapó, Paranapanema 3 and 4 Hydrographic Unit, in the state of Paraná, Brazil.

    Science.gov (United States)

    Nóbrega, M T; Serra, E; Silveira, H; Terassi, P M B; Bonifácio, C M

    2015-12-01

    The aim of this study is to characterize the Pirapó, Paranapanema 3 and 4 Hydrographic Unit, emphasizing its physical attributes and processes of use and occupation, responsible for the structure of the current landscape and the state of its water resources. The recognition of the landscape's spatial structure in the hydrographic unit and its drainage basins was obtained by integrated analysis of the main elements that compose it: geology, landforms (hypsometric and slope), soils, climate and land use. Analysis revealed that within each drainage basin several variations in the spatial structure of the landscape occur which produce an internal compartmentalization. Each compartment is defined by its own geo-ecological structure, physiognomic standards and dynamics, reflected in its potentialities and vulnerabilities and in the conditions of water resources in the wake of occupation and use over time.

  20. Research on properties of fine recycled aggregate for structural concrete from repeatedly recycling concrete waste%循环再生高性能混凝土细骨料性能研究

    Institute of Scientific and Technical Information of China (English)

    牟晓芳; 郑俊健; 李浩然; 朱平华

    2014-01-01

    In order to explore the possibility of repeatedly recycling the waste concrete from different sources for structural concrete ag-gregate,the experiment researched the performance of recycled fine aggregate from both secondary renewable single sources and mixed sources,analysing the mineral and chemical component,grading the test results according to Japanese technical standards for recycled ag-gregate,ASTM and China GB/T 25177-2010 and other relevant recycled aggregate standards,establishing a relationship between aggre-gate indicators through the data fitting.The experimental results show that:with the increase of the cycle,the apparent density of recycled fine aggregate,the water absorption and water demand ratio decreases while the intensity ratio increases;the surface absorption mortar con-tent of circulation recycled aggregate increases;compared with natural fine aggregate,the mass fraction of CaO from first recycled fine ag-gregate increased by an average of 5 times,which from the second recycled fine aggregate increased by an average of 10 times;the com-pressive strength radio of recycled mortar and the absorption mortar content shows a quadratic relationship ,the curve down first then up shows that with the increase of regeneration frequencies,the compressive strength radio of recycled mortar elevates;The secondary recy-cled aggregates are satisfied with the performance requirements of structural concrete with fine aggregate regardless of what the standards and criteria taken.%系统研究了由废弃混凝土二次再生制备的结构混凝土细骨料性能,分析了矿物与化学成分,依据日本JISA、美国ASTM和中国GB/T 25176-2010等相关再生细骨料标准对试验结果进行了等级评定,并建立了表观密度、胶砂强度与吸附砂浆含量之间的关系。结果表明:随着循环次数的增加,再生细骨料表观密度、吸水率、需水量比降低,胶砂强度比与细度模数增大,吸附的砂浆含量

  1. An examination of the origin and evolution of additional tandem repeats in the mitochondrial DNA control region of Japanese sika deer (Cervus Nippon).

    Science.gov (United States)

    Ba, Hengxing; Wu, Lang; Liu, Zongyue; Li, Chunyi

    2016-01-01

    Tandem repeat units are only detected in the left domain of the mitochondrial DNA control region in sika deer. Previous studies showed that Japanese sika deer have more tandem repeat units than its cousins from the Asian continent and Taiwan, which often have only three repeat units. To determine the origin and evolution of these additional repeat units in Japanese sika deer, we obtained the sequence of repeat units from an expanded dataset of the control region from all sika deer lineages. The functional constraint is inferred to act on the first repeat unit because this repeat has the least sequence divergence in comparison to the other units. Based on slipped-strand mispairing mechanisms, the illegitimate elongation model could account for the addition or deletion of these additional repeat units in the Japanese sika deer population. We also report that these additional repeat units could be occurring in the internal positions of tandem repeat regions, possibly via coupling with a homogenization mechanism within and among these lineages. Moreover, the increased number of repeat units in the Japanese sika deer population could reflect a balance between mutation and selection, as well as genetic drift.

  2. Airborne Radar Interferometric Repeat-Pass Processing

    Science.gov (United States)

    Hensley, Scott; Michel, Thierry R.; Jones, Cathleen E.; Muellerschoen, Ronald J.; Chapman, Bruce D.; Fore, Alexander; Simard, Marc; Zebker, Howard A.

    2011-01-01

    Earth science research often requires crustal deformation measurements at a variety of time scales, from seconds to decades. Although satellites have been used for repeat-track interferometric (RTI) synthetic-aperture-radar (SAR) mapping for close to 20 years, RTI is much more difficult to implement from an airborne platform owing to the irregular trajectory of the aircraft compared with microwave imaging radar wavelengths. Two basic requirements for robust airborne repeat-pass radar interferometry include the ability to fly the platform to a desired trajectory within a narrow tube and the ability to have the radar beam pointed in a desired direction to a fraction of a beam width. Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR) is equipped with a precision auto pilot developed by NASA Dryden that allows the platform, a Gulfstream III, to nominally fly within a 5 m diameter tube and with an electronically scanned antenna to position the radar beam to a fraction of a beam width based on INU (inertial navigation unit) attitude angle measurements.

  3. Abundant intergenic TAACTGA direct repeats and putative alternate RNA polymerase β´ subunits in marine Beggiatoaceae genomes: possible regulatory roles and origins

    Directory of Open Access Journals (Sweden)

    Barbara J. MacGregor

    2015-12-01

    Full Text Available The genome sequences of several giant marine sulfur-oxidizing bacteria present evidence of a possible post-transcriptional regulatory network that may have been transmitted to or from two distantly related bacteria lineages. The draft genome of a Cand. Maribeggiatoa filament from the Guaymas Basin (Gulf of California, Mexico seafloor contains 169 sets of TAACTGA direct repeats and one indirect repeat, with two to six copies per set. Related heptamers are rarely or never found as direct repeats. TAACTGA direct repeats are also found in some other Beggiatoaceae, Thiocystis violascens, a range of Cyanobacteria, and five Bacteroidetes. This phylogenetic distribution suggests they may have been transmitted horizontally, but no mechanism is evident. There is no correlation between total TAACTGA occurrences and repeats per genome. In most species the repeat units are relatively short, but longer arrays of up to 43 copies are found in several Bacteroidetes and Cyanobacteria. The majority of TAACTGA repeats in the Cand. Maribeggiatoa Orange Guaymas (BOGUAY genome are within several nucleotides upstream of a putative start codon, suggesting they may be binding sites for a post-transcriptional regulator. Candidates include members of the ribosomal protein S1, Csp (cold shock protein, and Csr (carbon storage regulator families. No pattern was evident in the predicted functions of the open reading frames (ORFs downstream of repeats, but some encode presumably essential products such as ribosomal proteins. Among these is an ORF encoding a possible alternate or modified RNA polymerase beta prime subunit, predicted to have the expected subunit interaction domains but lacking most catalytic residues. A similar ORF was found in the Thioploca ingrica draft genome, but in no others. In both species they are immediately upstream of putative sensor kinase genes with nearly identical domain structures. In the marine Beggiatoaceae, a role for the TAACTGA repeats in

  4. Why Not Start with Quarks? Teachers Investigate a Learning Unit on the Subatomic Structure of Matter with 12-Year-Olds

    Science.gov (United States)

    Wiener, Gerfried J.; Schmeling, Sascha M.; Hopf, Martin

    2017-01-01

    This paper describes the second in a series of studies exploring the acceptance of the subatomic structure of matter by 12-year-olds. The studies focus on a novel learning unit introducing an atomic model from electrons down to quarks, which is aimed to be used at an early stage in the physics curriculum. Three features are fundamental to the…

  5. Genetic structure and pathogenicity of populations of Phytophthora infestans from organic potato crops in France, Norway, Switzerland and the United Kingdom

    NARCIS (Netherlands)

    Flier, W.G.; Kroon, L.P.N.M.; Hermansen, A.; Raaij, van H.M.G.; Speiser, B.; Tamm, L.; Fuchs, J.G.; Lambion, J.; Razzaghian, J.; Andrivon, D.; Wilcockson, S.; Leifert, C.

    2007-01-01

    Genetic variation and pathogenicity of Pbytophthora infestans isolates collected from organic potato crops of the susceptible cv. Bintje and the moderately resistant cv. Sante were assessed in France, Norway, and the United Kingdom in 2001 and in Switzerland in 2001 and 2002. Population structures d

  6. Forest products research and development organizations in a worldwide setting: A review of structure, governance, and measures of performance of organizations outside the United States

    Science.gov (United States)

    Paul V. Ellefson; Michael A. Kilgore; Kenneth E. Skog; Christopher D. Risbrudt

    2007-01-01

    Located in 23 countries, 40 forest-products research and development organizations outside the United States were reviewed in 2004 and 2005. The intent was to obtain a better understanding of how such organizations are structured and administered and their performance judged. Investing over $600 million annually, the 40 organizations employed 7,000 to 7,500 scientists...

  7. Directionality switchable gain stabilized linear repeater

    Science.gov (United States)

    Ota, Takayuki; Ohmachi, Tadashi; Aida, Kazuo

    2004-10-01

    We propose a new approach to realize a bidirectional linear repeater suitable for future optical internet networks and fault location in repeater chain with OTDR. The proposed approach is the linear repeater of simple configuration whose directionality is rearranged dynamically by electrical control signal. The repeater is composed of a magneto-optical switch, a circulator, a dynamically gain stabilized unidirectional EDFA, and control circuits. The repeater directionality is rearranged as fast as 0.1ms by an electrical control pulse. It is experimentally confirmed that OTDR with the directionality switchable repeater is feasible for repeater chain. The detailed design and performance of the repeater are also discussed, including the multi-pass interference (MPI) which may arise in the proposed repeater, the effect of the MPI on SNR degradation of the repeater chain and the feed-forward EDFA gain control circuit.

  8. Structured expert elicitation about Listeria monocytogenes cross-contamination in the environment of retail deli operations in the United States.

    Science.gov (United States)

    Hoelzer, Karin; Oliver, Haley F; Kohl, Larry R; Hollingsworth, Jill; Wells, Martin T; Wiedmann, Martin

    2012-07-01

    Listeria monocytogenes is among the foodborne pathogens with the highest death toll in the United States. Ready-to-eat foods contaminated at retail are an important source of infection. Environmental sites in retail deli operations can be contaminated. However, commonly contaminated sites are unlikely to come into direct contact with food and the public health relevance of environmental contamination has remained unclear. To identify environmental sites that may pose a considerable cross-contamination risk, to elucidate potential transmission pathways, and to identify knowledge gaps, we performed a structured expert elicitation of 41 experts from state regulatory agencies and the food retail industry with practical experience in retail deli operations. Following the "Delphi" method, the elicitation was performed in three consecutive steps: questionnaire, review and discussion of results, second questionnaire. Hands and gloves were identified as important potential contamination sources. However, bacterial transfers to and from hands or gloves represented a major data gap. Experts agreed about transfer probabilities from cutting boards, scales, deli cases, and deli preparation sinks to product, and about transfer probabilities from floor drains, walk-in cooler floors, and knife racks to food contact surfaces. Comparison of experts' opinions to observational data revealed a tendency among experts with certain demographic characteristics and professional opinions to overestimate prevalence. Experts' votes clearly clustered into separate groups not defined by place of employment, even though industry experts may have been somewhat overrepresented in one cluster. Overall, our study demonstrates the value and caveats of expert elicitation to identify data gaps and prioritize research efforts.

  9. Measurement-based quantum repeaters

    CERN Document Server

    Zwerger, M; Briegel, H J

    2012-01-01

    We introduce measurement-based quantum repeaters, where small-scale measurement-based quantum processors are used to perform entanglement purification and entanglement swapping in a long-range quantum communication protocol. In the scheme, pre-prepared entangled states stored at intermediate repeater stations are coupled with incoming photons by simple Bell-measurements, without the need of performing additional quantum gates or measurements. We show how to construct the required resource states, and how to minimize their size. We analyze the performance of the scheme under noise and imperfections, with focus on small-scale implementations involving entangled states of few qubits. We find measurement-based purification protocols with significantly improved noise thresholds. Furthermore we show that already resource states of small size suffice to significantly increase the maximal communication distance. We also discuss possible advantages of our scheme for different set-ups.

  10. A Repeating Fast Radio Burst

    CERN Document Server

    Spitler, L G; Hessels, J W T; Bogdanov, S; Brazier, A; Camilo, F; Chatterjee, S; Cordes, J M; Crawford, F; Deneva, J; Ferdman, R D; Freire, P C C; Kaspi, V M; Lazarus, P; Lynch, R; Madsen, E C; McLaughlin, M A; Patel, C; Ransom, S M; Seymour, A; Stairs, I H; Stappers, B W; van Leeuwen, J; Zhu, W W

    2016-01-01

    Fast Radio Bursts are millisecond-duration astronomical radio pulses of unknown physical origin that appear to come from extragalactic distances. Previous follow-up observations have failed to find additional bursts at the same dispersion measures (i.e. integrated column density of free electrons between source and telescope) and sky position as the original detections. The apparent non-repeating nature of the fast radio bursts has led several authors to hypothesise that they originate in cataclysmic astrophysical events. Here we report the detection of ten additional bursts from the direction of FRB121102, using the 305-m Arecibo telescope. These new bursts have dispersion measures and sky positions consistent with the original burst. This unambiguously identifies FRB121102 as repeating and demonstrates that its source survives the energetic events that cause the bursts. Additionally, the bursts from FRB121102 show a wide range of spectral shapes that appear to be predominantly intrinsic to the source and wh...

  11. A further analysis of the relationship between yellow ripe-fruit color and the capsanthin-capsorubin synthase gene in pepper (Capsicum sp.) indicated a new mutant variant in C. annuum and a tandem repeat structure in promoter region.

    Science.gov (United States)

    Li, Zheng; Wang, Shu; Gui, Xiao-Ling; Chang, Xiao-Bei; Gong, Zhen-Hui

    2013-01-01

    Mature pepper (Capsicum sp.) fruits come in a variety of colors, including red, orange, yellow, brown, and white. To better understand the genetic and regulatory relationships between the yellow fruit phenotype and the capsanthin-capsorubin synthase gene (Ccs), we examined 156 Capsicum varieties, most of which were collected from Northwest Chinese landraces. A new ccs variant was identified in the yellow fruit cultivar CK7. Cluster analysis revealed that CK7, which belongs to the C. annuum species, has low genetic similarity to other yellow C. annuum varieties. In the coding sequence of this ccs allele, we detected a premature stop codon derived from a C to G change, as well as a downstream frame-shift caused by a 1-bp nucleotide deletion. In addition, the expression of the gene was detected in mature CK7 fruit. Furthermore, the promoter sequences of Ccs from some pepper varieties were examined, and we detected a 176-bp tandem repeat sequence in the promoter region. In all C. annuum varieties examined in this study, the repeat number was three, compared with four in two C. chinense accessions. The sequence similarity ranged from 84.8% to 97.7% among the four types of repeats, and some putative cis-elements were also found in every repeat. This suggests that the transcriptional regulation of Ccs expression is complex. Based on the analysis of the novel C. annuum mutation reported here, along with the studies of three mutation types in yellow C. annuum and C. chinense accessions, we suggest that the mechanism leading to the production of yellow color fruit may be not as complex as that leading to orange fruit production.

  12. A further analysis of the relationship between yellow ripe-fruit color and the capsanthin-capsorubin synthase gene in pepper (Capsicum sp. indicated a new mutant variant in C. annuum and a tandem repeat structure in promoter region.

    Directory of Open Access Journals (Sweden)

    Zheng Li

    Full Text Available Mature pepper (Capsicum sp. fruits come in a variety of colors, including red, orange, yellow, brown, and white. To better understand the genetic and regulatory relationships between the yellow fruit phenotype and the capsanthin-capsorubin synthase gene (Ccs, we examined 156 Capsicum varieties, most of which were collected from Northwest Chinese landraces. A new ccs variant was identified in the yellow fruit cultivar CK7. Cluster analysis revealed that CK7, which belongs to the C. annuum species, has low genetic similarity to other yellow C. annuum varieties. In the coding sequence of this ccs allele, we detected a premature stop codon derived from a C to G change, as well as a downstream frame-shift caused by a 1-bp nucleotide deletion. In addition, the expression of the gene was detected in mature CK7 fruit. Furthermore, the promoter sequences of Ccs from some pepper varieties were examined, and we detected a 176-bp tandem repeat sequence in the promoter region. In all C. annuum varieties examined in this study, the repeat number was three, compared with four in two C. chinense accessions. The sequence similarity ranged from 84.8% to 97.7% among the four types of repeats, and some putative cis-elements were also found in every repeat. This suggests that the transcriptional regulation of Ccs expression is complex. Based on the analysis of the novel C. annuum mutation reported here, along with the studies of three mutation types in yellow C. annuum and C. chinense accessions, we suggest that the mechanism leading to the production of yellow color fruit may be not as complex as that leading to orange fruit production.

  13. Comparative Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) of Streptococcus thermophilus St-I and its Bacteriophage-Insensitive Mutants (BIM) Derivatives.

    Science.gov (United States)

    Li, Wan; Bian, Xin; Evivie, Smith Etareri; Huo, Gui-Cheng

    2016-09-01

    The CRISPR-Cas (CRISPR together with CRISPR-associated proteins) modules are the adaptive immune system, acting as an adaptive and heritable immune system in bacteria and archaea. CRISPR-based immunity acts by integrating short virus sequences in the cell's CRISPR locus, allowing the cell to remember, recognize, and clear infections. In this study, the homology of CRISPRs sequence in BIMs (bacteriophage-insensitive mutants) of Streptococcus thermophilus St-I were analyzed. Secondary structures of the repeats and the PAMs (protospacer-associated motif) of each CRISPR locus were also predicted. Results showed that CRISPR1 has 27 repeat-spacer units, 5 of them had duplicates; CRISPR2 has one repeat-spacer unit; CRISPR3 has 28 repeat-spacer units. Only BIM1 had a new spacer acquisition in CRISPR3, while BIM2 and BIM3 had no new spacers' insertion, thus indicating that while most CRISPR1 were more active than CRISPR3, new spacer acquisition occurred just in CRSPR3 in some situations. These findings will help establish the foundation for the study of CRSPR-Cas systems in lactic acid bacteria.

  14. Repeatability of Harris Corner Detector

    Institute of Scientific and Technical Information of China (English)

    HU Lili

    2003-01-01

    Interest point detectors are commonly employed to reduce the amount of data to be processed. The ideal interest point detector would robustly select those features which are most appropriate or salient for the application and data at hand. This paper shows that interest points are geometrically stable under different transformations.This property makes interest points very successful in the context of image matching. To measure this property quantatively, we introduce a evaluation criterion: repeatability rate.

  15. On Methods of Establishing Design Diagrams for Structural Integrity of Slender Complex Types of Breakwater Armour Units

    DEFF Research Database (Denmark)

    Burcharth, Hans F.; Howell, Gary J.

    1988-01-01

    units to measure bending movements in a cross section of the units and the accelerations (impact speed) were first used by DHL in 1980. Recent developments were presented by Scott et al. 1986. Correct scaling of the most important material properties of concrete in small scale hydraulic model tests...... was first presented by NRC (Timco 1981 ). Work based on direct strain-gauge measurement of stresses on large concrete model armour units was presented by Nishigori et al. in 1986.So far, none of the mentioned methods have produced general applicable tools for the design of armour layers. This is mainly......Many of the recent dramatic failures of a number of large rubble mound breakwaters armoured with Dolosse and Tetrapods were caused by breakage of the concrete armour units. Breakage took place before the hydraulic stability of intact units in the armour layers expired. Thus there was not a balance...

  16. Unitals in Projective Planes

    CERN Document Server

    Barwick, Susan

    2008-01-01

    Unitals are key structures in projective planes, and have connections with other structures in algebra. This book presents a monograph on unitals embedded in finite projective planes. It offers a survey of the research literature on embedded unitals. It is suitable for graduate students and researchers who want to learn about this topic

  17. Ethical Leadership, Leader-Member Exchange and Feedback Seeking: A Double-Moderated Mediation Model of Emotional Intelligence and Work-Unit Structure

    Science.gov (United States)

    Qian, Jing; Wang, Bin; Han, Zhuo; Song, Baihe

    2017-01-01

    This research elucidates the role of ethical leadership in employee feedback seeking by examining how and when ethical leadership may exert a positive influence on feedback seeking. Using matched reports from 64 supervisors and 265 of their immediate employees from a hotel group located in a major city in China, we proposed and tested a moderated mediation model that examines leader-member exchange (LMX) as the mediator and emotional intelligence as well as work-unit structure as double moderators in the relationships between ethical leadership and followers’ feedback-seeking behavior from supervisors and coworkers. Our findings indicated that (1) LMX mediated the positive relationship between ethical leadership and feedback seeking from both ethical leaders and coworkers, and (2) emotional intelligence and work-unit structure served as joint moderators on the mediated positive relationship in such a way that the relationship was strongest when the emotional intelligence was high and work-unit structure was more of an organic structure rather than a mechanistic structure. PMID:28744251

  18. Potential Role of the Last Half Repeat in TAL Effectors Revealed by a Molecular Simulation Study

    Directory of Open Access Journals (Sweden)

    Hua Wan

    2016-01-01

    Full Text Available TAL effectors (TALEs contain a modular DNA-binding domain that is composed of tandem repeats. In all naturally occurring TALEs, the end of tandem repeats is invariantly a truncated half repeat. To investigate the potential role of the last half repeat in TALEs, we performed comparative molecular dynamics simulations for the crystal structure of DNA-bound TALE AvrBs3 lacking the last half repeat and its modeled structure having the last half repeat. The structural stability analysis indicates that the modeled system is more stable than the nonmodeled system. Based on the principle component analysis, it is found that the AvrBs3 increases its structural compactness in the presence of the last half repeat. The comparison of DNA groove parameters of the two systems implies that the last half repeat also causes the change of DNA major groove binding efficiency. The following calculation of hydrogen bond reveals that, by stabilizing the phosphate binding with DNA at the C-terminus, the last half repeat helps to adopt a compact conformation at the protein-DNA interface. It further mediates more contacts between TAL repeats and DNA nucleotide bases. Finally, we suggest that the last half repeat is required for the high-efficient recognition of DNA by TALE.

  19. Potential Role of the Last Half Repeat in TAL Effectors Revealed by a Molecular Simulation Study

    Science.gov (United States)

    Wan, Hua; Chang, Shan; Hu, Jian-ping; Tian, Xu-hong

    2016-01-01

    TAL effectors (TALEs) contain a modular DNA-binding domain that is composed of tandem repeats. In all naturally occurring TALEs, the end of tandem repeats is invariantly a truncated half repeat. To investigate the potential role of the last half repeat in TALEs, we performed comparative molecular dynamics simulations for the crystal structure of DNA-bound TALE AvrBs3 lacking the last half repeat and its modeled structure having the last half repeat. The structural stability analysis indicates that the modeled system is more stable than the nonmodeled system. Based on the principle component analysis, it is found that the AvrBs3 increases its structural compactness in the presence of the last half repeat. The comparison of DNA groove parameters of the two systems implies that the last half repeat also causes the change of DNA major groove binding efficiency. The following calculation of hydrogen bond reveals that, by stabilizing the phosphate binding with DNA at the C-terminus, the last half repeat helps to adopt a compact conformation at the protein-DNA interface. It further mediates more contacts between TAL repeats and DNA nucleotide bases. Finally, we suggest that the last half repeat is required for the high-efficient recognition of DNA by TALE. PMID:27803930

  20. First-principles investigation of the effect of charged unit cell on the electronic structure of two-dimensional MoS2

    Science.gov (United States)

    Shekaari, Ashkan; Abolhassani, Mohammad Reza; Lashgari, Hamed

    2017-01-01

    Density-functional theory has been applied to investigate the effect of charged unit cell on the structural and electronic properties of two-dimensional MoS2 within PBE-GGA. The charge of the unit cell of the monolayer changes from zero to n = ± 4 e with e the absolute value of the elementary electric charge. Variations of the lattice constant, Mo-S bond length, S-Mo-S bond angle, total energy, exchange and correlation contributions, and the Fermi level versus n have been calculated quantitatively, indicating decrease in the stability of the atomic structure of the monolayer with increase in the absolute value of n. It is found that the Fermi level for two-dimensional MoS2 is a function of both the number of electrons in allowed states and the inverse of the volume of the unit cell. The electronic properties of each monolayer have been also calculated via examining the related electronic band structure and density of states. Results broadly support the view that the effect of charged unit cell (n =+ e to - 4 e) on the electronic properties of MoS2 monolayer is manifested in the form of semiconductor-to-metal transition in addition to the Fermi level shift. It is also verified that as the negative charge of the unit cell increases from n = - e to - 4 e , there is an ever-increasing trend in the total number of allowed electronic states at the Fermi level, implying a direct correlation between electrical conductivity and the value of n in a way that the more negative the charge of the unit cell, the higher the electrical conductivity of the monolayer.

  1. Six Zn(II) and Cd(II) coordination polymers assembled from a similar binuclear building unit: tunable structures and luminescence properties.

    Science.gov (United States)

    Zhang, Liyan; Rong, Lulu; Hu, Guoli; Jin, Suo; Jia, Wei-Guo; Liu, Ji; Yuan, Guozan

    2015-04-21

    Six Zn(ii) and Cd(ii) coordination polymers were constructed by treating a 2-substituted 8-hydroxyquinolinate ligand containing a pyridyl group with zinc or cadmium salts, and characterized by a variety of techniques. Interestingly, based on a similar binuclear Zn(ii) or Cd(ii) building unit, the supramolecular structures of the six coordination polymers () exhibit an unprecedented structural diversification due to the different choices of metal salts. and represent a novel 2D framework containing 1D infinite right- and left-handed helical chains. and are 2D coordination frameworks based on binuclear Cd(ii) building units. For and , the L ligands can bridge binuclear building units forming a 1D infinite chain. Interestingly, the adjacent Cd2O2 planes of the 1D chain in are in parallel with each other, while the dihedral angle between the two Zn2O2 planes in is 83.43°. Photoluminescence properties revealed that the six coordination polymers exhibit redshifted emission maximum compared with the free ligand HL, which can be ascribed to an increased conformational rigidity and the fabrication of coplanar binuclear building units M2L2 in . Coordination polymers also display distinct fluorescence lifetimes and quantum yields because of their different metal centers and supramolecular structures.

  2. Repeating Patterns in Kindergarten: Findings from Children's Enactments of Two Activities

    Science.gov (United States)

    Tsamir, Pessia; Tirosh, Dina; Levenson, Esther S.; Barkai, Ruthi; Tabach, Michal

    2017-01-01

    This paper describes kindergarten children's engagement with two patterning activities. The first activity includes two tasks in which children are asked to choose possible ways for extending two different repeating patterns and the second activity calls for comparing different pairs of repeating patterns. Children's recognition of the unit of…

  3. Scanning for unstable trinucleotide repeats in neuropsychiatric disorders: Detection of a large CTG expansion in a schizophrenic patient

    Energy Technology Data Exchange (ETDEWEB)

    Sirugo, G.; Haaf, T.; Kidd, K.K. [and others

    1994-09-01

    Expansion of unstable trinucleotide repeats have been associated so far with seven human genetic disorders including fragile X, myotonic dystrophy and Huntington disease. This newly discovered class of genetic mutations is almost invariably associated with genetic anticipation. Anticipation has been recently reported in bipolar affective disorder and schizophrenia pedigrees, suggesting a possible implication of genes with unstable triplets in these disorders. To explore this hypothesis we have analyzed large schizophrenia and bipolar affective disorder kindreds by means of the Repeat Expansion Detection Method (RED) described by Schalling and modified in our laboratory. This method uses genomic DNA as a template for the annealing and ligation of repeat-specific oligonucleotides. The reactions were subjected to denaturing PAGE and then transferred onto nylon membrane by capillary transfer. The multimers were revealed after hybridization with an oligoprobe and 5 hours exposure on film. To date the kindreds have been screened for the presence of unstable (CTG)n. CTG multimers ranging from 51 to 119 CTG units were detected in both affected and normal individuals corresponding to a normal variation in length of one or more CTG loci. Although our results indicate that (CTG)n expansions are not the mechanism causing schziophrenia or bipolar affective disorder, in one schizophrenia patient we have detected a large (CTG)n constituted by at least 204 CTG units. The incomplete structure of the family does not allow us to determine if this large repeat segregates with the disease. Localization of this expanded locus by in situ hybridization is underway. Similar in situ studies using PCR-generated CCA multimers up to 1 kb in length as a probe have revealed the presence of long tracts of CCA repeats at discrete sites in the human genome. This shows the feasibility of the in situ approach to localize large arrays of triplets in the human genome.

  4. Sediments, structural framework, petroleum potential, environmental conditions, and operational considerations of the United States South Atlantic Outer Continental Shelf

    Science.gov (United States)

    ,

    1975-01-01

    The area designated for possible oil and gas lease sale in Bureau of Land Management memorandum 3310 #43 (722) and referred to therein as part of the United States South Atlantic Outer Continental Shelf (OCS) contains about 98,000 square kilometres of the continental margin seaward of the 3 mile offshore limit and within the 600 metre isobath. The designated area, offshore of North Carolina, South Carolina, Georgia, and Florida, encompasses parts of three physiographic provinces: the Continental Shelf, the Florida-Hatteras Slope, and the Blake Plateau. The structural framework of the U.3. South Atlantic region is dominated by the Southeast Georgia Embayment --an east-plunging depression recessed into the Atlantic Coastal Plain and shelf between Cape Fear, North Carolina and Jacksonville, Florida. The embayment is bounded to the north by the Cape Fear Arch and to southeast by the Peninsular Arch. Refraction data indicate a minor basement(?) ridge beneath the outer shelf between 30? and 32?N at 80?W. Drill hole data also suggest a gentle fold or accretionary structure (reef?) off the east coast of Florida. Several other structural features have been identified by refraction and reflection techniques and drilling. These are the Yamacraw Uplift, Burton High, Stone Arch, and the Suwannee Channel. Gravity and magnetic anomalies within the area probably result from emplacement of magma bodies along linear features representing fundamental crustal boundaries. Of these anomalies, the most prominent, is a segment of the East Coast Magnetic Anomaly which crosses the coast at Brunswick, Georgia. This anomaly has been interpreted as representing an ancient continental boundary where two formerly separate continental plates collided and were welded together. There may be as much as 5,000 m of sedimentary rocks in the Southeast Georgia Embayment out to the 600 m isobath. Basement rocks beneath the Southeast Georgia Embayment are expected to be similar to those exposed in the

  5. ACCA phosphopeptide recognition by the BRCT repeats of BRCA1.

    Science.gov (United States)

    Ray, Hind; Moreau, Karen; Dizin, Eva; Callebaut, Isabelle; Venezia, Nicole Dalla

    2006-06-16

    The tumour suppressor gene BRCA1 encodes a 220 kDa protein that participates in multiple cellular processes. The BRCA1 protein contains a tandem of two BRCT repeats at its carboxy-terminal region. The majority of disease-associated BRCA1 mutations affect this region and provide to the BRCT repeats a central role in the BRCA1 tumour suppressor function. The BRCT repeats have been shown to mediate phospho-dependant protein-protein interactions. They recognize phosphorylated peptides using a recognition groove that spans both BRCT repeats. We previously identified an interaction between the tandem of BRCA1 BRCT repeats and ACCA, which was disrupted by germ line BRCA1 mutations that affect the BRCT repeats. We recently showed that BRCA1 modulates ACCA activity through its phospho-dependent binding to ACCA. To delineate the region of ACCA that is crucial for the regulation of its activity by BRCA1, we searched for potential phosphorylation sites in the ACCA sequence that might be recognized by the BRCA1 BRCT repeats. Using sequence analysis and structure modelling, we proposed the Ser1263 residue as the most favourable candidate among six residues, for recognition by the BRCA1 BRCT repeats. Using experimental approaches, such as GST pull-down assay with Bosc cells, we clearly showed that phosphorylation of only Ser1263 was essential for the interaction of ACCA with the BRCT repeats. We finally demonstrated by immunoprecipitation of ACCA in cells, that the whole BRCA1 protein interacts with ACCA when phosphorylated on Ser1263.

  6. Origin and fate of repeats in bacteria.

    Science.gov (United States)

    Achaz, G; Rocha, E P C; Netter, P; Coissac, E

    2002-07-01

    We investigated 53 complete bacterial chromosomes for intrachromosomal repeats. In previous studies on eukaryote chromosomes, we proposed a model for the dynamics of repeats based on the continuous genesis of tandem repeats, followed by an active process of high deletion rate, counteracted by rearrangement events that may prevent the repeats from being deleted. The present study of long repeats in the genomes of Bacteria and Archaea suggests that our model of interspersed repeats dynamics may apply to them. Thus the duplication process might be a consequence of very ancient mechanisms shared by all three domains. Moreover, we show that there is a strong negative correlation between nucleotide composition bias and the repeat density of genomes. We hypothesise that in highly biased genomes, non-duplicated small repeats arise more frequently by random effects and are used as primers for duplication mechanisms, leading to a higher density of large repeats.

  7. Evaluating post-Katrina recovery in Mississippi using repeat photography.

    Science.gov (United States)

    Burton, Christopher; Mitchell, Jerry T; Cutter, Susan L

    2011-07-01

    Hurricane Katrina of August 2005 had extensive consequences for the state of Mississippi in the United States. Widespread infrastructure and property damage, massive social dislocation, and ecological loss remain among the many challenges faced by communities as they work towards 'normalcy'. This study employs repeat photography to understand differential recovery from Hurricane Katrina in Mississippi. Revealing change with conventional landscape photography, a process known as repeat photography, is common in the natural sciences. Simply stated, repeat photography is the practice of re-photographing the same scene as it appears in an earlier photograph. Photographs were taken at 131 sites every six months over a three-year period. Each photograph was assigned a recovery score and a spatially interpolated recovery surface was generated for each time period. The mapped and graphed results show disparities in the progression of recovery: some communities quickly entered the rebuilding process whereas others have lagged far behind.

  8. A Brief Review of Short Tandem Repeat Mutation

    Institute of Scientific and Technical Information of China (English)

    Hao Fan; Jia-You Chu

    2007-01-01

    Short tandem repeats (STRs) are short tandemly repeated DNA sequences that involve a repetitive unit of 1-6 bp. Because of their polymorphisms and high mutation rates, STRs are widely used in biological research. Strand-slippage replication is the predominant mutation mechanism of STRs, and the stepwise mutation model is regarded as the main mutation model. STR mutation rates can be influenced by many factors. Moreover, some trinucleotide repeats are associated with human neurodegenerative diseases. In order to deepen our knowledge of these diseases and broaden STR application, it is essential to understand the STR mutation process in detail. In this review, we focus on the current known information about STR mutation.

  9. Altitude of the top of the middle Fort Union hydrogeologic unit in the Powder River structural basin

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — These data represent the altitude, in feet above North American Vertical Datum of 1988 (NAVD88), of the middle Fort Union hydrogeologic unit in the Powder River...

  10. Altitude of the top of the Upper Hell Creek hydrogeologic unit in the Powder River structural basin

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — These data represent the altitude, in feet above North American Vertical Datum of 1988 (NAVD88), of the Upper Hell Creek hydrogeologic unit in the Powder River...

  11. The evolution and function of protein tandem repeats in plants.

    Science.gov (United States)

    Schaper, Elke; Anisimova, Maria

    2015-04-01

    Sequence tandem repeats (TRs) are abundant in proteomes across all domains of life. For plants, little is known about their distribution or contribution to protein function. We exhaustively annotated TRs and studied the evolution of TR unit variations for all Ensembl plants. Using phylogenetic patterns of TR units, we detected conserved TRs with unit number and order preserved during evolution, and those TRs that have diverged via recent TR unit gains/losses. We correlated the mode of evolution of TRs to protein function. TR number was strongly correlated with proteome size, with about one-half of all TRs recognized as common protein domains. The majority of TRs have been highly conserved over long evolutionary distances, some since the separation of red algae and green plants c. 1.6 billion yr ago. Conversely, recurrent recent TR unit mutations were rare. Our results suggest that the first TRs by far predate the first plants, and that TR appearance is an ongoing process with similar rates across the plant kingdom. Interestingly, the few detected highly mutable TRs might provide a source of variation for rapid adaptation. In particular, such TRs are enriched in leucine-rich repeats (LRRs) commonly found in R genes, where TR unit gain/loss may facilitate resistance to emerging pathogens.

  12. Roles of mammalian structural units, ligand cluster and polyvalency in the Abrus precatorius agglutinin and glycoprotein recognition process.

    Science.gov (United States)

    Wu, Albert M; Wu, June H; Liu, Jia-Hau; Chen, Yuen-Yuen; Singha, Biswajit; Chow, Lu-Ping; Lin, Jung-Yaw

    2009-10-01

    Previous studies on one of the toxic type 2 ribosome inactivating proteins (RIP), Abrus precatorius agglutinin (APA), have shown that the recognition domains of APA are restricted to monomers of Galbeta1-3GalNAc (T, Thomsen-Friedenreich glycotope) and Galbeta1-3/4GlcNAc (blood group precursor type I/II sequences); which are essential but play a minor role in the recognition process. In this study, APA recognition factors were expanded to include ligand clusters and polyvalent glycotopes by enzyme-linked lectinosorbent binding and inhibition assays. Based on the results of molar relative potency, the essential mammalian structural units are Galbeta1-3GalNAcalpha/beta1- (T(alpha)/T(beta))>Galalpha1-4Gal (E)>Galbeta1-3/4GlcNAc (I/II) and avidity for tri-/di-antennary II(beta), T, E and II monomers was found to be 7.1 x 10(2), 4.0, 5.5, 3.7 and 2.4 times higher than monomeric Gal. Among natural polyvalent glycotopes or clusters, high-density polyvalent T(alpha) and complex multivalent I(beta)/II(beta) glycotopes greatly enhanced the affinity for APA over 10(4) times. Based on these results, it is concluded that contribution of monomeric T(alpha), II(beta), I(beta), E(beta) and their clusters and polyvalency play critical roles in this recognition process. The binding intensities of these factors in decreasing order are: polyvalent T(alpha), II(beta)/I(beta) and E(beta)>tri-antennary II(beta)>monomeric T(alpha), T(beta), I and II>Gal>GalNAc (weak). As one of type 2 RIP lectins, these recognition factors of the B chain are likely to be crucial for attachment and endocytosis. A comparison of the differential recognition factors and combining sites of APA with those of other lectins (Ricinus communis agglutinin, RCA(1) and ricin) is also illustrated.

  13. Sediments, structural framework, petroleum potential, environmental conditions, and operational considerations of the United States North Atlantic Outer Continental Shelf

    Science.gov (United States)

    ,

    1975-01-01

    The area designated for possible oil and gas lease sale as modified from BLM memorandum 3310 #42 (722) and referred to therein as the North Atlantic Outer Continental Shelf (OCS) contains about 58,300 sq km of shelf beneath water depths of less than 200 m and lies chiefly within the Georges Bank basin. The oldest sediments drilled or dredged on the bordering Continental Slope are sandstone, clay, and silt of Upper Cretaceous age. In Upper Cretaceous exposures, on Marthas Vineyard and nearby New England islands, the predominant lithology appears to be clay. About 125 km northeast of the eastern tip of Georges Bank, the Shell B-93 well penetrated clays and silts of Upper and Lower Cretaceous age above dense Jurassic carbonate rocks which overlie a basement of lower Paleozoic slate, schist, quartzite, and granite. Structurally, the Georges Bank basin is a westerly trending trough which opens to the west-southwest. Post-Paleozoic sediments are more than 8 km thick in parts of the basin. Major structural features appear to be directly related to basement structures. Local anticlines, probably caused by differential compaction over basement flexures and horst blocks or by later uplift along basement faults are reflected principally in Lower Cretaceous and older sediments, though some of these features continue upward to within 0.7 of a second (about 650 m) of the seafloor. Tertiary deposits in the Georges Bank basin are probably up to a kilometre thick and are made up of poorly consolidated sand, silt, and clay. The Cretaceous section is inferred to be up to 3.5 km thick and to be mainly clastics -- shale, siltstone, calcareous shale, changing to limestone in the lowest part of the system. Jurassic rocks in the deepest part of the basin appear to be about 3.6 to 4.0 km thick and probably consist mainly of dense carbonates. Potential source rocks in the Georges Bank basin may include organic-rich Cretaceous shale and carbonaceous Jurassic limestone. By analogy with the

  14. Improving repeatability by improving quality

    Energy Technology Data Exchange (ETDEWEB)

    Ronen, Shuki; Ackers, Mark; Schlumberger, Geco-Prakla; Brink, Mundy

    1998-12-31

    Time lapse (4-D) seismic is a promising tool for reservoir characterization and monitoring. The method is apparently simple: to acquire data repeatedly over the same reservoir, process and interpret the data sets, then changes between the data sets indicate changes in the reservoir. A problem with time lapse seismic data is that reservoirs are a relatively small part of the earth and important reservoir changes may cause very small differences to the time lapse data. The challenge is to acquire and process economical time lapse data such that reservoir changes can be detected above the noise of varying acquisition and environment. 7 refs., 9 figs.

  15. Coordinated hybrid automatic repeat request

    KAUST Repository

    Makki, Behrooz

    2014-11-01

    We develop a coordinated hybrid automatic repeat request (HARQ) approach. With the proposed scheme, if a user message is correctly decoded in the first HARQ rounds, its spectrum is allocated to other users, to improve the network outage probability and the users\\' fairness. The results, which are obtained for single- and multiple-antenna setups, demonstrate the efficiency of the proposed approach in different conditions. For instance, with a maximum of M retransmissions and single transmit/receive antennas, the diversity gain of a user increases from M to (J+1)(M-1)+1 where J is the number of users helping that user.

  16. Analysis of tandem repeats in the genome of Chinese shrimp Fenneropenaeus chinensis

    Institute of Scientific and Technical Information of China (English)

    KONG Jie; GAO Huan

    2005-01-01

    Through random sequencing, we found a total of 884000 base-pairs (bp) of random genomic sequences in the genome of Chinese shrimp (Fenneropenaeus chinensis). Using bio-soft Tandem Repeat Finder (TRF) software, 2159 tandem repeats were found, in which there were 1714 microsatellites and 445 minisatellites, accounting for 79.4% and 20.6% of repeat sequences, respectively. The cumulative length of repeat sequences was found to be 116685 bp, accounting for 13.2% of the total DNA sequence; the cumulative length of microsatellites occupied 9.78% of the total DNA sequence, and that of minisatellites occupied 3.42%. In decreasing order, the 20 most abundant repeat sequence classes were as follows: AT (557), AC (471), AG (274), AAT (92), A (56), AAG (28), ATC (27), ATAG (27), AGG (18), ACT (15), C (11), AAC (11), ACAT (11), CAGA (10), AGAA (9), AGGG (7), CAAA (7), CGCA (6), ATAA (6), AGAGAA (6). Dinucleotide repeats, not only in the aspect of the number, but also in cumulative length, were the preponderant repeat type. There were few classes and low copy numbers of repeat units of the pentanucleotide repeat type, which included only three classes: AGAGA, GAGGC and AAAGA. The classes and copy numbers of heptanucleotide, eleven-nucleotide and thirteen-nucleotide primer-number-composed repeats were distinctly less than that of repeat types beside them.

  17. Crowding by a repeating pattern.

    Science.gov (United States)

    Rosen, Sarah; Pelli, Denis G

    2015-01-01

    Theinability to recognize a peripheral target among flankers is called crowding. For a foveal target, crowding can be distinguished from overlap masking by its sparing of detection, linear scaling with eccentricity, and invariance with target size.Crowding depends on the proximity and similarity of the flankers to the target. Flankers that are far from or dissimilar to the target do not crowd it. On a gray page, text whose neighboring letters have different colors, alternately black and white, has enough dissimilarity that it might escape crowding. Since reading speed is normally limited by crowding, escape from crowding should allow faster reading. Yet reading speed is unchanged (Chung & Mansfield, 2009). Why? A recent vernier study found that using alternating-color flankers produces strong crowding (Manassi, Sayim, & Herzog, 2012). Might that effect occur with letters and reading? Critical spacing is the minimum center-to-center target-flanker spacing needed to correctly identify the target. We measure it for a target letter surrounded by several equidistant flanker letters of the same polarity, opposite polarity, or mixed polarity: alternately white and black. We find strong crowding in the alternating condition, even though each flanker letter is beyond its own critical spacing (as measured in a separate condition). Thus a periodic repeating pattern can produce crowding even when the individual elements do not. Further, in all conditions we find that, once a periodic pattern repeats (two cycles), further repetition does not affect critical spacing of the innermost flanker.

  18. Simple sequence repeats in mycobacterial genomes

    Indian Academy of Sciences (India)

    Vattipally B Sreenu; Pankaj Kumar; Javaregowda Nagaraju; Hampapathalu A Nagarajaram

    2007-01-01

    Simple sequence repeats (SSRs) or microsatellites are the repetitive nucleotide sequences of motifs of length 1–6 bp. They are scattered throughout the genomes of all the known organisms ranging from viruses to eukaryotes. Microsatellites undergo mutations in the form of insertions and deletions (INDELS) of their repeat units with some bias towards insertions that lead to microsatellite tract expansion. Although prokaryotic genomes derive some plasticity due to microsatellite mutations they have in-built mechanisms to arrest undue expansions of microsatellites and one such mechanism is constituted by post-replicative DNA repair enzymes MutL, MutH and MutS. The mycobacterial genomes lack these enzymes and as a null hypothesis one could expect these genomes to harbour many long tracts. It is therefore interesting to analyse the mycobacterial genomes for distribution and abundance of microsatellites tracts and to look for potentially polymorphic microsatellites. Available mycobacterial genomes, Mycobacterium avium, M. leprae, M. bovis and the two strains of M. tuberculosis (CDC1551 and H37Rv) were analysed for frequencies and abundance of SSRs. Our analysis revealed that the SSRs are distributed throughout the mycobacterial genomes at an average of 220–230 SSR tracts per kb. All the mycobacterial genomes contain few regions that are conspicuously denser or poorer in microsatellites compared to their expected genome averages. The genomes distinctly show scarcity of long microsatellites despite the absence of a post-replicative DNA repair system. Such severe scarcity of long microsatellites could arise as a result of strong selection pressures operating against long and unstable sequences although influence of GC-content and role of point mutations in arresting microsatellite expansions can not be ruled out. Nonetheless, the long tracts occasionally found in coding as well as non-coding regions may account for limited genome plasticity in these genomes.

  19. Automatization and familiarity in repeated checking

    NARCIS (Netherlands)

    Dek, Eliane C P; van den Hout, Marcel A.; Giele, Catharina L.; Engelhard, Iris M.

    2014-01-01

    Repeated checking paradoxically increases memory uncertainty. This study investigated the underlying mechanism of this effect. We hypothesized that as a result of repeated checking, familiarity with stimuli increases, and automatization of the checking procedure occurs, which should result in decrea

  20. CDC Vital Signs: Preventing Repeat Teen Births

    Science.gov (United States)

    ... file Error processing SSI file Preventing Repeat Teen Births Recommend on Facebook Tweet Share Compartir On this ... Too many teens, ages 15–19, have repeat births. Nearly 1 in 5 births to teens, ages ...