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Sample records for adp-glucose pyrophosphorylase uncovered

  1. Multiple forms of ADP-glucose pyrophosphorylase from tomato fruit

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    Chen, B. Y.; Janes, H. W.

    1997-01-01

    ADP-glucose pyrophosphorylase (AGP) was purified from tomato (Lycopersicon esculentum Mill.) fruit to apparent homogeneity. By sodium dodecyl sulfate-polyacrylamide gel electrophoresis the enzyme migrated as two close bands with molecular weights of 50,000 and 51,000. Two-dimensional polyacrylamide gel electrophoresis analysis of the purified enzyme, however, revealed at least five major protein spots that could be distinguished by their slight differences in net charge and molecular weight. Whereas all of the spots were recognized by the antiserum raised against tomato fruit AGP holoenzyme, only three of them reacted strongly with antiserum raised against the potato tuber AGP large subunit, and the other two spots (with lower molecular weights) reacted specifically with antisera raised against spinach leaf AGP holoenzyme and the potato tuber AGP small subunit. The results suggest the existence of at least three isoforms of the AGP large subunit and two isoforms of the small subunit in tomato fruit in vivo. The native molecular mass of the enzyme determined by gel filtration was 220 +/- 10 kD, indicating a tetrameric structure for AGP from tomato fruit. The purified enzyme is very sensitive to 3-phosphoglycerate/inorganic phosphate regulation.

  2. Unraveling the activation mechanism of the potato tuber ADP-glucose pyrophosphorylase.

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    Carlos M Figueroa

    Full Text Available ADP-glucose pyrophosphorylase regulates the synthesis of glycogen in bacteria and of starch in plants. The enzyme from plants is mainly activated by 3-phosphoglycerate and is a heterotetramer comprising two small and two large subunits. Here, we found that two highly conserved residues are critical for triggering the activation of the potato tuber ADP-glucose pyrophosphorylase, as shown by site-directed mutagenesis. Mutations in the small subunit, which bears the catalytic function in this potato tuber form, had a more dramatic effect on disrupting the allosteric activation than those introduced in the large subunit, which is mainly modulatory. Our results strongly agree with a model where the modified residues are located in loops responsible for triggering the allosteric activation signal for this enzyme, and the sensitivity to this activation correlates with the dynamics of these loops. In addition, previous biochemical data indicates that the triggering mechanism is widespread in the enzyme family, even though the activator and the quaternary structure are not conserved.

  3. Cloning and characterization of ADP-glucose pyrophosphorylase small subunit gene in Cyperus esculentus (yellow nutsedge).

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    Cheng, C; Hu, J; Zhi, Y; Su, J J; Zhang, X K; Huang, B Q

    2015-01-01

    ADP-glucose pyrophosphorylase (ADPGlcPPase) controls the first committed step of starch synthesis by catalyzing the biosynthesis of ADP-glucose from glucose-phosphate and ATP. It is a tetrameric protein consisting of two small and two large subunits. The small subunits have a catalytic function, while the large subunits regulate the enzyme activity. Cyperus esculentus (yellow nutsedge) is a perennial C4 plant grown from rhizomes and tubers. Previous studies on yellow nutsedge have mostly focused on the morphology and cultivation of tubers, their application in food, and biochemical analyses of the tubers. In this study, the gene encoding the ADPGlcPPase small subunit (CeAGPS) in yellow nutsedge was cloned and characterized. The full-length CeAGPS cDNA sequence contained an 81-bp 5'-untranslated region (UTR), a 188-bp 3'-UTR, and a 1539-bp open reading frame encoding 512-amino acid residues. The genomic sequence of CeAGPS comprises a nine exon-eight intron structure similar to the previously reported cotton and Arabidopsis thaliana AGPS genes. The deduced translation product of the CeAGPS gene contained a well-conserved catalytic domain and regulatory elements typical of plant AGPS. Reverse transcriptase polymerase chain reaction amplification of the target gene in various plant parts using gene-specific primers indicated that the expression of CeAGPS was most abundant in the tuber, and relatively lower in nutsedge roots. PMID:26782478

  4. Regulatory properties of potato-Arabidopsis hybrid ADP-glucose pyrophosphorylase.

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    Ventriglia, Tiziana; Ballicora, Miguel A; Crevillén, Pedro; Preiss, Jack; Romero, José M

    2007-06-01

    In higher plants, ADP-glucose pyrophosphorylase (ADPGlc-PPase) is a heterotetrameric enzyme comprised of two small and two large subunits. Potato-Arabidopsis hybrid ADPGlc-PPases were generated and their regulatory properties analyzed. We show that ADPGlc-PPase subunits from two different species can interact, producing active enzymes with new regulatory properties. Depending on the subunit combinations, hybrid heterotetramers showed responses to allosteric effectors [3-phosphoglycerate (3-PGA) and Pi] in the micromolar or millimolar range. While hybrid potato small subunit (PSS) and the Arabidopsis large subunit APL1 showed an extremely sensitive response to 3-PGA and Pi, hybrid PSS/Arabidopsis APL2 was very insensitive to them. Intermediate responses were determined for other subunit combinations. PMID:17452341

  5. Substrate binding properties of potato tuber ADP-glucose pyrophosphorylase as determined by isothermal titration calorimetry.

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    Cakir, Bilal; Tuncel, Aytug; Green, Abigail R; Koper, Kaan; Hwang, Seon-Kap; Okita, Thomas W; Kang, ChulHee

    2015-06-01

    Substrate binding properties of the large (LS) and small (SS) subunits of potato tuber ADP-glucose pyrophosphorylase were investigated by using isothermal titration calorimetry. Our results clearly show that the wild type heterotetramer (S(WT)L(WT)) possesses two distinct types of ATP binding sites, whereas the homotetrameric LS and SS variant forms only exhibited properties of one of the two binding sites. The wild type enzyme also exhibited significantly increased affinity to this substrate compared to the homotetrameric enzyme forms. No stable binding was evident for the second substrate, glucose-1-phosphate, in the presence or absence of ATPγS suggesting that interaction of glucose-1-phosphate is dependent on hydrolysis of ATP and supports the Theorell-Chance bi bi reaction mechanism.

  6. Substrate binding properties of potato tuber ADP-glucose pyrophosphorylase as determined by isothermal titration calorimetry.

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    Cakir, Bilal; Tuncel, Aytug; Green, Abigail R; Koper, Kaan; Hwang, Seon-Kap; Okita, Thomas W; Kang, ChulHee

    2015-06-01

    Substrate binding properties of the large (LS) and small (SS) subunits of potato tuber ADP-glucose pyrophosphorylase were investigated by using isothermal titration calorimetry. Our results clearly show that the wild type heterotetramer (S(WT)L(WT)) possesses two distinct types of ATP binding sites, whereas the homotetrameric LS and SS variant forms only exhibited properties of one of the two binding sites. The wild type enzyme also exhibited significantly increased affinity to this substrate compared to the homotetrameric enzyme forms. No stable binding was evident for the second substrate, glucose-1-phosphate, in the presence or absence of ATPγS suggesting that interaction of glucose-1-phosphate is dependent on hydrolysis of ATP and supports the Theorell-Chance bi bi reaction mechanism. PMID:25953126

  7. Molecular characterization of multiple cDNA clones for ADP-glucose pyrophosphorylase from Arabidopsis thaliana.

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    Villand, P; Olsen, O A; Kleczkowski, L A

    1993-12-01

    PCR amplification of cDNA prepared from poly(A)+ RNA from aerial parts of Arabidopsis thaliana, using degenerate nucleotide primers based on conserved regions between the large and small subunits of ADP-glucose pyrophosphorylase (AGP), yielded four different cDNAs of ca. 550 nucleotides each. Based on derived amino acid sequences, the identities between the clones varied from 49 to 69%. Sequence comparison to previously published cDNAs for AGP from various species and tissues has revealed that three of the amplified cDNAs (ApL1, ApL2 and ApL3) correspond to the large subunit of AGP, and one cDNA (ApS) encodes the small subunit of AGP. Both ApL1 and ApS were subsequently found to be present in a cDNA library made from Arabidopsis leaves. All four PCR products are encoded by single genes, as found by genomic Southern analysis. PMID:8292792

  8. Two Arabidopsis ADP-glucose pyrophosphorylase large subunits (APL1 and APL2) are catalytic.

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    Ventriglia, Tiziana; Kuhn, Misty L; Ruiz, Ma Teresa; Ribeiro-Pedro, Marina; Valverde, Federico; Ballicora, Miguel A; Preiss, Jack; Romero, José M

    2008-09-01

    ADP-glucose (Glc) pyrophosphorylase (ADP-Glc PPase) catalyzes the first committed step in starch biosynthesis. Higher plant ADP-Glc PPase is a heterotetramer (alpha(2)beta(2)) consisting of two small and two large subunits. There is increasing evidence that suggests that catalytic and regulatory properties of the enzyme from higher plants result from the synergy of both types of subunits. In Arabidopsis (Arabidopsis thaliana), two genes encode small subunits (APS1 and APS2) and four large subunits (APL1-APL4). Here, we show that in Arabidopsis, APL1 and APL2, besides their regulatory role, have catalytic activity. Heterotetramers formed by combinations of a noncatalytic APS1 and the four large subunits showed that APL1 and APL2 exhibited ADP-Glc PPase activity with distinctive sensitivities to the allosteric activator (3-phosphoglycerate). Mutation of the Glc-1-P binding site of Arabidopsis and potato (Solanum tuberosum) isoforms confirmed these observations. To determine the relevance of these activities in planta, a T-DNA mutant of APS1 (aps1) was characterized. aps1 is starchless, lacks ADP-Glc PPase activity, APS1 mRNA, and APS1 protein, and is late flowering in long days. Transgenic lines of the aps1 mutant, expressing an inactivated form of APS1, recovered the wild-type phenotype, indicating that APL1 and APL2 have catalytic activity and may contribute to ADP-Glc synthesis in planta. PMID:18614708

  9. Two Arabidopsis ADP-Glucose Pyrophosphorylase Large Subunits (APL1 and APL2) Are Catalytic1

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    Ventriglia, Tiziana; Kuhn, Misty L.; Ruiz, Ma Teresa; Ribeiro-Pedro, Marina; Valverde, Federico; Ballicora, Miguel A.; Preiss, Jack; Romero, José M.

    2008-01-01

    ADP-glucose (Glc) pyrophosphorylase (ADP-Glc PPase) catalyzes the first committed step in starch biosynthesis. Higher plant ADP-Glc PPase is a heterotetramer (α2β2) consisting of two small and two large subunits. There is increasing evidence that suggests that catalytic and regulatory properties of the enzyme from higher plants result from the synergy of both types of subunits. In Arabidopsis (Arabidopsis thaliana), two genes encode small subunits (APS1 and APS2) and four large subunits (APL1–APL4). Here, we show that in Arabidopsis, APL1 and APL2, besides their regulatory role, have catalytic activity. Heterotetramers formed by combinations of a noncatalytic APS1 and the four large subunits showed that APL1 and APL2 exhibited ADP-Glc PPase activity with distinctive sensitivities to the allosteric activator (3-phosphoglycerate). Mutation of the Glc-1-P binding site of Arabidopsis and potato (Solanum tuberosum) isoforms confirmed these observations. To determine the relevance of these activities in planta, a T-DNA mutant of APS1 (aps1) was characterized. aps1 is starchless, lacks ADP-Glc PPase activity, APS1 mRNA, and APS1 protein, and is late flowering in long days. Transgenic lines of the aps1 mutant, expressing an inactivated form of APS1, recovered the wild-type phenotype, indicating that APL1 and APL2 have catalytic activity and may contribute to ADP-Glc synthesis in planta. PMID:18614708

  10. Investigation of the interaction between the large and small subunits of potato ADP-glucose pyrophosphorylase.

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    Ibrahim Baris

    2009-10-01

    Full Text Available ADP-glucose pyrophosphorylase (AGPase, a key allosteric enzyme involved in higher plant starch biosynthesis, is composed of pairs of large (LS and small subunits (SS. Current evidence indicates that the two subunit types play distinct roles in enzyme function. Recently the heterotetrameric structure of potato AGPase has been modeled. In the current study, we have applied the molecular mechanics generalized born surface area (MM-GBSA method and identified critical amino acids of the potato AGPase LS and SS subunits that interact with each other during the native heterotetrameric structure formation. We have further shown the role of the LS amino acids in subunit-subunit interaction by yeast two-hybrid, bacterial complementation assay and native gel. Comparison of the computational results with the experiments has indicated that the backbone energy contribution (rather than the side chain energies of the interface residues is more important in identifying critical residues. We have found that lateral interaction of the LS-SS is much stronger than the longitudinal one, and it is mainly mediated by hydrophobic interactions. This study will not only enhance our understanding of the interaction between the SS and the LS of AGPase, but will also enable us to engineer proteins to obtain better assembled variants of AGPase which can be used for the improvement of plant yield.

  11. Sucrose regulation of ADP-glucose pyrophosphorylase subunit genes transcript levels in leaves and fruits

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    Li, Xiangyang; Xing, Jinpeng; Gianfagna, Thomas J.; Janes, Harry W.

    2002-01-01

    ADP-glucose pyrophosphorylase (AGPase, EC2.7.7.27) is a key regulatory enzyme in starch biosynthesis. The enzyme is a heterotetramer with two S and two B subunits. In tomato, there are three multiple forms of the S subunit gene. Agp S1, S2 and B are highly expressed in fruit from 10 to 25 days after anthesis. Agp S3 is only weakly expressed in fruit. Sucrose significantly elevates expression of Agp S1, S2 and B in both leaves and fruits. Agp S1 exhibits the highest degree of regulation by sucrose. In fact, sucrose may be required for Agp S1 expression. For excised leaves incubated in water, no transcripts for Agp S1 could be detected in the absence of sucrose, whereas it took up to 16 h in water before transcripts were no longer detectable for Agp S2 and B. Neither Agp S3 nor the tubulin gene is affected by sucrose, demonstrating that this response is specifically regulated by a carbohydrate metabolic signal, and is not due to a general increase in metabolism caused by sucrose treatment. Truncated versions of the promoter for Agp S1 indicate that a specific region 1.3-3.0 kb upstream from the transcription site is responsible for sucrose sensitivity. This region of the S1 promoter contains several cis-acting elements present in the promoters of other genes that are also regulated by sucrose. c2002 Elsevier Science Ireland Ltd. All rights reserved.

  12. The different large subunit isoforms of Arabidopsis thaliana ADP-glucose pyrophosphorylase confer distinct kinetic and regulatory properties to the heterotetrameric enzyme.

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    Crevillén, Pedro; Ballicora, Miguel A; Mérida, Angel; Preiss, Jack; Romero, José M

    2003-08-01

    ADP-glucose pyrophosphorylase catalyzes the first and limiting step in starch biosynthesis and is allosterically regulated by the levels of 3-phosphoglycerate and phosphate in plants. ADP-glucose pyrophosphorylases from plants are heterotetramers composed of two types of subunits (small and large). In this study, the six Arabidopsis thaliana genes coding for ADP-glucose pyrophosphorylase isoforms (two small and four large subunits) have been cloned and expressed in an Escherichia coli mutant deficient in ADP-glucose pyrophosphorylase activity. The co-expression of the small subunit APS1 with the different Arabidopsis large subunits (APL1, APL2, APL3, and APL4) resulted in heterotetramers with different regulatory and kinetic properties. Heterotetramers composed of APS1 and APL1 showed the highest sensitivity to the allosteric effectors as well as the highest apparent affinity for the substrates (glucose-1-phosphate and ATP), whereas heterotetramers formed by APS1 and APL2 showed the lower response to allosteric effectors and the lower affinity for the substrates. No activity was detected for the second gene coding for a small subunit isoform (APS2) annotated in the Arabidopsis genome. This lack of activity is possibly due to the absence of essential amino acids involved in catalysis and/or in the binding of glucose-1-phosphate and 3-phosphoglycerate. Kinetic and regulatory properties of the different heterotetramers, together with sequence analysis has allowed us to make a distinction between sink and source enzymes, because the combination of different large subunits would provide a high plasticity to ADP-glucose pyrophosphorylase activity and regulation. This is the first experimental data concerning the role that all the ADP-glucose pyrophosphorylase isoforms play in a single plant species. This phenomenon could have an important role in vivo, because different large subunits would confer distinct regulatory properties to ADP-glucose pyrophosphorylase according

  13. The ancestral activation promiscuity of ADP-glucose pyrophosphorylases from oxygenic photosynthetic organisms

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    Kuhn Misty L

    2013-02-01

    Full Text Available Abstract Background ADP-glucose pyrophosphorylase (ADP-Glc PPase catalyzes the first committed step in the synthesis of glycogen in bacteria and starch in algae and plants. In oxygenic photosynthetic organisms, ADP-Glc PPase is mainly activated by 3-phosphoglycerate (3-PGA and to a lesser extent by other metabolites. In this work, we analyzed the activation promiscuity of ADP-Glc PPase subunits from the cyanobacterium Anabaena PCC 7120, the green alga Ostreococcus tauri, and potato (Solanum tuberosum tuber by comparing a specificity constant for 3-PGA, fructose-1,6-bisphosphate (FBP, fructose-6-phosphate, and glucose-6-phosphate. Results The 3-PGA specificity constant for the enzymes from Anabaena (homotetramer, O. tauri, and potato tuber was considerably higher than for other activators. O. tauri and potato tuber enzymes were heterotetramers comprising homologous small and large subunits. Conversely, the O. tauri small subunit (OtaS homotetramer was more promiscuous because its FBP specificity constant was similar to that for 3-PGA. To explore the role of both OtaS and OtaL (O. tauri large subunit in determining the specificity of the heterotetramer, we knocked out the catalytic activity of each subunit individually by site-directed mutagenesis. Interestingly, the mutants OtaSD148A/OtaL and OtaS/OtaLD171A had higher specificity constants for 3-PGA than for FBP. Conclusions After gene duplication, OtaS seemed to have lost specificity for 3-PGA compared to FBP. This was physiologically and evolutionarily feasible because co-expression of both subunits restored the specificity for 3-PGA of the resulting heterotetrameric wild type enzyme. This widespread promiscuity seems to be ancestral and intrinsic to the enzyme family. Its presence could constitute an efficient evolutionary mechanism to accommodate the ADP-Glc PPase regulation to different metabolic needs.

  14. ADP-glucose pyrophosphorylase gene plays a key role in the quality of corm and yield of cormels in gladiolus.

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    Seng, Shanshan; Wu, Jian; Sui, Juanjuan; Wu, Chenyu; Zhong, Xionghui; Liu, Chen; Liu, Chao; Gong, Benhe; Zhang, Fengqin; He, Junna; Yi, Mingfang

    2016-05-20

    Starch is the main storage compound in underground organs like corms. ADP-glucose pyrophosphorylase (AGPase) plays a key role in regulating starch biosynthesis in storage organs and is likely one of the most important determinant of sink strength. Here, we identify an AGPase gene (GhAGPS1) from gladiolus. The highest transcriptional levels of GhAGPS1 were observed in cormels and corms. Transformation of GhAGPS1 into Arabidopsis rescued the phenotype of aps1 mutant. Silencing GhAGPS1 in gladiolus corms by virus-induced gene silencing (VIGS) decreased the transcriptional levels of two genes and starch content. Transmission electron microscopy analyses of leaf and corm sections confirmed that starch biosynthesis was inhibited. Corm weight and cormel number reduced significantly in the silenced plants. Taken together, these results indicate that inhibiting the expression of AGPase gene could impair starch synthesis, which results in the lowered corm quality and cormel yield in gladiolus. PMID:27107698

  15. Molecular cloning and characterization of ADP-glucose pyrophosphorylase cDNA clones isolated from pea cotyledons.

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    Burgess, D; Penton, A; Dunsmuir, P; Dooner, H

    1997-02-01

    Three ADP-glucose pyrophosphorylase (ADPG-PPase) cDNA clones have been isolated and characterized from a pea cotyledon cDNA library. Two of these clones (Psagps1 and Psagps2) encode the small subunit of ADPG-PPase. The deduced amino acid sequences for these two clones are 95% identical. Expression of these two genes differs in that the Psagps2 gene shows comparatively higher expression in seeds relative to its expression in other tissues. Psagps2 expression also peaks midway through seed development at a time in which Psagps1 transcripts are still accumulating. The third cDNA isolated (Psagp11) encodes the large subunit of ADPG-PPase. It shows greater selectivity in expression than either of the small subunit clones. It is highly expressed in sink organs (seed, pod, and seed coat) and undetectable in leaves.

  16. ADP-glucose pyrophosphorylase is localized to both the cytoplasm and plastids in developing pericarp of tomato fruit

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    Chen, B. Y.; Wang, Y.; Janes, H. W.

    1998-01-01

    The intracellular location of ADP-glucose pyrophosphorylase (AGP) in developing pericarp of tomato (Lycopersicon esculentum Mill) has been investigated by immunolocalization. With the use of a highly specific anti-tomato fruit AGP antibody, the enzyme was localized in cytoplasm as well as plastids at both the light and electron microscope levels. The immunogold particles in plastids were localized in the stroma and at the surface of the starch granule, whereas those in the cytoplasm occurred in cluster-like patterns. Contrary to the fruit, the labeling in tomato leaf cells occurred exclusively in the chloroplasts. These data demonstrate that AGP is localized to both the cytoplasm and plastids in developing pericarp cells of tomato.

  17. [Enhancement of photoassimilate utilization by manipulation of ADP-glucose pyrophosphorylase gene]. Final progress report

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    Okita, T.W.

    1999-04-01

    Part 1 of this research focuses on patterns of gene expression of ADPG-pyrophosphorylase in native and transgenic potato plants. To elucidate the mechanism controlling AGP expression during plant development, the expression of the potato tuber AGP small subunit (sAGP) gene was analyzed in transgenic potato plants using a promoter-{beta}-glucuronidase expression system. Part II evaluated the structure-function relationships of AGP.

  18. Enhanced activity of ADP glucose pyrophosphorylase and formation of starch induced by Azospirillum brasilense in Chlorella vulgaris.

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    Choix, Francisco J; Bashan, Yoav; Mendoza, Alberto; de-Bashan, Luz E

    2014-05-10

    ADP-glucose pyrophosphorylase (AGPase) regulates starch biosynthesis in higher plants and microalgae. This study measured the effect of the bacterium Azospirillum brasilense on AGPase activity in the freshwater microalga Chlorella vulgaris and formation of starch. This was done by immobilizing both microorganisms in alginate beads, either replete with or deprived of nitrogen or phosphorus and all under heterotrophic conditions, using d-glucose or Na-acetate as the carbon source. AGPase activity during the first 72h of incubation was higher in C. vulgaris when immobilized with A. brasilense. This happened simultaneously with higher starch accumulation and higher carbon uptake by the microalgae. Either carbon source had similar effects on enzyme activity and starch accumulation. Starvation either by N or P had the same pattern on AGPase activity and starch accumulation. Under replete conditions, the population of C. vulgaris immobilized alone was higher than when immobilized together, but under starvation conditions A. brasilense induced a larger population of C. vulgaris. In summary, adding A. brasilense enhanced AGPase activity, starch formation, and mitigation of stress in C. vulgaris.

  19. Analysis of ADP-glucose pyrophosphorylase expression during turion formation induced by abscisic acid in Spirodela polyrhiza (greater duckweed

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    Wang Wenqin

    2012-01-01

    Full Text Available Abstract Background Aquatic plants differ in their development from terrestrial plants in their morphology and physiology, but little is known about the molecular basis of the major phases of their life cycle. Interestingly, in place of seeds of terrestrial plants their dormant phase is represented by turions, which circumvents sexual reproduction. However, like seeds turions provide energy storage for starting the next growing season. Results To begin a characterization of the transition from the growth to the dormant phase we used abscisic acid (ABA, a plant hormone, to induce controlled turion formation in Spirodela polyrhiza and investigated their differentiation from fronds, representing their growth phase, into turions with respect to morphological, ultra-structural characteristics, and starch content. Turions were rich in anthocyanin pigmentation and had a density that submerged them to the bottom of liquid medium. Transmission electron microscopy (TEM of turions showed in comparison to fronds shrunken vacuoles, smaller intercellular space, and abundant starch granules surrounded by thylakoid membranes. Turions accumulated more than 60% starch in dry mass after two weeks of ABA treatment. To further understand the mechanism of the developmental switch from fronds to turions, we cloned and sequenced the genes of three large-subunit ADP-glucose pyrophosphorylases (APLs. All three putative protein and exon sequences were conserved, but the corresponding genomic sequences were extremely variable mainly due to the invasion of miniature inverted-repeat transposable elements (MITEs into introns. A molecular three-dimensional model of the SpAPLs was consistent with their regulatory mechanism in the interaction with the substrate (ATP and allosteric activator (3-PGA to permit conformational changes of its structure. Gene expression analysis revealed that each gene was associated with distinct temporal expression during turion formation. APL2 and

  20. Sugars and light/dark exposure trigger differential regulation of ADP-glucose pyrophosphorylase genes in Arabidopsis thaliana (thale cress).

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    Sokolov, L N; Déjardin, A; Kleczkowski, L A

    1998-12-15

    Expression of four Arabidopsis (thale cress) genes corresponding to the small (ApS) and large subunits (ApL1, ApL2, ApL3) of ADP-glucose pyrophosphorylase (AGPase), a key enzyme of starch biosynthesis, was found to be profoundly and differentially regulated by sugar and light/dark exposures. Transcript levels of both ApL2 and ApL3, and to a lesser extent ApS, increased severalfold upon feeding sucrose or glucose to the detached leaves in the dark, whereas the mRNA content for ApL1 decreased under the same conditions. Glucose was, in general, less effective than sucrose in inducing regulation of AGPase genes, possibly due to observed limitations in its uptake when compared with sucrose uptake by detached leaves. Osmotic agents [sorbitol, poly(ethylene glycol)] had no effect on ApS, ApL2 and ApL3 transcript level, but they did mimic the effect of sucrose on ApL1 gene, suggesting that the latter is regulated by osmotic pressure rather than any particular sugar. For all the genes the sugar effect was closely mimicked by an exposure of the dark-pre-adapted leaves to the light. Under both dark and light conditions, sucrose fed to the detached leaves was found to be rapidly metabolized to hexoses and, to some extent, starch. Starch production reflected most probably an increase in substrate availability for AGPase reaction rather than being due to changes in AGPase protein content, since both the sugar feeding and light exposure had little or no effect on the activity of AGPase or on the levels of its small and large subunit proteins in leaf extracts. The data suggest tight translational or post-translational control, but they may also reflect spatial control of AGPase gene expression within a leaf. The sugar/light-dependent regulation of AGPase gene expression may represent a part of a general cellular response to the availability/allocation of carbohydrates during photosynthesis. PMID:9841881

  1. Inactivation of thioredoxin f1 leads to decreased light activation of ADP-glucose pyrophosphorylase and altered diurnal starch turnover in leaves of Arabidopsis plants.

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    Thormählen, Ina; Ruber, Joachim; von Roepenack-Lahaye, Edda; Ehrlich, Sven-Matthias; Massot, Vincent; Hümmer, Christine; Tezycka, Justyna; Issakidis-Bourguet, Emmanuelle; Geigenberger, Peter

    2013-01-01

    Chloroplast thioredoxin f (Trx f) is an important regulator of primary metabolic enzymes. However, genetic evidence for its physiological importance is largely lacking. To test the functional significance of Trx f in vivo, Arabidopsis mutants with insertions in the trx f1 gene were studied, showing a drastic decrease in Trx f leaf content. Knockout of Trx f1 led to strong attenuation in reductive light activation of ADP-glucose pyrophosphorylase (AGPase), the key enzyme of starch synthesis, in leaves during the day and in isolated chloroplasts, while sucrose-dependent redox activation of AGPase in darkened leaves was not affected. The decrease in light-activation of AGPase in leaves was accompanied by a decrease in starch accumulation, an increase in sucrose levels and a decrease in starch-to-sucrose ratio. Analysis of metabolite levels at the end of day shows that inhibition of starch synthesis was unlikely due to shortage of substrates or changes in allosteric effectors. Metabolite profiling by gas chromatography-mass spectrometry pinpoints only a small number of metabolites affected, including sugars, organic acids and ethanolamine. Interestingly, metabolite data indicate carbon shortage in trx f1 mutant leaves at the end of night. Overall, results provide in planta evidence for the role played by Trx f in the light activation of AGPase and photosynthetic carbon partitioning in plants.

  2. Regulatory properties of ADP glucose pyrophosphorylase are required for adjustment of leaf starch synthesis in different photoperiods.

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    Mugford, Sam T; Fernandez, Olivier; Brinton, Jemima; Flis, Anna; Krohn, Nicole; Encke, Beatrice; Feil, Regina; Sulpice, Ronan; Lunn, John E; Stitt, Mark; Smith, Alison M

    2014-12-01

    Arabidopsis (Arabidopsis thaliana) leaves synthesize starch faster in short days than in long days, but the mechanism that adjusts the rate of starch synthesis to daylength is unknown. To understand this mechanism, we first investigated whether adjustment occurs in mutants lacking components of the circadian clock or clock output pathways. Most mutants adjusted starch synthesis to daylength, but adjustment was compromised in plants lacking the GIGANTEA or FLAVIN-BINDING, KELCH REPEAT, F BOX1 components of the photoperiod-signaling pathway involved in flowering. We then examined whether the properties of the starch synthesis enzyme adenosine 5'-diphosphate-glucose pyrophosphorylase (AGPase) are important for adjustment of starch synthesis to daylength. Modulation of AGPase activity is known to bring about short-term adjustments of photosynthate partitioning between starch and sucrose (Suc) synthesis. We found that adjustment of starch synthesis to daylength was compromised in plants expressing a deregulated bacterial AGPase in place of the endogenous AGPase and in plants containing mutant forms of the endogenous AGPase with altered allosteric regulatory properties. We suggest that the rate of starch synthesis is in part determined by growth rate at the end of the preceding night. If growth at night is low, as in short days, there is a delay before growth recovers during the next day, leading to accumulation of Suc and stimulation of starch synthesis via activation of AGPase. If growth at night is fast, photosynthate is used for growth at the start of the day, Suc does not accumulate, and starch synthesis is not up-regulated.

  3. Structure Function Relationships of ADP-Glucose Pyrophosphorylase and Branching Enzyme: Manipulation of Their Genes for Alteration of Starch Quanlity and Quantity

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    Jack Preiss

    2006-02-16

    Conversion of the Potato tuber ADP-glucose Pyrophopshorylase Regulatory Subunit into a Catalytic Subunit. ADP-glucose synthesis, a rate-limiting reaction in starch synthesis, is catalyzed by ADP-glucose pyrophosphorylase (ADPGlc PPase). The enzyme in plants is allosterically activated by 3-phosphoglycerate (3PGA) and inhibited by inorganic phosphate (Pi) and is composed of two subunits as a heterotetramer, a2b2. Subunit a is the catalytic subunit and subunit b is designated as the regulatory subunit.The b subunit increases the affinty of the activator for the catalytic subunit. Recent results have shown that the subunits are derived from the same ancestor subunit as the regulatory subunit can be converted to a catalytically subunit via mutation of just two amino acids. Lys44 and Thr54 in the large subunit from potato tuber were converted to the homologous catalytic subunit residues, Arg33 and Lys43. The activity of the large subunit mutants cannot be readily tested with a co-expressed wild-type small (catalytic) subunit because of the intrinsic activity of the latter. We co-expressed the regulatory-subunit mutants with SmallD145N, an inactive S subunit in which the catalytic Asp145 was mutated. The activity of the small (catalytic) subunit was reduced more than three orders of magnitude. Coexpression of the L subunit double mutant LargeK44R/T54K with SmallD145N generated an enzyme with considerable activity, 10% and 18% of the wildtype enzyme, in the ADP-glucose synthetic and pyrophosphorolytic direction, respectively. Replacement of those two residues in the small subunit by the homologous amino acids in the L subunits (mutations R33K and K43T) decreased the activity one and two orders of magnitude. The wild-type enzyme and SmallD145NLargeK44R/T54K had very similar kinetic properties indicating that the substrate site has been conserved. The fact that only two mutations in the L subunit restored enzyme activity is very strong evidence that the large subunit is

  4. Analysis of Gene Expression of Seven Isoforms of ADP-glucose Pyrophosphorylase in Rice Endosperm under Different Temperature Conditions%不同温度下水稻胚乳AGPase各同工酶基因表达特征分析(英文)

    Institute of Scientific and Technical Information of China (English)

    袁定阳; 孙志忠; 谭炎宁; 段美娟

    2012-01-01

    [目的]分析不同温度对水稻胚乳中AGPase各同工酶基因表达水平的影响。[方法]以特青和泰国香米为材料,利用人工气候箱设置高温(日平均温度33℃)和适温(日平均温度25℃)2个温度处理,结合实时荧光定量PCR技术分析比较了水稻淀粉合成关键酶腺嘌呤-葡萄糖焦磷酸化酶(AGPase)7个同工酶基因AGPS1、AGPS2a、AGPS2b、AGPL1、AGPL2、AGPL3及AGPL4的表达特征。[结果]AGPase 3个同工酶基因AGPS2b、AGPL2和AGPL3表达较强,其中AGPL2相对表达量最高;AGPS2b、AGPL2和AGPL3在2个品种中的相对表达量在适温条件下的均高于高温处理,在特青胚乳中各时期2种温度处理下的相对表达量总体高于泰国香米中的相对表达量。[结论]本研究为进一步利用分子生物学技术培育稳定的优质水稻品种提供理论基础。%[Objective] This study aimed to analyze the effects of temperature on the expression of AGPase isoform genes in rice endosperm during milk stage. [Method] Different temperature treatments (33 and 25 ℃ of daily mean temperature for high and normal temperature treatments, respectively) and the real-time fluorescence quantitative PCR ( FQPCR) were used to analyze the expression patterns of seven isoforms (AGPS1, AGPS2a, AGPS2b, AGPL1, AGPL2, AGPL3 and AGPL4) of ADPglucose pyrophosphorylase (AGPase) which was the key enzyme in starch synthesis and metabolism in rice endosperm of two rice varieties Teqing and Thai Fragrant Rice. [Result] The AGPase isoforms AGPS2b, AGPL2 and AGPL3 had much higher expression than the other four isoforms, thus they were thought to be the main expression patterns of AGPase in rice endosperm. The relative expressions of AGPL2 was the highest among all the isoforms. The relative expressions of AGPS2b, AGPL2 and AGPL3 were higher in the normal temperature treatment than in the high temperature treatment in both rice varieties. The relative expression of the

  5. Trehalose 6-phosphate regulates starch synthesis via posttranslational redox activation of ADP-glucose pyrophosphorylase

    OpenAIRE

    Kolbe, A.; Tiessen, A.; Schluepmann, H.; Paul, M; Ulrich, S; P. Geigenberger

    2005-01-01

    Trehalose is the most widespread disaccharide in nature, occurring in bacteria, fungi, insects, and plants. Its precursor, trehalose 6-phosphate (T6P), is also indispensable for the regulation of sugar utilization and growth, but the sites of action are largely unresolved. Here we use genetic and biochemical approaches to investigate whether T6P acts to regulate starch synthesis in plastids of higher plants. Feeding of trehalose to Arabidopsis leaves led to stimulation of starch synthesis wit...

  6. Identification and characterization of UDP-glucose pyrophosphorylase in cyanobacteria Anabaena sp. PCC 7120.

    Science.gov (United States)

    Kawano, Yusuke; Sekine, Midori; Ihara, Masaki

    2014-05-01

    Exopolysaccharides produced by photosynthetic cyanobacteria have received considerable attention in recent years for their potential applications in the production of renewable biofuels. Particularly, cyanobacterial cellulose is one of the most promising products because it is extracellularly secreted as a non-crystalline form, which can be easily harvested from the media and converted into glucose units. In cyanobacteria, the production of UDP-glucose, the cellulose precursor, is a key step in the cellulose synthesis pathway. UDP-glucose is synthesized from UTP and glucose-1-phosphate (Glc-1P) by UDP-glucose pyrophosphorylase (UGPase), but this pathway in cyanobacteria has not been well characterized. Therefore, to elucidate the overall cellulose biosynthesis pathway in cyanobacteria, we studied the putative UGPase All3274 and seven other putative NDP-sugar pyrophosphorylases (NSPases), All4645, Alr2825, Alr4491, Alr0188, Alr3400, Alr2361, and Alr3921 of Anabaena sp. PCC 7120. Assays using the purified recombinant proteins revealed that All3274 exhibited UGPase activity, All4645, Alr2825, Alr4491, Alr0188, and Alr3921 exhibited pyrophosphorylase activities on ADP-glucose, CDP-glucose, dTDP-glucose, GDP-mannose, and UDP-N-acetylglucosamine, respectively. Further characterization of All3274 revealed that the kcat for UDP-glucose formation was one or two orders lower than those of other known UGPases. The activity and dimerization tendency of All3274 increased at higher enzyme concentrations, implying catalytic activation by dimerization. However, most interestingly, All3274 dimerization was inhibited by UTP and Glc-1P, but not by UDP-glucose. This study presents the first in vitro characterization of a cyanobacterial UGPase, and provides insights into biotechnological attempts to utilize the photosynthetic production of cellulose from cyanobacteria.

  7. 玉米淀粉合成焦磷酸化酶研究进展%Study Progress of Maize ADP- Glc pyrophosphorylase

    Institute of Scientific and Technical Information of China (English)

    陈江; 刘汉梅; 黄玉碧

    2012-01-01

    Maize starch is the main source of starch for humans, animals eating and the industrial use. The synthesis of which is orchestrated by four major enzymes, ADP -glucose pyrophosphorylase (AGPase) , starch synthase (SS) , starch - branching enzyme (SBE) and de - branchingenzyme (DBE). ADP - glucose pyrophosphorylase (AGPase) , catalyzing the rate - limiting step in starch biosynthesis in plants, play an important role in the synthesis process of starch. Through deeply studying to AGPase, we can reveal the mechanism of starch biosynthesis, by which we can control the starch synthesis by ourselves. This article aimed at a summary for maize AGPase's physicochemical property, regulation of enzyme activity, expression rules and the application of the breeding. Also this paper put forward opinions on the problems and predicted the future research of AGPase.%玉米是重要的食用、饲用和工业原料,淀粉是玉米种子的主要组成部分,其生物合成和积累主要由ADPG焦磷酸化酶(ADP - Glc pyrophosphorylase,AGPase)、淀粉合成酶(starch synthase,ss)、淀粉分支酶(starch branching enzyme,SBE)及去分支酶(de - branching enzyme,DBE)等一系列的酶催化形成.ADPG焦磷酸化酶作为淀粉合成代谢途径中关键限速酶,在玉米淀粉合成过程起到重要作用.通过对其深入研究,在揭示玉米淀粉生物合成的分子机理,实现玉米淀粉合成的人工调控等方面有重要意义.就玉米AGPase的理化性质,调控特性,表达规律及在育种中的应用进行综述,对研究中存在问题及未来AGPase的研究方向提出见解.

  8. Decreased expression of plastidial adenylate kinase in potato tubers results in an enhanced rate of respiration and a stimulation of starch synthesis that is attributable to post-translational redox-activation of ADP-glucose pyrophosphorylase

    OpenAIRE

    Oliver, S; Tiessen, A.; Fernie, A.; P. Geigenberger

    2008-01-01

    Adenine nucleotides are of general importance for many aspects of cell function, but their role in the regulation of biosynthetic processes is still unclear. It was previously reported that decreased expression of plastidial adenylate kinase, catalysing the interconversion of ATP and AMP to ADP, leads to increased adenylate pools and starch content in transgenic potato tubers. However, the underlying mechanisms were not elucidated. Here, it is shown that decreased expression of plastidial ade...

  9. A luminescence-based assay of UDP-sugar producing pyrophosphorylases

    OpenAIRE

    Decker, Daniel; Lindberg, Stina; Eriksson, Jonas; Kleczkowski, Leszek A.

    2014-01-01

    A coupled luminescence assay was applied to monitor pyrophosphate (PPi) production by either purified barley UDP-glucose pyrophosphorylase (UGPase) or purified Leishmania UDP-sugar pyrophosphorylase (USPase). In the assay, the PPi produced by the pyrophosphorylases was converted to ATP by ATP-sulfurylase, and the ATP produced was linked to luminescent light formation through the action of firefly luciferase. The assay allowed for a quantitative measurement of UGPase and USPase activities, dow...

  10. Biosynthesis of starch in chloroplasts.

    Science.gov (United States)

    Nomura, T; Nakayama, N; Murata, T; Akazawa, T

    1967-03-01

    The enzymic synthesis of ADP-glucose and UDP-glucose by chloroplastic pyrophosphorylase of bean and rice leaves has been demonstrated by paper chromatographic techniques. In both tissues, the activity of UDP-glucose-pyrophosphorylase was much higher than ADP-glucose-pyrophosphorylase. Glycerate-3-phosphate, phosphoenolpyruvate and fructose-1,6-diphosphate did not stimulate ADP-glucose formation by a pyrophosphorylation reaction. The major metabolic pathway for UDP-glucose utilization appears to be the synthesis of either sucrose or sucrose-P. On the other hand, a specific precursor role of ADP-glucose for synthesizing chloroplast starch by the ADP-glucose-starch transglucosylase reaction is supported by the coupled enzyme system of ADP-glucose-pyrophosphorylase and transglucosylase, isolated from chloroplasts. None of the glycolytic intermediates stimulated the glucose transfer in the enzyme sequence of reaction system employed. PMID:4292567

  11. Crystallization and preliminary X-ray characterization of the Vitis vinifera fucokinase:GDP-fucose pyrophosphorylase

    OpenAIRE

    Quirk, Stephen

    2012-01-01

    The Vitis vinifera dual-activity fucose and nucleotide-sugar metabolizing enzyme l-fucokinase:GDP-fucose pyrophosphorylase (FKP) has been purified to homogeneity and the 118.8 kDa monomeric protein has been crystallized by vapor diffusion in Zeppezauer tubes at 277 K.

  12. Starch-related Enzymes during Potato Tuber Dormancy and Sprouting

    NARCIS (Netherlands)

    Sergeeva, L.I.; Claassens, M.M.J.; Jamar, D.C.L.; Plas, van der L.H.W.; Vreugdenhil, D.

    2012-01-01

    Activities of enzymes presumably involved in starch biosynthesis (ADP-glucose pyrophosphorylase, AGPase) and/or breakdown (starch phosphorylase, STP; amylases) were determined during potato (Solanum tuberosum L.) tuber dormancy and sprouting. Overall activities of all these enzymes decreased during

  13. GenBank blastx search result: AK287557 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK287557 J065021C17 DQ021458.1 DQ021458 Nicotiana langsdorffii x Nicotiana sanderae clone agps...-1 ADP glucose pyrophosphorylase small subunit (AGPS-1) mRNA, partial cds. PLN 1e-84 0 ...

  14. UDP-sugar pyrophosphorylase controls the activity of proceeding sugar-1-kinases enzymes

    OpenAIRE

    Geserick, Claudia; Tenhaken, Raimund

    2013-01-01

    Plant cell wall synthesis requires a number of different nucleotide sugars which provide the building blocks of the different polymers. These nucleotide sugars are mainly provided by de novo synthesis but recycling pathways also contribute to the pools. The last enzyme of the recycling pathway is UDP-sugar pyrophosphorylase (USP), a single copy gene in Arabidopsis, of which a knockout is lethal for pollen development. Here we analyze the dependency between USP enzyme activity and the upstream...

  15. Identification of a GDP-mannose pyrophosphorylase gene from Sulfolobus solfataricus.

    Science.gov (United States)

    Sacchetti, Silvana; Bartolucci, Simonetta; Rossi, Mosè; Cannio, Raffaele

    2004-05-12

    An open reading frame (ORF) encoding a putative GDP-mannose pyrophosphorylase (SsoGMPP) was identified on the genome sequence of Sulfolobus solfataricus P2, the predicted gene product showing high amino acid sequence homology to several archaeal, bacterial, and eukaryal GDP-mannose pyrophosphorylases such as guanidine diphosphomannose pyrophosphorylases (GMPPs) from Saccharomyces cerevisiae and Arabidopsis thaliana. The sequence was PCR amplified from genomic DNA of S. solfataricus P2 and heterologous gene expression obtained as a fusion to glutathione S-transferase in Escherichia coli, under conditions suitable to reduce the formation of inclusion bodies. Specific assays performed at 60 degrees C revealed the presence of the archaeal synthesizing GDP-mannose enzyme activity in the cell extracts of the transformed E. coli. As a positive control, the same assays were performed at the mesophilic enzyme optimum temperature on the already characterized yeast recombinant GMPP. The recombinant protein was purified to homogeneity by glutathione sepharose affinity chromatography and its thermophilic nature could be verified. The enzyme was definitively identified by demonstrating its capability to catalyze also the reverse reaction of pyrophosphorolysis and, most interestingly, its high specificity for synthesizing GDP-mannose. PMID:15145064

  16. The subunit structure of potato tuber ADPglucose pyrophosphorylase. [Solanum tuberosum L

    Energy Technology Data Exchange (ETDEWEB)

    Okita, T.W.; Nakata, P.A.; Anderson, J.M. (Washington State Univ., Pullman (USA)); Sowokinos, J. (Univ. of Minnesota, St. Paul (USA)); Morell, M.; Preiss, J. (Michigan State Univ., East Lansing (USA))

    1990-06-01

    ADPglucose pyrophosphorylase has been extensively purified from potato (Solanum tuberosum L.) tuber tissue to study its structure. By employing a modified published procedure together with Mono Q chromatography, a near homogeneous enzyme preparation was obtained with substantial improvement in enzyme yield and specific activity. In single dimensional sodium dodecyl sulfate polyacrylamide gels, the enzyme migrated as a single polypeptide band with a mobility of about 50,000 daltons. Analysis by two-dimensional polyacrylamide gel electrophoresis, however, revealed the presence of two types of subunits which could be distinguished by their slight differences in net charge and molecular weight. The smaller potato tuber subunit was recognized by antiserum prepared against the smaller spinach leaf 51 kilodalton ADPglucose pyrophosphorylase subunit. In contrast, the anti-54 kilodalton raised against the spinach leaf subunit did not significantly react to the tuber enzyme subunits. The results are consistent with the hypothesis that the potato tuber ADPglucose pyrophosphorylase is not composed of a simple homotetramer as previously suggested, but is a product of two separate and distinct subunits as observed for the spinach leaf and maize enzymes.

  17. [Enhancement of photoassimilate utilization by manipulation of the ADPglucose pyrophosphorylase gene]. Progress report, [March 15, 1989--April 14, 1990

    Energy Technology Data Exchange (ETDEWEB)

    Okita, T.W.

    1990-12-31

    The long term aim of this project is to assess the feasibility of increasing the conversion of photosynthate into starch via manipulation of the gene that encodes for ADPglucose pyrophosphorylase, a key regulatory enzyme of starch biosynthesis. In developing storage tissues such as cereal seeds and tubers, starch biosynthesis is regulated by the gene activation and expression of ADPglucose pyrophosphorylase, starch synthase, branching enzyme and other ancillary starch modifying enzymes, as well as the allosteric-controlled behavior of ADPglucose pyrophosphorylase activity. During the last two years we have obtained information on the structure of this enzyme from both potato tuber and rice endosperm, using a combination of biochemical and molecular biological approaches. Moreover, we present evidence that this enzyme may be localized at discrete regions of the starch grain within the amyloplast, and plays a role in controlling overall starch biosynthesis in potato tubers.

  18. Crystallization and preliminary X-ray characterization of the Vitis vinifera fucokinase:GDP-fucose pyrophosphorylase

    International Nuclear Information System (INIS)

    The Vitis vinifera dual-activity fucose and nucleotide-sugar metabolizing enzyme l-fucokinase:GDP-fucose pyrophosphorylase (FKP) has been purified to homogeneity and the 118.8 kDa monomeric protein has been crystallized by vapor diffusion in Zeppezauer tubes at 277 K. The Vitis vinifera dual-activity fucose and nucleotide-sugar metabolizing enzyme l-fucokinase:GDP-fucose pyrophosphorylase (FKP) has been purified to homogeneity and the 118.8 kDa monomeric protein has been crystallized by vapor diffusion in Zeppezauer tubes at 277 K. Crystals of the apoenzyme diffracted to 2.6 Å resolution and belonged to the tetragonal space group P41212. There is a single FKP monomer in the asymmetric unit, giving a Matthews coefficient of 3.22 Å3 Da−1 and a solvent content of 61.8%. A complete native data set has been collected as a first step in determining the three-dimensional structure of this enzyme

  19. [Enhancement of photoassimilate utilization by manipulation of the ADPglucose pyrophosphorylase gene]. Summary of progress, [April 15, 1991--April 14, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Okita, T.W.

    1992-12-31

    The long term aim of this project is to assess the feasibility of increasing the conversion of photosynthate into starch via manipulation of genes encoding enzymes that may be rate-limiting in starch biosynthesis. In developing storage tissues such as tubers, starch biosynthesis is regulated by the gene activation and expression of ADPglucose pyrophosphorylase, starch synthase, branching enzyme and other ancillary starch modifying enzymes, as well as the allosteric-controlled behavior of ADPglucose pyrophosphorylase activity. In view of the regulatory role of ADPglucose pyrophosphorylase in starch biosynthesis at both the genetic and biochemical level, we have focused our attention on the genes that encode for this enzyme in potato tubers. The proposed objectives of the grant were to (1) analyze the structure of the tuber enzyme, (2) isolate and characterize the structure of its genes, and (3) identify the regulatory elements controlling ADPglucose pyrophosphorylase during plant development. During the last two and 1/2 years we have met or have made considerable progress in achieving these objectives as discussed in more detail below.

  20. Comparative study of structural models of Leishmania donovani and human GDP-mannose pyrophosphorylases.

    Science.gov (United States)

    Daligaux, Pierre; Bernadat, Guillaume; Tran, Linh; Cavé, Christian; Loiseau, Philippe M; Pomel, Sébastien; Ha-Duong, Tâp

    2016-01-01

    Leishmania is the parasite responsible for the neglected disease leishmaniasis. Its virulence and survival require biosynthesis of glycoconjugates, whose guanosine diphospho-d-mannose pyrophosphorylase (GDP-MP) is a key player. However, experimentally resolved structures of this enzyme are still lacking. We herein propose structural models of the GDP-MP from human and Leishmania donovani. Based on a multiple sequences alignment, the models were built with MODELLER and then carefully refined with all atom molecular dynamics simulations in explicit solvent. Their quality was evaluated against several standard criteria, including their ability to bind GDP-mannose assessed by redocking calculations. Special attention was given in this study to interactions of the catalytic site residues with the enzyme substrate and competitive inhibitors, opening the perspective of medicinal chemistry developments.

  1. Structure of uridine diphosphate N-acetylglucosamine pyrophosphorylase from Entamoeba histolytica.

    Science.gov (United States)

    Edwards, Thomas E; Gardberg, Anna S; Phan, Isabelle Q H; Zhang, Yang; Staker, Bart L; Myler, Peter J; Lorimer, Donald D

    2015-05-01

    Uridine diphosphate N-acetylglucosamine pyrophosphorylase (UAP) catalyzes the final step in the synthesis of UDP-GlcNAc, which is involved in cell-wall biogenesis in plants and fungi and in protein glycosylation. Small-molecule inhibitors have been developed against UAP from Trypanosoma brucei that target an allosteric pocket to provide selectivity over the human enzyme. A 1.8 Å resolution crystal structure was determined of UAP from Entamoeba histolytica, an anaerobic parasitic protozoan that causes amoebic dysentery. Although E. histolytica UAP exhibits the same three-domain global architecture as other UAPs, it appears to lack three α-helices at the N-terminus and contains two amino acids in the allosteric pocket that make it appear more like the enzyme from the human host than that from the other parasite T. brucei. Thus, allosteric inhibitors of T. brucei UAP are unlikely to target Entamoeba UAPs.

  2. Molecular cloning of a novel glucuronokinase/putative pyrophosphorylase from zebrafish acting in an UDP-glucuronic acid salvage pathway.

    Directory of Open Access Journals (Sweden)

    Roman Gangl

    Full Text Available In animals, the main precursor for glycosaminoglycan and furthermore proteoglycan biosynthesis, like hyaluronic acid, is UDP-glucuronic acid, which is synthesized via the nucleotide sugar oxidation pathway. Mutations in this pathway cause severe developmental defects (deficiency in the initiation of heart valve formation. In plants, UDP-glucuronic acid is synthesized via two independent pathways. Beside the nucleotide sugar oxidation pathway, a second minor route to UDP-glucuronic acid exist termed the myo-inositol oxygenation pathway. Within this myo-inositol is ring cleaved into glucuronic acid, which is subsequently converted to UDP-glucuronic acid by glucuronokinase and UDP-sugar pyrophosphorylase. Here we report on a similar, but bifunctional enzyme from zebrafish (Danio rerio which has glucuronokinase/putative pyrophosphorylase activity. The enzyme can convert glucuronic acid into UDP-glucuronic acid, required for completion of the alternative pathway to UDP-glucuronic acid via myo-inositol and thus establishes a so far unknown second route to UDP-glucuronic acid in animals. Glucuronokinase from zebrafish is a member of the GHMP-kinase superfamily having unique substrate specificity for glucuronic acid with a Km of 31 ± 8 µM and accepting ATP as the only phosphate donor (Km: 59 ± 9 µM. UDP-glucuronic acid pyrophosphorylase from zebrafish has homology to bacterial nucleotidyltransferases and requires UTP as nucleosid diphosphate donor. Genes for bifunctional glucuronokinase and putative UDP-glucuronic acid pyrophosphorylase are conserved among some groups of lower animals, including fishes, frogs, tunicates, and polychaeta, but are absent from mammals. The existence of a second pathway for UDP-glucuronic acid biosynthesis in zebrafish likely explains some previous contradictory finding in jekyll/ugdh zebrafish developmental mutants, which showed residual glycosaminoglycans and proteoglycans in knockout mutants of UDP

  3. Genetic and structural validation of Aspergillus fumigatus UDP-N-acetylglucosamine pyrophosphorylase as an antifungal target.

    Science.gov (United States)

    Fang, Wenxia; Du, Ting; Raimi, Olawale G; Hurtado-Guerrero, Ramon; Urbaniak, Michael D; Ibrahim, Adel F M; Ferguson, Michael A J; Jin, Cheng; van Aalten, Daan M F

    2013-08-01

    The sugar nucleotide UDP-N-acetylglucosamine (UDP-GlcNAc) is an essential metabolite in both prokaryotes and eukaryotes. In fungi, it is the precursor for the synthesis of chitin, an essential component of the fungal cell wall. UDP-N-acetylglucosamine pyrophosphorylase (UAP) is the final enzyme in eukaryotic UDP-GlcNAc biosynthesis, converting UTP and N-acetylglucosamine-1-phosphate (GlcNAc-1P) to UDP-GlcNAc. As such, this enzyme may provide an attractive target against pathogenic fungi. Here, we demonstrate that the fungal pathogen Aspergillus fumigatus possesses an active UAP (AfUAP1) that shows selectivity for GlcNAc-1P as the phosphosugar substrate. A conditional mutant, constructed by replacing the native promoter of the A. fumigatus uap1 gene with the Aspergillus nidulans alcA promoter, revealed that uap1 is essential for cell survival and important for cell wall synthesis and morphogenesis. The crystal structure of AfUAP1 was determined and revealed exploitable differences in the active site compared with the human enzyme. Thus AfUAP1 could represent a novel antifungal target and this work will assist the future discovery of small molecule inhibitors against this enzyme.

  4. GDP-mannose pyrophosphorylase is essential for cell wall integrity, morphogenesis and viability of Aspergillus fumigatus.

    Science.gov (United States)

    Jiang, Hechun; Ouyang, Haomiao; Zhou, Hui; Jin, Cheng

    2008-09-01

    GDP-mannose pyrophosphorylase (GMPP) catalyses the synthesis of GDP-mannose, which is the precursor for the mannose residues in glycoconjugates, using mannose 1-phosphate and GTP as substrates. Repression of GMPP in yeast leads to phenotypes including cell lysis, defective cell wall, and failure of polarized growth and cell separation. Although several GMPPs have been isolated and characterized in filamentous fungi, the physiological consequences of their actions are not clear. In this study, Afsrb1, which is a homologue of yeast SRB1/PSA1/VIG9, was identified in the Aspergillus fumigatus genome. The Afsrb1 gene was expressed in Escherichia coli, and recombinant AfSrb1 was functionally confirmed as a GMPP. By the replacement of the native Afsrb1 promoter with an inducible Aspergillus nidulans alcA promoter, the conditional inactivation mutant strain YJ-gmpp was constructed. The presence of 3 % glucose completely blocked transcription of P(alcA)-Afsrb1, and was lethal to strain YJ-gmpp. Repression of Afsrb1 expression in strain YJ-gmpp led to phenotypes including hyphal lysis, defective cell wall, impaired polarity maintenance, and branching site selection. Also, rapid germination and reduced conidiation were documented. However, in contrast to yeast, strain YJ-gmpp retained the ability to direct polarity establishment and septation. Our results showed that the Afsrb1 gene is essential for cell wall integrity, morphogenesis and viability of Aspergillus fumigatus.

  5. Purification, crystallization and preliminary X-ray characterization of the human GTP fucose pyrophosphorylase

    International Nuclear Information System (INIS)

    The human GTP fucose pyrophosphohydrolase protein has been crystallized via the hanging-drop technique over a reservoir of polyethylene glycol (MW 8000) and ethylene glycol. The orthorhombic crystals diffract to 2.8 Å resolution. The human nucleotide-sugar metabolizing enzyme GTP fucose pyrophosphorylase (GFPP) has been purified to homogeneity by an affinity chromatographic procedure that utilizes a novel nucleoside analog. This new purification regime results in a protein preparation that produces significantly better crystals than traditional purification methods. The purified 66.6 kDa monomeric protein has been crystallized via hanging-drop vapor diffusion at 293 K. Crystals of the native enzyme diffract to 2.8 Å and belong to the orthorhombic space group P212121. There is a single GFPP monomer in the asymmetric unit, giving a Matthews coefficient of 2.38 Å3 Da−1 and a solvent content of 48.2%. A complete native data set has been collected as a first step in determining the three-dimensional structure of this enzyme

  6. GDP-D-mannose pyrophosphorylase from Pogonatherum paniceum enhances salinity and drought tolerance of transgenic tobacco.

    Science.gov (United States)

    Ai, Taobo; Liao, Xuehong; Li, Rui; Fan, Linhong; Luo, Fengxue; Xu, Ying; Wang, Shenghua

    2016-01-01

    Pogonatherum paniceum is a highly drought- and salt-tolerant plant species that is typically used for ecological restoration and the conservation of soil and water in many countries. Understanding the molecular mechanisms underlying plant abiotic stress responses, especially to salinity and drought stresses, in species such as P. paniceum could be important to broader crop improvement efforts. GDP-D-mannose pyrophosphorylase (GMPase) is the limiting enzyme in the synthesis of L-ascorbic acid (AsA), which plays a crucial role in the detoxification of reactive oxygen species (ROS). We have cloned and characterized the cDNA of the PpGMP gene of P. paniceum encoding a GMPase. The full-length cDNA sequence contains 1411 nucleotides encoding a putative protein with 361 amino acid residues and an approximate molecular mass of 39.68 kDa. The GMPase transcript was up-regulated in P. paniceum plants subjected to salinity and drought stress, respectively. Transgenic tobacco expressing PpGMPase exhibited enhanced salinity and drought resistance, a higher seed germination rate, better growth performance, a higher AsA content, a more stable redox state, higher superoxide dismutase (SOD) activity, and lower levels of malonaldehyde (MDA) and H2O2 under drought and salinity stress. Taken together, expression of PpGMPase in tobacco conferred salinity and drought stress tolerance by increasing the content of AsA, thereby enhancing ROS-detoxifying functions. Thus, PpGMP is a potential candidate gene for crop improvement.

  7. Purification, crystallization and preliminary X-ray characterization of the human GTP fucose pyrophosphorylase

    Energy Technology Data Exchange (ETDEWEB)

    Quirk, Stephen; Seley-Radtke, Katherine L., E-mail: kseley@umbc.edu [Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Chemistry 405C, Baltimore, MD 21250 (United States)

    2006-04-01

    The human GTP fucose pyrophosphohydrolase protein has been crystallized via the hanging-drop technique over a reservoir of polyethylene glycol (MW 8000) and ethylene glycol. The orthorhombic crystals diffract to 2.8 Å resolution. The human nucleotide-sugar metabolizing enzyme GTP fucose pyrophosphorylase (GFPP) has been purified to homogeneity by an affinity chromatographic procedure that utilizes a novel nucleoside analog. This new purification regime results in a protein preparation that produces significantly better crystals than traditional purification methods. The purified 66.6 kDa monomeric protein has been crystallized via hanging-drop vapor diffusion at 293 K. Crystals of the native enzyme diffract to 2.8 Å and belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}. There is a single GFPP monomer in the asymmetric unit, giving a Matthews coefficient of 2.38 Å{sup 3} Da{sup −1} and a solvent content of 48.2%. A complete native data set has been collected as a first step in determining the three-dimensional structure of this enzyme.

  8. Uncovering Plagiarism - Author Profiling at PAN

    OpenAIRE

    Rosso, Paolo; RANGEL PARDO, FRANCISCO MANUEL

    2014-01-01

    PAN is a yearly workshop and evaluation lab on uncovering plagiarism, authorship, and social software misuse. Since 2009, PAN has been organizing benchmark activities on uncovering plagiarism, authorship, and social software misuse . An additional task - author profiling - has also recently been proposed. Author profiling, instead of focusing on individual authors, studies how language is shared by a class of people. Author profiling is a problem of growing importance in applications in foren...

  9. Enhancement of photoassimilate utilization by manipulation of the ADPglucose pyrophosphorylase gene. Progress report, [April 15, 1987--April 14, 1988

    Energy Technology Data Exchange (ETDEWEB)

    Okita, T.W.

    1988-12-31

    Many agronomically important crops are viewed as significant resources of renewable energy. Overall crop productivity could be increased if the efficiency of photoassimilate conversion into dry matter such as starch were improved in storage tissues. Starch production is controlled by the catalytic activity of ADPglucose pyrophosphorylase in the first step of starch biosynthesis. This research focuses on the genetic structure and molecular mechanisms by which it is controlled during plant development and how it is affected by environmental and hormonal conditions. The current goal is to isolate the genes for this enzyme present in both cereal endosperm and potato tuber tissues, and to elucidate its structure and the controlling sequences responsible for gene expression. The long term goal is the improvement of starch production in storage organs by manipulating this gene so that it encodes an enzyme refractive to inorganic phosphate inhibition.

  10. Distinct isoforms of ADPglucose pyrophosphatase and ADPglucose pyrophosphorylase occur in the suspension-cultured cells of sycamore (Acer pseudoplatanus L.).

    Science.gov (United States)

    Baroja-Fernández, E; Zandueta-Criado, A; Rodríguez-López, M; Akazawa, T; Pozueta-Romero, J

    2000-09-01

    The intracellular localizations of ADPglucose pyrophosphatase (AGPPase) and ADPglucose pyrophosphorylase (AGPase) have been studied using protoplasts prepared from suspension-cultured cells of sycamore (Acer pseudoplatanus L.). Subcellular fractionation studies revealed that all the AGPPase present in the protoplasts is associated with amyloplasts, whereas more than 60% of AGPase is in the extraplastidial compartment. Immunoblots of amyloplast- and extraplastid-enriched extracts further confirmed that AGPase is located mainly outside the amyloplast. Experiments carried out to identify possible different isoforms of AGPPase in the amyloplast revealed the presence of soluble and starch granule-bound isoforms. We thus propose that ADPglucose levels linked to starch biosynthesis in sycamore cells are controlled by enzymatic reactions catalyzing the synthesis and breakdown of ADPglucose, which take place both inside and outside the amyloplast.

  11. Enhancement of photoassimilate utilization by manipulation of the ADPglucose pyrophosphorylase genes. Progress report, [April 15, 1990--April 14, 1991

    Energy Technology Data Exchange (ETDEWEB)

    Okita, T.W.

    1990-12-31

    The long term goal of this project is to assess the feasibility of increasing the conversion of photosynthate a key regulatory enzyme in starch biosynthesis. In developing storage tissues such as cereal seeds and tubers, starch biosynthesis is primarily regulated by the gene activation, expression, and allosteric regulation of ADPglucose pyrophosphorylase, as well as starch synthase, and branching enzyme. During the last year we have elucidated the structure of both subunits which compose this tetrameric enzyme and determined the temporal and spatial expression of the genes encoding each subunit as well as their correlation to starch biosynthesis. Genomic clones to both subunits have also been isolated and the gene structure of the small subunit determined. Transgenic potato plants have been produced containing deletions of the small subunit promoter. Currently, cis acting elements and their involvement in spatial and temporal expression are under investigation.

  12. UDP-N-Acetyl glucosamine pyrophosphorylase as novel target for controlling Aedes aegypti – molecular modeling, docking and simulation studies

    Directory of Open Access Journals (Sweden)

    Bhagath Kumar Palaka

    2014-12-01

    Full Text Available Aedes aegypti is a vector that transmits diseases like dengue fever, chikungunya, and yellow fever. It is distributed in all tropical and subtropical regions of the world. According to WHO reports, 40% of the world’s population is currently at risk for dengue fever. As vaccines are not available for such diseases, controlling mosquito population becomes necessary. Hence, this study aims at UDP-N-acetyl glucosamine pyrophosphorylase of Aedes aegypti (AaUAP, an essential enzyme for chitin metabolim in insects, as a drug target. Structure of AaUAP was predicted and validated using in-silico approach. Further, docking studies were performed using a set of 10 inhibitors out of which NAG9 was found to have good docking score, which was further supported by simulation studies. Hence, we propose that NAG9 can be considered as a potential hit in designing new inhibitors to control Aedes aegypti.

  13. Alginate biosynthetic enzymes in mucoid and nonmucoid Pseudomonas aeruginosa: overproduction of phosphomannose isomerase, phosphomannomutase, and GDP-mannose pyrophosphorylase by overexpression of the phosphomannose isomerase (pmi) gene.

    OpenAIRE

    Sá-Correia, I.; Darzins, A; Wang, S K; Berry, A.; Chakrabarty, A M

    1987-01-01

    The specific activities of phosphomannose isomerase (PMI), phosphomannomutase (PMM), GDP-mannose pyrophosphorylase (GMP), and GDP-mannose dehydrogenase (GMD) were compared in a mucoid cystic fibrosis isolate of Pseudomonas aeruginosa and in two spontaneous nonmucoid revertants. In both revertants some or all of the alginate biosynthetic enzymes we examined appeared to be repressed, indicating that the loss of the mucoid phenotype may be a result of decreased formation of sugar-nucleotide prec...

  14. Cloning, expression, and mapping of GDP-D-mannose pyrophosphorylase cDNA from tomato (Lycopersicon esculentum).

    Science.gov (United States)

    Zou, Li-Ping; Li, Han-Xia; Ouyang, Bo; Zhang, Jun-Hong; Ye, Zhi-Biao

    2006-08-01

    GDP-D-mannose pyrophosphorylase (GMP, EC 2.7.7.22) catalyzes the synthesis of GDP-D-mannose and represents the first committed step in plant ascorbic acid biosynthesis. Using potato GMP cDNA sequence as a querying probe, 65 highly homologous tomato ESTs were obtained from dbEST of GenBank and the putative cDNA sequence of tomato GMP was assembled. The full-length GMP cDNA of tomato was cloned by RACE-PCR with primers designed according to the assembled cDNA sequence. The full-length cDNA sequence contained a complete open reading frame (ORF) of 1,086 bp, which encoded 361 amino acid residues. This gene was designated as LeGMP (GenBank accession No. AY605668). Homology analysis of LeGMP showed a 96% identity with potato GMP and the deduced amino acid showed 99%, 97%, 91% and 89% homology with GMP from potato, tobacco, alfalfa and Arabidopsis thaliana, respectively. Northern blot analysis showed that LeGMP was constitutively expressed in roots, stems, leaves, flowers and fruits of tomato; but the expression levels varied. LeGMP was mapped to 3-D using 75 tomato introgression lines (ILs), each containing a single homozygous RFLP-defined chromosome segment from the green-fruited species Lycopersicon pennellii. PMID:16939010

  15. Deletion of UDP-glucose pyrophosphorylase reveals a UDP-glucose independent UDP-galactose salvage pathway in Leishmania major

    Science.gov (United States)

    Lamerz, Anne-Christin; Damerow, Sebastian; Kleczka, Barbara; Wiese, Martin; van Zandbergen, Ger; Lamerz, Jens; Wenzel, Alexander; Hsu, Fong-Fu; Turk, John; Beverley, Stephen M.; Routier, Françoise H.

    2010-01-01

    The nucleotide sugar UDP-galactose (UDP-Gal) is essential for the biosynthesis of several abundant glycoconjugates forming the surface glycocalyx of the protozoan parasite Leishmania major. Current data suggest that UDP-Gal could arise de novo by epimerization of UDP-glucose (UDP-Glc) or by a salvage pathway involving phosphorylation of Gal and the action of UDP-glucose:α-d-galactose-1-phosphate uridylyltransferase as described by Leloir. Since both pathways require UDP-Glc, inactivation of the UDP-glucose pyrophosphorylase (UGP) catalyzing activation of glucose-1 phosphate to UDP-Glc was expected to deprive parasites of UDP-Gal required for Leishmania glycocalyx formation. Targeted deletion of the gene encoding UGP, however, only partially affected the synthesis of the Gal-rich phosphoglycans. Moreover, no alteration in the abundant Gal-containing glycoinositolphospholipids was found in the deletion mutant. Consistent with these findings, the virulence of the UGP-deficient mutant was only modestly affected. These data suggest that Leishmania elaborates a UDP-Glc independent salvage pathway for UDP-Gal biosynthesis. PMID:20335578

  16. 'Mystery shoppers' can uncover ED weaknesses.

    Science.gov (United States)

    2006-12-01

    One veteran "mystery shopper" has uncovered several common ED practices that can hurt patient satisfaction. You can learn from her observations to improve your ED's customer service: Be sure to let all of your patients know how long they might expect to wait before seeing a doctor. Wash your hands where the patient can see you, so they can be confident you are practicing good hygiene. Clearly explain all forms and discharge instructions to help ensure patient compliance. PMID:17209484

  17. Uncovering student ideas in physical science

    CERN Document Server

    Keeley, Page

    2014-01-01

    If you and your students can't get enough of a good thing, Volume 2 of Uncovering Student Ideas in Physical Science is just what you need. The book offers 39 new formative assessment probes, this time with a focus on electric charge, electric current, and magnets and electromagnetism. It can help you do everything from demystify electromagnetic fields to explain the real reason balloons stick to the wall after you rub them on your hair.

  18. Hepatitis C virus host cell interactions uncovered

    DEFF Research Database (Denmark)

    Gottwein, Judith; Bukh, Jens

    2007-01-01

      Insights into virus-host cell interactions as uncovered by Randall et al. (1) in a recent issue of PNAS further our understanding of the hepatitis C virus (HCV) life cycle, persistence, and pathogenesis and might lead to the identification of new therapeutic targets. HCV persistently infects 180...... treated. Therefore, there is a pressing need for the identification of novel drugs against hepatitis C. Although most research focuses on the development of HCV-specific antivirals, such as protease and polymerase inhibitors (3), cellular targets could be pursued and might allow the development of broad...

  19. Phytophthora sojae avirulence effector Avr3b is a secreted NADH and ADP-ribose pyrophosphorylase that modulates plant immunity.

    Directory of Open Access Journals (Sweden)

    Suomeng Dong

    2011-11-01

    Full Text Available Plants have evolved pathogen-associated molecular pattern (PAMP-triggered immunity (PTI and effector-triggered immunity (ETI to protect themselves from infection by diverse pathogens. Avirulence (Avr effectors that trigger plant ETI as a result of recognition by plant resistance (R gene products have been identified in many plant pathogenic oomycetes and fungi. However, the virulence functions of oomycete and fungal Avr effectors remain largely unknown. Here, we combined bioinformatics and genetics to identify Avr3b, a new Avr gene from Phytophthora sojae, an oomycete pathogen that causes soybean root rot. Avr3b encodes a secreted protein with the RXLR host-targeting motif and C-terminal W and Nudix hydrolase motifs. Some isolates of P. sojae evade perception by the soybean R gene Rps3b through sequence mutation in Avr3b and lowered transcript accumulation. Transient expression of Avr3b in Nicotiana benthamiana increased susceptibility to P. capsici and P. parasitica, with significantly reduced accumulation of reactive oxygen species (ROS around invasion sites. Biochemical assays confirmed that Avr3b is an ADP-ribose/NADH pyrophosphorylase, as predicted from the Nudix motif. Deletion of the Nudix motif of Avr3b abolished enzyme activity. Mutation of key residues in Nudix motif significantly impaired Avr3b virulence function but not the avirulence activity. Some Nudix hydrolases act as negative regulators of plant immunity, and thus Avr3b might be delivered into host cells as a Nudix hydrolase to impair host immunity. Avr3b homologues are present in several sequenced Phytophthora genomes, suggesting that Phytophthora pathogens might share similar strategies to suppress plant immunity.

  20. Clinical role modelling: uncovering hidden knowledge.

    Science.gov (United States)

    Davies, E

    1993-04-01

    Those responsible for the education of nurses are well aware of the need to reconcile the art and science of nursing so that future practitioners can be prepared to offer a humanistic and professional service to society. One way to assist students in this integration is to provide them with opportunities for role modelling as a means of discovering the knowledge embedded in clinical practice. A study of first-year undergraduate students undertaking a course which provides such opportunities in a number of practice settings was carried out to determine whether the observation of clinical role models does lead to knowledge discovery. The study, which used a grounded theory approach, indicated that the major aspect of nursing uncovered by the students through observation of clinical role models was that of provision of direct care. They articulated their values in relation to 'good' and 'bad' care and identified those attributes of nurses which they considered contributed to these care positions. In addition, they were able to recognize creativity and flexibility in practitioners and to relate these attributes to the ability to provide individualized, context-specific care. There was some uncovering of aspects of the nurse's role in maintaining their own professional competence, socializing neophytes into the profession and collaborating with the members of the multi-disciplinary health care team. PMID:8496511

  1. Uncovering the architecture of action semantics.

    Science.gov (United States)

    Watson, Christine E; Buxbaum, Laurel J

    2014-10-01

    Despite research suggesting that stored sensorimotor information about tool use is a component of the semantic representations of tools, little is known about the action features or organizing principles that underlie this knowledge. We used methods similar to those applied in other semantic domains to examine the "architecture" of action semantic knowledge. In Experiment 1, participants sorted photographs of tools into groups according to the similarity of their associated "use" actions and rated tools on dimensions related to action. The results suggest that the magnitude of arm movement, configuration of the hand, and manner of motion during tool use play a role in determining how tools cluster in action "semantic space." In Experiment 2, we validated the architecture uncovered in Experiment 1 using an implicit semantic task for which tool use knowledge was not ostensibly relevant (blocked cyclic word-picture matching). Using stimuli from Experiment 1, we found that participants performed more poorly during blocks of trials containing tools used with similar versus unrelated actions, and the amount of semantic interference depended on the magnitude of action similarity among tools. Thus, the degree of featural overlap between tool use actions plays a role in determining the overall semantic similarity of tools.

  2. Cloning a Full-length cDNA Encoding UDP-glucose Pyrophosphorylase from Amorpha fruticosa by PCR-based Methods

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A method based on degenerate Oligo-primed polymerase chain reaction (PCR) and random amplification of cDNA end (RACE) PCR for cloning a full-length cDNA is described. An Amorpha fruticosa cDNA clone encoding UDP-glucose pyrophosphorylase (UGP), a key enzyme producing UDP-glucose in the synthesis of sucrose and cell ulose, is cloned by using this method. We design 5' RACE primers based on UGP A1 fragment, which obtains from degenerate PCR. Inverse PCR and nested PCR enable cloning of the remainder 5' and 3' end fragments of the gene. The deduced amino acid sequence exhibits significant homology with the other UGP genes cloned. This method is more simple and inexpensive than screening cDNA library, and can be easily adapted to clone other genes.

  3. Uncovering Research Topics of Academic Communities of Scientific Collaboration Network

    OpenAIRE

    Hongqi Han; Shuo Xu; Jie Gui; Xiaodong Qiao; Lijun Zhu; Han Zhang

    2014-01-01

    In order to improve the quality of applications, such as recommendation or retrieval in knowledge-based service system, it is very helpful to uncover research topics of academic communities in scientific collaboration network (SCN). Previous research mainly focuses on network characteristics measurement and community evolution, but it remains largely understudied on how to uncover research topics of each community. This paper proposes a nonjoint approach, consisting of three simple steps: (1)...

  4. Macroscopic model for biological fixation and its uncover-ing idea in Chinese Mongolian traditional osteopathy

    Institute of Scientific and Technical Information of China (English)

    ZHAO Namula; LI Xue-en; WANG Mei; HU Da-lai

    2009-01-01

    Splintage external fixation in Chinese Mongolian oste-opathy is a biological macroscopic model. In this model, the ideas of self-life "unity of mind and body" and vital natural "correspondence of nature and human" combine the physi-ological and psychological self-fixation with supplementary external fixation of fracture using small splints. This model implies macroscopic ideas of uncovering fixation and healing: structural stability integrating geometrical "dy-namic" stability with mechanical "dynamic" equilibrium and the stability of state integrating statics with dynamics, and osteoblasts with osteoclasts, and psychological stability in-tegrating closed and open systems of human and nature. These ideas indicate a trend of development in modem osteopathy.

  5. Uncovering Curriculum: Language performance through culture by design

    Directory of Open Access Journals (Sweden)

    Jennifer Eddy

    2015-01-01

    Full Text Available This article discusses a model curriculum design framework designed to both uncover and integrate culture perspectives and performance assessment throughout the span of an articulated language program. For two years, the NALRC has hosted a leadership institute on curriculum design. This curricular framework aligns the three stages of Understanding by Design with the World Readiness (National standards. Uncovering Content: Assessment Design Aligning Performance and Transfer, facilitates design of performance based assessments derived from cultural perspectives and big ideas essential to understanding the culture or cultures. The framework can be used to design one course or an entire articulated program of study, minor, or major for any language. The framework enables continuity of recurring ideas, perspectives, and issues from beginning to end of a program. Students leave the program with key understandings, a core cadre of tasks that uncover these, and questions they will continue to unpack over time as they become self-directed learners.

  6. Cloning and sequencing of the Candida albicans homologue of SRB1/PSA1/VIG9, the essential gene encoding GDP-mannose pyrophosphorylase in Saccharomyces cerevisiae.

    Science.gov (United States)

    Warit, S; Walmsley, R M; Stateva, L I

    1998-09-01

    Two genomic fragments have been isolated from Candida albicans which strongly hybridize to SRB1/PSA1/VIG9, an essential gene which encodes GDP-mannose pyrophosphorylase in Saccharomyces cerevisiae. A common 2.5 kb Xbal-Pstl fragment has been identified, which Southern analysis suggests is most likely unique in the C. albicans genome. The fragment contains an ORF, which is 82% identical and 90% homologous to the Srb1p/Psa1p/Vig9p from S. cerevisiae, contains one additional amino acid at position 254 and is able to functionally complement the major phenotypic characteristics of S. cerevisiae srb1 null and conditional mutations. The authors therefore conclude that they have cloned and sequenced from C. albicans the bona fide homologue of SRB1/PSA1/VIG9, named hereafter CaSRB1. Northern analysis data indicate that the gene is expressed in C. albicans under conditions of growth in the yeast and hyphal form and suggest that its expression might be regulated. PMID:9782489

  7. Regulation of starch accumulation by granule-associated plant 14-3-3 proteins

    OpenAIRE

    Sehnke, Paul C.; Chung, Hwa-Jee; Wu, Ke; Ferl, Robert J.

    2001-01-01

    In higher plants the production of starch is orchestrated by chloroplast-localized biosynthetic enzymes, namely starch synthases, ADP-glucose pyrophosphorylase, and starch branching and debranching enzymes. Diurnal regulation of these enzymes, as well as starch-degrading enzymes, influences both the levels and composition of starch, and is dependent in some instances upon phosphorylation-linked regulation. The phosphoserine/threonine-binding 14-3-3 proteins partici...

  8. Metabolic consequences of infection of grapevine (Vitis vinifera L. cv. ‘Modra frankinja’ with flavescence dorée phytoplasma

    Directory of Open Access Journals (Sweden)

    Nina ePrezelj

    2016-05-01

    Full Text Available Flavescence dorée, caused by the quarantine phytoplasma FDp, represents the most devastating of the grapevine yellows diseases in Europe. In an integrated study we have explored the FDp–grapevine interaction in infected grapevines of cv. ‘Modra frankinja’ under natural conditions in the vineyard. In FDp-infected leaf vein-enriched tissues, the seasonal transcriptional profiles of 14 genes selected from various metabolic pathways showed an FDp-specific plant response compared to other grapevine yellows and uncovered a new association of the SWEET17a vacuolar transporter of fructose with pathogens. Non-targeted metabolome analysis from leaf vein-enriched tissues identified 22 significantly changed compounds with increased levels during infection. Several metabolites corroborated the gene expression study. Detailed investigation of the dynamics of carbohydrate metabolism revealed significant accumulation of sucrose and starch in the mesophyll of FDp-infected leaves, as well as significant up-regulation of genes involved in their biosynthesis. In addition, infected leaves had high activities of ADP-glucose pyrophosphorylase and, more significantly, sucrose synthase. The data support the conclusion that FDp infection inhibits phloem transport, resulting in accumulation of carbohydrates and secondary metabolites that provoke a source-sink transition and defence response status.

  9. UDP-glucose pyrophosphorylase2 (OsUgp2),a pollen-preferential gene in rice, plays a critical role in starch accumulation during pollen maturation

    Institute of Scientific and Technical Information of China (English)

    MU Hong; KE JianHao; LIU Wei; ZHUANG ChuXiong; YIP WingKin

    2009-01-01

    UDP-glucose pyrophosphorylase (UGPase) is predominantly present and plays significant role in car-bohydrate metabolism in plants. Two homologous UGPase genes, OsUgp1 and OsUgp2, exist in rice genome. OsUgp1 has recently been reported to be essential for callose deposition during pollen mother cell and meiosis stages as well as for seed carbohydrate metabolism. In this study, a full-length cDNA of OsUgp2 was isolated from rice anther. Northern blot and RNA in situ hybridization indicated that the expression of OsUgp2 was preferentially in pollen and developmentally regulated. No tran-scripts were found in leaf, stem, lemma/palea, ripening grain and florets before the uninucleate micro-spore developmental stage, but a large quantity of OsUgp2 mRNA was found in pollen at the binucleate and mature stages. The immunolocalizaUon of OsUgp2 showed a similar expression pattern to that by RNA in situ hybridization. The function of OsUgp2 was investigated by dsRNA-mediated transcriptional gene silencing. The pollen fertility of 16 independent transgenic rice plants was found between 25%and 90%, which was correlated with the amount of OsUgp2 mRNA. The results of morphological changes and starch variation during pollen development in transgenic rice showed that the abnormal feature of pollen development appeared after the uninucleate microspore stage. Starch failed to accu-mulate in pollen and thus led to sterile pollens. These results demonstrated that OsUgp2 is a pol-len-preferential "late gone" and plays a key role during pollen maturation, especially for starch accu-mulation. OsUgp2 complements OsUgpl to fulfill the UGPase's functions necessary for the full processof pollen development.

  10. Uncovering the systemic issues that reside in home care

    OpenAIRE

    Giannasi, Wynona

    2012-01-01

    This video clip comprises the Keynote Address: “Uncovering the systemic issues that reside in home care” held at the 21st Annual John K. Friesen Conference, "Innovations in Home Care: A Public Policy Perspective," MAY 16-17, 2012, Vancouver, BC. Presented by Wynona Giannasi, Partner, Howegroup – Public Sector Consultants, Vancouver BC. It is well known that jurisdictions with more comprehensive and integrated home care delivery systems are able to extend independent living for older p...

  11. Uncovering Student Ideas in Astronomy 45 Formative Assessment Probes

    CERN Document Server

    Keeley, Page

    2012-01-01

    What do your students know-or think they know-about what causes night and day, why days are shorter in winter, and how to tell a planet from a star? Find out with this book on astronomy, the latest in NSTA's popular Uncovering Student Ideas in Science series. The 45 astronomy probes provide situations that will pique your students' interest while helping you understand how your students think about key ideas related to the universe and how it operates.

  12. Molecular and biochemical analysis of the plastidic ADP-glucose transporter (ZmBT1) from Zea mays

    NARCIS (Netherlands)

    Kirchberger, S.; Leroch, M.; Huynen, M.A.; Wahl, M.; Neuhaus, H.E.; Tjaden, J.

    2007-01-01

    Physiological studies on the Brittle1 maize mutant have provided circumstantial evidence that ZmBT1 (Zea mays Brittle1 protein) is involved in the ADP-Glc transport into maize endosperm plastids, but up to now, no direct ADP-Glc transport mediated by ZmBT1 has ever been shown. The heterologous synth

  13. Molecular and biochemical analysis of the plastidic ADP-glucose transporter (ZmBT1) from Zea mays.

    NARCIS (Netherlands)

    Kirchberger, S.; Leroch, M.; Huynen, M.A.; Wahl, M.; Neuhaus, H.E.; Tjaden, J.

    2007-01-01

    Physiological studies on the Brittle1 maize mutant have provided circumstantial evidence that ZmBT1 (Zea mays Brittle1 protein) is involved in the ADP-Glc transport into maize endosperm plastids, but up to now, no direct ADP-Glc transport mediated by ZmBT1 has ever been shown. The heterologous synth

  14. Rice GDP-mannose pyrophosphorylase OsVTC1-1 and OsVTC1-3 play different roles in ascorbic acid synthesis.

    Science.gov (United States)

    Qin, Hua; Deng, Zaian; Zhang, Chuanyu; Wang, Yayun; Wang, Juan; Liu, Hai; Zhang, Zhili; Huang, Rongfeng; Zhang, Zhijin

    2016-02-01

    GDP-D-mannose pyrophosphorylase (GMPase) catalyzes the synthesis of GDP-D-mannose, which is a precursor for ascorbic acid (AsA) synthesis in plants. The rice genome encodes three GMPase homologs OsVTC1-1, OsVTC1-3 and OsVTC1-8, but their roles in AsA synthesis are unclear. The overexpression of OsVTC1-1 or OsVTC1-3 restored the AsA synthesis of vtc1-1 in Arabidopsis, while that of OsVTC1-8 did not, indicating that only OsVTC1-1 and OsVTC1-3 are involved in AsA synthesis in rice. Similar to Arabidopsis VTC1, the expression of OsVTC1-1 was high in leaves, induced by light, and inhibited by dark. Unlike OsVTC1-1, the expression level of OsVTC1-3 was high in roots and quickly induced by the dark, while the transcription level of OsVTC1-8 did not show obvious changes under constant light or dark treatments. In OsVTC1-1 RNAi plants, the AsA content of rice leaves decreased, and the AsA production induced by light was limited. In contrast, OsVTC1-3 RNAi lines altered AsA synthesis levels in rice roots, but not in the leaves or under the light/dark treatment. The enzyme activity showed that OsVTC1-1 and OsVTC1-3 had higher GMPase activities than OsVTC1-8 in vitro. Our data showed that, unlike in Arabidopsis, the rice GPMase homologous proteins illustrated a new model in AsA synthesis: OsVTC1-1 may be involved in the AsA synthesis, which takes place in leaves, while OsVTC1-3 may be responsible for AsA synthesis in roots. The different roles of rice GMPase homologous proteins in AsA synthesis may be due to their differences in transcript levels and enzyme activities.

  15. Uncover the Ideology Behind News Reports Through Transitivity Analysis

    Institute of Scientific and Technical Information of China (English)

    董亚男

    2015-01-01

    When people read the reports relating to Occupy Central from different news papers, they get completely different feelings towards the event. To find out how this phenomenon happened, this paper is going to apply transitivity analysis to the news reports. The reports are selected from China Daily, CNN and BBC respectively. To have a deep application of this method, only verbal process wil be taken into consideration. This paper wil discuss the proportion of verbal process from the two sides (Occupy Central people as one side and people against them as the other), the message delivered by the verbal process, the sequence and the transformation of verbal process. The purpose is to uncover the ideology hidden behind the seemingly objective news reports through transitivity analysis.

  16. Laughing It Off: Uncovering the Everyday Work Experience of Nurses

    Directory of Open Access Journals (Sweden)

    Valerie M. Adams

    2007-03-01

    Full Text Available During research towards her doctoral dissertation, the author noticed that nurses understated the conditions in which they worked. Seeking to understand how nursing culture shapes how nurses describe their work, she developed a “toolbox” of reflexive methods. She used metaphors of nursing and emotion expressed as laughter to identify aspects of nursing culture in semistructured interviews with nurses working in Australian residential aged care facilities. She also incorporated autoethnography, as she had worked as a registered nurse while studying economics. The inclusion of her voice in the data illustrates the difference between nursing culture and another worldview. These pluralist methods made explicit some of the effects of gendered socialization, such as understatement and self-consciousness, and demonstrate how they are embedded in nursing culture. Awareness of such norms is important for understanding marketized caring labor. This combination of methods has significance for uncovering workplace culture in other forms of marketized caring.

  17. Uncovering Transcriptional Regulatory Networks by Sparse Bayesian Factor Model

    Science.gov (United States)

    Meng, Jia; Zhang, Jianqiu(Michelle); Qi, Yuan(Alan); Chen, Yidong; Huang, Yufei

    2010-12-01

    The problem of uncovering transcriptional regulation by transcription factors (TFs) based on microarray data is considered. A novel Bayesian sparse correlated rectified factor model (BSCRFM) is proposed that models the unknown TF protein level activity, the correlated regulations between TFs, and the sparse nature of TF-regulated genes. The model admits prior knowledge from existing database regarding TF-regulated target genes based on a sparse prior and through a developed Gibbs sampling algorithm, a context-specific transcriptional regulatory network specific to the experimental condition of the microarray data can be obtained. The proposed model and the Gibbs sampling algorithm were evaluated on the simulated systems, and results demonstrated the validity and effectiveness of the proposed approach. The proposed model was then applied to the breast cancer microarray data of patients with Estrogen Receptor positive ([InlineEquation not available: see fulltext.]) status and Estrogen Receptor negative ([InlineEquation not available: see fulltext.]) status, respectively.

  18. Uncovering Transcriptional Regulatory Networks by Sparse Bayesian Factor Model

    Directory of Open Access Journals (Sweden)

    Qi Yuan(Alan

    2010-01-01

    Full Text Available Abstract The problem of uncovering transcriptional regulation by transcription factors (TFs based on microarray data is considered. A novel Bayesian sparse correlated rectified factor model (BSCRFM is proposed that models the unknown TF protein level activity, the correlated regulations between TFs, and the sparse nature of TF-regulated genes. The model admits prior knowledge from existing database regarding TF-regulated target genes based on a sparse prior and through a developed Gibbs sampling algorithm, a context-specific transcriptional regulatory network specific to the experimental condition of the microarray data can be obtained. The proposed model and the Gibbs sampling algorithm were evaluated on the simulated systems, and results demonstrated the validity and effectiveness of the proposed approach. The proposed model was then applied to the breast cancer microarray data of patients with Estrogen Receptor positive ( status and Estrogen Receptor negative ( status, respectively.

  19. Uncovering transcriptional interactions via an adaptive fuzzy logic approach

    Directory of Open Access Journals (Sweden)

    Chen Chung-Ming

    2009-12-01

    Full Text Available Abstract Background To date, only a limited number of transcriptional regulatory interactions have been uncovered. In a pilot study integrating sequence data with microarray data, a position weight matrix (PWM performed poorly in inferring transcriptional interactions (TIs, which represent physical interactions between transcription factors (TF and upstream sequences of target genes. Inferring a TI means that the promoter sequence of a target is inferred to match the consensus sequence motifs of a potential TF, and their interaction type such as AT or RT is also predicted. Thus, a robust PWM (rPWM was developed to search for consensus sequence motifs. In addition to rPWM, one feature extracted from ChIP-chip data was incorporated to identify potential TIs under specific conditions. An interaction type classifier was assembled to predict activation/repression of potential TIs using microarray data. This approach, combining an adaptive (learning fuzzy inference system and an interaction type classifier to predict transcriptional regulatory networks, was named AdaFuzzy. Results AdaFuzzy was applied to predict TIs using real genomics data from Saccharomyces cerevisiae. Following one of the latest advances in predicting TIs, constrained probabilistic sparse matrix factorization (cPSMF, and using 19 transcription factors (TFs, we compared AdaFuzzy to four well-known approaches using over-representation analysis and gene set enrichment analysis. AdaFuzzy outperformed these four algorithms. Furthermore, AdaFuzzy was shown to perform comparably to 'ChIP-experimental method' in inferring TIs identified by two sets of large scale ChIP-chip data, respectively. AdaFuzzy was also able to classify all predicted TIs into one or more of the four promoter architectures. The results coincided with known promoter architectures in yeast and provided insights into transcriptional regulatory mechanisms. Conclusion AdaFuzzy successfully integrates multiple types of

  20. 16 CFR 1611.34 - Only uncovered or exposed parts of wearing apparel to be tested.

    Science.gov (United States)

    2010-01-01

    ... apparel to be tested. 1611.34 Section 1611.34 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION... § 1611.34 Only uncovered or exposed parts of wearing apparel to be tested. In determining whether an... uncovered or exposed part of such article of wearing apparel shall be tested according to the...

  1. 77 FR 30501 - Uncovered Innerspring Units From the People's Republic of China: Initiation of Anticircumvention...

    Science.gov (United States)

    2012-05-23

    ... Innerspring Units From South Africa and Vietnam, USITC Pub. 4051, Inv. Nos. 731-TA-1141-1142 at I-11 (December... International Trade Administration Uncovered Innerspring Units From the People's Republic of China: Initiation... units from the People's Republic of China (``PRC'').\\1\\ \\1\\ See Uncovered Innerspring Units From...

  2. Charting the Vasculome: Uncovering the Principles of Vascular Organization

    Science.gov (United States)

    Oppenheim, Jacob; Magnasco, Marcelo

    2014-03-01

    The efficient distribution of resources in any system requires a carefully designed architecture that is both space filling and efficient. While the principles of such networks are beginning to be uncovered in plants, they remain poorly elucidated in the case of higher animals. We have developed a high-throughput, easily implemented method of mapping vascular networks in mammalian tissue. By combining high resolution, rapid fluorescence blockface imaging with serial sectioning, we are able to map the vasculature of the rat liver at a resolution of 10 microns, revealing the structure above the level of the capillaries, constituting the largest vascular dataset yet assembled. We have developed algorithms for the efficient three-dimensional reconstruction from two-dimensional images, allowing skeletonization and investigation of its geometry and topology. We are able to calculate the scaling properties of these networks as well as the frequency of loops at each level. Using sophisticated topological tools, we are beginning to elucidate the principles of their organization. Ultimately, a greater understanding of vasculature is necessary for the success of efforts in synthetic and regenerative biology along with the better understanding of the growth and development of cancers.

  3. Uncovering patterns of technology use in consumer health informatics.

    Science.gov (United States)

    Hung, Man; Conrad, Jillian; Hon, Shirley D; Cheng, Christine; Franklin, Jeremy D; Tang, Philip

    2013-11-01

    Internet usage and accessibility has grown at a staggering rate, influencing technology use for healthcare purposes. The amount of health information technology (Health IT) available through the Internet is immeasurable and growing daily. Health IT is now seen as a fundamental aspect of patient care as it stimulates patient engagement and encourages personal health management. It is increasingly important to understand consumer health IT patterns including who is using specific technologies, how technologies are accessed, factors associated with use, and perceived benefits. To fully uncover consumer patterns it is imperative to recognize common barriers and which groups they disproportionately affect. Finally, exploring future demand and predictions will expose significant opportunities for health IT. The most frequently used health information technologies by consumers are gathering information online, mobile health (mHealth) technologies, and personal health records (PHRs). Gathering health information online is the favored pathway for healthcare consumers as it is used by more consumers and more frequently than any other technology. In regard to mHealth technologies, minority Americans, compared with White Americans utilize social media, mobile Internet, and mobile applications more frequently. Consumers believe PHRs are the most beneficial health IT. PHR usage is increasing rapidly due to PHR integration with provider health systems and health insurance plans. Key issues that have to be explicitly addressed in health IT are privacy and security concerns, health literacy, unawareness, and usability. Privacy and security concerns are rated the number one reason for the slow rate of health IT adoption.

  4. Losartan ameliorates dystrophic epidermolysis bullosa and uncovers new disease mechanisms.

    Science.gov (United States)

    Nyström, Alexander; Thriene, Kerstin; Mittapalli, Venugopal; Kern, Johannes S; Kiritsi, Dimitra; Dengjel, Jörn; Bruckner-Tuderman, Leena

    2015-07-20

    Genetic loss of collagen VII causes recessive dystrophic epidermolysis bullosa (RDEB)-a severe skin fragility disorder associated with lifelong blistering and disabling progressive soft tissue fibrosis. Causative therapies for this complex disorder face major hurdles, and clinical implementation remains elusive. Here, we report an alternative evidence-based approach to ameliorate fibrosis and relieve symptoms in RDEB. Based on the findings that TGF-β activity is elevated in injured RDEB skin, we targeted TGF-β activity with losartan in a preclinical setting. Long-term treatment of RDEB mice efficiently reduced TGF-β signaling in chronically injured forepaws and halted fibrosis and subsequent fusion of the digits. In addition, proteomics analysis of losartan- vs. vehicle-treated RDEB skin uncovered changes in multiple proteins related to tissue inflammation. In line with this, losartan reduced inflammation and diminished TNF-α and IL-6 expression in injured forepaws. Collectively, the data argue that RDEB fibrosis is a consequence of a cascade encompassing tissue damage, TGF-β-mediated inflammation, and matrix remodeling. Inhibition of TGF-β activity limits these unwanted outcomes and thereby substantially ameliorates long-term symptoms.

  5. Uncovering Cryptic Parasitoid Diversity in Horismenus (Chalcidoidea, Eulophidae.

    Directory of Open Access Journals (Sweden)

    Sarah G Kenyon

    Full Text Available Horismenus parasitoids are an abundant and understudied group of eulophid wasps found mainly in the New World. Recent surveys based on morphological analyses in Costa Rica have quadrupled the number of named taxa, with more than 400 species described so far. This recent revision suggests that there is still a vast number of unknown species to be identified. As Horismenus wasps have been widely described as parasitoids of insect pests associated with crop plants, it is of high importance to properly establish the extant diversity of the genus, in order to provide biological control practitioners with an exhaustive catalog of putative control agents. In this study, we first collected Horismenus wasps from wild Phaseolus bean seeds in Central Mexico and Arizona to assess the genetic relatedness of three morphologically distinct species with overlapping host and geographical ranges. Sequence data from two nuclear and two mitochondrial gene regions uncovered three cryptic species within each of the three focal species (i.e., H. missouriensis, H. depressus and H. butcheri. The monophyly of each cryptic group is statistically supported (except in two of them represented by one single tip in which monophyly cannot be tested. The phylogenetic reconstruction is discussed with respect to differences between gene regions as well as likely reasons for the differences in variability between species.

  6. Uncovering the mechanism(s) of deep brain stimulation

    Energy Technology Data Exchange (ETDEWEB)

    Li Gang; Yu Chao; Lin Ling; Lu, Stephen C-Y [Inspiring Technical Laboratory, College of Precision Instruments and Opto-Electronics Engineering, Tianjin University, Tianjin 300072 (China)

    2005-01-01

    Deep brain stimulators, often called 'pacemakers for the brain', are implantable devices which continuously deliver impulse stimulation to specific targeted nuclei of deep brain structure, namely deep brain stimulation (DBS). To date, deep brain stimulation (DBS) is the most effective clinical technique for the treatment of several medically refractory movement disorders (e.g., Parkinson's disease, essential tremor, and dystonia). In addition, new clinical applications of DBS for other neurologic and psychiatric disorders (e.g., epilepsy and obsessive-compulsive disorder) have been put forward. Although DBS has been effective in the treatment of movement disorders and is rapidly being explored for the treatment of other neurologic disorders, the scientific understanding of its mechanisms of action remains unclear and continues to be debated in the scientific community. Optimization of DBS technology for present and future therapeutic applications will depend on identification of the therapeutic mechanism(s) of action. The goal of this review is to address our present knowledge of the effects of high-frequency stimulation within the central nervous system and comment on the functional implications of this knowledge for uncovering the mechanism(s) of DBS.

  7. Uncovering the mechanism(s) of deep brain stimulation

    Science.gov (United States)

    Gang, Li; Chao, Yu; Ling, Lin; C-Y Lu, Stephen

    2005-01-01

    Deep brain stimulators, often called `pacemakers for the brain', are implantable devices which continuously deliver impulse stimulation to specific targeted nuclei of deep brain structure, namely deep brain stimulation (DBS). To date, deep brain stimulation (DBS) is the most effective clinical technique for the treatment of several medically refractory movement disorders (e.g., Parkinson's disease, essential tremor, and dystonia). In addition, new clinical applications of DBS for other neurologic and psychiatric disorders (e.g., epilepsy and obsessive-compulsive disorder) have been put forward. Although DBS has been effective in the treatment of movement disorders and is rapidly being explored for the treatment of other neurologic disorders, the scientific understanding of its mechanisms of action remains unclear and continues to be debated in the scientific community. Optimization of DBS technology for present and future therapeutic applications will depend on identification of the therapeutic mechanism(s) of action. The goal of this review is to address our present knowledge of the effects of high-frequency stimulation within the central nervous system and comment on the functional implications of this knowledge for uncovering the mechanism(s) of DBS.

  8. Uncovering Aberrant Mutant PKA Function with Flow Cytometric FRET

    Directory of Open Access Journals (Sweden)

    Shin-Rong Lee

    2016-03-01

    Full Text Available Biology has been revolutionized by tools that allow the detection and characterization of protein-protein interactions (PPIs. Förster resonance energy transfer (FRET-based methods have become particularly attractive as they allow quantitative studies of PPIs within the convenient and relevant context of living cells. We describe here an approach that allows the rapid construction of live-cell FRET-based binding curves using a commercially available flow cytometer. We illustrate a simple method for absolutely calibrating the cytometer, validating our binding assay against the gold standard isothermal calorimetry (ITC, and using flow cytometric FRET to uncover the structural and functional effects of the Cushing-syndrome-causing mutation (L206R on PKA’s catalytic subunit. We discover that this mutation not only differentially affects PKAcat’s binding to its multiple partners but also impacts its rate of catalysis. These findings improve our mechanistic understanding of this disease-causing mutation, while illustrating the simplicity, general applicability, and power of flow cytometric FRET.

  9. Urban association rules: uncovering linked trips for shopping behavior

    CERN Document Server

    Yoshimura, Yuji; Hobin, Juan N Bautista; Ratti, Carlo; Blat, Josep

    2016-01-01

    In this article, we introduce the method of urban association rules and its uses for extracting frequently appearing combinations of stores that are visited together to characterize shoppers' behaviors. The Apriori algorithm is used to extract the association rules (i.e., if -> result) from customer transaction datasets in a market-basket analysis. An application to our large-scale and anonymized bank card transaction dataset enables us to output linked trips for shopping all over the city: the method enables us to predict the other shops most likely to be visited by a customer given a particular shop that was already visited as an input. In addition, our methodology can consider all transaction activities conducted by customers for a whole city in addition to the location of stores dispersed in the city. This approach enables us to uncover not only simple linked trips such as transition movements between stores but also the edge weight for each linked trip in the specific district. Thus, the proposed methodo...

  10. Uncovering Multiple Populations in Globular Clusters with Washington Photometry

    Science.gov (United States)

    Geisler, Douglas; Cummings, Jeff; Villanova, Sandro; Carraro, Giovanni

    2015-01-01

    Globular Clusters (GCs), long considered as ideal Simple Stellar Populations, are now known to harbor a wide variety of chemical inhomogeneities. Multiple populations (MP) are being found in a growing number of Galactic globular clusters (GCs) via both photometric and spectroscopic techniques. Indeed, it has been suggested that a GC is an object that possesses MP. A definitive investigation of MP in GCs will undoubtedly provide a profound improvement in our understanding of their formation and evolution.However, most studies employ either high resolution VLT spectroscopy, HST photometry or inefficient filters from the ground. A ground-based photometric system which is both efficient and effective would be especially excellent for uncovering MP. We demonstrate that the Washington system meets these goals. The Washington C filter, in addition to being specifically designed for the purpose of detecting MPs, is both much broader and redder than competing UV filters, making it far more efficient at detecting MPs and much less sensitive to reddening and extinction.Our analysis of the well-studied GC NGC 1851 shows indeed that the C filter is both very efficient and effective at detecting its previously discovered MPs in the RGB and SGB, using relatively little telescope time on only a 1-meter telescope. Remarkably, we have also detected an intrinsically broad MS best characterized by two distinct but heavily overlapping populations that cannot be explained by binaries, field stars, or photometric errors. Detailed analysis shows that the MS distribution is in very good agreement with that seen on the RGB. This is the first time MPs in a MS have been discovered from the ground, and just as strikingly, using only a 1-meter telescope. The Washington system thus proves to be a very powerful tool for investigating MPs, and holds particular promise for extragalactic objects where photons are limited.

  11. 78 FR 65711 - Uncovered Innerspring Units From China, South Africa, and Vietnam Institution of Five-Year Reviews

    Science.gov (United States)

    2013-11-01

    ... orders on imports of uncovered innerspring units from South Africa and Vietnam (73 FR 75390 and 75391... uncovered innerspring units from China (74 FR 7661). The Commission is conducting reviews to determine... COMMISSION Uncovered Innerspring Units From China, South Africa, and Vietnam Institution of Five-Year...

  12. UDP-glucose pyrophosphorylase influences polysaccharide synthesis, cell wall components, and hyphal branching in Ganoderma lucidum via regulation of the balance between glucose-1-phosphate and UDP-glucose.

    Science.gov (United States)

    Li, Mengjiao; Chen, Tianxi; Gao, Tan; Miao, Zhigang; Jiang, Ailiang; Shi, Liang; Ren, Ang; Zhao, Mingwen

    2015-09-01

    UDP-glucose pyrophosphorylase (UGP) is a key enzyme involved in carbohydrate metabolism, but there are few studies on the functions of this enzyme in fungi. The ugp gene of Ganoderma lucidum was cloned, and enzyme kinetic parameters of the UGP recombinant protein were determined in vitro, revealing that this protein was functional and catalyzed the reversible conversion between Glc-1-P and UDP-Glc. ugp silencing by RNA interference resulted in changes in the levels of the intermediate metabolites Glc-1-P and UDP-Glc. The compounds and structure of the cell wall in the silenced strains were also altered compared with those in the wild-type strains. Moreover, the number of hyphal branches was also changed in the silenced strains. To verify the role of UGP in hyphal branching, a ugp-overexpressing strain was constructed. The results showed that the number of hyphal branches was influenced by UGP. The mechanism underlying hyphal branching was further investigated by adding exogenous Glc-1-P. Our results showed that hyphal branching was regulated by a change in the cytosolic Ca(2+) concentration, which was affected by the level of the intermediate metabolite Glc-1-P, in G. lucidum. Our findings indicate the existence of an interaction between carbon metabolism and Ca(2+) signaling in this fungus.

  13. Reducing AsA leads to leaf lesion and defence response in knock-down of the AsA biosynthetic enzyme GDP-D-mannose pyrophosphorylase gene in tomato plant.

    Science.gov (United States)

    Zhang, Chanjuan; Ouyang, Bo; Yang, Changxian; Zhang, Xiaohui; Liu, Hui; Zhang, Yuyang; Zhang, Junhong; Li, Hanxia; Ye, Zhibiao

    2013-01-01

    As a vital antioxidant, L-ascorbic acid (AsA) affects diverse biological processes in higher plants. Lack of AsA in cell impairs plant development. In the present study, we manipulated a gene of GDP-mannose pyrophosphorylase which catalyzes the conversion of D-mannose-1-P to GDP-D-mannose in AsA biosynthetic pathway and found out the phenotype alteration of tomato. In the tomato genome, there are four members of GMP gene family and they constitutively expressed in various tissues in distinct expression patterns. As expected, over-expression of SlGMP3 increased total AsA contents and enhanced the tolerance to oxidative stress in tomato. On the contrary, knock-down of SlGMP3 significantly decreased AsA contents below the threshold level and altered the phenotype of tomato plants with lesions and further senescence. Further analysis indicated the causes for this symptom could result from failing to instantly deplete the reactive oxygen species (ROS) as decline of free radical scavenging activity. More ROS accumulated in the leaves and then triggered expressions of defence-related genes and mimic symptom occurred on the leaves similar to hypersensitive responses against pathogens. Consequently, the photosynthesis of leaves was dramatically fallen. These results suggested the vital roles of AsA as an antioxidant in leaf function and defence response of tomato.

  14. Reducing AsA leads to leaf lesion and defence response in knock-down of the AsA biosynthetic enzyme GDP-D-mannose pyrophosphorylase gene in tomato plant.

    Directory of Open Access Journals (Sweden)

    Chanjuan Zhang

    Full Text Available As a vital antioxidant, L-ascorbic acid (AsA affects diverse biological processes in higher plants. Lack of AsA in cell impairs plant development. In the present study, we manipulated a gene of GDP-mannose pyrophosphorylase which catalyzes the conversion of D-mannose-1-P to GDP-D-mannose in AsA biosynthetic pathway and found out the phenotype alteration of tomato. In the tomato genome, there are four members of GMP gene family and they constitutively expressed in various tissues in distinct expression patterns. As expected, over-expression of SlGMP3 increased total AsA contents and enhanced the tolerance to oxidative stress in tomato. On the contrary, knock-down of SlGMP3 significantly decreased AsA contents below the threshold level and altered the phenotype of tomato plants with lesions and further senescence. Further analysis indicated the causes for this symptom could result from failing to instantly deplete the reactive oxygen species (ROS as decline of free radical scavenging activity. More ROS accumulated in the leaves and then triggered expressions of defence-related genes and mimic symptom occurred on the leaves similar to hypersensitive responses against pathogens. Consequently, the photosynthesis of leaves was dramatically fallen. These results suggested the vital roles of AsA as an antioxidant in leaf function and defence response of tomato.

  15. Deepest Image of Exploded Star Uncovers Bipolar Jets

    Science.gov (United States)

    2004-08-01

    A spectacular new image of Cassiopeia A from NASA's Chandra X-ray Observatory released today has nearly 200 times more data than the "First Light" Chandra image of this object made five years ago. The new image reveals clues that the initial explosion caused by the collapse of a massive star was far more complicated than suspected. Chandra Broadband Image of Cassiopeia A Chandra Broadband Image of Cassiopeia A "Although this young supernova remnant has been intensely studied for years, this deep observation is the most detailed ever made of the remains of an exploded star," said Martin Laming of the Naval Research Laboratory in Washington, D.C. Laming is part of a team of scientists led by Una Hwang of the Goddard Space Flight Center in Greenbelt, Maryland. "It is a gold mine of data that astronomers will be panning through for years to come." The one-million-second (about 11.5-day) observation of Cassiopeia A uncovered two large, opposed jet-like structures that extend to about 10 light years from the center of the remnant. Clouds of iron that have remained nearly pure for the approximately 340 years since the explosion were also detected. "The presence of the bipolar jets suggests that jets could be more common in relatively normal supernova explosions than supposed by astronomers," said Hwang. A paper by Hwang, Laming and others on the Cassiopeia A observation will appear in an upcoming issue of The Astrophysical Journal Letters. Chandra Enhanced Silicon Image of Cassiopeia A Chandra Enhanced Silicon Image of Cassiopeia A X-ray spectra show that the jets are rich in silicon atoms and relatively poor in iron atoms. In contrast, fingers of almost pure iron gas extend in a direction nearly perpendicular to the jets. This iron was produced in the central, hottest regions of the star. The high silicon and low iron abundances in the jets indicate that massive, matter-dominated jets were not the immediate cause of the explosion, as these should have carried out large

  16. Endoscopic removal of a spontaneously fractured biliary uncovered self-expandable metal stent.

    Science.gov (United States)

    Kawakubo, Kazumichi; Isayama, Hiroyuki; Tsujino, Takeshi; Nakai, Yousuke; Sasahira, Naoki; Kogure, Hirofumi; Hamada, Tsuyoshi; Nagano, Rie; Miyabayashi, Kouji; Yamamoto, Keisuke; Mohri, Dai; Sasaki, Takashi; Ito, Yukiko; Yamamoto, Natsuyo; Hirano, Kenji; Tada, Minoru; Koike, Kazuhiko

    2012-05-01

    Self-expandable metal stents (SEMS) are widely used for the palliative treatment of unresectable malignant biliary obstruction. However, the long-term durability of SEMSs in biliary strictures is not clear. We describe a case of endoscopic removal of spontaneously fractured uncovered biliary SEMS. A 59-year-old woman presented to our institution with a 1-year history of recurrent cholangitis. Her medical history included a proctectomy for rectal cancer and right hemihepatectomy for liver metastasis 10 years earlier. Five years after these operations, she developed a benign hilar stricture and had an uncovered SEMS placed in another hospital. Endoscopic retrograde cholangiopancreatography demonstrated that the SEMS was torn in half and the distal part of the stent was floating in the dilated common bile duct. The papillary orifice was dilated by endoscopic papillary large balloon dilation (EPLBD) using a 15-mm wire-guided balloon catheter. Subsequently, we inserted biopsy forceps into the bile duct and grasped the distal end of the broken SEMS under fluoroscopy. We successfully removed the fragment of the SEMS from the bile duct, along with the endoscope. The patient was discharged without complications. Placement of an uncovered biliary SEMS is not the preferred treatment for benign biliary strictures. Spontaneous fracture of an uncovered biliary SEMS is an extremely rare complication. We should be aware that stent fracture can occur when placing uncovered biliary SEMSs in patients with a long life expectancy. EPLBD is very useful for retrieving the fractured fragment of SEMS. PMID:22507093

  17. Uncovering flux line correlations in superconductors by reverse monte carlo refinement of neutron scattering data

    OpenAIRE

    Laver, M.; Forgan, E. M.; Abrahamsen, Asger Bech; Bowell, C.; Geue, T.; Cubitt, R.

    2008-01-01

    We describe the use of reverse Monte Carlo refinement to extract structural information from angle-resolved data of a Bragg peak. Starting with small-angle neutron scattering data, the positional order of an ensemble of flux lines in superconducting Nb is revealed. We discuss the uncovered correlation functions in the light of topical theories, in particular, the "Bragg glass" paradigm.

  18. Using Text Mining to Uncover Students' Technology-Related Problems in Live Video Streaming

    Science.gov (United States)

    Abdous, M'hammed; He, Wu

    2011-01-01

    Because of their capacity to sift through large amounts of data, text mining and data mining are enabling higher education institutions to reveal valuable patterns in students' learning behaviours without having to resort to traditional survey methods. In an effort to uncover live video streaming (LVS) students' technology related-problems and to…

  19. Learning "through" Computers: Uncovering Students' Thought Processes while Solving Physics Problems

    Science.gov (United States)

    Soong, Benson

    2008-01-01

    This paper presents a study that illustrates how the author and an in service secondary school teacher used basic synchronous computer mediated communications (CMC) technology to help them uncover students' physics preconceptions and thought processes (including their misconceptions and misunderstandings) in a real class setting. In this paper, I…

  20. Epistemically Virtuous Risk Management : Financial Due Diligence and Uncovering the Madoff Fraud

    NARCIS (Netherlands)

    de Bruin, Boudewijn; Luetge, Christoph; Jauernig, Johanna

    2014-01-01

    The chapter analyses how Bernard Madoff’s Ponzi scheme was uncovered by Harry Markopolos, an employee of Rampart Investment Management, LLC, and the contribution of so-called epistemic virtues to Markopolos’ success. After Rampart had informed the firm about an allegedly highly successful hedge fund

  1. Uncovering One Trilingual Child's Multi-Literacies Development across Informal and Formal Learning Contexts

    Science.gov (United States)

    Kim, Mi Song

    2016-01-01

    Due to globalisation and rapid technological change, today's educators need to help students develop multi-literacy competencies to enable them to function successfully in our culturally and linguistically diverse (CLD) and increasingly connected global and digital society. A qualitative, longitudinal case study attempted to uncover the…

  2. Uncovering flux line correlations in superconductors by reverse monte carlo refinement of neutron scattering data

    DEFF Research Database (Denmark)

    Laver, M.; Forgan, E.M.; Abrahamsen, Asger Bech;

    2008-01-01

    We describe the use of reverse Monte Carlo refinement to extract structural information from angle-resolved data of a Bragg peak. Starting with small-angle neutron scattering data, the positional order of an ensemble of flux lines in superconducting Nb is revealed. We discuss the uncovered correl...

  3. 77 FR 12227 - Long Term 2 Enhanced Surface Water Treatment Rule: Uncovered Finished Water Reservoirs; Public...

    Science.gov (United States)

    2012-02-29

    ... AGENCY 40 CFR Parts 141 and 142 Long Term 2 Enhanced Surface Water Treatment Rule: Uncovered Finished Water Reservoirs; Public Meeting AGENCY: Environmental Protection Agency (EPA). ACTION: Notice of public... requirement in the Long Term 2 Enhanced Surface Water Treatment Rule (LT2 rule). At this meeting, EPA...

  4. Uncovering Expertise-Related Differences in Troubleshooting Performance: Combining Eye Movement and Concurrent Verbal Protocol Data

    NARCIS (Netherlands)

    Van Gog, Tamara; Paas, Fred; Van Merriënboer, Jeroen

    2007-01-01

    This study explored the value of eye movement data for uncovering relatively small expertise-related differences in electrical circuit-troubleshooting performance, and describes that value in relation to concurrent verbal protocols. Results show that in the ‘problem orientation’ phase, higher expert

  5. Feminist Approaches to Triangulation: Uncovering Subjugated Knowledge and Fostering Social Change in Mixed Methods Research

    Science.gov (United States)

    Hesse-Biber, Sharlene

    2012-01-01

    This article explores the deployment of triangulation in the service of uncovering subjugated knowledge and promoting social change for women and other oppressed groups. Feminist approaches to mixed methods praxis create a tight link between the research problem and the research design. An analysis of selected case studies of feminist praxis…

  6. Uncovering the Motivating Factors behind Writing in English in en EFL Context

    Science.gov (United States)

    Büyükyavuz, Oya; Çakir, Ismail

    2014-01-01

    Writing in a language, whether the target or native, is regarded as a complex activity operating on multiple cognitive levels. This study aimed to uncover the factors which motivate teacher trainees of English to write in English in an EFL context. The study also investigated the differences in the ways teacher trainees are motivated in terms of…

  7. Community Mapping in Action: Uncovering Resources and Assets for Young Children and Their Families

    Science.gov (United States)

    Ordonez-Jasis, Rosario; Myck-Wayne, Janice

    2012-01-01

    Community mapping is a promising practice that can assist early intervention/early childhood special education (EI/ECSE) professionals uncover the depth and diversity of community needs, resources, and learning opportunities, in the neighborhoods surrounding their schools. Community mapping is an inquiry-based method that situates learning in the…

  8. Uncovering Influence through Social Network Analysis: The Role of Schools in Education for Sustainable Development

    Science.gov (United States)

    Kolleck, Nina

    2016-01-01

    This paper examines the implementation of Education for Sustainable Development (ESD) in Germany and explores the possibilities of Social Network Analysis (SNA) for uncovering influential actors in educational policy innovation processes. From the theoretical perspective, an actor's influence is inferred from its relative position within…

  9. Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels

    DEFF Research Database (Denmark)

    Kilpeläinen, Tuomas O; Carli, Jayne F Martin; Skowronski, Alicja A;

    2016-01-01

    Leptin is an adipocyte-secreted hormone, the circulating levels of which correlate closely with overall adiposity. Although rare mutations in the leptin (LEP) gene are well known to cause leptin deficiency and severe obesity, no common loci regulating circulating leptin levels have been uncovered...

  10. Uncovering Special Nuclear Materials by Low-energy Nuclear Reaction Imaging

    OpenAIRE

    P. B. Rose; Erickson, A. S.; Mayer, M.; Nattress, J.; Jovanovic, I

    2016-01-01

    Weapons-grade uranium and plutonium could be used as nuclear explosives with extreme destructive potential. The problem of their detection, especially in standard cargo containers during transit, has been described as “searching for a needle in a haystack” because of the inherently low rate of spontaneous emission of characteristic penetrating radiation and the ease of its shielding. Currently, the only practical approach for uncovering well-shielded special nuclear materials is by use of act...

  11. THE SIGNIFICANCE OF CRIMINALISTIC THEORY OF INFORMATION FOR THE PROCESS OF UNCOVERING AND INVESTIGATION OF CRIMES

    OpenAIRE

    Pisarev, Evgeniy

    2014-01-01

    The article proves the necessity of development of general criminalistic theory of information and application of informational approach in the process of uncovering and investigation of the crimes. The place of criminalistic informatiology is determined in general theory of criminalistics as its element. The author proceeds from the fact that the evidence in criminal procedure legislation is determined as the data; this circumstance predetermines the process of collection of evidence as the ...

  12. Multi-frequency complex network from time series for uncovering oil-water flow structure

    Science.gov (United States)

    Gao, Zhong-Ke; Yang, Yu-Xuan; Fang, Peng-Cheng; Jin, Ning-De; Xia, Cheng-Yi; Hu, Li-Dan

    2015-02-01

    Uncovering complex oil-water flow structure represents a challenge in diverse scientific disciplines. This challenge stimulates us to develop a new distributed conductance sensor for measuring local flow signals at different positions and then propose a novel approach based on multi-frequency complex network to uncover the flow structures from experimental multivariate measurements. In particular, based on the Fast Fourier transform, we demonstrate how to derive multi-frequency complex network from multivariate time series. We construct complex networks at different frequencies and then detect community structures. Our results indicate that the community structures faithfully represent the structural features of oil-water flow patterns. Furthermore, we investigate the network statistic at different frequencies for each derived network and find that the frequency clustering coefficient enables to uncover the evolution of flow patterns and yield deep insights into the formation of flow structures. Current results present a first step towards a network visualization of complex flow patterns from a community structure perspective.

  13. Thermal Behavior of a Single Spent Fuel in Water Pool Storage Under Partially Uncovered Condition

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Woo Ram; Park, Hee Sung; Song, Sub Lee; Lee, Jae Young [Handong Global Univ, Pohang (Korea, Republic of)

    2015-10-15

    LOCA in SFP can be led by a partial drain-down or a boil off scenario. In order to predict the response and consequence in such case, exact model on the partially uncovered SFP has to be established. Most studies on accidents in SFP have been done by safety analysis codes such as ATHLET-CD, ASTEC, MAAP, and MELCOR. However, an experimental investigation has not been conducted so far. Schultz et al.(2014) studied experimentally the response of air cooled BWR fuel assembly which is blocked at lower side fluid path. In this study, we experimentally investigated the thermal response of a partially uncovered single nuclear fuel rod (SNFR) in the SFP. The SNFR was 1/4 scaled down in axial length. 1-dimensional numerical analysis model was developed and compared with the result of experiment. An experimental study was conducted for obtaining transient temperature profile data of a modeled single nuclear fuel rod in heating condition under partially uncovered condition. Numerical prediction model was developed also and the prediction result was compared with the experimental result.

  14. Endoscopic management of occluded biliary uncovered metal stents:A multicenter experience

    Institute of Scientific and Technical Information of China (English)

    Panagiotis Katsinelos; Kostas Fasoulas; Stefanos Atmatzidis; Christos Zavos; Jannis Kountouras; Athanasios Beltsis; Grigoris Chatzimavroudis; Dimitris Paikos; George Paroutoglou; Dimitris Kapetanos; Sotiris Terzoudis; Georgia Lazaraki; Ioannis Pilpilidis

    2011-01-01

    AIM:To compare diverse endoscopic interventions in the management of occluded uncovered self-expanding metal stents(SEMSs)that had been placed for palliative treatment of unresectable malignant biliary obstruction.METHODS:A retrospective review was undertaken in 4 tertiary endoscopic centers to determine optimal management of different types of occluded SEMSs.The technical success of performed treatment in occluded SEMSs,the patency of the stent,the need for re-intervention and the financial costs of each treatment were analyzed.RESULTS:Fifty four patients were included in the analysis;21 received Hanaro,19 Wallstent and 14 Flexus.For the relief of obstruction,a plastic stent was inserted in 24 patients,a second SEMS in 25 and mechanical cleaning was performed in 5 patients.The overall median second patency rates between second SEMSs and plastic stents did not differ(133 d for SEMSs vs 106 d for plastic stents;P = 0.856).Similarly,no difference was found between the overall survival of SEMS and plastic stent groups,and no procedure-related complications occurred.Incremental cost analysis showed that successive plastic stenting was a cost-saving strategy at least in Greece.CONCLUSION:Insertion of uncovered SEMSs or plastic stents is a safe and effective treatment for occluded uncovered SEMSs;insertion of plastic stents appears to be the most cost-effective strategy.

  15. 番茄GDP-D-甘露糖焦磷酸化酶cDNA的克隆、表达及定位%Cloning, Expression, and Mapping of GDP-D-mannose Pyrophosphorylase cDNA from Tomato (Lycopersicon esculentum)

    Institute of Scientific and Technical Information of China (English)

    邹礼平; 李汉霞; 欧阳波; 张俊红; 叶志彪

    2006-01-01

    GDP-D-mannose pyrophosphorylase (GMP, EC 2.7.7.22) catalyzes the synthesis of GDP-D-mannose and represents the first committed step in plant ascorbic acid biosynthesis. Using potato GMP cDNA sequence as a querying probe, 65 highly homologous tomato ESTs were obtained from dbEST of GenBank and the putative cDNA sequence of tomato GMP was assembled.The full-length GMP cDNA of tomato was cloned by RACE-PCR with primers designed according to the assembled cDNA sequence. The full-length cDNA sequence contained a complete open reading frame (ORF) of 1 086 bp, which encoded 361 amino acid residues. This gene was designated as LeGMP (GenBank accession No. AY605668). Homology analysis of LeGMP showed a 96% identity with potato GMP and the deduced amino acid showed 99%, 97%, 91% and 89% homology with GMP from potato,tobacco, alfalfa and Arabidopsis thaliana, respectively. Northern blot analysis showed that LeGMP was constitutively expressed in roots, stems, leaves, flowers and fruits of tomato; but the expression levels varied. LeGMP was mapped to 3-D using 75 tomato introgression lines (ILs), each containing a single homozygous RFLP-defined chromosome segment from the green-fruited species Lycopersicon pennellii.%GDP-D-甘露糖焦磷酸化酶催化GDP-D-甘露糖的合成,是植物抗坏血酸生物合成途径中上游的关键酶.以马铃薯GDP-D-甘露糖焦磷酸化酶cDNA序列为信息探针,在GenBank dbEST数据库中找到65条高度同源的番茄EST序列,通过序列拼接及RACE-PCR得到了番茄该基因的全长cDNA序列,命名为LeGMP.LeGMP与马铃薯GDP-D-甘露糖焦磷酸化酶cDNA序列一致率为96%,推导的氨基酸序列与马铃薯、烟草、紫苜蓿、拟南芥的GDP-D-甘露糖焦磷酸化酶基因的一致率分别为99%、97%、91%、89%.经Northern杂交分析,LeGMP在番茄根、茎、叶、花、果实中都有表达,但表达水平有差异.利用75个番茄远缘杂交重组系(IL系)将LeGMP定位在番茄第3

  16. Uncovering Sundanese Values by Analyzing Symbolic Meaning of Ménak Priangan Clothing (1800-1942)

    Science.gov (United States)

    Karmila, M.; Suciati; Widiaty, I.

    2016-04-01

    This study investigates symbolic meanings found in the Sunda ethnic clothing, particularly the Menak Priangan clothing. This study aims to uncover and document those symbolic meanings found in the Menak Priangan clothing as an effort to develop Sunda cultural artefacts of West Java. This study on Menak Priangan clothing applies ethnography (visual) and aesthetic methods. The visual method is utilized in order to uncover local cultural (Sunda) values found in Menak Priangan clothing visualization, including: design, model, name, and representing colours, which then directed towards local Sundanese aesthetic concepts living within the Priangan community. Furthermore, aesthetic method is used to explore role of aesthetic values in empowering visual cultural values within certain community, particularly Sunda aesthetic values. The study results show that since the 19th century, Sunda ethnic clothing was limited to Priangan Sunda only, while traditional clothing wearing by Priangan people reflects their social strata, consisting of: a. Menak Gede (Menak pangluhurna: mayor), bearing raden title, b. Menak Leutik/Santana (mayor assistant), titles: asep, mas, agus, ujang, (Nyimas for woman), c. Somah/Cacah: ordinary people/lower class. Clothing is a cultural phenomenon within certain culture reflecting such society experiences. For Menak people, clothing and its accessories have important meanings. They wear such traditional clothing and accessories as a symbol of power they have within bureaucratic structure and as a symbol of social status they bear within traditional community structure.

  17. Animal models of Huntington's disease: implications in uncovering pathogenic mechanisms and developing therapies

    Institute of Scientific and Technical Information of China (English)

    Lin-hui WANG; Zheng-hong QIN

    2006-01-01

    Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder, which is caused by an abnormal expansion of Cytosine Adenine Guanine (CAG) trinucleotide repeat in the gene making huntingtin (Htt). Despite intensive research efforts devoted to investigate molecular mechanisms of pathogenesis, effective therapy for this devastating disease is still not available at present. The development of various animal models of HD has offered alternative approaches in the study of HD molecular pathology. Many HD models, including chemical-induced models and genetic models, mimic some aspects of HD symptoms and pathology. To date, however, there is no ideal model which replicates all of the essential features of neuropathology and progressive motor and cognitive impairments of human HD. As a result, our understanding of molecular mechanisms of pathogenesis in HD is still limited. A new model is needed in order to uncover the pathogenesis and to develop novel therapies for HD. In this review we discussed usefulness and limitations of various animal and cellular models of HD in uncovering molecular mechanisms of pathogenesis and developing novel therapies for HD.

  18. From detecting astrocyte connectivity to uncovering drug effects in living tissues

    CERN Document Server

    Pires, Marcelo; Vaz, Sandra; Sebastião, Ana; Lind, Pedro G

    2013-01-01

    We introduce a simple procedure of multivariate signal analysis to uncover the connectivity structure among cells composing a living tissue and describe how to apply it for extracting insight on the effect of drugs in the tissue. The procedure is based in the covariance matrix of time resolved activity signals. By determining the time-lag that maximizes covariance one derives the weight of the corresponding connection between cells. Introducing simple constraints, it is possible to conclude if pairs of cells are connected or not and in which direction. After testing the method against synthetic data we apply it to study propagation of $Ca^{2+}$ waves in astrocytes, with the aim of uncovering the cell connectivity structure. Our method shows to be particularly suited for this type of networking signal propagation where signals are pulse-like and have short time-delays, and is shown to be superior to standard methods, namely a multivariate Granger algorithm. Finally, based the statistical analysis of the connec...

  19. Strategies and approaches in plasmidome studies – uncovering plasmid diversity disregarding of linear elements?

    Directory of Open Access Journals (Sweden)

    Julian Rafael Dib

    2015-05-01

    Full Text Available The term plasmid was originally coined for circular, extrachromosomal genetic elements. Today, plasmids are widely recognised not only as important factors facilitating genome restructuring but also as vehicles for the dissemination of beneficial characters within bacterial communities. Plasmid diversity has been uncovered by means of culture–dependent or –independent approaches, such as endogenous or exogenous plasmid isolation as well as PCR-based detection or transposon-aided capture, respectively. High-throughput-sequencing made possible to cover total plasmid populations in a given environment, i.e. the plasmidome, and allowed to address the quality and significance of self-replicating genetic elements. Since such efforts were and still are rather restricted to circular molecules, here we put equal emphasis on the linear plasmids which – despite their frequent occurrence in a large number of bacteria – are largely neglected in prevalent plasmidome conceptions.

  20. Health Detectives: Uncovering the Mysteries of Disease (LBNL Science at the Theater)

    Energy Technology Data Exchange (ETDEWEB)

    Bissell, Mina; Canaria, Christie; Celnicker, Susan; Karpen, Gary

    2012-04-23

    In this April 23, 2012 Science at the Theater event, Berkeley Lab scientists discuss how they uncover the mysteries of disease in unlikely places. Speakers and topics include: World-renowned cancer researcher Mina Bissell's pioneering research on the role of the cellular microenvironment in breast cancer has changed the conversation about the disease. How does DNA instability cause disease? To find out, Christie Canaria images neural networks to study disorders such as Huntington's disease. Fruit flies can tell us a lot about ourselves. Susan Celniker explores the fruit fly genome to learn how our genome works. DNA is not destiny. Gary Karpen explores how environmental factors shape genome function and disease through epigenetics.

  1. Uncovered Interest Parity in Central and Eastern Europe: Convergence and the Global Financial Crisis

    Directory of Open Access Journals (Sweden)

    Fabio Filipozzi

    2012-12-01

    Full Text Available This paper presents tests of uncovered interest parity in Croatia, the Czech Republic, Hungary, Poland and Romania; all countries in Central and Eastern Europe with floating exchange rates. Data are monthly and the trading horizon is three months. The estimations show that the UIP hypothesis is rejected for the full sample from 1999 to 2011 for all five countries. A number of reasons for the rejection were investigated. Rolling regressions show that standard versions of the UIP essentially lose all explanatory power in 2008-10, which was a period in which the global financial crisis led to instability in currency and interest markets in Central and Eastern Europe. Two indicators of global risk aversion were also found to enter significantly in the many UIP estimations. Finally, the size of the interest rates spread also seems to be of importance, at least for Poland and Romania

  2. Strategies and approaches in plasmidome studies—uncovering plasmid diversity disregarding of linear elements?

    Science.gov (United States)

    Dib, Julián R.; Wagenknecht, Martin; Farías, María E.; Meinhardt, Friedhelm

    2015-01-01

    The term plasmid was originally coined for circular, extrachromosomal genetic elements. Today, plasmids are widely recognized not only as important factors facilitating genome restructuring but also as vehicles for the dissemination of beneficial characters within bacterial communities. Plasmid diversity has been uncovered by means of culture-dependent or -independent approaches, such as endogenous or exogenous plasmid isolation as well as PCR-based detection or transposon-aided capture, respectively. High-throughput-sequencing made possible to cover total plasmid populations in a given environment, i.e., the plasmidome, and allowed to address the quality and significance of self-replicating genetic elements. Since such efforts were and still are rather restricted to circular molecules, here we put equal emphasis on the linear plasmids which—despite their frequent occurrence in a large number of bacteria—are largely neglected in prevalent plasmidome conceptions. PMID:26074886

  3. Uncover the Aesthetic Simplicity Associated with Mass Transfer in Energy Materials

    Institute of Scientific and Technical Information of China (English)

    Jiang-Wei Li; Jia Li; Ke-Chun Wen

    2016-01-01

    Aesthetics, referred frequently to as a philosophical term, has played a starring role in forming and evolving a number of aspects of human society, including arts, politics, economics, ethics, etc. Indeed, exploring and investigating the aesthetic phenomena in the scientific field have aroused insightful research findings, which in turn has stimulated research interests in such a science-aesthetics field. In particular, better-evaluated aesthetic aspects of the materials field are expected to be uncovered upon the exceedingly-exposed fundamental breakthroughs in researching the basic structure and functionality of materials. In this report, we glimpse into the aesthetic simplicity of energy materials and comprehend specifically the mass transfer functionalities of key categories of energy materials through an intuitive and bottom-up approach. Our effort aspires to shed new lights on the functionality understanding and manipulation of functional materials in general.

  4. Intraductal radiofrequency ablation of tumour ingrowth into an uncovered metal stent used for inoperable cholangiocarcinoma.

    Science.gov (United States)

    Lui, K L; Li, K K

    2013-12-01

    A 91-year-old woman diagnosed to have an inoperable cholangiocarcinoma had an uncovered metal stent inserted for palliative drainage. About 1.5 years later, tumour ingrowth into the metal stent caused cholangitis. Intraductal radiofrequency ablation was applied to create local coagulative tumour necrosis and the necrotic tissue was removed via a balloon catheter. A plastic stent was inserted to empirically treat any ensuing potential bile duct injury. The patient was discharged without complication with good palliative drainage. Intraductal radiofrequency ablation is a new technique for the treatment of metal stent occlusion due to tumour ingrowths. This is the first case report of this relatively safe and feasible new technique for the treatment of tumour ingrowth into a metal stent used as palliation for malignant biliary obstruction. PMID:24310661

  5. Uncovering the overlapping community structure of complex networks in nature and society

    CERN Document Server

    Pálla, G; Farkas, I; Vicsek, T; Palla, Gergely; Derenyi, Imre; Farkas, Illes; Vicsek, Tamas

    2005-01-01

    Many complex systems in nature and society can be described in terms of networks capturing the intricate web of connections among the units they are made of. A key question is how to interpret the global organization of such networks as the coexistence of their structural subunits (communities) associated with more highly interconnected parts. Identifying these a priori unknown building blocks (such as functionally related proteins, industrial sectors and groups of people) is crucial to the understanding of the structural and functional properties of networks. The existing deterministic methods used for large networks find separated communities, whereas most of the actual networks are made of highly overlapping cohesive groups of nodes. Here we introduce an approach to analysing the main statistical features of the interwoven sets of overlapping communities that makes a step towards uncovering the modular structure of complex systems. After defining a set of new characteristic quantities for the statistics of...

  6. Systems-level approach to uncovering diffusive states and their transitions from single particle trajectories

    CERN Document Server

    Koo, Peter K

    2016-01-01

    The stochastic motions of a diffusing particle contain information concerning the particle's interactions with binding partners and with its local environment. However, accurate determination of the underlying diffusive properties, beyond normal diffusion, has remained challenging when analyzing particle trajectories on an individual basis. Here, we introduce the maximum likelihood estimator (MLE) for confined diffusion and fractional Brownian motion. We demonstrate that this MLE yields improved estimation over traditional mean square displacement analyses. We also introduce a model selection scheme (that we call mleBIC) that classifies individual trajectories to a given diffusion mode. We demonstrate the statistical limitations of classification via mleBIC using simulated data. To overcome these limitations, we introduce a new version of perturbation expectation-maximization (pEMv2), which simultaneously analyzes a collection of particle trajectories to uncover the system of interactions which give rise to u...

  7. Uncovering the role of p53 splice variants in human malignancy: a clinical perspective

    Directory of Open Access Journals (Sweden)

    Surget S

    2013-12-01

    Full Text Available Sylvanie Surget,1,2 Marie P Khoury,1,2 Jean-Christophe Bourdon1,21Dundee Cancer Centre, 2Jacqui Wood Cancer Centre, Ninewells Hospital, University of Dundee, Dundee, UKAbstract: Thirty-five years of research on p53 gave rise to more than 68,000 articles and reviews, but did not allow the uncovering of all the mysteries that this major tumor suppressor holds. How p53 handles the different signals to decide the appropriate cell fate in response to a stress and its implication in tumorigenesis and cancer progression remains unclear. Nevertheless, the uncovering of p53 isoforms has opened new perspectives in the cancer research field. Indeed, the human TP53 gene encodes not only one but at least twelve p53 protein isoforms, which are produced in normal tissues through alternative initiation of translation, usage of alternative promoters, and alternative splicing. In recent years, it became obvious that the different p53 isoforms play an important role in regulating cell fate in response to different stresses in normal cells by differentially regulating gene expression. In cancer cells, abnormal expression of p53 isoforms contributes actively to cancer formation and progression, regardless of TP53 mutation status. They can also be associated with response to treatment, depending on the cell context. The determination of p53 isoform expression and p53 mutation status helps to define different subtypes within a particular cancer type, which would have different responses to treatment. Thus, the understanding of the regulation of p53 isoform expression and their biological activities in relation to the cellular context would constitute an important step toward the improvement of the diagnostic, prognostic, and predictive values of p53 in cancer treatment. This review aims to summarize the involvement of p53 isoforms in cancer and to highlight novel potential therapeutic targets.Keywords: p53, isoforms, p63, p73, alternative splicing, cancer

  8. Metabolism of human insulin after subcutaneous administration: A possible means to uncover insulin misuse.

    Science.gov (United States)

    Thomas, Andreas; Brinkkötter, Paul; Schänzer, Wilhelm; Thevis, Mario

    2015-10-15

    The misuse of insulin for performance enhancement in sport or as toxic agent has frequently been reported in the past. In contrast to synthetic insulin analogues, the administration of recombinant human insulin is hardly recognized by mass spectrometry. The present study was designed to uncover the misuse of recombinant human insulin for doping control purposes as well as for forensic applications. It is hypothesized that an altered metabolite profile of circulating insulin prevails after subcutaneous administration due to exposure of insulin to epidermal proteases. In vitro experiments with skin tissue lysates (S9 fraction and microsomes), different biological fluids (urine, serum, plasma) and recombinant human insulin were performed and the deriving metabolites were characterized by liquid chromatography coupled to high resolution mass spectrometry (HRMS). Afterwards, authentic blood samples of patients suffering from diabetes mellitus and a control group of healthy humans were analysed. Therefore, a method using protein precipitation, ultrafiltration and antibody-coated magnetic beads for purification with subsequent separation by nano-scale liquid chromatography coupled a Q Exactive mass spectrometer was applied. Several metabolites of insulin with C-terminally truncated sequences of the B-chain (and A-chain in minor extent) were identified within this study. Here, the DesB30 human insulin represents the major metabolite in all experiments. This metabolite is frequently found in urine samples due to degradation processes and, thus, disqualifies this matrix for the intended purposes. In contrast, blood samples do commonly not contain DesB30 insulin, which was corroborated by data obtained from the control group. In post-administration blood samples, minute but distinct amounts (approx. 50 pg mL(-1)) of DesB30 insulin were found and suggest the use of this analyte as potential marker for subcutaneous human insulin administration, supporting the attempts to

  9. Uncovering Time-Varying Parameters with the Kalman-Filter and the Flexible Least Squares: a Monte Carlo Study

    OpenAIRE

    Zsolt Darvas; Balázs Varga

    2012-01-01

    Using Monte Carlo methods, we compare the ability of the Kalman-filter, the Kalman-smoother and the flexible least squares (FLS) to uncover the parameters of an autoregression. We find that the ordinary least squares (OLS) estimator performs much better that the time-varying coefficient methods when the parameters are in fact constant, but the OLS does very poorly when parameters change. Neither the FLS, nor the Kalman-filter and Kalman-smoother can uncover sudden changes in parameters. But w...

  10. Uncovering the Links between Prospective Teachers' Personal Responsibility, Academic Optimism, Hope, and Emotions about Teaching: A Mediation Analysis

    Science.gov (United States)

    Eren, Altay

    2014-01-01

    Prospective teachers' sense of personal responsibility has not been examined together with their academic optimism, hope, and emotions about teaching in a single study to date. However, to consider hope, academic optimism, and emotions about teaching together with personal responsibility is important to uncover the factors affecting…

  11. Water Balance Components in Covered and Uncovered Soil Growing Irrigated Muskmelon

    Directory of Open Access Journals (Sweden)

    Paulo Leonel Libardi

    2015-10-01

    Full Text Available ABSTRACT Knowledge of the terms (or processes of the soil water balance equation or simply the components of the soil water balance over the cycle of an agricultural crop is essential for soil and water management. Thus, the aim of this study was to analyze these components in a Cambissolo Háplico (Haplocambids growing muskmelon (Cucumis melo L. under drip irrigation, with covered and uncovered soil, in the municipality of Baraúna, State of Rio Grande do Norte, Brazil (05º 04’ 48” S, 37º 37’ 00” W. Muskmelon, variety AF-646, was cultivated in a flat experimental area (20 × 50 m. The crop was spaced at 2.00 m between rows and 0.35 m between plants, in a total of ten 50-m-long plant rows. At points corresponding to ⅓ and ⅔ of each plant row, four tensiometers (at a distance of 0.1 m from each other were set up at the depths of 0.1, 0.2, 0.3, and 0.4 m, adjacent to the irrigation line (0.1 m from the plant row, between two selected plants. Five random plant rows were mulched using dry leaves of banana (Musa sp. along the drip line, forming a 0.5-m-wide strip, which covered an area of 25 m2 per of plant row with covered soil. In the other five rows, there was no covering. Thus, the experiment consisted of two treatments, with 10 replicates, in four phenological stages: initial (7-22 DAS - days after sowing, growing (22-40 DAS, fruiting (40-58 DAS and maturation (58-70 DAS. Rainfall was measured with a rain gauge and water storage was estimated by the trapezoidal method, based on tensiometer readings and soil water retention curves. For soil water flux densities at 0.3 m, the tensiometers at the depths of 0.2, 0.3, and 0.4 m were considered; the tensiometer at 0.3 m was used to estimate soil water content from the soil water retention curve at this depth, and the other two to calculate the total potential gradient. Flux densities were calculated through use of the Darcy-Buckingham equation, with hydraulic conductivity determined by

  12. Uncovering the pKa dependent fluorescence quenching of carbon dots induced by chlorophenols

    Science.gov (United States)

    Zhang, Yu; Wang, Yu; Guan, Yafeng; Feng, Liang

    2015-03-01

    Fluorescence quenching induced by targets is always an alluring strategy to elucidate the possible photoluminescence origin of carbon dots. In this study, a new kind of N, S co-doped carbon dots (NSCDs) was synthesized and the fluorescence of NSCDs was surprisingly found to be quenched by chlorophenols (CPs) in a pKa dependent mode. Detailed investigation of this behavior demonstrated that phenolate was the responsible species and N and/or S dopants in NSCDs failed to play a role in the fluorescence quenching. Further evidence uncovered that the quenching was a static one, where a non-fluorescent intermediate was formed between electron-deficient C&z.dbd;O on the CDs surface and the electron-rich phenolic oxygen anion of chlorophenolate via nucleophilic addition. Moreover, one of the main photoluminescence origins of this kind of CDs was derived, namely surface emissive sites mostly attributed to carbonyl groups.Fluorescence quenching induced by targets is always an alluring strategy to elucidate the possible photoluminescence origin of carbon dots. In this study, a new kind of N, S co-doped carbon dots (NSCDs) was synthesized and the fluorescence of NSCDs was surprisingly found to be quenched by chlorophenols (CPs) in a pKa dependent mode. Detailed investigation of this behavior demonstrated that phenolate was the responsible species and N and/or S dopants in NSCDs failed to play a role in the fluorescence quenching. Further evidence uncovered that the quenching was a static one, where a non-fluorescent intermediate was formed between electron-deficient C&z.dbd;O on the CDs surface and the electron-rich phenolic oxygen anion of chlorophenolate via nucleophilic addition. Moreover, one of the main photoluminescence origins of this kind of CDs was derived, namely surface emissive sites mostly attributed to carbonyl groups. Electronic supplementary information (ESI) available: Texts, figures and tables giving partial experimental procedures, detailed characterizations

  13. Combining Novel Simulation Methods and Nucleation Theory to Uncover the Secrets of Gas Hydrates

    Energy Technology Data Exchange (ETDEWEB)

    Keyes, Thomas [Boston Univ., MA (United States). Dept. of Chemistry

    2016-04-14

    Conventional computer simulation methods fail for some of the most important problems. With the design and application of innovative algorithms, this project achieved a breakthrough for the case of systems undergoing first-order phase transitions. We gave a complete simulation protocol based upon a well optimized version of our "generalized replica exchange method". The transition of primary interest was gas hydrate formation, a process of significance for climate science and natural gas retrieval. Since hydrates consist of guest molecules in the cages of a water matrix, β ice, the freezing and melting of water was also studied. New information was uncovered about the transition pathways and thermodynamics. Some highlights are 1. the finding that in a very dilute solution without deep supercooling, representative of real-world conditions and very challenging to conventional algorithms, methane can act as a catalyst to drive the formation of large amounts of β ice with empty cages as metastable intermediates, which might be filled by additional methane in a mechanism for hydrate formation, and 2. illumination of the role of metastable cubic ice in water freezing, with determination of the surface tensions of the cubic, hexagonal, and β ices, and the free energy difference of cubic vs hexagonal ice. Work was begun on lipid systems, bilayers and nanoreactors promising for energy-related photoreductions, and targets for future research. Our methods yielded what is arguably the most complete description of the composite lipid/water phases and the transition pathways among them.

  14. Gene Expression Deconvolution for Uncovering Molecular Signatures in Response to Therapy in Juvenile Idiopathic Arthritis.

    Directory of Open Access Journals (Sweden)

    Ang Cui

    Full Text Available Gene expression-based signatures help identify pathways relevant to diseases and treatments, but are challenging to construct when there is a diversity of disease mechanisms and treatments in patients with complex diseases. To overcome this challenge, we present a new application of an in silico gene expression deconvolution method, ISOpure-S1, and apply it to identify a common gene expression signature corresponding to response to treatment in 33 juvenile idiopathic arthritis (JIA patients. Using pre- and post-treatment gene expression profiles only, we found a gene expression signature that significantly correlated with a reduction in the number of joints with active arthritis, a measure of clinical outcome (Spearman rho = 0.44, p = 0.040, Bonferroni correction. This signature may be associated with a decrease in T-cells, monocytes, neutrophils and platelets. The products of most differentially expressed genes include known biomarkers for JIA such as major histocompatibility complexes and interleukins, as well as novel biomarkers including α-defensins. This method is readily applicable to expression datasets of other complex diseases to uncover shared mechanistic patterns in heterogeneous samples.

  15. Uncovering Special Nuclear Materials by Low-energy Nuclear Reaction Imaging

    Science.gov (United States)

    Rose, P. B.; Erickson, A. S.; Mayer, M.; Nattress, J.; Jovanovic, I.

    2016-01-01

    Weapons-grade uranium and plutonium could be used as nuclear explosives with extreme destructive potential. The problem of their detection, especially in standard cargo containers during transit, has been described as “searching for a needle in a haystack” because of the inherently low rate of spontaneous emission of characteristic penetrating radiation and the ease of its shielding. Currently, the only practical approach for uncovering well-shielded special nuclear materials is by use of active interrogation using an external radiation source. However, the similarity of these materials to shielding and the required radiation doses that may exceed regulatory limits prevent this method from being widely used in practice. We introduce a low-dose active detection technique, referred to as low-energy nuclear reaction imaging, which exploits the physics of interactions of multi-MeV monoenergetic photons and neutrons to simultaneously measure the material’s areal density and effective atomic number, while confirming the presence of fissionable materials by observing the beta-delayed neutron emission. For the first time, we demonstrate identification and imaging of uranium with this novel technique using a simple yet robust source, setting the stage for its wide adoption in security applications. PMID:27087555

  16. Uncovering molecular relaxation processes with nonlinear spectroscopies in the deep UV

    International Nuclear Information System (INIS)

    Highlights: • We discuss the outlook for multidimensional spectroscopies in the deep UV. • Photophysics are examined in small DNA components at cryogenic temperatures. • Wavepacket motions are detected in ring-opening systems with 2DUV spectroscopy. • Measurements of electronic wavepacket motions in molecules are proposed. - Abstract: Nonlinear laser spectroscopies in the deep UV spectral range are motivated by studies of biological systems and elementary processes in small molecules. This perspective article discusses recent technical advances in this area with a particular emphasis on diffractive optic based approaches to four-wave mixing spectroscopies. Applications to two classes of systems illustrate present experimental capabilities. First, experiments on DNA components at cryogenic temperatures are used to uncover features of excited state potential energy surfaces and vibrational cooling mechanisms. Second, sub-200 fs internal conversion processes and coherent wavepacket motions are investigated in cyclohexadiene and α-terpinene. Finally, we propose new experimental directions that combine methods for producing few-cycle UV laser pulses in noble gases with incoherent detection methods (e.g., photoionization) in experiments with time resolution near a singlefemtosecond. These measurements are motivated by knowledge of extremely fast non-adiabatic dynamics and the resolution of electronic wavepacket motions in molecules

  17. Gene Expression Deconvolution for Uncovering Molecular Signatures in Response to Therapy in Juvenile Idiopathic Arthritis.

    Science.gov (United States)

    Cui, Ang; Quon, Gerald; Rosenberg, Alan M; Yeung, Rae S M; Morris, Quaid

    2016-01-01

    Gene expression-based signatures help identify pathways relevant to diseases and treatments, but are challenging to construct when there is a diversity of disease mechanisms and treatments in patients with complex diseases. To overcome this challenge, we present a new application of an in silico gene expression deconvolution method, ISOpure-S1, and apply it to identify a common gene expression signature corresponding to response to treatment in 33 juvenile idiopathic arthritis (JIA) patients. Using pre- and post-treatment gene expression profiles only, we found a gene expression signature that significantly correlated with a reduction in the number of joints with active arthritis, a measure of clinical outcome (Spearman rho = 0.44, p = 0.040, Bonferroni correction). This signature may be associated with a decrease in T-cells, monocytes, neutrophils and platelets. The products of most differentially expressed genes include known biomarkers for JIA such as major histocompatibility complexes and interleukins, as well as novel biomarkers including α-defensins. This method is readily applicable to expression datasets of other complex diseases to uncover shared mechanistic patterns in heterogeneous samples. PMID:27244050

  18. MARS A Cosmic Stepping Stone Uncovering Humanity’s Cosmic Context

    CERN Document Server

    Nolan, Kevin

    2008-01-01

    The questions of our origin and cosmic abundance of life are among the most compelling facing humanity. We have determined much about the nature and origin of the Universe and our place in it, but with virtually all evidence of our origin long since gone from our world and an unimaginably vast Universe still to explore, defining answers are difficult to obtain. For all of the difficulties facing us however, the planet Mars may act as a ‘cosmic stepping stone’ in uncovering some of the answers. Although different today, the origin and early history of both Earth and Mars may have been similar enough to consider an origin to life on both. But because Mars’ planetary processes collapsed over three billion years ago – just as life was beginning to flourish on Earth – a significant and unique record of activity from that era perhaps relevant to the origin of life still resides there today. In recognition of this, both the US and Europe are currently engaged in one of the most ambitious programs of explor...

  19. Uncovering cryptic species diversity of a termite community in a West African savanna.

    Science.gov (United States)

    Hausberger, Barbara; Kimpel, Dorothea; van Neer, Abbo; Korb, Judith

    2011-12-01

    To uncover the termite species diversity of a natural African savanna ecosystem, we combined morphological analyses and sequencing of three gene fragments (cytochrome oxidase I, cytochrome oxidase II and 28SrDNA, total length about 2450 bp) to infer putative species from phylogenetic trees. We identified 18 putative species clusters with high support values and which we retrieved consistently. Samples from two genera (Ancistrotermes and Microcerotermes) were excluded from the mitochondrial phylogenetic analyses as they might represent nuclear mitochondrial sequences (NUMTs). In total, our data suggest a species richness of at least 20 species, all but one belonging to the Termitidae (higher termites), and among them the fungus-growing Macrotermitinae were most prevalent with at least nine putative species. Within the fungus-growers the most species-rich genus was Microtermes and its four putative species were all cryptic species. Their abundance in the samples suggests that they play an important ecological role which is completely unstudied also due to the lack of reliable identification means. Our study shows that morphological traits are unreliable means of species identification for several termite taxa. Yet reliable and consistent identification is necessary for studying the functional role of termites in ecosystem and global processes.

  20. Percutaneous Treatment of Malignant Jaundice Due to Extrahepatic Cholangiocarcinoma: Covered Viabil Stent Versus Uncovered Wallstents

    International Nuclear Information System (INIS)

    To compare clinical effectiveness of Viabil-covered stents versus uncovered metallic Wallstents, for palliation of malignant jaundice due to extrahepatic cholangiocarcinoma, 60 patients were enrolled in a prospective and randomized study. In half of the patients a bare Wallstent was used, and in the other half a Viabil biliary stent. Patients were followed up until death. Primary patency, survival, complication rates, and mean cost were calculated in both groups. Stent dysfunction occurred in 9 (30%) patients in the bare stent group after a mean period of 133.1 days and in 4 (13.3%) patients in the covered stent group after a mean of 179.5 days. The incidence of stent dysfunction was significantly lower in the covered stent group (P = 0.046). Tumor ingrowth occurred exclusively in the bare stent group (P = 0.007). Median survival was 180.5 days for the Wallstent and 243.5 days for the Viabil group (P = 0.039). Complications and mean cost were similar in the two groups. Viabil stent-grafts proved to be significantly superior to Wallstents for the palliation of malignant jaundice due to extrahepatic cholangiocarcinoma, with comparable cost and complication rates. Appropriate patient selection should be performed prior to stent placement.

  1. Percutaneous treatment of malignant jaundice due to extrahepatic cholangiocarcinoma: covered Viabil stent versus uncovered Wallstents.

    Science.gov (United States)

    Krokidis, Miltiadis; Fanelli, Fabrizio; Orgera, Gianluigi; Bezzi, Mario; Passariello, Roberto; Hatzidakis, Adam

    2010-02-01

    To compare clinical effectiveness of Viabil-covered stents versus uncovered metallic Wallstents, for palliation of malignant jaundice due to extrahepatic cholangiocarcinoma, 60 patients were enrolled in a prospective and randomized study. In half of the patients a bare Wallstent was used, and in the other half a Viabil biliary stent. Patients were followed up until death. Primary patency, survival, complication rates, and mean cost were calculated in both groups. Stent dysfunction occurred in 9 (30%) patients in the bare stent group after a mean period of 133.1 days and in 4 (13.3%) patients in the covered stent group after a mean of 179.5 days. The incidence of stent dysfunction was significantly lower in the covered stent group (P = 0.046). Tumor ingrowth occurred exclusively in the bare stent group (P = 0.007). Median survival was 180.5 days for the Wallstent and 243.5 days for the Viabil group (P = 0.039). Complications and mean cost were similar in the two groups. Viabil stent-grafts proved to be significantly superior to Wallstents for the palliation of malignant jaundice due to extrahepatic cholangiocarcinoma, with comparable cost and complication rates. Appropriate patient selection should be performed prior to stent placement. PMID:19495871

  2. Uncovering Special Nuclear Materials by Low-energy Nuclear Reaction Imaging

    Science.gov (United States)

    Rose, P. B.; Erickson, A. S.; Mayer, M.; Nattress, J.; Jovanovic, I.

    2016-04-01

    Weapons-grade uranium and plutonium could be used as nuclear explosives with extreme destructive potential. The problem of their detection, especially in standard cargo containers during transit, has been described as “searching for a needle in a haystack” because of the inherently low rate of spontaneous emission of characteristic penetrating radiation and the ease of its shielding. Currently, the only practical approach for uncovering well-shielded special nuclear materials is by use of active interrogation using an external radiation source. However, the similarity of these materials to shielding and the required radiation doses that may exceed regulatory limits prevent this method from being widely used in practice. We introduce a low-dose active detection technique, referred to as low-energy nuclear reaction imaging, which exploits the physics of interactions of multi-MeV monoenergetic photons and neutrons to simultaneously measure the material’s areal density and effective atomic number, while confirming the presence of fissionable materials by observing the beta-delayed neutron emission. For the first time, we demonstrate identification and imaging of uranium with this novel technique using a simple yet robust source, setting the stage for its wide adoption in security applications.

  3. Systematic Triple-Mutant Analysis Uncovers Functional Connectivity between Pathways Involved in Chromosome Regulation

    Directory of Open Access Journals (Sweden)

    James E. Haber

    2013-06-01

    Full Text Available Genetic interactions reveal the functional relationships between pairs of genes. In this study, we describe a method for the systematic generation and quantitation of triple mutants, termed triple-mutant analysis (TMA. We have used this approach to interrogate partially redundant pairs of genes in S. cerevisiae, including ASF1 and CAC1, two histone chaperones. After subjecting asf1Δ cac1Δ to TMA, we found that the Swi/Snf Rdh54 protein compensates for the absence of Asf1 and Cac1. Rdh54 more strongly associates with the chromatin apparatus and the pericentromeric region in the double mutant. Moreover, Asf1 is responsible for the synthetic lethality observed in cac1Δ strains lacking the HIRA-like proteins. A similar TMA was carried out after deleting both CLB5 and CLB6, cyclins that regulate DNA replication, revealing a strong functional connection to chromosome segregation. This approach can reveal functional redundancies that cannot be uncovered through traditional double-mutant analyses.

  4. Unexpected novel relational links uncovered by extensive developmental profiling of nuclear receptor expression.

    Directory of Open Access Journals (Sweden)

    Stéphanie Bertrand

    2007-11-01

    Full Text Available Nuclear receptors (NRs are transcription factors that are implicated in several biological processes such as embryonic development, homeostasis, and metabolic diseases. To study the role of NRs in development, it is critically important to know when and where individual genes are expressed. Although systematic expression studies using reverse transcriptase PCR and/or DNA microarrays have been performed in classical model systems such as Drosophila and mouse, no systematic atlas describing NR involvement during embryonic development on a global scale has been assembled. Adopting a systems biology approach, we conducted a systematic analysis of the dynamic spatiotemporal expression of all NR genes as well as their main transcriptional coregulators during zebrafish development (101 genes using whole-mount in situ hybridization. This extensive dataset establishes overlapping expression patterns among NRs and coregulators, indicating hierarchical transcriptional networks. This complete developmental profiling provides an unprecedented examination of expression of NRs during embryogenesis, uncovering their potential function during central nervous system and retina formation. Moreover, our study reveals that tissue specificity of hormone action is conferred more by the receptors than by their coregulators. Finally, further evolutionary analyses of this global resource led us to propose that neofunctionalization of duplicated genes occurs at the levels of both protein sequence and RNA expression patterns. Altogether, this expression database of NRs provides novel routes for leading investigation into the biological function of each individual NR as well as for the study of their combinatorial regulatory circuitry within the superfamily.

  5. Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels.

    Science.gov (United States)

    Kilpeläinen, Tuomas O; Carli, Jayne F Martin; Skowronski, Alicja A; Sun, Qi; Kriebel, Jennifer; Feitosa, Mary F; Hedman, Åsa K; Drong, Alexander W; Hayes, James E; Zhao, Jinghua; Pers, Tune H; Schick, Ursula; Grarup, Niels; Kutalik, Zoltán; Trompet, Stella; Mangino, Massimo; Kristiansson, Kati; Beekman, Marian; Lyytikäinen, Leo-Pekka; Eriksson, Joel; Henneman, Peter; Lahti, Jari; Tanaka, Toshiko; Luan, Jian'an; Del Greco M, Fabiola; Pasko, Dorota; Renström, Frida; Willems, Sara M; Mahajan, Anubha; Rose, Lynda M; Guo, Xiuqing; Liu, Yongmei; Kleber, Marcus E; Pérusse, Louis; Gaunt, Tom; Ahluwalia, Tarunveer S; Ju Sung, Yun; Ramos, Yolande F; Amin, Najaf; Amuzu, Antoinette; Barroso, Inês; Bellis, Claire; Blangero, John; Buckley, Brendan M; Böhringer, Stefan; I Chen, Yii-Der; de Craen, Anton J N; Crosslin, David R; Dale, Caroline E; Dastani, Zari; Day, Felix R; Deelen, Joris; Delgado, Graciela E; Demirkan, Ayse; Finucane, Francis M; Ford, Ian; Garcia, Melissa E; Gieger, Christian; Gustafsson, Stefan; Hallmans, Göran; Hankinson, Susan E; Havulinna, Aki S; Herder, Christian; Hernandez, Dena; Hicks, Andrew A; Hunter, David J; Illig, Thomas; Ingelsson, Erik; Ioan-Facsinay, Andreea; Jansson, John-Olov; Jenny, Nancy S; Jørgensen, Marit E; Jørgensen, Torben; Karlsson, Magnus; Koenig, Wolfgang; Kraft, Peter; Kwekkeboom, Joanneke; Laatikainen, Tiina; Ladwig, Karl-Heinz; LeDuc, Charles A; Lowe, Gordon; Lu, Yingchang; Marques-Vidal, Pedro; Meisinger, Christa; Menni, Cristina; Morris, Andrew P; Myers, Richard H; Männistö, Satu; Nalls, Mike A; Paternoster, Lavinia; Peters, Annette; Pradhan, Aruna D; Rankinen, Tuomo; Rasmussen-Torvik, Laura J; Rathmann, Wolfgang; Rice, Treva K; Brent Richards, J; Ridker, Paul M; Sattar, Naveed; Savage, David B; Söderberg, Stefan; Timpson, Nicholas J; Vandenput, Liesbeth; van Heemst, Diana; Uh, Hae-Won; Vohl, Marie-Claude; Walker, Mark; Wichmann, Heinz-Erich; Widén, Elisabeth; Wood, Andrew R; Yao, Jie; Zeller, Tanja; Zhang, Yiying; Meulenbelt, Ingrid; Kloppenburg, Margreet; Astrup, Arne; Sørensen, Thorkild I A; Sarzynski, Mark A; Rao, D C; Jousilahti, Pekka; Vartiainen, Erkki; Hofman, Albert; Rivadeneira, Fernando; Uitterlinden, André G; Kajantie, Eero; Osmond, Clive; Palotie, Aarno; Eriksson, Johan G; Heliövaara, Markku; Knekt, Paul B; Koskinen, Seppo; Jula, Antti; Perola, Markus; Huupponen, Risto K; Viikari, Jorma S; Kähönen, Mika; Lehtimäki, Terho; Raitakari, Olli T; Mellström, Dan; Lorentzon, Mattias; Casas, Juan P; Bandinelli, Stefanie; März, Winfried; Isaacs, Aaron; van Dijk, Ko W; van Duijn, Cornelia M; Harris, Tamara B; Bouchard, Claude; Allison, Matthew A; Chasman, Daniel I; Ohlsson, Claes; Lind, Lars; Scott, Robert A; Langenberg, Claudia; Wareham, Nicholas J; Ferrucci, Luigi; Frayling, Timothy M; Pramstaller, Peter P; Borecki, Ingrid B; Waterworth, Dawn M; Bergmann, Sven; Waeber, Gérard; Vollenweider, Peter; Vestergaard, Henrik; Hansen, Torben; Pedersen, Oluf; Hu, Frank B; Eline Slagboom, P; Grallert, Harald; Spector, Tim D; Jukema, J W; Klein, Robert J; Schadt, Erik E; Franks, Paul W; Lindgren, Cecilia M; Leibel, Rudolph L; Loos, Ruth J F

    2016-01-01

    Leptin is an adipocyte-secreted hormone, the circulating levels of which correlate closely with overall adiposity. Although rare mutations in the leptin (LEP) gene are well known to cause leptin deficiency and severe obesity, no common loci regulating circulating leptin levels have been uncovered. Therefore, we performed a genome-wide association study (GWAS) of circulating leptin levels from 32,161 individuals and followed up loci reaching P<10(-6) in 19,979 additional individuals. We identify five loci robustly associated (P<5 × 10(-8)) with leptin levels in/near LEP, SLC32A1, GCKR, CCNL1 and FTO. Although the association of the FTO obesity locus with leptin levels is abolished by adjustment for BMI, associations of the four other loci are independent of adiposity. The GCKR locus was found associated with multiple metabolic traits in previous GWAS and the CCNL1 locus with birth weight. Knockdown experiments in mouse adipose tissue explants show convincing evidence for adipogenin, a regulator of adipocyte differentiation, as the novel causal gene in the SLC32A1 locus influencing leptin levels. Our findings provide novel insights into the regulation of leptin production by adipose tissue and open new avenues for examining the influence of variation in leptin levels on adiposity and metabolic health. PMID:26833098

  6. Multiple omics uncovers host-gut microbial mutualism during prebiotic fructooligosaccharide supplementation.

    Science.gov (United States)

    Kato, Tamotsu; Fukuda, Shinji; Fujiwara, Akemi; Suda, Wataru; Hattori, Masahira; Kikuchi, Jun; Ohno, Hiroshi

    2014-10-01

    Fructooligosaccharide (FOS), a prebiotic well known for its health-promoting properties, can improve the human gut ecosystem most likely through changes in its microbial composition. However, the detailed mechanism(s) of action of FOS in the modulation of the gut ecosystem remain(s) obscure. Traditional methods of profiling microbes and metabolites could barely show any significant features due to the existence of large interindividual differences, but our novel microbe-metabolite correlation approach, combined with faecal immunoglobulin A (IgA) measurements, has revealed that the induction of mucosal IgA by FOS supplementation correlated with the presence of specific bacteria. Furthermore, the metabolic dynamics of butyrate, L-phenylalanine, L-lysine and tyramine were positively correlated with that of these bacteria and IgA production, whereas p-cresol was negatively correlated. Taken together, our focused intraindividual analysis with omics approaches is a powerful strategy for uncovering the gut molecular network and could provide a new vista for understanding the human gut ecosystem. PMID:24848698

  7. CHANG-ES VIII: Uncovering Hidden AGN Activity in Radio Polarization

    CERN Document Server

    Irwin, Judith A; Damas-Segovia, A; Beck, Rainer; English, Jayanne; Heald, George; Henriksen, Richard N; Krause, Marita; Li, Jiang-Tao; Rand, Richard J; Wang, Q Daniel; Wiegert, Theresa; Kamieneski, Patrick; Paré, Dylan; Sullivan, Kendall

    2016-01-01

    We report on C-band (5 - 7 GHz) observations of the galaxy, NGC~2992, from the CHANG-ES sample. This galaxy displays an embedded nuclear double-lobed radio morphology within its spiral disk, as revealed in linearly polarized emission but {\\it not} in total intensity emission. The radio lobes are kpc-sized, similar to what has been observed in the past for other Seyfert galaxies, and show ordered magnetic fields. NGC~2992 has shown previous evidence for AGN-related activity, but not the linearly polarized radio features that we present here. We draw attention to this galaxy as the first clear example (and prototype) of bipolar radio outflow that is revealed in linearly polarized emission only. Such polarization observations, which are unobscured by dust, provide a new tool for uncovering hidden weak AGN activity which may otherwise be masked by brighter unpolarized emission within which it is embedded. The radio lobes observed in NGC~2992 are interacting with the surrounding interstellar medium and offer new o...

  8. Uncovering Special Nuclear Materials by Low-energy Nuclear Reaction Imaging.

    Science.gov (United States)

    Rose, P B; Erickson, A S; Mayer, M; Nattress, J; Jovanovic, I

    2016-04-18

    Weapons-grade uranium and plutonium could be used as nuclear explosives with extreme destructive potential. The problem of their detection, especially in standard cargo containers during transit, has been described as "searching for a needle in a haystack" because of the inherently low rate of spontaneous emission of characteristic penetrating radiation and the ease of its shielding. Currently, the only practical approach for uncovering well-shielded special nuclear materials is by use of active interrogation using an external radiation source. However, the similarity of these materials to shielding and the required radiation doses that may exceed regulatory limits prevent this method from being widely used in practice. We introduce a low-dose active detection technique, referred to as low-energy nuclear reaction imaging, which exploits the physics of interactions of multi-MeV monoenergetic photons and neutrons to simultaneously measure the material's areal density and effective atomic number, while confirming the presence of fissionable materials by observing the beta-delayed neutron emission. For the first time, we demonstrate identification and imaging of uranium with this novel technique using a simple yet robust source, setting the stage for its wide adoption in security applications.

  9. Uncovering Special Nuclear Materials by Low-energy Nuclear Reaction Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Rose Jr., P.B.; Erickson, A. S.; Mayer, Michael F.; Nattress, J.; Jovanovic , I

    2016-04-18

    Weapons-grade uranium and plutonium could be used as nuclear explosives with extreme destructive potential. The problem of their detection, especially in standard cargo containers during transit, has been described as “searching for a needle in a haystack” because of the inherently low rate of spontaneous emission of characteristic penetrating radiation and the ease of its shielding. Currently, the only practical approach for uncovering well-shielded special nuclear materials is by use of active interrogation using an external radiation source. However, the similarity of these materials to shielding and the required radiation doses that may exceed regulatory limits prevent this method from being widely used in practice. We introduce a low-dose active detection technique, referred to as low-energy nuclear reaction imaging, which exploits the physics of interactions of multi-MeV monoenergetic photons and neutrons to simultaneously measure the material’s areal density and effective atomic number, while confirming the presence of fissionable materials by observing the beta-delayed neutron emission. For the first time, we demonstrate identification and imaging of uranium with this novel technique using a simple yet robust source, setting the stage for its wide adoption in security applications.

  10. Novel resistance functions uncovered using functional metagenomic investigations of resistance reservoirs

    Directory of Open Access Journals (Sweden)

    Erica C. Pehrsson

    2013-06-01

    Full Text Available Rates of infection with antibiotic-resistant bacteria have increased precipitously over the past several decades, with far-reaching healthcare and societal costs. Recent evidence has established a link between antibiotic resistance genes in human pathogens and those found in non-pathogenic, commensal, and environmental organisms, prompting deeper investigation of natural and human-associated reservoirs of antibiotic resistance. Functional metagenomic selections, in which shotgun-cloned DNA fragments are selected for their ability to confer survival to an indicator host, have been increasingly applied to the characterization of many antibiotic resistance reservoirs. These experiments have demonstrated that antibiotic resistance genes are highly diverse and widely distributed, many times bearing little to no similarity to known sequences. Through unbiased selections for survival to antibiotic exposure, functional metagenomics can improve annotations by reducing the discovery of false-positive resistance and by allowing for the identification of previously unrecognizable resistance genes. In this review, we summarize the novel resistance functions uncovered using functional metagenomic investigations of natural and human-impacted resistance reservoirs. Examples of novel antibiotic resistance genes include those highly divergent from known sequences, those for which sequence is entirely unable to predict resistance function, bifunctional resistance genes, and those with unconventional, atypical resistance mechanisms. Overcoming antibiotic resistance in the clinic will require a better understanding of existing resistance reservoirs and the dissemination networks that govern horizontal gene exchange, informing best practices to limit the spread of resistance-conferring genes to human pathogens.

  11. Gene Expression Deconvolution for Uncovering Molecular Signatures in Response to Therapy in Juvenile Idiopathic Arthritis

    Science.gov (United States)

    Rosenberg, Alan M.; Yeung, Rae S. M.; Morris, Quaid

    2016-01-01

    Gene expression-based signatures help identify pathways relevant to diseases and treatments, but are challenging to construct when there is a diversity of disease mechanisms and treatments in patients with complex diseases. To overcome this challenge, we present a new application of an in silico gene expression deconvolution method, ISOpure-S1, and apply it to identify a common gene expression signature corresponding to response to treatment in 33 juvenile idiopathic arthritis (JIA) patients. Using pre- and post-treatment gene expression profiles only, we found a gene expression signature that significantly correlated with a reduction in the number of joints with active arthritis, a measure of clinical outcome (Spearman rho = 0.44, p = 0.040, Bonferroni correction). This signature may be associated with a decrease in T-cells, monocytes, neutrophils and platelets. The products of most differentially expressed genes include known biomarkers for JIA such as major histocompatibility complexes and interleukins, as well as novel biomarkers including α-defensins. This method is readily applicable to expression datasets of other complex diseases to uncover shared mechanistic patterns in heterogeneous samples. PMID:27244050

  12. Proteomic Analysis of Cytokeratin Isoforms Uncovers Association with Survival in Lung Adenocarcinoma

    Directory of Open Access Journals (Sweden)

    Tarek G. Gharib

    2002-01-01

    Full Text Available Cytokeratins. (CK are intermediate filaments whose expression is often altered in epithelial cancer. Systematic identification of lung adenocarcinoma proteins using two-dimensional polyacrylamide gel electrophoresis and mass spectrometry has uncovered numerous CK isoforms. In this study, 93 lung adenocarcinomas. (64 stage I and 29 stage III and 10 uninvolved lung samples were quantitatively examined for protein expression. Fourteen of 21 isoforms of CK 7, 8, 18, 19 occurred at significantly higher levels. (P<.05 in tumors compared to uninvolved adjacent tissue. Specific isoforms of the four types of CK identified correlated with either clinical outcome or individual clinical-pathological parameters. All five of the CK7 isoforms associated with patient survival represented cleavage products. Two of five CK7 isoforms. (nos. 2165 and 2091, one of eight CK8 isoforms. (no. 439, one of three CK19 isoforms. (no. 1955 were associated with survival and significantly correlated to their mRNA levels, suggesting that transcription underlies overexpression of these CK isoforms. Our data indicate substantial heterogeneity among CK in lung adenocarcinomas resulting from posttranslational modifications, some of which correlated with patient survival and other clinical parameters. Therefore, specific isoforms of individual CK may have utility as diagnostic or predictive markers in lung adenocarcinomas.

  13. Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels

    Science.gov (United States)

    Kilpeläinen, Tuomas O.; Carli, Jayne F. Martin; Skowronski, Alicja A.; Sun, Qi; Kriebel, Jennifer; Feitosa, Mary F; Hedman, Åsa K.; Drong, Alexander W.; Hayes, James E.; Zhao, Jinghua; Pers, Tune H.; Schick, Ursula; Grarup, Niels; Kutalik, Zoltán; Trompet, Stella; Mangino, Massimo; Kristiansson, Kati; Beekman, Marian; Lyytikäinen, Leo-Pekka; Eriksson, Joel; Henneman, Peter; Lahti, Jari; Tanaka, Toshiko; Luan, Jian'an; Greco M, Fabiola Del; Pasko, Dorota; Renström, Frida; Willems, Sara M.; Mahajan, Anubha; Rose, Lynda M.; Guo, Xiuqing; Liu, Yongmei; Kleber, Marcus E.; Pérusse, Louis; Gaunt, Tom; Ahluwalia, Tarunveer S.; Ju Sung, Yun; Ramos, Yolande F.; Amin, Najaf; Amuzu, Antoinette; Barroso, Inês; Bellis, Claire; Blangero, John; Buckley, Brendan M.; Böhringer, Stefan; I Chen, Yii-Der; de Craen, Anton J. N.; Crosslin, David R.; Dale, Caroline E.; Dastani, Zari; Day, Felix R.; Deelen, Joris; Delgado, Graciela E.; Demirkan, Ayse; Finucane, Francis M.; Ford, Ian; Garcia, Melissa E.; Gieger, Christian; Gustafsson, Stefan; Hallmans, Göran; Hankinson, Susan E.; Havulinna, Aki S; Herder, Christian; Hernandez, Dena; Hicks, Andrew A.; Hunter, David J.; Illig, Thomas; Ingelsson, Erik; Ioan-Facsinay, Andreea; Jansson, John-Olov; Jenny, Nancy S.; Jørgensen, Marit E.; Jørgensen, Torben; Karlsson, Magnus; Koenig, Wolfgang; Kraft, Peter; Kwekkeboom, Joanneke; Laatikainen, Tiina; Ladwig, Karl-Heinz; LeDuc, Charles A.; Lowe, Gordon; Lu, Yingchang; Marques-Vidal, Pedro; Meisinger, Christa; Menni, Cristina; Morris, Andrew P.; Myers, Richard H.; Männistö, Satu; Nalls, Mike A.; Paternoster, Lavinia; Peters, Annette; Pradhan, Aruna D.; Rankinen, Tuomo; Rasmussen-Torvik, Laura J.; Rathmann, Wolfgang; Rice, Treva K.; Brent Richards, J; Ridker, Paul M.; Sattar, Naveed; Savage, David B.; Söderberg, Stefan; Timpson, Nicholas J.; Vandenput, Liesbeth; van Heemst, Diana; Uh, Hae-Won; Vohl, Marie-Claude; Walker, Mark; Wichmann, Heinz-Erich; Widén, Elisabeth; Wood, Andrew R.; Yao, Jie; Zeller, Tanja; Zhang, Yiying; Meulenbelt, Ingrid; Kloppenburg, Margreet; Astrup, Arne; Sørensen, Thorkild I. A.; Sarzynski, Mark A.; Rao, D. C.; Jousilahti, Pekka; Vartiainen, Erkki; Hofman, Albert; Rivadeneira, Fernando; Uitterlinden, André G.; Kajantie, Eero; Osmond, Clive; Palotie, Aarno; Eriksson, Johan G.; Heliövaara, Markku; Knekt, Paul B.; Koskinen, Seppo; Jula, Antti; Perola, Markus; Huupponen, Risto K.; Viikari, Jorma S.; Kähönen, Mika; Lehtimäki, Terho; Raitakari, Olli T.; Mellström, Dan; Lorentzon, Mattias; Casas, Juan P.; Bandinelli, Stefanie; März, Winfried; Isaacs, Aaron; van Dijk, Ko W.; van Duijn, Cornelia M.; Harris, Tamara B.; Bouchard, Claude; Allison, Matthew A.; Chasman, Daniel I.; Ohlsson, Claes; Lind, Lars; Scott, Robert A.; Langenberg, Claudia; Wareham, Nicholas J.; Ferrucci, Luigi; Frayling, Timothy M.; Pramstaller, Peter P.; Borecki, Ingrid B.; Waterworth, Dawn M.; Bergmann, Sven; Waeber, Gérard; Vollenweider, Peter; Vestergaard, Henrik; Hansen, Torben; Pedersen, Oluf; Hu, Frank B.; Eline Slagboom, P; Grallert, Harald; Spector, Tim D.; Jukema, J.W.; Klein, Robert J.; Schadt, Erik E; Franks, Paul W.; Lindgren, Cecilia M.; Leibel, Rudolph L.; Loos, Ruth J. F.

    2016-01-01

    Leptin is an adipocyte-secreted hormone, the circulating levels of which correlate closely with overall adiposity. Although rare mutations in the leptin (LEP) gene are well known to cause leptin deficiency and severe obesity, no common loci regulating circulating leptin levels have been uncovered. Therefore, we performed a genome-wide association study (GWAS) of circulating leptin levels from 32,161 individuals and followed up loci reaching P<10−6 in 19,979 additional individuals. We identify five loci robustly associated (P<5 × 10−8) with leptin levels in/near LEP, SLC32A1, GCKR, CCNL1 and FTO. Although the association of the FTO obesity locus with leptin levels is abolished by adjustment for BMI, associations of the four other loci are independent of adiposity. The GCKR locus was found associated with multiple metabolic traits in previous GWAS and the CCNL1 locus with birth weight. Knockdown experiments in mouse adipose tissue explants show convincing evidence for adipogenin, a regulator of adipocyte differentiation, as the novel causal gene in the SLC32A1 locus influencing leptin levels. Our findings provide novel insights into the regulation of leptin production by adipose tissue and open new avenues for examining the influence of variation in leptin levels on adiposity and metabolic health. PMID:26833098

  14. Uncovering phenotypes of poor-pitch singing: The Sung Performance Battery (SPB

    Directory of Open Access Journals (Sweden)

    Magdalena eBerkowska

    2013-10-01

    Full Text Available Singing is as natural as speaking for humans. Increasing evidence shows that the layman can carry a tune (e.g., when asked to sing a well-known song or to imitate single pitches, intervals and short melodies. Yet, important individual differences exist in the general population with regard to singing proficiency. Some individuals are particularly inaccurate or imprecise in producing or imitating pitch information (poor-pitch singers, thus showing a variety of singing phenotypes. Unfortunately, so far there is not a standard set of tasks for assessing singing proficiency in the general population, allowing to uncover and characterize individual profiles of poor-pitch singing. Different tasks and analysis methods are typically used in various experiments, making the comparison of the results across studies arduous. To fill this gap we propose here a new tool for assessing singing proficiency (the Sung Performance Battery, SPB. The SPB starts from the assessment of participants’ vocal range followed by five tasks: 1 single-pitch matching, 2 pitch-interval matching, 3 novel-melody matching, 4 singing from memory of familiar melodies (with lyrics and on a syllable, and 5 singing of familiar melodies (with lyrics and on a syllable at a slow tempo indicated by a metronome. Data analysis via acoustical methods provides objective measures of pitch accuracy and precision in terms of absolute and relative pitch. The SPB has been tested in a group of 50 occasional singers. The results indicate that the battery is useful for characterizing proficient singing and for detecting cases of inaccurate and/or imprecise singing.

  15. The proteome and phosphoproteome of maize pollen uncovers fertility candidate proteins.

    Science.gov (United States)

    Chao, Qing; Gao, Zhi-Fang; Wang, Yue-Feng; Li, Zhe; Huang, Xia-He; Wang, Ying-Chun; Mei, Ying-Chang; Zhao, Biligen-Gaowa; Li, Liang; Jiang, Yu-Bo; Wang, Bai-Chen

    2016-06-01

    Maize is unique since it is both monoecious and diclinous (separate male and female flowers on the same plant). We investigated the proteome and phosphoproteome of maize pollen containing modified proteins and here we provide a comprehensive pollen proteome and phosphoproteome which contain 100,990 peptides from 6750 proteins and 5292 phosphorylated sites corresponding to 2257 maize phosphoproteins, respectively. Interestingly, among the total 27 overrepresented phosphosite motifs we identified here, 11 were novel motifs, which suggested different modification mechanisms in plants compared to those of animals. Enrichment analysis of pollen phosphoproteins showed that pathways including DNA synthesis/chromatin structure, regulation of RNA transcription, protein modification, cell organization, signal transduction, cell cycle, vesicle transport, transport of ions and metabolisms, which were involved in pollen development, the following germination and pollen tube growth, were regulated by phosphorylation. In this study, we also found 430 kinases and 105 phosphatases in the maize pollen phosphoproteome, among which calcium dependent protein kinases (CDPKs), leucine rich repeat kinase, SNF1 related protein kinases and MAPK family proteins were heavily enriched and further analyzed. From our research, we also uncovered hundreds of male sterility-associated proteins and phosphoproteins that might influence maize productivity and serve as targets for hybrid maize seed production. At last, a putative complex signaling pathway involving CDPKs, MAPKs, ubiquitin ligases and multiple fertility proteins was constructed. Overall, our data provides new insight for further investigation of protein phosphorylation status in mature maize pollen and construction of maize male sterile mutants in the future. PMID:26969016

  16. Uncovering paradoxes from physicians' experiences of patient-centered ward-round.

    Science.gov (United States)

    Bååthe, Fredrik; Ahlborg, Gunnar; Edgren, Lars; Lagström, Annica; Nilsson, Kerstin

    2016-05-01

    Purpose The purpose of this paper is to uncover paradoxes emerging from physicians' experiences of a patient-centered and team-based ward round, in an internal medicine department. Design/methodology/approach Abductive reasoning relates empirical material to complex responsive processes theory in a dialectical process to further understandings. Findings This paper found the response from physicians, to a patient-centered and team-based ward round, related to whether the new demands challenged or confirmed individual physician's professional identity. Two empirically divergent perspectives on enacting the role of physician during ward round emerged: We-perspective and I-perspective, based on where the physician's professional identity was centered. Physicians with more of a We-perspective experienced challenges with the new round, while physicians with more of an I-perspective experienced alignment with their professional identity and embraced the new round. When identity is challenged, anxiety is aroused, and if anxiety is not catered to, then resistance is likely to follow and changes are likely to be hampered. Practical implications For change processes affecting physicians' professional identity, it is important for managers and change leaders to acknowledge paradox and find a balance between new knowledge that needs to be learnt and who the physician is becoming in this new procedure. Originality/value This paper provides increased understanding about how physicians' professional identity is interacting with a patient-centered ward round. It adds to the knowledge about developing health care in line with recent societal requests and with sustainable physician engagement. PMID:27198705

  17. Uncovering highly obfuscated plagiarism cases using fuzzy semantic-based similarity model

    Directory of Open Access Journals (Sweden)

    Salha M. Alzahrani

    2015-07-01

    Full Text Available Highly obfuscated plagiarism cases contain unseen and obfuscated texts, which pose difficulties when using existing plagiarism detection methods. A fuzzy semantic-based similarity model for uncovering obfuscated plagiarism is presented and compared with five state-of-the-art baselines. Semantic relatedness between words is studied based on the part-of-speech (POS tags and WordNet-based similarity measures. Fuzzy-based rules are introduced to assess the semantic distance between source and suspicious texts of short lengths, which implement the semantic relatedness between words as a membership function to a fuzzy set. In order to minimize the number of false positives and false negatives, a learning method that combines a permission threshold and a variation threshold is used to decide true plagiarism cases. The proposed model and the baselines are evaluated on 99,033 ground-truth annotated cases extracted from different datasets, including 11,621 (11.7% handmade paraphrases, 54,815 (55.4% artificial plagiarism cases, and 32,578 (32.9% plagiarism-free cases. We conduct extensive experimental verifications, including the study of the effects of different segmentations schemes and parameter settings. Results are assessed using precision, recall, F-measure and granularity on stratified 10-fold cross-validation data. The statistical analysis using paired t-tests shows that the proposed approach is statistically significant in comparison with the baselines, which demonstrates the competence of fuzzy semantic-based model to detect plagiarism cases beyond the literal plagiarism. Additionally, the analysis of variance (ANOVA statistical test shows the effectiveness of different segmentation schemes used with the proposed approach.

  18. Treatment of gastric outlet and duodenal obstructions with uncovered expandable metal stents

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    AIM: To investigate and evaluate the technical feasibility and clinical effectiveness of fluoroscopically guided peroral uncovered expandable metal stent placement to treat gastric outlet and duodenal obstructions. METHODS: Fifteen consecutive patients underwent peroral placement of WallstentTM Enteral Endoprosthesis to treat gastric outlet and duodenal obstructions (14 malignant, 1 benign). All procedures were completed under fluoroscopic guidance without endoscopic assistance. Follow-up was completed until the patients died or were lost, and the clinical outcomes were analyzed. RESULTS: The technique success rate was 100%, and the oral intake was maintained in 12 of 14 patients varying from 7 d to 270 d. Two patients remained unable to resume oral intake, although their stents were proven to be patent with the barium study. One patient with acute necrotizing pancreatitis underwent enteral stenting to treat intestinal obstruction, and nausea and vomiting disappeared. Ten patients died during the followup period, and their mean oral intake time was 50 d. No procedure-related complications occurred. Stent migration to the gastric antrum occurred in one patient 1 year after the procedure, a tumor grew at the proximal end of the stent in another patient 38 d post-stent insertion. CONCLUSION: Fluoroscopically guided peroral metal stent implantation is a safe and effective method to treat malignant gastrointestinal obstructions, and complications can be ignored based on our short-term study. Indications for this procedure should be discreetly considered because a few patients may not benefit from gastrointestinal insertion, but some benign gastrointestinal obstructions can be treated using this procedure.

  19. Quick determination of gas pressure before uncovering coal in cross-cuts and shafts

    Institute of Scientific and Technical Information of China (English)

    JIANG Cheng-lin; DENG Su-hua; ZHANG Chao-jie; CHENG Song-li; LV Shu-wen; WANG Chen; LI Xiao-wei; CHEN Yu-jia; XIE Qing-xue; LIU Ying; TANG Jun; YANG Fei-long; WANG Fa-kai

    2008-01-01

    The determination of gas pressure before uncovering coal in cross-cuts and in shafts is one of the important steps in predicting coal and gas outbursts. However, the time spent for testing gas pressure is, at present, very long, seriously affecting the application of outburst prediction techniques in opening coal seams in cross-cuts and shafts. In order to reduce the time needed in gas pressure tests and to improve the accuracy of tests, we analyzed the process of gas pressure tests and examined the effect of the length of boreholes in coal seams in tests. The result shows that 1) the shorter the borehole, the easier the real pressure value of gas can be obtained and 2) the main factors affecting the time spent in gas pressure tests are the length of the borehole in coal seams,the gas emission time after the borehole has been formed and the quality of the borehole-sealing. The longer the length of the borehole, the longer the gas emission time and the larger the pressure-relief circle formed around the borehole, the longer the time needed for pressure tests. By controlling the length of the borehole in a test case in the Huainan mining area, and adopting a quick sealing technique using a sticky liquid method, the sealing quality was clearly improved and the gas emission time as well as the amount of gas discharged greatly decreased. Before the method described, the time required for the gas pressure to increase during the pressure test process, was more than 10 days. With our new method the required time is only 5 hours. In addition, the accuracy of the gas pressure test is greatly improved.

  20. Uncovering China’s transport CO2 emission patterns at the regional level

    International Nuclear Information System (INIS)

    With China’s rapid economic development, its transport sector has experienced a dramatic growth, leading to a large amount of related CO2 emission. This paper aims to uncover China’s transport CO2 emission patterns at the regional and provincial level. We first present the CO2 emission features from transport sector in 30 Chinese provinces, including per capita emissions, emission intensities, and historical evolution of annual CO2 emission. We then quantify the related driving forces by adopting both period-wise and time-series LMDI analysis. Results indicate that significant regional CO2 emission disparities exist in China’s transport sector. The eastern region had higher total CO2 emissions and per capita CO2 emissions, but lower CO2 emission intensities in its transport sector. The western region had higher CO2 emission intensities and experienced a rapid CO2 emission increase. The CO2 emission increments in the eastern provinces were mainly contributed by both economic activity effect and population effect, while energy intensity partially offset the emission growth and energy structure had a marginal effect. However, in the central and western provinces, both economic activity effect and energy intensity effect induced the CO2 emission increases, while the effects from population and energy structure change were limited. - Highlights: • The CO2 emission features from transport sector in 30 Chinese provinces were presented. • The driving forces of CO2 emissions from transport sector were quantified. • Regional disparities on China’s transport sector CO2 emission exist. • Region-specific mitigation policies on transport sector CO2 emission are needed

  1. Multivariate weighted recurrence network inference for uncovering oil-water transitional flow behavior in a vertical pipe.

    Science.gov (United States)

    Gao, Zhong-Ke; Yang, Yu-Xuan; Cai, Qing; Zhang, Shan-Shan; Jin, Ning-De

    2016-06-01

    Exploring the dynamical behaviors of high water cut and low velocity oil-water flows remains a contemporary and challenging problem of significant importance. This challenge stimulates us to design a high-speed cycle motivation conductance sensor to capture spatial local flow information. We systematically carry out experiments and acquire the multi-channel measurements from different oil-water flow patterns. Then we develop a novel multivariate weighted recurrence network for uncovering the flow behaviors from multi-channel measurements. In particular, we exploit graph energy and weighted clustering coefficient in combination with multivariate time-frequency analysis to characterize the derived complex networks. The results indicate that the network measures are very sensitive to the flow transitions and allow uncovering local dynamical behaviors associated with water cut and flow velocity. These properties render our method particularly useful for quantitatively characterizing dynamical behaviors governing the transition and evolution of different oil-water flow patterns. PMID:27368782

  2. Multivariate weighted recurrence network inference for uncovering oil-water transitional flow behavior in a vertical pipe

    Science.gov (United States)

    Gao, Zhong-Ke; Yang, Yu-Xuan; Cai, Qing; Zhang, Shan-Shan; Jin, Ning-De

    2016-06-01

    Exploring the dynamical behaviors of high water cut and low velocity oil-water flows remains a contemporary and challenging problem of significant importance. This challenge stimulates us to design a high-speed cycle motivation conductance sensor to capture spatial local flow information. We systematically carry out experiments and acquire the multi-channel measurements from different oil-water flow patterns. Then we develop a novel multivariate weighted recurrence network for uncovering the flow behaviors from multi-channel measurements. In particular, we exploit graph energy and weighted clustering coefficient in combination with multivariate time-frequency analysis to characterize the derived complex networks. The results indicate that the network measures are very sensitive to the flow transitions and allow uncovering local dynamical behaviors associated with water cut and flow velocity. These properties render our method particularly useful for quantitatively characterizing dynamical behaviors governing the transition and evolution of different oil-water flow patterns.

  3. Effects and Mechanisms of P and K Nutrients on Yield and Protein Content of Fodder Rice

    Institute of Scientific and Technical Information of China (English)

    TANG Xiang-ru; YU Tie-qiao

    2002-01-01

    Effects and mechanisms of P and K nutrients on yield and protein content of Weiyou 56, a fodder hybrid rice combination, were studied through pot experiment and biochemical analysis. The results showed that the increase of P and K nutrients enhanced the activities of PEP carboxylase (PEPC), glutamine synthase (GS) and sucrose phosphate synthase (SPS) in leaves, sucrose synthase (SS), ADP glucose pyrophosphorylase (ADPGP) and GS in grains, and the chlorophyll content in leaves, soluble sugar and starch content in grains,protein N and total N content in leaves and grains. Howerer, they decreased soluble sugar content in leaves and led to an increase of protein content in brown rice, biomass, grain yield and harvest index. Excessive P nutrients slightly reduced SPS and ADPG activity in leaves and grains respectively.

  4. Differential SAGE analysis in Arabidopsis uncovers increased transcriptome complexity in response to low temperature

    Directory of Open Access Journals (Sweden)

    Parkin Isobel AP

    2008-09-01

    Full Text Available Abstract Background Abiotic stress, including low temperature, limits the productivity and geographical distribution of plants, which has led to significant interest in understanding the complex processes that allow plants to adapt to such stresses. The wide range of physiological, biochemical and molecular changes that occur in plants exposed to low temperature require a robust global approach to studying the response. We have employed Serial Analysis of Gene Expression (SAGE to uncover changes in the transcriptome of Arabidopsis thaliana over a time course of low temperature stress. Results Five SAGE libraries were generated from A. thaliana leaf tissue collected at time points ranging from 30 minutes to one week of low temperature treatment (4°C. Over 240,000 high quality SAGE tags, corresponding to 16,629 annotated genes, provided a comprehensive survey of changes in the transcriptome in response to low temperature, from perception of the stress to acquisition of freezing tolerance. Interpretation of these data was facilitated by representing the SAGE data by gene identifier, allowing more robust statistical analysis, cross-platform comparisons and the identification of genes sharing common expression profiles. Simultaneous statistical calculations across all five libraries identified 920 low temperature responsive genes, only 24% of which overlapped with previous global expression analysis performed using microarrays, although similar functional categories were affected. Clustering of the differentially regulated genes facilitated the identification of novel loci correlated with the development of freezing tolerance. Analysis of their promoter sequences revealed subsets of genes that were independent of CBF and ABA regulation and could provide a mechanism for elucidating complementary signalling pathways. The SAGE data emphasised the complexity of the plant response, with alternate pre-mRNA processing events increasing at low temperatures

  5. No Place to Hide: Missing Primitive Stars Outside Milky Way Uncovered

    Science.gov (United States)

    2010-02-01

    After years of successful concealment, the most primitive stars outside our Milky Way galaxy have finally been unmasked. New observations using ESO's Very Large Telescope have been used to solve an important astrophysical puzzle concerning the oldest stars in our galactic neighbourhood - which is crucial for our understanding of the earliest stars in the Universe. "We have, in effect, found a flaw in the forensic methods used until now," says Else Starkenburg, lead author of the paper reporting the study. "Our improved approach allows us to uncover the primitive stars hidden among all the other, more common stars." Primitive stars are thought to have formed from material forged shortly after the Big Bang, 13.7 billion years ago. They typically have less than one thousandth the amount of chemical elements heavier than hydrogen and helium found in the Sun and are called "extremely metal-poor stars" [1]. They belong to one of the first generations of stars in the nearby Universe. Such stars are extremely rare and mainly observed in the Milky Way. Cosmologists think that larger galaxies like the Milky Way formed from the merger of smaller galaxies. Our Milky Way's population of extremely metal-poor or "primitive" stars should already have been present in the dwarf galaxies from which it formed, and similar populations should be present in other dwarf galaxies. "So far, evidence for them has been scarce," says co-author Giuseppina Battaglia. "Large surveys conducted in the last few years kept showing that the most ancient populations of stars in the Milky Way and dwarf galaxies did not match, which was not at all expected from cosmological models." Element abundances are measured from spectra, which provide the chemical fingerprints of stars [2]. The Dwarf galaxies Abundances and Radial-velocities Team [3] used the FLAMES instrument on ESO's Very Large Telescope to measure the spectra of over 2000 individual giant stars in four of our galactic neighbours, the Fornax

  6. A distinctive avian assemblage (Aves: Passeriformes) in Western Darién, Panama is uncovered through a disease surveillance program.

    Science.gov (United States)

    Miller, Matthew J

    2014-06-01

    Basic knowledge about the distribution of flora and fauna is lacking for most tropical areas. Improving our knowledge of the tropical biota will help address contemporary global problems, including emerging tropical diseases. Less appreciated is the role that applied studies can have in improving our understanding of basic biological patterns and processes in the tropics. Here, I describe a novel avifauna assemblage uncovered in Western Darién province in the Republic of Panama that was uncovered during a vector-borne disease surveillance program. I compared the passerine bird species composition at 16 sites using records from recent ornithological expeditions sponsored by the Smithsonian Tropical Research Institute in Central and Eastern Panama. Based on the results of a Mantel test, geographic distance did not correlate with pairwise distinctiveness of sites. instead, based on an index of distinctiveness modified from the Chao-Jaccard index, most sites were more or less similarly distinctive, with one site, Aruza Abajo, significantly more distinctive than the rest. I found that the distinctiveness of this site was due not only to the presence of several rare and range-restricted taxa, but also to the absence of taxa that are common elsewhere. This finding provides more evidence of high species composition turnover (beta-diversity) in the Panamanian biota, which appears to be driven by a combination of soil and climate differences over narrow distances. PMID:25102652

  7. Realizing full coverage of perovskite film on substrate surface during solution processing: Characterization and elimination of uncovered surface

    Science.gov (United States)

    Li, Yan; He, Xue-Long; Ding, Bin; Gao, Li-Li; Yang, Guan-Jun; Li, Cheng-Xin; Li, Chang-Jiu

    2016-07-01

    The full coverage of the perovskite film on the substrate surface is of significant importance for the high performance perovskite solar cells. In order to obtain full coverage perovskite films by one-step deposition method, the microstructures of both uncovered areas and covered areas of the CH3NH3PbI3 film are comparatively investigated. Results show that the uncovered area indeed has an ultra-thin layer of CH3NH3PbI3 film which is too thin to cover the rough surface morphology of the substrate, and the localized solute accumulation due to long crystal growth time is responsible for the non-full coverage of the perovskite film. Then by decreasing the crystal growth time, the localized solute accumulation is eliminated gradually and subsequently a full coverage of perovskite film on substrate surface is realized. As a result, the perovskite solar cells show a conversion efficiency of ∼13% with the uniform and full coverage perovskite film.

  8. Clinical exome sequencing for cerebellar ataxia and spastic paraplegia uncovers novel gene–disease associations and unanticipated rare disorders

    Science.gov (United States)

    van de Warrenburg, Bart P; Schouten, Meyke I; de Bot, Susanne T; Vermeer, Sascha; Meijer, Rowdy; Pennings, Maartje; Gilissen, Christian; Willemsen, Michèl AAP; Scheffer, Hans; Kamsteeg, Erik-Jan

    2016-01-01

    Cerebellar ataxia (CA) and hereditary spastic paraplegia (HSP) are two of the most prevalent motor disorders with extensive locus and allelic heterogeneity. We implemented clinical exome sequencing, followed by filtering data for a ‘movement disorders' gene panel, as a generic test to increase variant detection in 76 patients with these disorders. Segregation analysis or phenotypic re-evaluation was utilized to substantiate findings. Disease-causing variants were identified in 9 of 28 CA patients, and 8 of 48 HSP patients. In addition, possibly disease-causing variants were identified in 1 and 8 of the remaining CA and HSP patients, respectively. In 10 patients with CA, the total disease-causing or possibly disease-causing variants were detected in 8 different genes, whereas 16 HSP patients had such variants in 12 different genes. In the majority of cases, the identified variants were compatible with the patient phenotype. Interestingly, in some patients variants were identified in genes hitherto related to other movement disorders, such as TH variants in two siblings with HSP. In addition, rare disorders were uncovered, for example, a second case of HSP caused by a VCP variant. For some patients, exome sequencing results had implications for treatment, exemplified by the favorable L-DOPA treatment in a patient with HSP due to ATP13A2 variants (Parkinson type 9). Thus, clinical exome sequencing in this cohort of CA and HSP patients suggests broadening of disease spectra, revealed novel gene–disease associations, and uncovered unanticipated rare disorders. In addition, clinical exome sequencing results have shown their value in guiding practical patient management. PMID:27165006

  9. Computing the origin and evolution of the ribosome from its structure — Uncovering processes of macromolecular accretion benefiting synthetic biology

    Directory of Open Access Journals (Sweden)

    Gustavo Caetano-Anollés

    2015-01-01

    Full Text Available Accretion occurs pervasively in nature at widely different timeframes. The process also manifests in the evolution of macromolecules. Here we review recent computational and structural biology studies of evolutionary accretion that make use of the ideographic (historical, retrodictive and nomothetic (universal, predictive scientific frameworks. Computational studies uncover explicit timelines of accretion of structural parts in molecular repertoires and molecules. Phylogenetic trees of protein structural domains and proteomes and their molecular functions were built from a genomic census of millions of encoded proteins and associated terminal Gene Ontology terms. Trees reveal a ‘metabolic-first’ origin of proteins, the late development of translation, and a patchwork distribution of proteins in biological networks mediated by molecular recruitment. Similarly, the natural history of ancient RNA molecules inferred from trees of molecular substructures built from a census of molecular features shows patchwork-like accretion patterns. Ideographic analyses of ribosomal history uncover the early appearance of structures supporting mRNA decoding and tRNA translocation, the coevolution of ribosomal proteins and RNA, and a first evolutionary transition that brings ribosomal subunits together into a processive protein biosynthetic complex. Nomothetic structural biology studies of tertiary interactions and ancient insertions in rRNA complement these findings, once concentric layering assumptions are removed. Patterns of coaxial helical stacking reveal a frustrated dynamics of outward and inward ribosomal growth possibly mediated by structural grafting. The early rise of the ribosomal ‘turnstile’ suggests an evolutionary transition in natural biological computation. Results make explicit the need to understand processes of molecular growth and information transfer of macromolecules.

  10. Variation in the Slope Coefficient of the Fama Regression for Testing Uncovered Interest Rate Parity: Evidence from Fixed and Time-varying Coefficient Approaches

    NARCIS (Netherlands)

    C. de Koning (Camiel); S. Straetmans

    1997-01-01

    textabstractWe investigate the potential presence of time variation in the coefficients of the ''Fama regression'' for Uncovered Interest Rate Parity. We implement coefficient constancy tests, rolling regression techniques, and stochastic coefficient models based on state space modelling. Among six

  11. Effects of Variation in Activities of Starch-Sugar Metabolic Enzymes on Reducing Sugar Accumulation and Processing Quality of Potato Tubers

    Institute of Scientific and Technical Information of China (English)

    CHENG Shan-han; SU Zhen-hong; XIE Cong-hua; LIU Jun

    2004-01-01

    The experiment was designed,via storing potato tubers of cv.E-Potatol and E-Potato3 in different temperatures,to explore the variation patterns of reducing sugar(RS)and total sugar(TS)contents and enzyme activities that are involved in the pathway of starch-sugar metabolism aiming at identifying the main factors that influence the chip color.The results showed that low temperature in storage was a main factor that accelerated the accumulation of RS of the stored tubers and a very significant linear relationship existed between RS content and chip color index(CCI)of the tubers.Further analysis elucidated that when tubers stored at 4℃,the activities of ADP glucose pyrophosphorylase(AGPase),UDP glucose pyrophosphorylase(UGPase)and sucrose synthase(SuSy)were negatively exponential to the RS content significantly while that of acid invertase and alkaline invertase was significantly linear to RS content.It suggested that these enzymes could play main roles in the cold sweetening of potato tubers through regulating starch-sugar metabolism.

  12. Atmospheric pollution history at Linfen (China) uncovered by magnetic and chemical parameters of sediments from a water reservoir

    International Nuclear Information System (INIS)

    We studied magnetic and chemical parameters of sediments from sediments of a water reservoir at Linfen (China) in order to quantitatively reconstruct the atmospheric pollution history in this region. The results show that the main magnetic phases are magnetite and maghemite originating from the surrounding catchment and from anthropogenic activities, and there is a significant positive relationship between magnetic concentration parameters and heavy metals concentrations, indicating that magnetic proxies can be used to monitor the anthropogenic pollution. In order to uncover the atmospheric pollution history, we combined the known events of environmental improvement with variations of magnetic susceptibility (χ) and heavy metals along the cores to obtain a detailed chronological framework. In addition, air comprehensive pollution index (ACPI) was reconstructed from regression equation among magnetic and chemical parameters as well as atmospheric monitoring data. Based on these results, the atmospheric pollution history was successfully reconstructed. - Highlights: • Magnetic proxies can be used to monitor the heavy mental pollution in sediments. • Accurate age model was obtained using known events of environmental improvement. • Regression equation was obtained among sediment records and monitoring data. • Atmospheric pollution history was quantitatively reconstructed. - Atmospheric pollution history was quantitatively reconstructed using magnetic and chemical records of reservoir sediments combined with atmospheric monitoring data

  13. COMBINED UNCOVERED SHEET-AND-TUBE PVT-COLLECTOR SYSTEM WITH BUILT-IN STORAGE WATER HEATER

    Directory of Open Access Journals (Sweden)

    Muhammad Abid

    2012-02-01

    Full Text Available This work describes the design and investigation of a simple combined uncovered sheet-and-tube photo-voltaic-thermal (PVT collector system. The PVT-collector system consists of a support, standard PV module (1.22x0.305m, area=0.37m2, fill factor=0.75, sheet-and-tube water collector and storage tank-heater. The collector was fixed under PV module. Inclination angle of the PVT-collector to the horizontal plane was 45 degree. The storage tank-heater played double role i.e. for storage of hot water and for water heating. The PVT-collector system could work in the fixed and tracking modes of operation. During investigations of PVT-collector in natural conditions, solar irradiance, voltage and current of PV module, ambient temperature and water temperature in storage tank were measured. Average thermal and electrical powers of the PVT-collector system at the tracking mode of operation observed were 39W and 21W, with efficiencies of 15% and 8% respectively at the input power of 260W. The maximum temperature of the water obtained was 42oC. The system was observed efficient for low-temperature applications. The PVT-collector system may be used as a prototype for design of PVT-collector system for domestic application, teaching aid and for demonstration purposes.

  14. Uncovering the composition of microbial community structure and metagenomics among three gut locations in pigs with distinct fatness.

    Science.gov (United States)

    Yang, Hui; Huang, Xiaochang; Fang, Shaoming; Xin, Wenshui; Huang, Lusheng; Chen, Congying

    2016-01-01

    Uncovering the phylogenetic composition of microbial community and the potential functional capacity of microbiome in different gut locations is of great importance to pig production. Here we performed a comparative analysis of gut microbiota and metagenomics among jejunum, ileum and cecum in pigs with distinct fatness. 16S rRNA gene sequencing revealed dramatic differences of microbial composition, diversity and species abundance between small intestine and cecum. Clostridium and SMB53 were enriched in the small intestine, while Prevotella, Treponema, Ruminococcus and Faecalibacterium showed a higher abundance in the cecum. Functional capacity analysis of gut microbiome revealed that the microbiome of small intestine plays important roles in the metabolism of small molecule nutrients, while the microbiome of cecum has the stronger ability to degrade xylan, pectin and cellulose. We identified tens of fatness associated-bacterial species including Escherichia spp. that showed a notable increase of relative abundance in all three gut locations of high fatness pigs. We further suggested that the potential pathogens, inflammation process, and microbial metabolism and nutrient sensing are involved in the high fatness of pigs. These results improve our knowledge about microbiota compositions in different gut locations, and give an insight into the effect of gut microbiota on porcine fatness. PMID:27255518

  15. Meta-analysis of cancer transcriptomes: A new approach to uncover molecular pathological events in different cancer tissues

    Directory of Open Access Journals (Sweden)

    Sundus Iqbal

    2014-03-01

    Full Text Available To explore secrets of metastatic cancers, individual expression of true sets of respective genes must spread across the tissue. In this study, meta-analysis for transcriptional profiles of oncogenes was carried out to hunt critical genes or networks helping in metastasizing cancers. For this, transcriptomic analysis of different cancerous tissues causing leukemia, lung, liver, spleen, colorectal, colon, breast, bladder, and kidney cancers was performed by extracting microarray expression data from online resource; Gene Expression Omnibus. A newly developed bioinformatics technique; Dynamic Impact Approach (DIA was applied for enrichment analysis of transcriptional profiles using Database for Annotation Visualization and Integrated Discovery (DAVID. Furthermore, oPOSSUM (v. 2.0 and Cytoscape (v. 2.8.2 were used for in-depth analysis of transcription factors and regulatory gene networks respectively. DAVID analysis uncovered the most significantly enriched pathways in molecular functions that were 'Ubiquitin thiolesterase activity' up regulated in blood, breast, bladder, colorectal, lung, spleen, prostrate cancer. 'Transforming growth factor beta receptor activity' was inhibited in all cancers except leukemia, colon and liver cancer. oPOSSUM further revealed highly over-represented Transcription Factors (TFs; Broad-complex_3, Broad-complex_4, and Foxd3 except for leukemia and bladder cancer. From these findings, it is possible to target genes and networks, play a crucial role in the development of cancer. In the future, these transcription factors can serve as potential candidates for the therapeutic drug targets which can impede the deadly spread.

  16. Uncovering Prepositional Senses

    DEFF Research Database (Denmark)

    Lassen, Tine

    . These rules were transformed into a dictionary of prepositional senses, where, given a preposition and a sense, ontological affinities are expressed as restrictions on the ontological types of the arguments. Thus, the essential results of this research is knowledge about the relations that subset of Danish......This dissertation is concerned with the semantics of Danish prepositions in an ontology-based information retrieval framework. In such a framework, conceptual indexing of texts is needed and, for us, the goal of this indexing process is to index texts based on the conceptual content of larger text...... chunks – ideally based on the conceptual content of sentences. The conceptual content of text chunks is mapped into a so-called generative ontology, which is to be understood as a non-finite set of concepts. Basically, a generative ontology consists of a given finite ontology ordered by the ISA relation...

  17. Uncovering the real Broadmoor.

    Science.gov (United States)

    2016-09-21

    Can nurses use the example of Broadmoor to enhance their own practice? Stephanie Jones-Berry reports behind the scenes in England's most infamous psychiatric hospital. Contrary to the sensational tabloid stories, she discusses the hospital's supportive ethos. Ms Jones-Berry talks to Broadmoor nurses about how the hospital's inclusive approach helps service users overcome mental health issues and how nurses work collaboratively with patients. She also interviews a former high-risk service user whose experiences at Broadmoor allowed him to transition back into the community and is now involved with mandatory induction training for staff. PMID:27654566

  18. Uncovering undetected hypoglycemic events

    Directory of Open Access Journals (Sweden)

    Unger J

    2012-03-01

    Full Text Available Jeff UngerCatalina Research Institute, Chino, CA, USAAbstract: Hypoglycemia is the rate-limiting factor that often prevents patients with diabetes from safely and effectively achieving their glycemic goals. Recent studies have reported that severe hypoglycemia is associated with a significant increase in the adjusted risks of major macrovascular events, major microvascular events, and mortality. Minor hypoglycemic episodes can also have serious implications for patient health, psychological well being, and adherence to treatment regimens. Hypoglycemic events can impact the health economics of the patient, their employer, and third-party payers. Insulin treatment is a key predictor of hypoglycemia, with one large population-based study reporting an overall prevalence of 7.1% (type 1 diabetes mellitus and 7.3% (type 2 diabetes mellitus in insulin-treated patients, compared with 0.8% in patients with type 2 diabetes treated with an oral sulfonylurea. Patients with type 1 diabetes typically experience symptomatic hypoglycemia on average twice weekly and severe hypoglycemia once annually. The progressive loss of islet cell function in patients with type 2 diabetes results in a higher risk of both symptomatic and unrecognized hypoglycemia over time. Patients with diabetes who become hypoglycemic are also more susceptible to developing defective counter-regulation, also known as hypoglycemia awareness autonomic failure, which is life-threatening and must be aggressively addressed. In patients unable to recognize hypoglycemia symptoms, frequent home monitoring or use of continuous glucose sensors are critical. Primary care physicians play a key role in the prevention and management of hypoglycemia in patients with diabetes, particularly in those requiring intensive insulin therapy, yet physicians are often unaware of the multitude of consequences of hypoglycemia or how to deal with them. Careful monitoring, adherence to guidelines, and use of optimal treatment combinations are all important steps toward improving care in patients with diabetes. The most important goals are for primary care physicians to recognize that every patient treated with antihyperglycemic medications is at risk of iatrogenic hypoglycemia and to ask patients about hypoglycemia at every visit.Keywords: hypoglycemia, insulin analogs, type 1 diabetes mellitus, type 2 diabetes mellitus

  19. Uncovering the Cornfield

    DEFF Research Database (Denmark)

    Carter, Dale

    2015-01-01

    Observers agree that a pivotal factor in the abandonment of the Beach Boys’ Smile album in 1967 was the hostility shown by group members to some of Brian Wilson co-writer Van Dyke Parks’s lyrics. The latter still tend, however, to be cited more than they are analyzed. This reading of the song...

  20. Uncovering foveal crowding?

    Science.gov (United States)

    Lev, Maria; Yehezkel, Oren; Polat, Uri

    2014-02-12

    Visual crowding, as context modulation, reduce the ability to recognize objects in clutter, sets a fundamental limit on visual perception and object recognition. It's considered that crowding does not exist in the fovea and extensive efforts explored crowding in the periphery revealed various models that consider several aspects of spatial processing. Studies showed that spatial and temporal crowding are correlated, suggesting a tradeoff between spatial and temporal processing of crowding. We hypothesized that limiting stimulus availability should decrease object recognition in clutter. Here we show, for the first time, that robust contour interactions exist in the fovea for much larger target-flanker spacing than reported previously: participants overcome crowded conditions for long presentations times but exhibit contour interaction effects for short presentation times. Thus, by enabling enough processing time in the fovea, contour interactions can be overcome, enabling object recognition. Our results suggest that contemporary models of context modulation should include both time and spatial processing.

  1. Uncovering the unarchived web

    OpenAIRE

    Samar, Thaer; Huurdeman, H.C.; Ben-David, A.; Kamps, J.; Vries, de, H.J.C.

    2014-01-01

    Many national and international heritage institutes realize the importance of archiving the web for future culture heritage. Web archiving is currently performed either by harvesting a national domain, or by crawling a pre-defined list of websites selected by the archiving institution. In either method, crawling results in more information being harvested than just the websites intended for preservation; which could be used to reconstruct impressions of pages that existed on the live web of t...

  2. Uncovering the unarchived web

    NARCIS (Netherlands)

    Samar, T.; Huurdeman, H.C.; Ben-David, A.; Kamps, J.; Vries, A.P. de

    2014-01-01

    Many national and international heritage institutes realize the importance of archiving the web for future culture heritage. Web archiving is currently performed either by harvesting a national domain, or by crawling a pre-defined list of websites selected by the archiving institution. In either met

  3. Sporty materials uncovered

    OpenAIRE

    Kevin Edwards

    2004-01-01

    Materials in Sports Equipment is a welcome addition to books on materials engineering, says Kevin Edwards. It fills a gap in coverage of the important sports market, where advances in materials can lead to improved performance.

  4. Uncovering Earth's virome.

    Science.gov (United States)

    Paez-Espino, David; Eloe-Fadrosh, Emiley A; Pavlopoulos, Georgios A; Thomas, Alex D; Huntemann, Marcel; Mikhailova, Natalia; Rubin, Edward; Ivanova, Natalia N; Kyrpides, Nikos C

    2016-08-25

    Viruses are the most abundant biological entities on Earth, but challenges in detecting, isolating, and classifying unknown viruses have prevented exhaustive surveys of the global virome. Here we analysed over 5 Tb of metagenomic sequence data from 3,042 geographically diverse samples to assess the global distribution, phylogenetic diversity, and host specificity of viruses. We discovered over 125,000 partial DNA viral genomes, including the largest phage yet identified, and increased the number of known viral genes by 16-fold. Half of the predicted partial viral genomes were clustered into genetically distinct groups, most of which included genes unrelated to those in known viruses. Using CRISPR spacers and transfer RNA matches to link viral groups to microbial host(s), we doubled the number of microbial phyla known to be infected by viruses, and identified viruses that can infect organisms from different phyla. Analysis of viral distribution across diverse ecosystems revealed strong habitat-type specificity for the vast majority of viruses, but also identified some cosmopolitan groups. Our results highlight an extensive global viral diversity and provide detailed insight into viral habitat distribution and host–virus interactions. PMID:27533034

  5. Uncovering Plagiarism Networks

    OpenAIRE

    Freire, Manuel; Cebrian, Manuel; del Rosal, Emilio

    2007-01-01

    Plagiarism detection in educational programming assignments is still a problematic issue in terms of resource waste, ethical controversy, legal risks, and technical complexity. This paper presents AC, a modular plagiarism detection system. The design is portable across platforms and assignment formats and provides easy extraction into the internal assignment representation. Multiple similarity measures have been incorporated, both existing and newly-developed. Statistical analysis and several...

  6. Uncovering the Missing Routes

    DEFF Research Database (Denmark)

    Tsirogiannis, Constantinos; Tsirogiannis, Christos

    2016-01-01

    In the present work we model and analyse the global network of the illegal trade in antiquities. Our goal is to use this network to estimate for any given artefact the potential sequence of people in the network among whom this artefact was traded. For this reason, we have implemented and evaluated...

  7. The discovery uncovered

    CERN Multimedia

    Antonella Del Rosso

    2016-01-01

    Almost exactly one hundred years after the publication of Einstein’s paper on General Relativity, the LIGO and Virgo collaborations have published a paper in which they show a gravitational signal emitted by the merger of two black holes. The signal has been observed with 5-sigma accuracy and is the first direct observation of gravitational waves.   On Thursday, 11 February, Barry Clark Barish, one of the fathers of the LIGO experiment, presented the latest results in a packed Auditorium. Ripples in space-time, the fabric of the Universe: this is how we can picture gravitational waves. In his visionary paper published in June 1916, Einstein predicted that masses deform space-time and, therefore, any change in their position causes a distortion that propagates at the speed of light, resulting in gravitational waves.   It wasn’t until 1975, almost 60 years later, that Russell Hulse and Joseph Taylor, who were awarded the Nobel Prize in 1993, inferred t...

  8. Genome engineering uncovers 54 evolutionarily conserved and testis-enriched genes that are not required for male fertility in mice.

    Science.gov (United States)

    Miyata, Haruhiko; Castaneda, Julio M; Fujihara, Yoshitaka; Yu, Zhifeng; Archambeault, Denise R; Isotani, Ayako; Kiyozumi, Daiji; Kriseman, Maya L; Mashiko, Daisuke; Matsumura, Takafumi; Matzuk, Ryan M; Mori, Masashi; Noda, Taichi; Oji, Asami; Okabe, Masaru; Prunskaite-Hyyrylainen, Renata; Ramirez-Solis, Ramiro; Satouh, Yuhkoh; Zhang, Qian; Ikawa, Masahito; Matzuk, Martin M

    2016-07-12

    Gene-expression analysis studies from Schultz et al. estimate that more than 2,300 genes in the mouse genome are expressed predominantly in the male germ line. As of their 2003 publication [Schultz N, Hamra FK, Garbers DL (2003) Proc Natl Acad Sci USA 100(21):12201-12206], the functions of the majority of these testis-enriched genes during spermatogenesis and fertilization were largely unknown. Since the study by Schultz et al., functional analysis of hundreds of reproductive-tract-enriched genes have been performed, but there remain many testis-enriched genes for which their relevance to reproduction remain unexplored or unreported. Historically, a gene knockout is the "gold standard" to determine whether a gene's function is essential in vivo. Although knockout mice without apparent phenotypes are rarely published, these knockout mouse lines and their phenotypic information need to be shared to prevent redundant experiments. Herein, we used bioinformatic and experimental approaches to uncover mouse testis-enriched genes that are evolutionarily conserved in humans. We then used gene-disruption approaches, including Knockout Mouse Project resources (targeting vectors and mice) and CRISPR/Cas9, to mutate and quickly analyze the fertility of these mutant mice. We discovered that 54 mutant mouse lines were fertile. Thus, despite evolutionary conservation of these genes in vertebrates and in some cases in all eukaryotes, our results indicate that these genes are not individually essential for male mouse fertility. Our phenotypic data are highly relevant in this fiscally tight funding period and postgenomic age when large numbers of genomes are being analyzed for disease association, and will prevent unnecessary expenditures and duplications of effort by others. PMID:27357688

  9. A genome-wide immunodetection screen in S. cerevisiae uncovers novel genes involved in lysosomal vacuole function and morphology.

    Directory of Open Access Journals (Sweden)

    Florante Ricarte

    Full Text Available Vacuoles of yeast Saccharomyces cerevisiae are functionally analogous to mammalian lysosomes. Both are cellular organelles responsible for macromolecular degradation, ion/pH homeostasis, and stress survival. We hypothesized that undefined gene functions remain at post-endosomal stage of vacuolar events and performed a genome-wide screen directed at such functions at the late endosome and vacuole interface - ENV genes. The immunodetection screen was designed to identify mutants that internally accumulate precursor form of the vacuolar hydrolase carboxypeptidase Y (CPY. Here, we report the uncovering and initial characterizations of twelve ENV genes. The small size of the collection and the lack of genes previously identified with vacuolar events are suggestive of the intended exclusive functional interface of the screen. Most notably, the collection includes four novel genes ENV7, ENV9, ENV10, and ENV11, and three genes previously linked to mitochondrial processes - MAM3, PCP1, PPE1. In all env mutants, vesicular trafficking stages were undisturbed in live cells as assessed by invertase and active α-factor secretion, as well as by localization of the endocytic fluorescent marker FM4-64 to the vacuole. Several mutants exhibit defects in stress survival functions associated with vacuoles. Confocal fluorescence microscopy revealed the collection to be significantly enriched in vacuolar morphologies suggestive of fusion and fission defects. These include the unique phenotype of lumenal vesicles within vacuoles in the novel env9Δ mutant and severely fragmented vacuoles upon deletion of GET4, a gene recently implicated in tail anchored membrane protein insertion. Thus, our results establish new gene functions in vacuolar function and morphology, and suggest a link between vacuolar and mitochondrial events.

  10. Uncovering ultrastructural defences in Daphnia magna--an interdisciplinary approach to assess the predator-induced fortification of the carapace.

    Directory of Open Access Journals (Sweden)

    Max Rabus

    Full Text Available The development of structural defences, such as the fortification of shells or exoskeletons, is a widespread strategy to reduce predator attack efficiency. In unpredictable environments these defences may be more pronounced in the presence of a predator. The cladoceran Daphnia magna (Crustacea: Branchiopoda: Cladocera has been shown to develop a bulky morphotype as an effective inducible morphological defence against the predatory tadpole shrimp Triops cancriformis (Crustacea: Branchiopoda: Notostraca. Mediated by kairomones, the daphnids express an increased body length, width and an elongated tail spine. Here we examined whether these large scale morphological defences are accompanied by additional ultrastructural defences, i.e. a fortification of the exoskeleton. We employed atomic force microscopy (AFM based nanoindentation experiments to assess the cuticle hardness along with tapping mode AFM imaging to visualise the surface morphology for predator exposed and non-predator exposed daphnids. We used semi-thin sections of the carapace to measure the cuticle thickness, and finally, we used fluorescence microscopy to analyse the diameter of the pillars connecting the two carapace layers. We found that D. magna indeed expresses ultrastructural defences against Triops predation. The cuticle in predator exposed individuals is approximately five times harder and two times thicker than in control daphnids. Moreover, the pillar diameter is significantly increased in predator exposed daphnids. These predator-cue induced changes in the carapace architecture should provide effective protection against being crushed by the predator's mouthparts and may add to the protective effect of bulkiness. This study highlights the potential of interdisciplinary studies to uncover new and relevant aspects even in extensively studied fields of research.

  11. Upregulation of glycans containing 3' fucose in a subset of pancreatic cancers uncovered using fusion-tagged lectins.

    Science.gov (United States)

    Singh, Sudhir; Pal, Kuntal; Yadav, Jessica; Tang, Huiyuan; Partyka, Katie; Kletter, Doron; Hsueh, Peter; Ensink, Elliot; Kc, Birendra; Hostetter, Galen; Xu, H Eric; Bern, Marshall; Smith, David F; Mehta, Anand S; Brand, Randall; Melcher, Karsten; Haab, Brian B

    2015-06-01

    The fucose post-translational modification is frequently increased in pancreatic cancer, thus forming the basis for promising biomarkers, but a subset of pancreatic cancer patients does not elevate the known fucose-containing biomarkers. We hypothesized that such patients elevate glycan motifs with fucose in linkages and contexts different from the known fucose-containing biomarkers. We used a database of glycan array data to identify the lectins CCL2 to detect glycan motifs with fucose in a 3' linkage; CGL2 for motifs with fucose in a 2' linkage; and RSL for fucose in all linkages. We used several practical methods to test the lectins and determine the optimal mode of detection, and we then tested whether the lectins detected glycans in pancreatic cancer patients who did not elevate the sialyl-Lewis A glycan, which is upregulated in ∼75% of pancreatic adenocarcinomas. Patients who did not upregulate sialyl-Lewis A, which contains fucose in a 4' linkage, tended to upregulate fucose in a 3' linkage, as detected by CCL2, but they did not upregulate total fucose or fucose in a 2' linkage. CCL2 binding was high in cancerous epithelia from pancreatic tumors, including areas negative for sialyl-Lewis A and a related motif containing 3' fucose, sialyl-Lewis X. Thus, glycans containing 3' fucose may complement sialyl-Lewis A to contribute to improved detection of pancreatic cancer. Furthermore, the use of panels of recombinant lectins may uncover details about glycosylation that could be important for characterizing and detecting cancer.

  12. Genome engineering uncovers 54 evolutionarily conserved and testis-enriched genes that are not required for male fertility in mice

    Science.gov (United States)

    Miyata, Haruhiko; Castaneda, Julio M.; Fujihara, Yoshitaka; Yu, Zhifeng; Archambeault, Denise R.; Isotani, Ayako; Kiyozumi, Daiji; Kriseman, Maya L.; Mashiko, Daisuke; Matsumura, Takafumi; Matzuk, Ryan M.; Mori, Masashi; Noda, Taichi; Oji, Asami; Okabe, Masaru; Prunskaite-Hyyrylainen, Renata; Ramirez-Solis, Ramiro; Satouh, Yuhkoh; Zhang, Qian; Ikawa, Masahito; Matzuk, Martin M.

    2016-01-01

    Gene-expression analysis studies from Schultz et al. estimate that more than 2,300 genes in the mouse genome are expressed predominantly in the male germ line. As of their 2003 publication [Schultz N, Hamra FK, Garbers DL (2003) Proc Natl Acad Sci USA 100(21):12201–12206], the functions of the majority of these testis-enriched genes during spermatogenesis and fertilization were largely unknown. Since the study by Schultz et al., functional analysis of hundreds of reproductive-tract–enriched genes have been performed, but there remain many testis-enriched genes for which their relevance to reproduction remain unexplored or unreported. Historically, a gene knockout is the “gold standard” to determine whether a gene’s function is essential in vivo. Although knockout mice without apparent phenotypes are rarely published, these knockout mouse lines and their phenotypic information need to be shared to prevent redundant experiments. Herein, we used bioinformatic and experimental approaches to uncover mouse testis-enriched genes that are evolutionarily conserved in humans. We then used gene-disruption approaches, including Knockout Mouse Project resources (targeting vectors and mice) and CRISPR/Cas9, to mutate and quickly analyze the fertility of these mutant mice. We discovered that 54 mutant mouse lines were fertile. Thus, despite evolutionary conservation of these genes in vertebrates and in some cases in all eukaryotes, our results indicate that these genes are not individually essential for male mouse fertility. Our phenotypic data are highly relevant in this fiscally tight funding period and postgenomic age when large numbers of genomes are being analyzed for disease association, and will prevent unnecessary expenditures and duplications of effort by others. PMID:27357688

  13. PPARalpha siRNA-treated expression profiles uncover the causal sufficiency network for compound-induced liver hypertrophy.

    Directory of Open Access Journals (Sweden)

    Xudong Dai

    2007-03-01

    Full Text Available Uncovering pathways underlying drug-induced toxicity is a fundamental objective in the field of toxicogenomics. Developing mechanism-based toxicity biomarkers requires the identification of such novel pathways and the order of their sufficiency in causing a phenotypic response. Genome-wide RNA interference (RNAi phenotypic screening has emerged as an effective tool in unveiling the genes essential for specific cellular functions and biological activities. However, eliciting the relative contribution of and sufficiency relationships among the genes identified remains challenging. In the rodent, the most widely used animal model in preclinical studies, it is unrealistic to exhaustively examine all potential interactions by RNAi screening. Application of existing computational approaches to infer regulatory networks with biological outcomes in the rodent is limited by the requirements for a large number of targeted permutations. Therefore, we developed a two-step relay method that requires only one targeted perturbation for genome-wide de novo pathway discovery. Using expression profiles in response to small interfering RNAs (siRNAs against the gene for peroxisome proliferator-activated receptor alpha (Ppara, our method unveiled the potential causal sufficiency order network for liver hypertrophy in the rodent. The validity of the inferred 16 causal transcripts or 15 known genes for PPARalpha-induced liver hypertrophy is supported by their ability to predict non-PPARalpha-induced liver hypertrophy with 84% sensitivity and 76% specificity. Simulation shows that the probability of achieving such predictive accuracy without the inferred causal relationship is exceedingly small (p < 0.005. Five of the most sufficient causal genes have been previously disrupted in mouse models; the resulting phenotypic changes in the liver support the inferred causal roles in liver hypertrophy. Our results demonstrate the feasibility of defining pathways mediating drug

  14. Risk of Post-ERCP Pancreatitis after placement of Covered versus Uncovered Self-Expandable Biliary Metal Stents: A Systematic Review and Meta-Analysis

    OpenAIRE

    Yaseen Alastal; Tariq Hammad; Muhammad Ali Khan; Khalil, Basmah W.; Sobia Khan; Mohammad Kashif Ismail; Ali Nawras; Aijaz Sofi

    2008-01-01

    Background Self-expandable metal stents are commonly used in the management of malignant biliary obstruction due to higher patency rates compared to plastic stents. Development of covered self-expandable metal stents has led to extended stent patency compared to uncovered self-expandable metal stents. However, there are concerns that deployment of covered self-expandable metal stents may be associated with higher risk of post-endoscopic retrograde cholangio-pancreatography pancreatitis, acute...

  15. Serial insertion of bilateral uncovered metal stents for malignant hilar obstruction using an 8 Fr biliary system: a case series of 17 consecutive patients

    OpenAIRE

    Hsieh, Jennifer; Thosani, Amar; Grunwald, Matthew; Nagula, Satish; Bucobo, Juan Carlos; Jonathan M Buscaglia

    2015-01-01

    Controversy exists over the need for unilateral versus bilateral stent placement in patients with malignant obstruction at the biliary hilum. Placement of bilateral uncovered self-expanding metal stent (UCSEMS) at this location is technically challenging, and generally associated with lower rates of procedural success. Serial insertion of side-by-side UCSEMS may be especially difficult when simultaneous deployment is not possible using larger stent delivery catheters. In this single-center, r...

  16. Comparative analysis of the Photorhabdus luminescens and the Yersinia enterocolitica genomes: uncovering candidate genes involved in insect pathogenicity

    Directory of Open Access Journals (Sweden)

    Fuchs Thilo M

    2008-01-01

    Full Text Available Abstract Background Photorhabdus luminescens and Yersinia enterocolitica are both enteric bacteria which are associated with insects. P. luminescens lives in symbiosis with soil nematodes and is highly pathogenic towards insects but not to humans. In contrast, Y. enterocolitica is widely found in the environment and mainly known to cause gastroenteritis in men, but has only recently been shown to be also toxic for insects. It is expected that both pathogens share an overlap of genetic determinants that play a role within the insect host. Results A selective genome comparison was applied. Proteins belonging to the class of two-component regulatory systems, quorum sensing, universal stress proteins, and c-di-GMP signalling have been analysed. The interorganismic synopsis of selected regulatory systems uncovered common and distinct signalling mechanisms of both pathogens used for perception of signals within the insect host. Particularly, a new class of LuxR-like regulators was identified, which might be involved in detecting insect-specific molecules. In addition, the genetic overlap unravelled a two-component system that is unique for the genera Photorhabdus and Yersinia and is therefore suggested to play a major role in the pathogen-insect relationship. Our analysis also highlights factors of both pathogens that are expressed at low temperatures as encountered in insects in contrast to higher (body temperature, providing evidence that temperature is a yet under-investigated environmental signal for bacterial adaptation to various hosts. Common degradative metabolic pathways are described that might be used to explore nutrients within the insect gut or hemolymph, thus enabling the proliferation of P. luminescens and Y. enterocolitica in their invertebrate hosts. A strikingly higher number of genes encoding insecticidal toxins and other virulence factors in P. luminescens compared to Y. enterocolitica correlates with the higher virulence of P

  17. Characterization of the serine acetyltransferase gene family of Vitis vinifera uncovers differences in regulation of OAS synthesis in woody plants

    Directory of Open Access Journals (Sweden)

    Silvia eTavares

    2015-02-01

    Full Text Available In higher plants cysteine biosynthesis is catalyzed by O-acetylserine(thiollyase (OASTL and represents the last step of the assimilatory sulfate reduction pathway. It is mainly regulated by provision of O-acetylserine (OAS, the nitrogen/carbon containing backbone for fixation of reduced sulfur. OAS is synthesized by Serine acetyltransferase (SERAT, which reversibly interacts with OASTL in the cysteine synthase complex (CSC. In this study we identify and characterize the SERAT protein family of the crop plant Vitis vinifera. The identified four members of the VvSERAT gene family are assigned to three distinct groups upon their sequence similarities to Arabidopsis SERATs. Expression of fluorescently labelled VvSERAT proteins uncover that the sub-cellular localization of VvSERAT1;1 and VvSERAT3;1 is the cytosol and that VvSERAT2;1 and VvSERAT2;2 localize in addition in plastids and mitochondria, respectively. The purified VvSERATs of group 1 and 2 have higher enzymatic activity than VvSERAT3;1, which display a characteristic C-terminal extension also present in AtSERAT3;1. VvSERAT1;1 and VvSERAT2;2 are evidenced to form the CSC. CSC formation activates VvSERAT2;2, by releasing CSC-associated VvSERAT2;2 from cysteine inhibition. Thus, subcellular distribution of SERAT isoforms and CSC formation in cytosol and mitochondria is conserved between Arabidopsis and grapevine. Surprisingly, VvSERAT2;1 lack the canonical C-terminal tail of plant SERATs, does not form the CSC and is almost insensitive to cysteine inhibition (IC50 = 1.9 mM cysteine. Upon sulfate depletion VvSERAT2;1 is strongly induced at the transcriptional level, while transcription of other VvSERATs is almost unaffected in sulfate deprived grapevine cell suspension cultures. Application of abiotic stresses to soil grown grapevine plants revealed isoform-specific induction of VvSERAT2;1 in leaves upon drought, whereas high light- or temperature- stress hardly trigger VvSERAT2;1 transcription.

  18. Covered versus Uncovered Self-Expandable Metal Stents for Managing Malignant Distal Biliary Obstruction: A Meta-Analysis.

    Directory of Open Access Journals (Sweden)

    Jinjin Li

    Full Text Available To compare the efficacy of using covered self-expandable metal stents (CSEMSs and uncovered self-expandable metal stents (UCSEMSs to treat objective jaundice caused by an unresectable malignant tumor.We performed a comprehensive electronic search from 1980 to May 2015. All randomized controlled trials comparing the use of CSEMSs and UCSEMSs to treat malignant distal biliary obstruction were included.The analysis included 1417 patients enrolled in 14 trials. We did not detect significant differences between the UCSEMS group and the CSEMS group in terms of cumulative stent patency (hazard ratio (HR 0.93, 95% confidence interval (CI 0.19-4.53; p = 0.93, I2 = 0%, patient survival (HR 0.77, 95% CI 0.05-10.87; p = 0.85, I2 = 0%, overall stent dysfunction (relative ratio (RR 0.85, M-H, random, 95% CI 0.57-1.25; p = 0.83, I2 = 63%, the overall complication rate (RR 1.26, M-H, fixed, 95% CI 0.94-1.68; p = 0.12, I2 = 0% or the change in serum bilirubin (weighted mean difference (WMD -0.13, IV fixed, 95% CI 0.56-0.3; p = 0.55, I2 = 0%. However, we did detect a significant difference in the main causes of stent dysfunction between the two groups. In particular, the CSEMS group exhibited a lower rate of tumor ingrowth (RR 0.25, M-H, random, 95% CI 0.12-0.52; p = 0.002, I2 = 40% but a higher rate of tumor overgrowth (RR 1.76, M-H, fixed, 95% CI 1.03-3.02; p = 0.04, I2 = 0%. Patients with CSEMSs also exhibited a higher migration rate (RR 9.33, M-H, fixed, 95% CI 2.54-34.24; p = 0.008, I2 = 0% and a higher rate of sludge formation (RR 2.47, M-H, fixed, 95% CI 1.36-4.50; p = 0.003, I2 = 0%.Our meta-analysis indicates that there is no significant difference in primary stent patency and stent dysfunction between CSEMSs and UCSEMSs during the period from primary stent insertion to primary stent dysfunction or patient death. However, when taking further management for occluded stents into consideration, CSEMSs is a better choice for patients with malignant biliary

  19. Transcript profiles uncover temporal and stress-induced changes of metabolic pathways in germinating sugar beet seeds

    Directory of Open Access Journals (Sweden)

    Windhövel Andrea

    2008-12-01

    Full Text Available Abstract Background With a cultivation area of 1.75 Mio ha and sugar yield of 16.7 Mio tons in 2006, sugar beet is a crop of great economic importance in Europe. The productivity of sugar beet is determined significantly by seed vigour and field emergence potential; however, little is known about the molecular mechanisms underlying these traits. Both traits exhibit large variations within sugar beet germplasm that have been difficult to ascribe to either environmental or genetic causes. Among potential targets for trait improvement, an enhancement of stress tolerance is considered because of the high negative influence of environmental stresses on trait parameters. Extending our knowledge of genetic and molecular determinants of sugar beet germination, stress response and adaptation mechanisms would facilitate the detection of new targets for breeding crop with an enhanced field emergence potential. Results To gain insight into the sugar beet germination we initiated an analysis of gene expression in a well emerging sugar beet hybrid showing high germination potential under various environmental conditions. A total of 2,784 ESTs representing 2,251 'unigenes' was generated from dry mature and germinating seeds. Analysis of the temporal expression of these genes during germination under non-stress conditions uncovered drastic transcriptional changes accompanying a shift from quiescent to metabolically active stages of the plant life cycle. Assay of germination under stressful conditions revealed 157 genes showing significantly different expression patterns in response to stress. As deduced from transcriptome data, stress adaptation mechanisms included an alteration in reserve mobilization pathways, an accumulation of the osmoprotectant glycine betaine, late embryogenesis abundant proteins and detoxification enzymes. The observed transcriptional changes are supposed to be regulated by ABA-dependent signal transduction pathway. Conclusion This study

  20. Risk of Post-ERCP Pancreatitis after placement of Covered versus Uncovered Self-Expandable Biliary Metal Stents: A Systematic Review and Meta-Analysis

    Directory of Open Access Journals (Sweden)

    Yaseen Alastal

    2008-09-01

    Full Text Available Background Self-expandable metal stents are commonly used in the management of malignant biliary obstruction due to higher patency rates compared to plastic stents. Development of covered self-expandable metal stents has led to extended stent patency compared to uncovered self-expandable metal stents. However, there are concerns that deployment of covered self-expandable metal stents may be associated with higher risk of post-endoscopic retrograde cholangio-pancreatography pancreatitis, acute cholecystitis and stent migration. Objective We performed this meta-analysis to assess the risk of post-endoscopic retrograde cholangio-pancreatography pancreatitis and other adverse events (acute cholecystitis and stent migration with biliary covered self-expandable metal stents compared to uncovered self-expandable metal stents. We also assessed the proportion of stent patency at 6 and 12 months between the two groups. Methods We searched MedLine, EMBASE, Cochrane database, ISI Web of Science and Scopus from January 1989 through June, 2014, to identify randomized controlled trials and observational studies that provided data on the risk of post-endoscopic retrograde cholangio-pancreatography pancreatitis and other adverse events following the placement of covered self-expandable metal stents versus uncovered self-expandable metal stents in patients with biliary obstruction. The Mantel–Haenszel method was used to pool data of post-endoscopic retrograde cholangio- pancreatography pancreatitis, acute cholecystitis, stent migration and proportion of stent patency over 6 and 12 months into fixed or random effect model of meta-analyses. Odds ratio was used to generate an overall effect estimate of the outcome. Results Eight studies (6 randomized controlled trials and 2 observational studies with a total of 1078 patients were included in the meta-analysis. The pooled odds ratio with 95% confidence intervals for risk of post-endoscopic retrograde cholangio

  1. AB039. Novel Y-chromosomal microdeletions associated with non-obstructive azoospermia uncovered by high throughput sequencing of sequence-tagged sites (STSs)

    OpenAIRE

    Li, Zesong

    2016-01-01

    Y-chromosomal microdeletion (YCM) serves as an important genetic factor in non-obstructive azoospermia (NOA). Multiplex polymerase chain reaction (PCR) is routinely used to detect YCMs by tracing sequence-tagged sites (STSs) in the Y chromosome. Here we introduce a novel methodology in which we sequence 1,787 (post-filtering) STSs distributed across the entire male-specific Y chromosome (MSY) in parallel to uncover known and novel YCMs. We validated this approach with 766 Chinese men with NOA...

  2. Global gene expression analysis using RNA-seq uncovered a new role for SR1/CAMTA3 transcription factor in salt stress.

    Science.gov (United States)

    Prasad, Kasavajhala V S K; Abdel-Hameed, Amira A E; Xing, Denghui; Reddy, Anireddy S N

    2016-01-01

    Abiotic and biotic stresses cause significant yield losses in all crops. Acquisition of stress tolerance in plants requires rapid reprogramming of gene expression. SR1/CAMTA3, a member of signal responsive transcription factors (TFs), functions both as a positive and a negative regulator of biotic stress responses and as a positive regulator of cold stress-induced gene expression. Using high throughput RNA-seq, we identified ~3000 SR1-regulated genes. Promoters of about 60% of the differentially expressed genes have a known DNA binding site for SR1, suggesting that they are likely direct targets. Gene ontology analysis of SR1-regulated genes confirmed previously known functions of SR1 and uncovered a potential role for this TF in salt stress. Our results showed that SR1 mutant is more tolerant to salt stress than the wild type and complemented line. Improved tolerance of sr1 seedlings to salt is accompanied with the induction of salt-responsive genes. Furthermore, ChIP-PCR results showed that SR1 binds to promoters of several salt-responsive genes. These results suggest that SR1 acts as a negative regulator of salt tolerance by directly repressing the expression of salt-responsive genes. Overall, this study identified SR1-regulated genes globally and uncovered a previously uncharacterized role for SR1 in salt stress response. PMID:27251464

  3. 人工环境下无覆盖土壤散湿量计算%Uncovered soil moisture gain calculation in artificial environment

    Institute of Scientific and Technical Information of China (English)

    胡晨炯; 邓辉炼

    2012-01-01

    Considering the situation of a ruins protection hall with a large floor proportion of uncovered soil in Guangzhou and borrowing some ideas from the calculation method and well-developed empirical formula of groundwater evaporation rate in hydro science, puts forward a method for calculating the uncovered soil moisture gain in artificial environment. In this method, outside evaporation capacity is characterized with the evaporation of exposed water surface and the water supply capacity of soil is characterized with groundwater evaporation coefficient. The design effect of the project indicates that the precision of the calculation method can meet the demand of engineering.%针对广州某遗址保护大厅内多为裸露土壤的情况,借鉴水利科学中潜水蒸发量的计算方法及成熟的相关经验公式,提出了人工环境下无覆盖土壤散湿量的计算方法.在该计算方法中,用暴露水面的蒸发量来表征外界蒸发能力,用潜水蒸发系数来表征土壤的输水能力.设计效果表明,该方法的计算精度能满足工程实际的需要.

  4. 冬小麦籽粒淀粉合成相关酶活性的日变化%Diurnal Changes in Activities of Related Enzymes to Starch Synthesis in Grains of Winter Wheat

    Institute of Scientific and Technical Information of China (English)

    姜东; 曹卫星; 戴廷波; 荆奇

    2004-01-01

    The conversion from sucrose to starch in grains is a key process during yield formation of wheat. In a field study, diurnal changes in ATP content and activities of enzymes catalyzing starch synthesis in grains of two winter wheat ( Triticum aestivum L.) cv. Lumai 22 and Lumai 14 were investigated.The enzymes included sucrose synthase (SS; EC 2.4.1.13), ADP-glucose pyrophosphorylase (ADPGPPase;EC 2.7.7.27), soluble starch synthase (SSS), and starch granule-bound synthase (GBSS; EC 2.4.1.21).Activities of these enzymes and ATP content showed obvious diurnal patterns. The enzyme activities were generally higher during the nighttime than the daytime, but ATP content showed an opposite pattern.It was found that the super-optimum air temperature could be partly responsible for the low enzyme activities during the daytime. The possible factors influenced the diurnal changes in activities of the enzymes for starch synthesis in wheat grain were discussed.%蔗糖向淀粉的转化是决定小麦籽粒产量的重要因素.田间条件下研究了两个小麦(Triticum aestivum L.)品种"鲁麦22"和"鲁麦14"籽粒淀粉合成相关酶:蔗糖合酶(sucrose synthase,SS)、腺苷二磷酸葡萄糖焦磷酸化酶(ADP-glucose pyrophosphorylase,ADPGPPase)、可溶性淀粉合酶(soluble starch synthase,SSS)、束缚态淀粉合酶(starch granule-bound synthase,GBSS)的活性以及籽粒ATP含量的日变化.结果表明,上述酶活性呈现明显的昼夜变化特征,酶活性一般在白天较低,而在夜间呈现较高活性,而籽粒ATP含量趋势相反.相关分析表明,白天较低的酶活性可能与气温超过其适宜温度有关.对籽粒淀粉合成相关酶活性日变化的可能因子进行了讨论.

  5. Uncovering Voter Preference Structures Using a Best-Worst Scaling Procedure: Method and Empirical Example in the British General Election of 2010

    DEFF Research Database (Denmark)

    Ormrod, Robert P.; Savigny, Heather

    Best-Worst scaling (BWS) is a method that can provide insights into the preference structures of voters. By asking voters to select the ‘best’ and ‘worst’ option (‘most important’ and ‘least important’ media in our investigation) from a short list of alternatives it is possible to uncover...... the relative importance of each of the options. Using a Balanced Incomplete Block research design we reduce the number of comparisons to the number of media, thus reducing fatigue and complexity problems associated with the standard paired-preference scale from which BWS is developed. Scale variables can...... amount of information provided by seven alternative media. Results indicate that voters in our sample gained the most information about the election campaign through the broadcast and print media and the leadership debate, whilst Party-controlled media such as party websites and election posters provided...

  6. Serial insertion of bilateral uncovered metal stents for malignant hilar obstruction using an 8 Fr biliary system: a case series of 17 consecutive patients.

    Science.gov (United States)

    Hsieh, Jennifer; Thosani, Amar; Grunwald, Matthew; Nagula, Satish; Bucobo, Juan Carlos; Buscaglia, Jonathan M

    2015-10-01

    Controversy exists over the need for unilateral versus bilateral stent placement in patients with malignant obstruction at the biliary hilum. Placement of bilateral uncovered self-expanding metal stent (UCSEMS) at this location is technically challenging, and generally associated with lower rates of procedural success. Serial insertion of side-by-side UCSEMS may be especially difficult when simultaneous deployment is not possible using larger stent delivery catheters. In this single-center, retrospective case series of all patients who underwent bilateral placement of uncovered Wallflex(TM) biliary stents between July 2008 and July 2014, we evaluate the feasibility, technical success, and safety of patients undergoing serial insertion of bilateral UCSEMS using the 8 Fr Wallflex(TM) biliary system for malignant hilar obstruction. A total of 17 patients were included. Primary cholangiocarcinoma, Bismuth IV, was the most common diagnosis. Mean procedure time was 54.4 minutes. Overall procedural technical success was achieved in 17/17 patients. Stricture dilation was necessary prior to Wallflex(TM) insertion in 8/17 patients (47.1%). Transpapillary extension of two stents was performed in all patients. There were no cases of stent deployment malfunction, or inability to insert or deploy the 2(nd) stent. Nine of 17 patients (52.9%) required inpatient hospitalization following ERCP; the most common indications were abdominal pain and need for IV antibiotics. There was one case of ERCP-related cholangitis otherwise; there were no other major complications. Bilateral, serial insertion of UCSEMS using the 8 Fr Wallflex(TM) biliary system in malignant hilar obstruction is feasible with an excellent technical success profile. Using this device for side-by-side deployment of UCSEMS appears to be safe in the majority of patients. PMID:26605283

  7. Parvin overexpression uncovers tissue-specific genetic pathways and disrupts F-actin to induce apoptosis in the developing epithelia in Drosophila.

    Directory of Open Access Journals (Sweden)

    Maria Chountala

    Full Text Available Parvin is a putative F-actin binding protein important for integrin-mediated cell adhesion. Here we used overexpression of Drosophila Parvin to uncover its functions in different tissues in vivo. Parvin overexpression caused major defects reminiscent of metastatic cancer cells in developing epithelia, including apoptosis, alterations in cell shape, basal extrusion and invasion. These defects were closely correlated with abnormalities in the organization of F-actin at the basal epithelial surface and of integrin-matrix adhesion sites. In wing epithelium, overexpressed Parvin triggered increased Rho1 protein levels, predominantly at the basal side, whereas in the developing eye it caused a rough eye phenotype and severely disrupted F-actin filaments at the retina floor of pigment cells. We identified genes that suppressed these Parvin-induced dominant effects, depending on the cell type. Co-expression of both ILK and the apoptosis inhibitor DIAP1 blocked Parvin-induced lethality and apoptosis and partially ameliorated cell delamination in epithelia, but did not rescue the elevated Rho1 levels, the abnormal organization of F-actin in the wing and the assembly of integrin-matrix adhesion sites. The rough eye phenotype was suppressed by coexpression of either PTEN or Wech, or by knock-down of Xrp1. Two main conclusions can be drawn from our studies: (1, high levels of cytoplasmic Parvin are toxic in epithelial cells; (2 Parvin in a dose dependent manner affects the organization of actin cytoskeleton in both wing and eye epithelia, independently of its role as a structural component of the ILK-PINCH-Parvin complex that mediates the integrin-actin link. Thus, distinct genetic interactions of Parvin occur in different cell types and second site modifier screens are required to uncover such genetic circuits.

  8. Integration of small RNAs, degradome and transcriptome sequencing in hyperaccumulator Sedum alfredii uncovers a complex regulatory network and provides insights into cadmium phytoremediation.

    Science.gov (United States)

    Han, Xiaojiao; Yin, Hengfu; Song, Xixi; Zhang, Yunxing; Liu, Mingying; Sang, Jiang; Jiang, Jing; Li, Jihong; Zhuo, Renying

    2016-06-01

    The hyperaccumulating ecotype of Sedum alfredii Hance is a cadmium (Cd)/zinc/lead co-hyperaccumulating species of Crassulaceae. It is a promising phytoremediation candidate accumulating substantial heavy metal ions without obvious signs of poisoning. However, few studies have focused on the regulatory roles of miRNAs and their targets in the hyperaccumulating ecotype of S. alfredii. Here, we combined analyses of the transcriptomics, sRNAs and the degradome to generate a comprehensive resource focused on identifying key regulatory miRNA-target circuits under Cd stress. A total of 87 721 unigenes and 356 miRNAs were identified by deep sequencing, and 79 miRNAs were differentially expressed under Cd stress. Furthermore, 754 target genes of 194 miRNAs were validated by degradome sequencing. A gene ontology (GO) enrichment analysis of differential miRNA targets revealed that auxin, redox-related secondary metabolism and metal transport pathways responded to Cd stress. An integrated analysis uncovered 39 pairs of miRNA targets that displayed negatively correlated expression profiles. Ten miRNA-target pairs also exhibited negative correlations according to a real-time quantitative PCR analysis. Moreover, a coexpression regulatory network was constructed based on profiles of differentially expressed genes. Two hub genes, ARF4 (auxin response factor 4) and AAP3 (amino acid permease 3), which might play central roles in the regulation of Cd-responsive genes, were uncovered. These results suggest that comprehensive analyses of the transcriptomics, sRNAs and the degradome provided a useful platform for investigating Cd hyperaccumulation in S. alfredii, and may provide new insights into the genetic engineering of phytoremediation. PMID:26801211

  9. DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data.

    Science.gov (United States)

    Vlachos, Ioannis S; Vergoulis, Thanasis; Paraskevopoulou, Maria D; Lykokanellos, Filopoimin; Georgakilas, Georgios; Georgiou, Penny; Chatzopoulos, Serafeim; Karagkouni, Dimitra; Christodoulou, Foteini; Dalamagas, Theodore; Hatzigeorgiou, Artemis G

    2016-07-01

    Differential expression analysis (DEA) is one of the main instruments utilized for revealing molecular mechanisms in pathological and physiological conditions. DIANA-mirExTra v2.0 (http://www.microrna.gr/mirextrav2) performs a combined DEA of mRNAs and microRNAs (miRNAs) to uncover miRNAs and transcription factors (TFs) playing important regulatory roles between two investigated states. The web server uses as input miRNA/RNA-Seq read count data sets that can be uploaded for analysis. Users can combine their data with 350 small-RNA-Seq and 65 RNA-Seq in-house analyzed libraries which are provided by DIANA-mirExTra v2.0.The web server utilizes miRNA:mRNA, TF:mRNA and TF:miRNA interactions derived from extensive experimental data sets. More than 450 000 miRNA interactions and 2 000 000 TF binding sites from specific or high-throughput techniques have been incorporated, while accurate miRNA TSS annotation is obtained from microTSS experimental/in silico framework. These comprehensive data sets enable users to perform analyses based solely on experimentally supported information and to uncover central regulators within sequencing data: miRNAs controlling mRNAs and TFs regulating mRNA or miRNA expression. The server also supports predicted miRNA:gene interactions from DIANA-microT-CDS for 4 species (human, mouse, nematode and fruit fly). DIANA-mirExTra v2.0 has an intuitive user interface and is freely available to all users without any login requirement. PMID:27207881

  10. Functional and gene network analyses of transcriptional signatures characterizing pre-weaned bovine mammary parenchyma or fat pad uncovered novel inter-tissue signaling networks during development

    Directory of Open Access Journals (Sweden)

    Lewin Harris A

    2010-05-01

    Full Text Available Abstract Background The neonatal bovine mammary fat pad (MFP surrounding the mammary parenchyma (PAR is thought to exert proliferative effects on the PAR through secretion of local modulators of growth induced by systemic hormones. We used bioinformatics to characterize transcriptomics differences between PAR and MFP from ~65 d old Holstein heifers. Data were mined to uncover potential crosstalk through the analyses of signaling molecules preferentially expressed in one tissue relative to the other. Results Over 9,000 differentially expressed genes (DEG; False discovery rate ≤ 0.05 were found of which 1,478 had a ≥1.5-fold difference between PAR and MFP. Within the DEG highly-expressed in PAR vs. MFP (n = 736 we noted significant enrichment of functions related to cell cycle, structural organization, signaling, and DNA/RNA metabolism. Only actin cytoskeletal signaling was significant among canonical pathways. DEG more highly-expressed in MFP vs. PAR (n = 742 belong to lipid metabolism, signaling, cell movement, and immune-related functions. Canonical pathways associated with metabolism and signaling, particularly immune- and metabolism-related were significantly-enriched. Network analysis uncovered a central role of MYC, TP53, and CTNNB1 in controlling expression of DEG highly-expressed in PAR vs. MFP. Similar analysis suggested a central role for PPARG, KLF2, EGR2, and EPAS1 in regulating expression of more highly-expressed DEG in MFP vs. PAR. Gene network analyses revealed putative inter-tissue crosstalk between cytokines and growth factors preferentially expressed in one tissue (e.g., ANGPTL1, SPP1, IL1B in PAR vs. MFP; ADIPOQ, IL13, FGF2, LEP in MFP vs. PAR with DEG preferentially expressed in the other tissue, particularly transcription factors or pathways (e.g., MYC, TP53, and actin cytoskeletal signaling in PAR vs. MFP; PPARG and LXR/RXR Signaling in MFP vs. PAR. Conclusions Functional analyses underscored a reciprocal influence in

  11. Influence of crop load on the expression patterns of starch metabolism genes in alternate-bearing citrus trees.

    Science.gov (United States)

    Nebauer, Sergio G; Renau-Morata, Begoña; Lluch, Yolanda; Baroja-Fernández, Edurne; Pozueta-Romero, Javier; Molina, Rosa-Victoria

    2014-07-01

    The fruit is the main sink organ in Citrus and captures almost all available photoassimilates during its development. Consequently, carbohydrate partitioning and starch content depend on the crop load of Citrus trees. Nevertheless, little is known about the mechanisms controlling the starch metabolism at the tree level in relation to presence of fruit. The aim of this study was to find the relation between the seasonal variation of expression and activity of the genes involved in carbon metabolism and the partition and allocation of carbohydrates in 'Salustiana' sweet orange trees with different crop loads. Metabolisable carbohydrates, and the expression and activity of the enzymes involved in sucrose and starch metabolism, including sucrose transport, were determined during the year in the roots and leaves of 40-year-old trees bearing heavy crop loads ('on' trees) and trees with almost no fruits ('off' trees). Fruit altered photoassimilate partitioning in trees. Sucrose content tended to be constant in roots and leaves, and surplus fixed carbon is channeled to starch production. Differences between 'on' and 'off' trees in starch content can be explained by differences in ADP-glucose pyrophosphorylase (AGPP) expression/activity and α-amylase activity which varies depending on crop load. The observed relation of AGPP and UGPP (UDP-glucose pyrophosphorylase) is noteworthy and indicates a direct link between sucrose and starch synthesis. Furthermore, different roles for sucrose transporter SUT1 and SUT2 have been proposed. Variation in soluble sugars content cannot explain the differences in gene expression between the 'on' and 'off' trees. A still unknown signal from fruit should be responsible for this control. PMID:24747724

  12. Structure, function and regulation of the enzymes in the starch biosynthetic pathway.

    Energy Technology Data Exchange (ETDEWEB)

    Geiger, Jim

    2013-11-30

    structure of ADP- Glucose pyrophosphorylase from potato in its inhibited conformation, and bound to both ATP and ADP-glucose. In addition, we have determined the first structure of glycogen synthase in its "closed", catalytically active conformation bound to ADP-glucose. We also determined the structure of glycogen synthase bound to malto-oligosaccharides, showing for the first time that an enzyme in the starch biosynthetic pathway recognizes glucans not just in its active site but on binding sites on the surface of the enzyme ten’s of Angstroms from the active site. In addition our structure of a glycogen branching enzyme bound to malto-oligosaccharides identified seven distinct binding sites distributed about the surface of the enzyme. We will now determine the function of these sites to get a molecular-level picture of exactly how these enzymes interact with their polymeric substrates and confer specificity leading to the complex structure of the starch granule. We will extend our studies to other isoforms of the enzymes, to understand how their structures give rise to their distinct function. Our goal is to understand what accounts for the various functional differences between SS and SBE isoforms at a molecular level.

  13. Structure, function and regulation of the enzymes in the starch biosynthetic pathway.

    Energy Technology Data Exchange (ETDEWEB)

    Geiger, Jim

    2013-11-30

    structure of ADP- Glucose pyrophosphorylase from potato in its inhibited conformation, and bound to both ATP and ADP-glucose. In addition, we have determined the first structure of glycogen synthase in its "closed", catalytically active conformation bound to ADP-glucose. We also determined the structure of glycogen synthase bound to malto-oligosaccharides, showing for the first time that an enzyme in the starch biosynthetic pathway recognizes glucans not just in its active site but on binding sites on the surface of the enzyme ten’s of Angstroms from the active site. In addition our structure of a glycogen branching enzyme bound to malto-oligosaccharides identified seven distinct binding sites distributed about the surface of the enzyme. We will now determine the function of these sites to get a molecular-level picture of exactly how these enzymes interact with their polymeric substrates and confer specificity leading to the complex structure of the starch granule. We will extend our studies to other isoforms of the enzymes, to understand how their structures give rise to their distinct function. Our goal is to understand what accounts for the various functional differences between SS and SBE isoforms at a molecular level.

  14. Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role

    KAUST Repository

    Kleftogiannis, Dimitrios A.

    2013-06-01

    Traditional biology was forced to restate some of its principles when the microRNA (miRNA) genes and their regulatory role were firstly discovered. Typically, miRNAs are small non-coding RNA molecules which have the ability to bind to the 3\\'untraslated region (UTR) of their mRNA target genes for cleavage or translational repression. Existing experimental techniques for their identification and the prediction of the target genes share some important limitations such as low coverage, time consuming experiments and high cost reagents. Hence, many computational methods have been proposed for these tasks to overcome these limitations. Recently, many researchers emphasized on the development of computational approaches to predict the participation of miRNA genes in regulatory networks and to analyze their transcription mechanisms. All these approaches have certain advantages and disadvantages which are going to be described in the present survey. Our work is differentiated from existing review papers by updating the methodologies list and emphasizing on the computational issues that arise from the miRNA data analysis. Furthermore, in the present survey, the various miRNA data analysis steps are treated as an integrated procedure whose aims and scope is to uncover the regulatory role and mechanisms of the miRNA genes. This integrated view of the miRNA data analysis steps may be extremely useful for all researchers even if they work on just a single step. © 2013 Elsevier Inc.

  15. Evaluation of chronic lymphocytic leukemia by oligonucleotide-based microarray analysis uncovers novel aberrations not detected by FISH or cytogenetic analysis

    Directory of Open Access Journals (Sweden)

    Kolquist Kathryn A

    2011-11-01

    Full Text Available Abstract Background Cytogenetic evaluation is a key component of the diagnosis and prognosis of chronic lymphocytic leukemia (CLL. We performed oligonucleotide-based comparative genomic hybridization microarray analysis on 34 samples with CLL and known abnormal karyotypes previously determined by cytogenetics and/or fluorescence in situ hybridization (FISH. Results Using a custom designed microarray that targets >1800 genes involved in hematologic disease and other malignancies, we identified additional cryptic aberrations and novel findings in 59% of cases. These included gains and losses of genes associated with cell cycle regulation, apoptosis and susceptibility loci on 3p21.31, 5q35.2q35.3, 10q23.31q23.33, 11q22.3, and 22q11.23. Conclusions Our results show that microarray analysis will detect known aberrations, including microscopic and cryptic alterations. In addition, novel genomic changes will be uncovered that may become important prognostic predictors or treatment targets for CLL in the future.

  16. Novel Y-chromosomal microdeletions associated with non-obstructive azoospermia uncovered by high throughput sequencing of sequence-tagged sites (STSs).

    Science.gov (United States)

    Liu, Xiao; Li, Zesong; Su, Zheng; Zhang, Junjie; Li, Honggang; Xie, Jun; Xu, Hanshi; Jiang, Tao; Luo, Liya; Zhang, Ruifang; Zeng, Xiaojing; Xu, Huaiqian; Huang, Yi; Mou, Lisha; Hu, Jingchu; Qian, Weiping; Zeng, Yong; Zhang, Xiuqing; Xiong, Chengliang; Yang, Huanming; Kristiansen, Karsten; Cai, Zhiming; Wang, Jun; Gui, Yaoting

    2016-01-01

    Y-chromosomal microdeletion (YCM) serves as an important genetic factor in non-obstructive azoospermia (NOA). Multiplex polymerase chain reaction (PCR) is routinely used to detect YCMs by tracing sequence-tagged sites (STSs) in the Y chromosome. Here we introduce a novel methodology in which we sequence 1,787 (post-filtering) STSs distributed across the entire male-specific Y chromosome (MSY) in parallel to uncover known and novel YCMs. We validated this approach with 766 Chinese men with NOA and 683 ethnically matched healthy individuals and detected 481 and 98 STSs that were deleted in the NOA and control group, representing a substantial portion of novel YCMs which significantly influenced the functions of spermatogenic genes. The NOA patients tended to carry more and rarer deletions that were enriched in nearby intragenic regions. Haplogroup O2* was revealed to be a protective lineage for NOA, in which the enrichment of b1/b3 deletion in haplogroup C was also observed. In summary, our work provides a new high-resolution portrait of deletions in the Y chromosome. PMID:26907467

  17. AB039. Novel Y-chromosomal microdeletions associated with non-obstructive azoospermia uncovered by high throughput sequencing of sequence-tagged sites (STSs)

    Science.gov (United States)

    Li, Zesong

    2016-01-01

    Y-chromosomal microdeletion (YCM) serves as an important genetic factor in non-obstructive azoospermia (NOA). Multiplex polymerase chain reaction (PCR) is routinely used to detect YCMs by tracing sequence-tagged sites (STSs) in the Y chromosome. Here we introduce a novel methodology in which we sequence 1,787 (post-filtering) STSs distributed across the entire male-specific Y chromosome (MSY) in parallel to uncover known and novel YCMs. We validated this approach with 766 Chinese men with NOA and 683 ethnically matched healthy individuals and detected 481 and 98 STSs that were deleted in the NOA and control group, representing a substantial portion of novel YCMs which significantly influenced the functions of spermatogenic genes. The NOA patients tended to carry more and rarer deletions that were enriched in nearby intragenic regions. Haplogroup O2* was revealed to be a protective lineage for NOA, in which the enrichment of b1/b3 deletion in haplogroup C was also observed. In summary, our work provides a new high-resolution portrait of deletions in the Y chromosome.

  18. Reverse genetic screen for loss-of-function mutations uncovers a frameshifting deletion in the melanophilin gene accountable for a distinctive coat color in Belgian Blue cattle.

    Science.gov (United States)

    Li, Wanbo; Sartelet, Arnaud; Tamma, Nico; Coppieters, Wouter; Georges, Michel; Charlier, Carole

    2016-02-01

    In the course of a reverse genetic screen in the Belgian Blue cattle breed, we uncovered a 10-bp deletion (c.87_96del) in the first coding exon of the melanophilin gene (MLPH), which introduces a premature stop codon (p.Glu32Aspfs*1) in the same exon, truncating 94% of the protein. Recessive damaging mutations in the MLPH gene are well known to cause skin, hair, coat or plumage color dilution phenotypes in numerous species, including human, mice, dog, cat, mink, rabbit, chicken and quail. Large-scale array genotyping undertaken to identify p.Glu32Aspfs*1 homozygous mutant animals revealed a mutation frequency of 5% in the breed and allowed for the identification of 10 homozygous mutants. As expression of a colored coat requires at least one wild-type allele at the co-dominant Roan locus encoded by the KIT ligand gene (KITLG), homozygous mutants for p.Ala227Asp corresponding with the missense mutation were excluded. The six remaining colored calves displayed a distinctive dilution phenotype as anticipated. This new coat color was named 'cool gray'. It is the first damaging mutation in the MLPH gene described in cattle and extends the already long list of species with diluted color due to recessive mutations in MLPH and broadens the color palette of gray in this breed. PMID:26582259

  19. RNA-Seq and Gene Network Analysis Uncover Activation of an ABA-Dependent Signalosome During the Cork Oak Root Response to Drought.

    Science.gov (United States)

    Magalhães, Alexandre P; Verde, Nuno; Reis, Francisca; Martins, Inês; Costa, Daniela; Lino-Neto, Teresa; Castro, Pedro H; Tavares, Rui M; Azevedo, Herlânder

    2015-01-01

    Quercus suber (cork oak) is a West Mediterranean species of key economic interest, being extensively explored for its ability to generate cork. Like other Mediterranean plants, Q. suber is significantly threatened by climatic changes, imposing the need to quickly understand its physiological and molecular adaptability to drought stress imposition. In the present report, we uncovered the differential transcriptome of Q. suber roots exposed to long-term drought, using an RNA-Seq approach. 454-sequencing reads were used to de novo assemble a reference transcriptome, and mapping of reads allowed the identification of 546 differentially expressed unigenes. These were enriched in both effector genes (e.g., LEA, chaperones, transporters) as well as regulatory genes, including transcription factors (TFs) belonging to various different classes, and genes associated with protein turnover. To further extend functional characterization, we identified the orthologs of differentially expressed unigenes in the model species Arabidopsis thaliana, which then allowed us to perform in silico functional inference, including gene network analysis for protein function, protein subcellular localization and gene co-expression, and in silico enrichment analysis for TFs and cis-elements. Results indicated the existence of extensive transcriptional regulatory events, including activation of ABA-responsive genes and ABF-dependent signaling. We were then able to establish that a core ABA-signaling pathway involving PP2C-SnRK2-ABF components was induced in stressed Q. suber roots, identifying a key mechanism in this species' response to drought.

  20. RNA-Seq and gene network analysis uncover activation of an ABA-dependent signalosome during the cork oak root response to drought

    Directory of Open Access Journals (Sweden)

    Alexandre Papadopoulos Magalhães

    2016-01-01

    Full Text Available Quercus suber (cork oak is a West Mediterranean species of key economic interest, being extensively explored for its ability to generate cork. Like other Mediterranean plants, Q. suber is significantly threatened by climatic changes, imposing the need to quickly understand its physiological and molecular adaptability to drought stress imposition. In the present report, we uncovered the differential transcriptome of Q. suber roots exposed to long-term drought, using an RNA-Seq approach. 454 sequencing reads were used to de novo assemble a reference transcriptome, and mapping of reads allowed the identification of 546 differentially expressed unigenes. These were enriched in both effector genes (e.g. LEA, chaperones, transporters as well as regulatory genes, including transcription factors (TFs belonging to various different classes, and genes associated with protein turnover. To further extend functional characterization, we identified the orthologs of differentially expressed unigenes in the model species Arabidopsis thaliana, which then allowed us to perform in silico functional inference, including gene network analysis for protein function, protein subcellular localization and gene co-expression, and in silico enrichment analysis for TFs and cis-elements. Results indicated the existence of extensive transcriptional regulatory events, including activation of ABA-responsive genes and ABF-dependent signaling. We were then able to establish that all components of a core ABA-signaling pathway involving PP2C-SnRK2-ABF components was induced in stressed Q. suber roots, identifying a key mechanism in this species’ response to drought.

  1. A joint modeling approach for uncovering associations between gene expression, bioactivity and chemical structure in early drug discovery to guide lead selection and genomic biomarker development.

    Science.gov (United States)

    Perualila-Tan, Nolen; Kasim, Adetayo; Talloen, Willem; Verbist, Bie; Göhlmann, Hinrich W H; Shkedy, Ziv

    2016-08-01

    The modern drug discovery process involves multiple sources of high-dimensional data. This imposes the challenge of data integration. A typical example is the integration of chemical structure (fingerprint features), phenotypic bioactivity (bioassay read-outs) data for targets of interest, and transcriptomic (gene expression) data in early drug discovery to better understand the chemical and biological mechanisms of candidate drugs, and to facilitate early detection of safety issues prior to later and expensive phases of drug development cycles. In this paper, we discuss a joint model for the transcriptomic and the phenotypic variables conditioned on the chemical structure. This modeling approach can be used to uncover, for a given set of compounds, the association between gene expression and biological activity taking into account the influence of the chemical structure of the compound on both variables. The model allows to detect genes that are associated with the bioactivity data facilitating the identification of potential genomic biomarkers for compounds efficacy. In addition, the effect of every structural feature on both genes and pIC50 and their associations can be simultaneously investigated. Two oncology projects are used to illustrate the applicability and usefulness of the joint model to integrate multi-source high-dimensional information to aid drug discovery. PMID:27269248

  2. Why do most Gitano/Romani students not complete compulsory secondary education in Spain? Uncovering the view of the educational community using concept mapping

    Directory of Open Access Journals (Sweden)

    Álvarez Arturo

    2016-01-01

    Full Text Available This paper describes the results of research that used Concept Mapping to study the causes of the high rates of school failure among the students of the Gitano or Spanish Romani minority. A sample of 52 members of a school community—pupils, families and teachers—participated in the research. Data were collected in focus groups. Generated ideas were sorted and rated by participants. A multidimensional scaling of sorted data resulted in a map of points. A cluster analysis with the points’ coordinates was run. The results uncovered a model of six clusters: ethnic differences, families, adolescent risk behaviours, students’ attitudes and values, curriculum gap, and finally effects of compensatory education and attention to diversity programmes. The relationships among the clusters point to three sources of concern: cultural and gender issues within the family setting that encourage girls to drop out of school; lack of motivation and educational orientation of the students; and structural problems of the educational system that contribute to maintain the educational gap between minority and majority students.

  3. Climate change adaptation: Uncovering constraints to the use of adaptation strategies among food crop farmers in South-west, Nigeria using principal component analysis (PCA

    Directory of Open Access Journals (Sweden)

    Moradeyo Adebanjo Otitoju

    2016-12-01

    Full Text Available This study focused on the constraints to the use of climate variability/change adaptation strategies in South-west Nigeria. Multistage random technique was employed to select the location and the respondents. Descriptive statistics and principal component analysis (PCA were the analytical tools engaged in this study. The constraints to climate variability and change examined before did not use PCA but generalized factor analysis. Hence, there is need to examine these constraints extensively using PCA. Uncovering the constraints to the use of climate variability/change adaptation strategies among crop framers is important to give a realistic direction in the development of farmer-inclusive climate policies in Nigeria. The PCA result showed that the principal constraints that the farmers faced in climate change adaptation were public, institutional and labour constraint; land, neighbourhood norms and religious beliefs constraint; high cost of inputs, technological and information constraint; farm distance, access to climate information, off-farm job and credit constraint; and poor agricultural programmes and service delivery constraint. These findings pointed out the need for both the government and non-government organizations to intensify efforts on institutional, technological and farmers’ friendly land tenure and information systems as effective measures to guide inclusive climate change adaptation policies and development in South-west Nigeria.

  4. Reverse genetic screen for loss-of-function mutations uncovers a frameshifting deletion in the melanophilin gene accountable for a distinctive coat color in Belgian Blue cattle.

    Science.gov (United States)

    Li, Wanbo; Sartelet, Arnaud; Tamma, Nico; Coppieters, Wouter; Georges, Michel; Charlier, Carole

    2016-02-01

    In the course of a reverse genetic screen in the Belgian Blue cattle breed, we uncovered a 10-bp deletion (c.87_96del) in the first coding exon of the melanophilin gene (MLPH), which introduces a premature stop codon (p.Glu32Aspfs*1) in the same exon, truncating 94% of the protein. Recessive damaging mutations in the MLPH gene are well known to cause skin, hair, coat or plumage color dilution phenotypes in numerous species, including human, mice, dog, cat, mink, rabbit, chicken and quail. Large-scale array genotyping undertaken to identify p.Glu32Aspfs*1 homozygous mutant animals revealed a mutation frequency of 5% in the breed and allowed for the identification of 10 homozygous mutants. As expression of a colored coat requires at least one wild-type allele at the co-dominant Roan locus encoded by the KIT ligand gene (KITLG), homozygous mutants for p.Ala227Asp corresponding with the missense mutation were excluded. The six remaining colored calves displayed a distinctive dilution phenotype as anticipated. This new coat color was named 'cool gray'. It is the first damaging mutation in the MLPH gene described in cattle and extends the already long list of species with diluted color due to recessive mutations in MLPH and broadens the color palette of gray in this breed.

  5. Deletion of chloroplast NADPH-dependent thioredoxin reductase results in inability to regulate starch synthesis and causes stunted growth under short-day photoperiods.

    Science.gov (United States)

    Lepistö, Anna; Pakula, Eveliina; Toivola, Jouni; Krieger-Liszkay, Anja; Vignols, Florence; Rintamäki, Eevi

    2013-09-01

    Plastid-localized NADPH-dependent thioredoxin reductase C (NTRC) is a unique NTR enzyme containing both reductase and thioredoxin domains in a single polypeptide. Arabidopsis thaliana NTRC knockout lines (ntrc) show retarded growth, especially under short-day (SD) photoperiods. This study identified chloroplast processes that accounted for growth reduction in SD-acclimated ntrc. The strongest reduction in ntrc growth occurred under photoperiods with nights longer than 14 h, whereas knockout of the NTRC gene did not alter the circadian-clock-controlled growth of Arabidopsis. Lack of NTRC modulated chloroplast reactive oxygen species (ROS) metabolism, but oxidative stress was not the primary cause of retarded growth of SD-acclimated ntrc. Scarcity of starch accumulation made ntrc leaves particularly vulnerable to photoperiods with long nights. Direct interaction of NTRC and ADP-glucose pyrophosphorylase, a key enzyme in starch synthesis, was confirmed by yeast two-hybrid analysis. The ntrc line was not able to maximize starch synthesis during the light period, which was particularly detrimental under SD conditions. Acclimation of Arabidopsis to SD conditions also involved an inductive rise of ROS production in illuminated chloroplasts that was not counterbalanced by the activation of plastidial anti-oxidative systems. It is proposed that knockout of NTRC challenges redox regulation of starch synthesis, resulting in stunted growth of the mutant lines acclimated to the SD photoperiod.

  6. Proteomic analysis reveals key proteins and phosphoproteins upon seed germination of wheat (Triticum aestivum L.

    Directory of Open Access Journals (Sweden)

    Kun eDong

    2015-11-01

    Full Text Available Wheat (Triticum aestivum L. is one of the oldest cultivated crops and the second most important food crop in the world. Seed germination is the key developmental process in plant growth and development, and poor germination directly affects plant growth and subsequent grain yield. In this study, we performed the first dynamic proteome analysis of wheat seed germination using a two-dimensional differential gel electrophoresis (2D-DIGE-based proteomic approach. A total of 166 differentially expressed protein (DEP spots representing 73 unique proteins were identified, which are mainly involved in storage, stress/defense/detoxification, carbohydrate metabolism, photosynthesis, cell metabolism, and transcription/translation/ transposition. The identified DEPs and their dynamic expression profiles generally correspond to three distinct seed germination phases after imbibition: storage degradation, physiological processes/morphogenesis, and photosynthesis. Some key DEPs involved in storage substance degradation and plant defense mechanisms, such as globulin 3, sucrose synthase type I, serpin, beta-amylase, and plastid ADP-glucose pyrophosphorylase (AGPase small subunit, were found to be phosphorylated during seed germination. Particularly, the phosphorylation site Ser355 was found to be located in the enzyme active region of beta-amylase, which promotes substrate binding. Phosphorylated modification of several proteins could promote storage substance degradation and environmental stress defense during seed germination. The central metabolic pathways involved in wheat seed germination are proposed herein, providing new insights into the molecular mechanisms of cereal seed germination.

  7. Expression Profiling of Cassava Storage Roots Reveals an Active Process of Glycolysis/Gluconeogenesis

    Institute of Scientific and Technical Information of China (English)

    Jun Yang; Dong An; Peng Zhang

    2011-01-01

    Mechanisms related to the development of cassava storage roots and starch accumulation remain largely unknown. To evaluate genome-wide expression patterns during tuberization, a 60 mer oligonucleotide microarray representing 20 840 cassava genes was designed to identify differentially expressed transcripts in fibrous roots, developing storage roots and mature storage roots. Using a random variance model and the traditional twofold change method for statistical analysis, 912 and 3 386 upregulated and downregulated genes related to the three developmental phases were identified. Among 25 significantly changed pathways identified, glycolysislgluconeogenesis was the most evident one. Rate-limiting enzymes were identified from each individual pathway, for example, enolase, L-lactate dehydrogenase and aldehyde dehydrogenase for glycolysis/gluconeogenesis, and ADP-glucose pyrophosphorylase, starch branching enzyme and glucan phosphorylase for sucrose and starch metabolism. This study revealed that dynamic changes in at least 16% of the total transcripts, including transcription fac-tors, oxidoreductasesltransferaseslhydrolases, hormone-related genes, and effectors of homeostasis. The reliability of these differentially expressed genes was verified by quantitative real-time reverse transcription-polymerase chain reaction. These studies should facilitate our understanding of the storage root formation and cassava improvement.

  8. Alteration of the interconversion of pyruvate and malate in the plastid or cytosol of ripening tomato fruit invokes diverse consequences on sugar but similar effects on cellular organic acid, metabolism, and transitory starch accumulation.

    Science.gov (United States)

    Osorio, Sonia; Vallarino, José G; Szecowka, Marek; Ufaz, Shai; Tzin, Vered; Angelovici, Ruthie; Galili, Gad; Fernie, Alisdair R

    2013-02-01

    The aim of this work was to investigate the effect of decreased cytosolic phosphoenolpyruvate carboxykinase (PEPCK) and plastidic NADP-dependent malic enzyme (ME) on tomato (Solanum lycopersicum) ripening. Transgenic tomato plants with strongly reduced levels of PEPCK and plastidic NADP-ME were generated by RNA interference gene silencing under the control of a ripening-specific E8 promoter. While these genetic modifications had relatively little effect on the total fruit yield and size, they had strong effects on fruit metabolism. Both transformants were characterized by lower levels of starch at breaker stage. Analysis of the activation state of ADP-glucose pyrophosphorylase correlated with the decrease of starch in both transformants, which suggests that it is due to an altered cellular redox status. Moreover, metabolic profiling and feeding experiments involving positionally labeled glucoses of fruits lacking in plastidic NADP-ME and cytosolic PEPCK activities revealed differential changes in overall respiration rates and tricarboxylic acid (TCA) cycle flux. Inactivation of cytosolic PEPCK affected the respiration rate, which suggests that an excess of oxaloacetate is converted to aspartate and reintroduced in the TCA cycle via 2-oxoglutarate/glutamate. On the other hand, the plastidic NADP-ME antisense lines were characterized by no changes in respiration rates and TCA cycle flux, which together with increases of pyruvate kinase and phosphoenolpyruvate carboxylase activities indicate that pyruvate is supplied through these enzymes to the TCA cycle. These results are discussed in the context of current models of the importance of malate during tomato fruit ripening.

  9. Simultaneous boosting of source and sink capacities doubles tuber starch yield of potato plants.

    Science.gov (United States)

    Jonik, Claudia; Sonnewald, Uwe; Hajirezaei, Mohammad-Reza; Flügge, Ulf-Ingo; Ludewig, Frank

    2012-12-01

    An important goal in biotechnological research is to improve the yield of crop plants. Here, we genetically modified simultaneously source and sink capacities in potato (Solanum tuberosum cv. Desirée) plants to improve starch yield. Source capacity was increased by mesophyll-specific overexpression of a pyrophosphatase or, alternatively, by antisense expression of the ADP-glucose pyrophosphorylase in leaves. Both approaches make use of re-routing photoassimilates to sink organs at the expense of leaf starch accumulation. Simultaneous increase in sink capacity was accomplished by overexpression of two plastidic metabolite translocators, that is, a glucose 6-phosphate/phosphate translocator and an adenylate translocator in tubers. Employing such a 'pull' approach, we have previously shown that potato starch content and yield can be increased when sink strength is elevated. In the current biotechnological approach, we successfully enhanced source and sink capacities by a combination of 'pull' and 'push' approaches using two different attempts. A doubling in tuber starch yield was achieved. This successful approach might be transferable to other crop plants in the future.

  10. Simultaneous boosting of source and sink capacities doubles tuber starch yield of potato plants.

    Science.gov (United States)

    Jonik, Claudia; Sonnewald, Uwe; Hajirezaei, Mohammad-Reza; Flügge, Ulf-Ingo; Ludewig, Frank

    2012-12-01

    An important goal in biotechnological research is to improve the yield of crop plants. Here, we genetically modified simultaneously source and sink capacities in potato (Solanum tuberosum cv. Desirée) plants to improve starch yield. Source capacity was increased by mesophyll-specific overexpression of a pyrophosphatase or, alternatively, by antisense expression of the ADP-glucose pyrophosphorylase in leaves. Both approaches make use of re-routing photoassimilates to sink organs at the expense of leaf starch accumulation. Simultaneous increase in sink capacity was accomplished by overexpression of two plastidic metabolite translocators, that is, a glucose 6-phosphate/phosphate translocator and an adenylate translocator in tubers. Employing such a 'pull' approach, we have previously shown that potato starch content and yield can be increased when sink strength is elevated. In the current biotechnological approach, we successfully enhanced source and sink capacities by a combination of 'pull' and 'push' approaches using two different attempts. A doubling in tuber starch yield was achieved. This successful approach might be transferable to other crop plants in the future. PMID:22931170

  11. Can fast-growing plantation trees escape biochemical down-regulation of photosynthesis when grown throughout their complete production cycle in the open air under elevated carbon dioxide?

    Science.gov (United States)

    Davey, P A; Olcer, H; Zakhleniuk, O; Bernacchi, C J; Calfapietra, C; Long, S P; Raines, C A

    2006-07-01

    Poplar trees sustain close to the predicted increase in leaf photosynthesis when grown under long-term elevated CO2 concentration ([CO2]). To investigate the mechanisms underlying this response, carbohydrate accumulation and protein expression were determined over four seasons of growth. No increase in the levels of soluble carbohydrates was observed in the young expanding or mature sun leaves of the three poplar genotypes during this period. However, substantial increases in starch levels were observed in the mature leaves of all three poplar genotypes grown in elevated [CO2]. Despite the very high starch levels, no changes in the expression of photosynthetic Calvin cycle proteins, or in the starch biosynthetic enzyme ADP-glucose pyrophosphorylase (AGPase), were observed. This suggested that no long-term photosynthetic acclimation to CO2 occurred in these plants. Our data indicate that poplar trees are able to 'escape' from long-term, acclimatory down-regulation of photosynthesis through a high capacity for starch synthesis and carbon export. These findings show that these poplar genotypes are well suited to the elevated [CO2] conditions forecast for the middle of this century and may be particularly suited for planting for the long-term carbon sequestration into wood. PMID:17080946

  12. Systematic Analysis of Pericarp Starch Accumulation and Degradation during Wheat Caryopsis Development.

    Directory of Open Access Journals (Sweden)

    Xurun Yu

    Full Text Available Although wheat (Triticum aestivum L. pericarp starch granule (PSG has been well-studied, our knowledge of its features and mechanism of accumulation and degradation during pericarp growth is poor. In the present study, developing wheat caryopses were collected and starch granules were extracted from their pericarp to investigate the morphological and structural characteristics of PSGs using microscopy, X-ray diffraction and Fourier transform infrared spectroscopy techniques. Relative gene expression levels of ADP-glucose pyrophosphorylase (APGase, granule-bound starch synthase II (GBSS II, and α-amylase (AMY were quantified by quantitative real-time polymerase chain reaction. PSGs presented as single or multiple starch granules and were synthesized both in the amyloplast and chloroplast in the pericarp. PSG degradation occurred in the mesocarp, beginning at 6 days after anthesis. Amylose contents in PSGs were lower and relative degrees of crystallinity were higher at later stages of development than at earlier stages. Short-range ordered structures in the external regions of PSGs showed no differences in the developing pericarp. When hydrolyzed by α-amylase, PSGs at various developmental stages showed high degrees of enzymolysis. Expression levels of AGPase, GBSS II, and AMY were closely related to starch synthesis and degradation. These results help elucidate the mechanisms of accumulation and degradation as well as the functions of PSG during wheat caryopsis development.

  13. Comparative Proteomic Analysis of Two Barley Cultivars (Hordeum vulgare L.) with Contrasting Grain Protein Content

    Science.gov (United States)

    Guo, Baojian; Luan, Haiye; Lin, Shen; Lv, Chao; Zhang, Xinzhong; Xu, Rugen

    2016-01-01

    Grain protein contents (GPCs) of barley seeds are significantly different between feed and malting barley cultivars. However, there is still no insight into the proteomic analysis of seed proteins between feed and malting barley cultivars. Also, the genetic control of barley GPC is still unclear. GPCs were measured between mature grains of Yangsimai 3 and Naso Nijo. A proteome profiling of differentially expressed protein was established by using a combination of 2-DE and tandem mass spectrometry. In total, 502 reproducible protein spots in barley seed proteome were detected with a pH range of 4–7 and 6–11, among these 41 protein spots (8.17%) were detected differentially expressed between Yangsimai 3 and Naso Nijo. Thirty-four protein spots corresponding to 23 different proteins were identified, which were grouped into eight categories, including stress, protein degradation and post-translational modification, development, cell, signaling, glycolysis, starch metabolism, and other functions. Among the identified proteins, enolase (spot 274) and small subunit of ADP-glucose pyrophosphorylase (spot 271) are exclusively expressed in barley Yangsimai 3, which may be involved in regulating seed protein expression. In addition, malting quality is characterized by an accumulation of serpin protein, Alpha-amylase/trypsin inhibitor CMb and Alpha-amylase inhibitor BDAI-1. Most noticeably, globulin, an important storage protein in barley seed, undergoes post-translational processing in both cultivars, and also displays different expression patterns. PMID:27200019

  14. Structural Comparison, Substrate Specificity, and Inhibitor Binding of AGPase Small Subunit from Monocot and Dicot: Present Insight and Future Potential

    Directory of Open Access Journals (Sweden)

    Kishore Sarma

    2014-01-01

    Full Text Available ADP-glucose pyrophosphorylase (AGPase is the first rate limiting enzyme of starch biosynthesis pathway and has been exploited as the target for greater starch yield in several plants. The structure-function analysis and substrate binding specificity of AGPase have provided enormous potential for understanding the role of specific amino acid or motifs responsible for allosteric regulation and catalytic mechanisms, which facilitate the engineering of AGPases. We report the three-dimensional structure, substrate, and inhibitor binding specificity of AGPase small subunit from different monocot and dicot crop plants. Both monocot and dicot subunits were found to exploit similar interactions with the substrate and inhibitor molecule as in the case of their closest homologue potato tuber AGPase small subunit. Comparative sequence and structural analysis followed by molecular docking and electrostatic surface potential analysis reveal that rearrangements of secondary structure elements, substrate, and inhibitor binding residues are strongly conserved and follow common folding pattern and orientation within monocot and dicot displaying a similar mode of allosteric regulation and catalytic mechanism. The results from this study along with site-directed mutagenesis complemented by molecular dynamics simulation will shed more light on increasing the starch content of crop plants to ensure the food security worldwide.

  15. Experiment 9: ASTROCULTURE: Growth and Starch Accumulation of Potato Tuber

    Science.gov (United States)

    Tibbitts, Theodore W.; Brown, Christopher S.; Croxdale, Judith G.; Wheeler, Raymond M.

    1998-01-01

    Potato explants (leaf, small stem section, and axillary bud) flown on STS-73 developed tubers of 1.5 cm diameter and 1.7 g mass during the 16-day period of space flight. The experiment was undertaken in the ASTROCULTURE(TM) experiment package under controlled temperature, humidity, lighting, and carbon dioxide concentrations. The tubers that formed in the explant system under microgravity had the same gross morphology, the same anatomical configuration of cells and tissues, and the same sizes, shapes, and surface character of starch granules as tubers formed in a 1 g environment. The total accumulation of starch and other energy containing compounds was similar in space flight and ground control tubers. Enzyme activity of starch synthase, starch phosphorylase, and total hydrolase was similar in space flight and ground controls, but activity of ADP-glucose pyrophosphorylase was reduced in the space flight tuber tissue. This experiment documented that potatoes will metabolize and accumulate starch as effectively in space flight as on the ground. Thus, this data provides the potential for effective utilization of potatoes in life support systems of space bases.

  16. Space Experiment on Tuber Development and Starch Accumulation for CELSS

    Science.gov (United States)

    Tibbitts,Theodore W.; Croxdale, Judith C.; Brown, Christopher S.

    1997-01-01

    Potato explants (leaf, small stem section, and axillary bud), flown on STS-73, developed tubers of 1.5 cm diameter and 1.7 g mass during the 16 day period of spaceflight. The experiment was undertaken in the ASTROCULTURE(Trademark) experiment package under controlled temperature, humidity, lighting, and carbon dioxide concentrations. The tubers formed in the explant system under microgravity had the same gross morphology, the same anatomical configuration of cells and tissues, and the same sizes, shapes, and surface character of starch granules as tubers formed in a 1 g environment. The total accumulation of starch and other energy containing compounds was singular in space flight and ground control tubers. Enzyme activity of starch synthase, starch phosphorylase, and total hydrolase was similar in spaceflight and ground controls but activity of ADP-glucose pyrophosphorylase was reduced in the spaceflight tuber tissue. This experiment documented that potatoes will metabolize and accumulate starch as effectively in spaceflight as on the ground and thus this data provides the potential for effective utilization of potatoes in life support systems of space bases.

  17. Leaf Photosynthesis in Response to Removing Fruit During Different Phenological Stages of Fruit Development in Peach Trees

    Institute of Scientific and Technical Information of China (English)

    LI Wei-dong; LI Shao-hua; WU Ben-hong; YANG Jian-min; WANG Hong-qing

    2005-01-01

    Removing fruit (RF) and retaining fruit (CK) were carried out during different phenological stages of fruit development on one-year-old shoot of Okubo peach trees [Prunus persica (L.) Batsch.] under preventing exportation of the assimilates to the non experimental parts of the tree by girdling one-year-old shoot and keeping the same leaves between RF and CK.The results showed that fruit removal significantly decreased net photosynthetic rate (Pn), stomatal conductance (Gs)and transpiration rate (E), but significantly increased leaf surface temperature (TLeaf) at about midday as compared with CK.Internal CO2 concentration, soluble sugar content, reductive sugar content, starch content except that during the final rapid fruit growth stage, ADP-glucose pyrophosphorylase and amylase activities in source leaves were not significantly affected by fruit removal. There was a significantly positive parabolic correlation between Pn and Gs, and a strong positive linear correlation between Pn and E. Moreover, Pn increased with increased TLeaf if Tieaf was below 38℃, then decreased sharply when TLeaf exceeded the above critical temperature for both RF and CK. Pn of RF was lower, however,than that of CK in the same TLea, especially if TLeaf exceeded 38℃. It is suggested that the decreased stomatal aperture and increased TLeaf may be the important mechanism in regulating photosynthesis under a decreased strength of sink demand by RF in fruit trees.

  18. Changes in the Activities of Enzymes Involved in Starch Synthesis in the Kernel During Grain Filling in Winter Wheat Cultivars of Different Spike Types

    Institute of Scientific and Technical Information of China (English)

    GAO Song-jie; WANG Wen-jing; GUO Tian-cai; HAN Jin-feng

    2003-01-01

    Two winter wheat(Triticum aestivum L. ) cultivars, large-spike type Yumai66 amd small-spike type Yumai49, were used to study the activities of enzymes involved in starch synthesis in the kernel during grain filling. Starch accumulated faster in the kernel of Yumai49 than Yumai66 up to 25 d after anthesis,thereafter starch accumulated faster in the kernel of Yumai66. Starch accumulation in Yumai66 peaked at 20 -25 d after anthesis, while in Yumai49 starch accumulation peaked at 15 -20 d after anthesis and 25 -30 d after anthesis. The first peak was much higher than that of the second. Sucrose content and sucrose synthase activity peaked at 20 and 15 d after anthesis in Yumai66 and Yumai49, respectively. The sucrose content and sucrose synthase activity in Yumai66 were higher than that in Yunai49 during grain filling. ADP-glucose pyrophosphorylase and starch branching enzyme activity in the kernel of Yumai66 peaked at 20 d after anthesis,while soluble starch synthase activity peaked at 10 and 20 d after anthesis. The second peak was much higher than that of the first.

  19. Characterization and Expression Analysis of Starch Branching Enzymes in Sweet Potato

    Institute of Scientific and Technical Information of China (English)

    QIN Hua; ZHOU Shuang; ZHANG Yi-zheng

    2013-01-01

    Spatial and temporal expression patterns of Sbe1 and Sbe2 that encode starch branching enzyme (SBE) I and II, respectively, in sweet potato (Ipomoea batatas L.) were analyzed. Expression of both genes in Escherichia coli indicate that both genes encoded active SBE. Analysis with real-time quantitative polymerase chain reaction technique indicates that IbSbe1 mRNA was expressed at very low levels in leaves but was the predominant isoform in tuberous root while the reverse case was found for IbSbe2. The expression pattern of IbSbe1, closely resembles that of AGPase S, a gene coding for one of the subunits of ADP-glucose pyrophosphorylase, which is the key regulatory enzyme in the starch biosynthetic pathway. Western analysis detected at least two isoforms of SBE I in tuberous roots, those two isoforms showed adverse expression patterns with the development of the tuberous roots. Expression of the two IbSbe genes exhibited a diurnal rhythm during a 12-h cycle when fed a continuous solution of sucrose. Abscisic acid (ABA) was aother potent inducer of IbSbe expression, but bypassed the semidian oscillator.

  20. Changes in Activities of Key Enzymes for Starch Synthesis and Glutamine Synthetase in Grains of Progenies from a Rice Cross During Grain Filling

    Institute of Scientific and Technical Information of China (English)

    LI Xiao-guang; LIU Hai-ying; JIN Zheng-xun; LIU Hong-liang; HUANG Xing; XU Mei-lan; ZHANG Feng-zhuan

    2010-01-01

    The progenies differed in amylose and protein contents in grains, which derived from a rice cross, Dongnong 423×Toukei 180, were used to study changes in the activities of ADP-glucose pyrophosphorylase (AGPP), soluble starch synthetase (SSS), starch branching enzyme (SBE) and glutamine synthetase (GS) in rice grains during grain filling. The activities of AGPP, SSS and SBE gradually increased and then declined as a single-peak curve with the process of grain filling in the progenies with high and low amylose contents in grains. The progenies with high amylose content peaked earlier in the AGPP, SSS and SBE activities and had higher AGPP, SSS and SBE activities at the early grain filling stage than those with low amylose content. The GS activity peaked earlier and was higher at the late stage of grain filling in the progenies with high protein content than in those with low protein content. It is suggested that the activities of key enzymes for starch synthesis and glutamine synthetase could be changed in oriented breeding for amylose and protein contents in grains.

  1. Progress on Key Enzymes Involved in Crop Starch Synthesis and Their Gene Expression%作物淀粉合成关键酶及其基因表达的研究进展

    Institute of Scientific and Technical Information of China (English)

    谭彩霞; 封超年; 陈静; 郭静; 郭文善; 朱新开; 李春燕; 彭永欣

    2008-01-01

    ADP-葡萄糖焦磷酸化酶(ADP-glucose pyrophosphorylase polypetide,AGPase)、颗粒结合淀粉合成酶(Granule-bound starch synthase,GBSS)、可溶性淀粉合成酶(Soluble starch synthase,SSS)、淀粉分支酶(Starch branching enzyme,SBE)、淀粉去分支酶(Starch debranching enzyme,DBE)等是淀粉合成过程中的关键酶.本文主要介绍了前人关于这五种酶各同工型的结构、功能、各同工酶基因在不同组织和不同生育时期的表达特异性,及它们的基因表达与淀粉合成的关系等方面的研究进展,旨在为相关研究提供参考.

  2. Effects of the activities of key enzymes involved in starch biosynthesis on the fine structure of amylopectin in developing rice (Oryza sativa L.) endosperms

    Institute of Scientific and Technical Information of China (English)

    L(U) Bing; GUO ZhiGang; LIANG JianSheng

    2008-01-01

    The dynamic changes of the activities of enzymes involving in starch biosynthesis, including ADP-glucose pyrophosphorylase (AGPase), soluble starch synthases (SSS), starch branching enzyme (SBE) and starch debranching enzymes (DBE) were studied, and changes of fine structure of amy-Iopectin were characterized by isoamylase treatment during rice grain development, using trans anti-waxy gene rice plants. The relationships between the activities of those key enzymes were also analyzed. The amylose synthesis was significantly inhibited in transgenic Wanjing 9522, but the total starch content and final grain weight were less affected as compared with those of non-transgenic Wanjing 9522 rice cultivar. Analyses on the changes of activities of enzymes involving in starch bio-synthesis showed that different enzyme activities were expressed differently during rice endosperm development. Soluble starch synthase is relatively highly expressed in earlier stage of endosperm de-velopment, whilst maximal expression of granule-bound starch synthase (GBSS) occurred in mid-stage of endosperm development. No obvious differences in changes of the activities of AGPase and SBE between two rice cultivars investigated, except the DBEs. Distribution patterns of branches of amy-Iopectin changed continually during the development of rice grains and varied between two rice culti-vars. It was suggested that amylopectin synthesis be prior to the synthesis of amylose and different enzymes have different roles in controlling syntheses of branches of amylopectin.

  3. Effect of Soil Texture on Starch Accumulation and Activities of Key Enzymes of Starch Synthesis in the Kernel of ZM 9023

    Institute of Scientific and Technical Information of China (English)

    WANG Wen-jing; ZHAN Hai-hong

    2008-01-01

    Three kinds of soil texture (clay-loam, mid-loam, and sand-loam soil) were used to study the effects of soil texture on starch accumulating rate and the changes in activities of the key enzymes of starch synthesis in the kernel during grain filling in high gluten content wheat ZM 9023, under conditions of pond culture. The content of starch and its components were measured according to the method of double-wave length described by Bao (1996). ADP-glucose pyrophosphorylase (AGPP) activity was tested according to the method described by Doehlert et al. (1988). Soluble starch synthase (SSS) and starch branching enzyme (SBE) activities were tested according to the method described by Nakamura et al. (1989). The amylose, amylopectin, and total starch accumulating rate in the kernel of ZM 9023 were found to be a single-peak curve in three different soil textures during grain filling, and peaked 20, 15, and 15 d after anthesis, respectively. The activities of the enzymes, AGPP, SSS, and SBE, in the kernel of ZM 9023 had a single-peaked curve, which peaked 20, 15, and 15 d after anthesis, respectively. The activities of the above three enzymes of ZM 9023 were higher in the sand-loam soil. The accumulating peak of amylose formed later compared to that of amylopectin. The sand-loam soil could help high gluten content cultivars to synthesize starch.

  4. Effects of the activities of key enzymes involved in starch biosynthesis on the fine structure of amylopectin in developing rice (Oryza sativa L.) endosperms.

    Science.gov (United States)

    Lü, Bing; Guo, ZhiGang; Liang, JianSheng

    2008-10-01

    The dynamic changes of the activities of enzymes involving in starch biosynthesis, including ADP-glucose pyrophosphorylase (AGPase), soluble starch synthases (SSS), starch branching enzyme (SBE) and starch debranching enzymes (DBE) were studied, and changes of fine structure of amylopectin were characterized by isoamylase treatment during rice grain development, using trans anti-waxy gene rice plants. The relationships between the activities of those key enzymes were also analyzed. The amylose synthesis was significantly inhibited in transgenic Wanjing 9522, but the total starch content and final grain weight were less affected as compared with those of non-transgenic Wanjing 9522 rice cultivar. Analyses on the changes of activities of enzymes involving in starch biosynthesis showed that different enzyme activities were expressed differently during rice endosperm development. Soluble starch synthase is relatively highly expressed in earlier stage of endosperm development, whilst maximal expression of granule-bound starch synthase (GBSS) occurred in mid-stage of endosperm development. No obvious differences in changes of the activities of AGPase and SBE between two rice cultivars investigated, except the DBEs. Distribution patterns of branches of amylopectin changed continually during the development of rice grains and varied between two rice cultivars. It was suggested that amylopectin synthesis be prior to the synthesis of amylose and different enzymes have different roles in controlling syntheses of branches of amylopectin.

  5. Influence of tryptophan and indole-3-acetic acid on starch accumulation in the synthetic mutualistic Chlorella sorokiniana-Azospirillum brasilense system under heterotrophic conditions.

    Science.gov (United States)

    Palacios, Oskar A; Choix, Francisco J; Bashan, Yoav; de-Bashan, Luz E

    2016-06-01

    This study measured the relations between tryptophan production, the phytohormone indole-3-acetic acid (IAA) and the metabolism and accumulation of starch during synthetic mutualism between the microalgae Chlorella sorokiniana and the microalgae growth-promoting bacteria Azospirillum brasilense, created by co-immobilization in alginate beads. Experiments used two wild-type A. brasilense strains (Cd and Sp6) and an IAA-attenuated mutant (SpM7918) grown under nitrogen-replete and nitrogen-starved conditions tested under dark, heterotrophic and aerobic growth conditions. Under all incubating conditions, C. sorokiniana, but not A. brasilense, produced tryptophan. A significant correlation between IAA-production by A. brasilense and starch accumulation in C. sorokiniana was found, since the IAA-attenuated mutant was not producing increased starch levels. The highest ADP-glucose pyrophosphorylase (AGPase) activity, starch content and glucose uptake were found during the interaction of A. brasilense wild type strains with the microalgae. When the microalgae were grown alone, they produced only small amounts of starch. Supplementation with synthetic IAA to C. sorokiniana grown alone enhanced the above parameters, but only transiently. Activity of α-amylase decreased under nitrogen-replete conditions, but increased under nitrogen-starved conditions. In summary, this study demonstrated that, during synthetic mutualism, the exchange of tryptophan and IAA between the partners is a mechanism that governs several changes in starch metabolism of C. sorokiniana, yielding an increase in starch content.

  6. Effects of Weak Light on Starch Accumulation and Starch Synthesis Enzyme Activities in Rice at the Grain Filling Stage

    Institute of Scientific and Technical Information of China (English)

    LI Tian; Ryu OHSUGI; Tohru YAMAGISHI; Haruto SASAKI

    2006-01-01

    Dynamic changes of starch, amylose, sucrose contents and the activities of starch synthesis enzymes under shading treatments after flowering were studied using two dce varieties IR72 (indica) and Nipponbare (japonica) as materials. Under shading treatments, the starch,amylose and sucrose contents decreased, while ADP-glucose pyrophosphorylase (ADPGPPase) activity only changed a little, soluble starch synthase activity and granule bound starch synthase activity decreased, soluble starch branching enzyme (SSBE, Q-enzyme) activity and granule bound starch branching enzyme (GBSBE, Q-enzyme) activity increased, and starch debranching enzyme (DBE, R-enzyme) activity vaded with varieties. Correlation analyses showed that the changes of starch content were positively and significantly correlated with the changes of sucrose content in the weak light. Both ADPGPPase activity and SSBE activity were positively and significantly correlated with starch accumulation rate. It was implied that the decline of starch synthase activities was related to the decrease of starch content and the increase of the activity of starch branching enzyme played an important role in the decrease of the ratio of amylose to the total starch under the weak light.

  7. Effects of the activities of key enzymes involved in starch biosynthesis on the fine structure of amylopectin in developing rice (Oryza sativa L.) endosperms

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The dynamic changes of the activities of enzymes involving in starch biosynthesis, including ADP-glucose pyrophosphorylase (AGPase), soluble starch synthases (SSS), starch branching enzyme (SBE) and starch debranching enzymes (DBE) were studied, and changes of fine structure of amy- lopectin were characterized by isoamylase treatment during rice grain development, using trans anti-waxy gene rice plants. The relationships between the activities of those key enzymes were also analyzed. The amylose synthesis was significantly inhibited in transgenic Wanjing 9522, but the total starch content and final grain weight were less affected as compared with those of non-transgenic Wanjing 9522 rice cultivar. Analyses on the changes of activities of enzymes involving in starch bio- synthesis showed that different enzyme activities were expressed differently during rice endosperm development. Soluble starch synthase is relatively highly expressed in earlier stage of endosperm de- velopment, whilst maximal expression of granule-bound starch synthase (GBSS) occurred in mid-stage of endosperm development. No obvious differences in changes of the activities of AGPase and SBE between two rice cultivars investigated, except the DBEs. Distribution patterns of branches of amy- lopectin changed continually during the development of rice grains and varied between two rice culti- vars. It was suggested that amylopectin synthesis be prior to the synthesis of amylose and different enzymes have different roles in controlling syntheses of branches of amylopectin.

  8. Systematic Analysis of Pericarp Starch Accumulation and Degradation during Wheat Caryopsis Development.

    Science.gov (United States)

    Yu, Xurun; Li, Bo; Wang, Leilei; Chen, Xinyu; Wang, Wenjun; Wang, Zhong; Xiong, Fei

    2015-01-01

    Although wheat (Triticum aestivum L.) pericarp starch granule (PSG) has been well-studied, our knowledge of its features and mechanism of accumulation and degradation during pericarp growth is poor. In the present study, developing wheat caryopses were collected and starch granules were extracted from their pericarp to investigate the morphological and structural characteristics of PSGs using microscopy, X-ray diffraction and Fourier transform infrared spectroscopy techniques. Relative gene expression levels of ADP-glucose pyrophosphorylase (APGase), granule-bound starch synthase II (GBSS II), and α-amylase (AMY) were quantified by quantitative real-time polymerase chain reaction. PSGs presented as single or multiple starch granules and were synthesized both in the amyloplast and chloroplast in the pericarp. PSG degradation occurred in the mesocarp, beginning at 6 days after anthesis. Amylose contents in PSGs were lower and relative degrees of crystallinity were higher at later stages of development than at earlier stages. Short-range ordered structures in the external regions of PSGs showed no differences in the developing pericarp. When hydrolyzed by α-amylase, PSGs at various developmental stages showed high degrees of enzymolysis. Expression levels of AGPase, GBSS II, and AMY were closely related to starch synthesis and degradation. These results help elucidate the mechanisms of accumulation and degradation as well as the functions of PSG during wheat caryopsis development. PMID:26394305

  9. Uncover the recruiter in you!

    CERN Multimedia

    2013-01-01

    2013 saw the launch of the one-day training course "Selecting the best person for CERN". So far, 10 courses have taken place and over 100 participants have taken part in this interactive, hands on experience.   The course has been met with much enthusiasm and positive feedback, with participants not only feeling better prepared and organised for the recruitment boards, but also equipped with concrete tools on how to prepare and conduct an effective selection interview. Following on from this success, further sessions are planned in 2014: we look forward to welcoming recruiting supervisors and board members who are likely to take part in a recruitment process, whether for LD or LD2IC, and who are interested in finding out more about how to get the most out of this important process! To enrol to this course, please follow this link: "Selecting the best person for CERN".

  10. ESA uncovers Geminga's `hot spot'

    Science.gov (United States)

    2004-07-01

    16 July 2004 Astronomers using ESA’s X-ray observatory XMM-Newton have detected a small, bright ‘hot spot’ on the surface of the neutron star called Geminga, 500 light-years away. The hot spot is the size of a football field and is caused by the same mechanism producing Geminga’s X-ray tails. This discovery identifies the missing link between the X-ray and gamma-ray emission from Geminga. hi-res Size hi-res: 1284 kb Credits: ESA, P. Caraveo (IASF, Milan) Geminga's hot spot This figure shows the effects of charged particles accelerated in the magnetosphere of Geminga. Panel (a) shows an image taken with the EPIC instrument on board the XMM-Newton observatory. The bright tails, made of particles kicked out by Geminga’s strong magnetic field, trail the neutron star as it moves about in space. Panel (b) shows how electrically charged particles interact with Geminga’s magnetic field. For example, if electrons (blue) are kicked out by the star, positrons (in red) hit the star’s magnetic poles like in an ‘own goal’. Panel (c) illustrates the size of Geminga’s magnetic field (blue) compared to that of the star itself at the centre (purple). The magnetic field is tilted with respect to Geminga’s rotation axis (red). Panel (d) shows the magnetic poles of Geminga, where charged particles hit the surface of the star, creating a two-million degrees hot spot, a region much hotter than the surroundings. As the star spins on its rotation axis, the hot spot comes into view and then disappears, causing the periodic colour change seen by XMM-Newton. An animated version of the entire sequence can be found at: Click here for animated GIF [low resolution, animated GIF, 5536 KB] Click here for AVI [high resolution, AVI with DIVX compression, 19128 KB] hi-res Size hi-res: 371 kb Credits: ESA, P. Caraveo (IASF, Milan) Geminga's hot spot, panel (a) Panel (a) shows an image taken with the EPIC instrument on board the XMM-Newton observatory. The bright tails, made of particles kicked out by Geminga’s strong magnetic field, trail the neutron star as it moves about in space. hi-res Size hi-res: 377 kb Credits: ESA, P. Caraveo (IASF, Milan) Geminga's hot spot, panel (b) Panel (b) shows how electrically charged particles interact with Geminga’s magnetic field. For example, if electrons (blue) are kicked out by the star, positrons (red) hit the star’s magnetic poles like in an ‘own goal’. hi-res Size hi-res: 435 kb Credits: ESA, P. Caraveo (IASF, Milan) Geminga's hot spot, panel (c) Panel (c) illustrates the size of Geminga’s magnetic field (blue) compared to that of the star itself at the centre (purple). The magnetic field is tilted with respect to Geminga’s rotation axis (red). hi-res Size hi-res: 121 kb Credits: ESA, P. Caraveo (IASF, Milan) Geminga's hot spot, panel (d) Panel (d) shows the magnetic poles of Geminga, where charged particles hit the surface of the star, creating a two-million degree hot spot, a region much hotter than the surroundings. As the star spins on its rotation axis, the hot spot comes into view and then disappears, causing the periodic colour change seen by XMM-Newton. Neutron stars are the smallest kind of stars known. They are the super-dense remnants of massive stars that died in cataclysmic explosions called supernovae. They have been thrown through space like cannonballs and set spinning at a furious rate, with magnetic fields hundreds of billions of times stronger than Earth’s. In the case of Geminga, this cannonball contains one and a half times the mass of the Sun, squeezed into a sphere just 20 kilometres across and spinning four times every second. A cloud bustling with electrically charged particles surrounds Geminga. These particles are shepherded by its magnetic and electric fields. ESA’s XMM-Newton observatory had already discovered that some of these particles are ejected into space, forming tails that stream behind the neutron star as it hurtles along. Scientists did not know whether Geminga’s tails are formed by electrons or by their twin particles with an opposite e

  11. Disordered Collarettes and Uncovered Tables

    DEFF Research Database (Denmark)

    Nørgaard, Nina

    2007-01-01

    This article examines the use of negative polarity as a stylistic device in James Joyce's short story, "Two Gallants" (1992 [1914]). The article begins with a brief account of various approaches to negative polarity, focusing in particular on theoretical paradigms that favour the pragmatic...

  12. Genome-wide analyses of Nkx2-1 binding to transcriptional target genes uncover novel regulatory patterns conserved in lung development and tumors.

    Directory of Open Access Journals (Sweden)

    Jean-Bosco Tagne

    Full Text Available The homeodomain transcription factor Nkx2-1 is essential for normal lung development and homeostasis. In lung tumors, it is considered a lineage survival oncogene and prognostic factor depending on its expression levels. The target genes directly bound by Nkx2-1, that could be the primary effectors of its functions in the different cellular contexts where it is expressed, are mostly unknown. In embryonic day 11.5 (E11.5 mouse lung, epithelial cells expressing Nkx2-1 are predominantly expanding, and in E19.5 prenatal lungs, Nkx2-1-expressing cells are predominantly differentiating in preparation for birth. To evaluate Nkx2-1 regulated networks in these two cell contexts, we analyzed genome-wide binding of Nkx2-1 to DNA regulatory regions by chromatin immunoprecipitation followed by tiling array analysis, and intersected these data to expression data sets. We further determined expression patterns of Nkx2-1 developmental target genes in human lung tumors and correlated their expression levels to that of endogenous NKX2-1. In these studies we uncovered differential Nkx2-1 regulated networks in early and late lung development, and a direct function of Nkx2-1 in regulation of the cell cycle by controlling the expression of proliferation-related genes. New targets, validated in Nkx2-1 shRNA transduced cell lines, include E2f3, Cyclin B1, Cyclin B2, and c-Met. Expression levels of Nkx2-1 direct target genes identified in mouse development significantly correlate or anti-correlate to the levels of endogenous NKX2-1 in a dosage-dependent manner in multiple human lung tumor expression data sets, supporting alternative roles for Nkx2-1 as a transcriptional activator or repressor, and direct regulator of cell cycle progression in development and tumors.

  13. ModuleFinder and CoReg: alternative tools for linking gene expression modules with promoter sequences motifs to uncover gene regulation mechanisms in plants

    OpenAIRE

    Whelan James; Millar A Harvey; Holt Kathryn E

    2006-01-01

    Abstract Background Uncovering the key sequence elements in gene promoters that regulate the expression of plant genomes is a huge task that will require a series of complementary methods for prediction, substantial innovations in experimental validation and a much greater understanding of the role of combinatorial control in the regulation of plant gene expression. Results To add to this larger process and to provide alternatives to existing prediction methods, we have developed several tool...

  14. ModuleFinder and CoReg: alternative tools for linking gene expression modules with promoter sequences motifs to uncover gene regulation mechanisms in plants

    Directory of Open Access Journals (Sweden)

    Whelan James

    2006-04-01

    Full Text Available Abstract Background Uncovering the key sequence elements in gene promoters that regulate the expression of plant genomes is a huge task that will require a series of complementary methods for prediction, substantial innovations in experimental validation and a much greater understanding of the role of combinatorial control in the regulation of plant gene expression. Results To add to this larger process and to provide alternatives to existing prediction methods, we have developed several tools in the statistical package R. ModuleFinder identifies sets of genes and treatments that we have found to form valuable sets for analysis of the mechanisms underlying gene co-expression. CoReg then links the hierarchical clustering of these co-expressed sets with frequency tables of promoter elements. These promoter elements can be drawn from known elements or all possible combinations of nucleotides in an element of various lengths. These sets of promoter elements represent putative cis-acting regulatory elements common to sets of co-expressed genes and can be prioritised for experimental testing. We have used these new tools to analyze the response of transcripts for nuclear genes encoding mitochondrial proteins in Arabidopsis to a range of chemical stresses. ModuleFinder provided a subset of co-expressed gene modules that are more logically related to biological functions than did subsets derived from traditional hierarchical clustering techniques. Importantly ModuleFinder linked responses in transcripts for electron transport chain components, carbon metabolism enzymes and solute transporter proteins. CoReg identified several promoter motifs that helped to explain the patterns of expression observed. Conclusion ModuleFinder identifies sets of genes and treatments that form useful sets for analysis of the mechanisms behind co-expression. CoReg links the clustering tree of expression-based relationships in these sets with frequency tables of promoter

  15. Early motor deficits in mouse disease models are reliably uncovered using an automated home-cage wheel-running system: a cross-laboratory validation.

    Science.gov (United States)

    Mandillo, Silvia; Heise, Ines; Garbugino, Luciana; Tocchini-Valentini, Glauco P; Giuliani, Alessandro; Wells, Sara; Nolan, Patrick M

    2014-03-01

    Deficits in motor function are debilitating features in disorders affecting neurological, neuromuscular and musculoskeletal systems. Although these disorders can vary greatly with respect to age of onset, symptomatic presentation, rate of progression and severity, the study of these disease models in mice is confined to the use of a small number of tests, most commonly the rotarod test. To expand the repertoire of meaningful motor function tests in mice, we tested, optimised and validated an automated home-cage-based running-wheel system, incorporating a conventional wheel with evenly spaced rungs and a complex wheel with particular rungs absent. The system enables automated assessment of motor function without handler interference, which is desirable in longitudinal studies involving continuous monitoring of motor performance. In baseline studies at two test centres, consistently significant differences in performance on both wheels were detectable among four commonly used inbred strains. As further validation, we studied performance in mutant models of progressive neurodegenerative diseases--Huntington's disease [TgN(HD82Gln)81Dbo; referred to as HD mice] and amyotrophic lateral sclerosis [Tg(SOD1G93A)(dl)1/GurJ; referred to as SOD1 mice]--and in a mutant strain with subtle gait abnormalities, C-Snap25(Bdr)/H (Blind-drunk, Bdr). In both models of progressive disease, as with the third mutant, we could reliably and consistently detect specific motor function deficits at ages far earlier than any previously recorded symptoms in vivo: 7-8 weeks for the HD mice and 12 weeks for the SOD1 mice. We also conducted longitudinal analysis of rotarod and grip strength performance, for which deficits were still not detectable at 12 weeks and 23 weeks, respectively. Several new parameters of motor behaviour were uncovered using principal component analysis, indicating that the wheel-running assay could record features of motor function that are independent of rotarod

  16. CoCoRaHS (The Community Collaborative Rain, Hail and Snow Network): Analysis of Participant Survey Data to Uncover Learning through Participation

    Science.gov (United States)

    Holzer, M. A.; Zimmerman, T.; Doesken, N. J.; Reges, H. W.; Newman, N.; Turner, J.; Schwalbe, Z.

    2010-12-01

    CoCoRaHS (The Community Collaborative Rain, Hail and Snow network) is based out of Fort Collins Colorado and is an extremely successful citizen science project with over 15,000 volunteers collecting valuable precipitation data. Forecasters and scientists use data from this dense network to illuminate and illustrate the high small-scale variability of precipitation across the nation. This presentation will discuss the results of a survey of CoCoRaHS participants as related to 1) citizen scientists’ motivation and learning; 2) the challenges of identifying how people learn science in citizen science projects; and 3) a potential research-based framework for how people learn through engaging in the data collection within in a citizen science project. A comprehensive survey of 14,500 CoCoRaHS observers was recently conducted to uncover participant perceptions of numerous aspects of the CoCoRaHS program, including its goal of increasing climate literacy. The survey yielded a response rate of over 50%, and included measures of motivation, engagement and learning. In relationship to motivation and learning, the survey revealed that most (57.1%) observers would make precipitation observations regardless of being a CoCoRaHS volunteer, therefore their motivation is related to their inherent level of interest in weather. Others are motivated by their desire to learn more about weather and climate, they want to contribute to a scientific project, they think its fun, and/or it provides a sense of community. Because so many respondents already had knowledge and interest in weather and climate, identifying how and what people learn through participating was a challenge. However, the narrow project focus of collecting and reporting of local precipitation assisted in identifying aspects of learning. For instance, most (46.4%) observers said they increased their knowledge about the local variability in precipitation even though they had been collecting precipitation data for many

  17. Purification, crystallization and preliminary X-ray characterization of the human GTP fucose pyrophosphorylase

    OpenAIRE

    Quirk, Stephen; Seley-Radtke, Katherine L.

    2006-01-01

    The human GTP fucose pyrophosphohydrolase protein has been crystallized via the hanging-drop technique over a reservoir of polyethylene glycol (MW 8000) and ethylene glycol. The orthorhombic crystals diffract to 2.8 Å resolution.

  18. 高瓦斯突出煤层组井筒快速揭煤关键技术%The key technology of uncovering coal quickly on the shaft in the outburst coal seam group with high gas

    Institute of Scientific and Technical Information of China (English)

    吴爱军; 程国军; 王法凯

    2015-01-01

    The first auxiliary shaft of Panyidong project department is served for minting area above-850m ,it will cross the high gas and outburst group be made of 13-1coal and 12coal . The In order to accelerate uncovering coal safely ,a number of new technology of outburst prevention were adopted by Project department :At first ,the coal seam gas pressure has been rapidly determined used the method of high gas inflation;At the same time ,the self-developed corer was used to achieve complete coal-core ,and the specific information of coal seam were mastered .After the uncovered coal has been verified and has no outburst ,large diameter drillings were constructed by the expansion slot hole and were used to speed up the gas emissions . After a series of rigorous organization and tight construction ,the whole process of uncovering coal is in less than 20 days ,and nearly a third of the time was shorten compared with conventional process ,a win-win situation of the economic and security benefits are gained .%潘一东项目部第一副井主要是服务于-850m以上的开采水平,该井筒要穿越13-1煤与12煤组成的高瓦斯突出煤层组,为了实现安全快速的揭煤,该项目部根据现场的实际情况,采用了多项新技术实施防突措施:首先使用高压充气法快速测定了煤层瓦斯压力,与此同时利用自行研制的取芯器实现完整钻取煤芯,掌握了煤层具体信息;在验证所揭煤层无突出危险性后,再利用扩槽钻头施工大直径的钻孔以加快瓦斯的排放。经过一系列严密组织和紧张施工,整个揭煤过程不到20天,较常规工艺缩短了近1/3的时间,取得了经济效益和安全效益的双赢。

  19. Definitive Metabolite Identification Coupled with Automated Ligand Identification System (ALIS) Technology: A Novel Approach to Uncover Structure-Activity Relationships and Guide Drug Design in a Factor IXa Inhibitor Program.

    Science.gov (United States)

    Zhang, Ting; Liu, Yong; Yang, Xianshu; Martin, Gary E; Yao, Huifang; Shang, Jackie; Bugianesi, Randal M; Ellsworth, Kenneth P; Sonatore, Lisa M; Nizner, Peter; Sherer, Edward C; Hill, Susan E; Knemeyer, Ian W; Geissler, Wayne M; Dandliker, Peter J; Helmy, Roy; Wood, Harold B

    2016-03-10

    A potent and selective Factor IXa (FIXa) inhibitor was subjected to a series of liver microsomal incubations, which generated a number of metabolites. Using automated ligand identification system-affinity selection (ALIS-AS) methodology, metabolites in the incubation mixture were prioritized by their binding affinities to the FIXa protein. Microgram quantities of the metabolites of interest were then isolated through microisolation analytical capabilities, and structurally characterized using MicroCryoProbe heteronuclear 2D NMR techniques. The isolated metabolites recovered from the NMR experiments were then submitted directly to an in vitro FIXa enzymatic assay. The order of the metabolites' binding affinity to the Factor IXa protein from the ALIS assay was completely consistent with the enzymatic assay results. This work showcases an innovative and efficient approach to uncover structure-activity relationships (SARs) and guide drug design via microisolation-structural characterization and ALIS capabilities. PMID:26871940

  20. Numerical Simulation of Coal and Gas Outburst Process in Uncovering Frozen Coal Seam in Cross - Cut%石门揭露冻结煤层瓦斯突出过程的数值模拟

    Institute of Scientific and Technical Information of China (English)

    谢雄刚; 冯涛; 余照阳

    2012-01-01

    针对新提出的石门揭煤注液冻结防突方法,根据煤与瓦斯突出与煤层力学性能、煤层冻结温度之间的关系,结合人工冻结工程实践,采用岩石破裂过程分析RFPA2D系统,确定模型尺寸和边界条件,建立了石门揭露冻结煤层过程气固耦合数学模型。设定冻结温度下煤层的单轴抗压强度、弹性模量及瓦斯压力等相关参数,数值模拟了不同冻结温度下龙家山煤矿-400m水平2#石门揭露6#煤层过程。数值模拟表明:当6#煤层温度降为-10--20℃时,该石门揭煤工作面突出危险性将大为降低。综合冻结时间、能源消耗和防突效果,选定-10℃作为该石门揭露冻结煤层控制温度,可以提高突出矿井石门揭煤工程的经济效益。%Aiming at a new- presented outburst prevention method by injecting liquid and freezing in uncovering coal seam in cross - cut, according to the relationship among the coal and gas outburst, the mechanical properties and coal seam freezing temperature, and combining with artificial freezing engineering practice, with the reek failure process analysis software - RFDA2D, the paper determines the model sizes and boundary conditions and establishes gas and solid coupling mathematics model of uncovering frozen coal seam in cross - cut. Setting the interrelated parameters of gas pressure, uniaxial compressive strength and elastic modulus of coal seam under freezing temperature, the paper simulates the process of uncovering 6# freezing coal seam in 2# cross - cut of - 400 levels in Longjias- hart mine under the different freezing temperature. The simulation shows that when the temperature of 6# frozen coal seam drops to - 15 - -20℃, the gas outburst risk of the working face in 2# rock cross -cut will be greatly reduced. Integrating freezing time, energy consumption and outburst prevention effect, -10℃ is selected as the frozen seam control temperature of the working face, which can

  1. Feedback inhibition of starch degradation in Arabidopsis leaves mediated by trehalose 6-phosphate.

    Science.gov (United States)

    Martins, Marina Camara Mattos; Hejazi, Mahdi; Fettke, Joerg; Steup, Martin; Feil, Regina; Krause, Ursula; Arrivault, Stéphanie; Vosloh, Daniel; Figueroa, Carlos María; Ivakov, Alexander; Yadav, Umesh Prasad; Piques, Maria; Metzner, Daniela; Stitt, Mark; Lunn, John Edward

    2013-11-01

    Many plants accumulate substantial starch reserves in their leaves during the day and remobilize them at night to provide carbon and energy for maintenance and growth. In this paper, we explore the role of a sugar-signaling metabolite, trehalose-6-phosphate (Tre6P), in regulating the accumulation and turnover of transitory starch in Arabidopsis (Arabidopsis thaliana) leaves. Ethanol-induced overexpression of trehalose-phosphate synthase during the day increased Tre6P levels up to 11-fold. There was a transient increase in the rate of starch accumulation in the middle of the day, but this was not linked to reductive activation of ADP-glucose pyrophosphorylase. A 2- to 3-fold increase in Tre6P during the night led to significant inhibition of starch degradation. Maltose and maltotriose did not accumulate, suggesting that Tre6P affects an early step in the pathway of starch degradation in the chloroplasts. Starch granules isolated from induced plants had a higher orthophosphate content than granules from noninduced control plants, consistent either with disruption of the phosphorylation-dephosphorylation cycle that is essential for efficient starch breakdown or with inhibition of starch hydrolysis by β-amylase. Nonaqueous fractionation of leaves showed that Tre6P is predominantly located in the cytosol, with estimated in vivo Tre6P concentrations of 4 to 7 µm in the cytosol, 0.2 to 0.5 µm in the chloroplasts, and 0.05 µm in the vacuole. It is proposed that Tre6P is a component in a signaling pathway that mediates the feedback regulation of starch breakdown by sucrose, potentially linking starch turnover to demand for sucrose by growing sink organs at night.

  2. Metabolic and enzymatic changes associated with carbon mobilization, utilization and replenishment triggered in grain amaranth (Amaranthus cruentus in response to partial defoliation by mechanical injury or insect herbivory

    Directory of Open Access Journals (Sweden)

    Castrillón-Arbeláez Paula

    2012-09-01

    Full Text Available Abstract Background Amaranthus cruentus and A. hypochondriacus are crop plants grown for grain production in subtropical countries. Recently, the generation of large-scale transcriptomic data opened the possibility to study representative genes of primary metabolism to gain a better understanding of the biochemical mechanisms underlying tolerance to defoliation in these species. A multi-level approach was followed involving gene expression analysis, enzyme activity and metabolite measurements. Results Defoliation by insect herbivory (HD or mechanical damage (MD led to a rapid and transient reduction of non-structural carbohydrates (NSC in all tissues examined. This correlated with a short-term induction of foliar sucrolytic activity, differential gene expression of a vacuolar invertase and its inhibitor, and induction of a sucrose transporter gene. Leaf starch in defoliated plants correlated negatively with amylolytic activity and expression of a β-amylase-1 gene and positively with a soluble starch synthase gene. Fatty-acid accumulation in roots coincided with a high expression of a phosphoenolpyruvate/phosphate transporter gene. In all tissues there was a long-term replenishment of most metabolite pools, which allowed damaged plants to maintain unaltered growth and grain yield. Promoter analysis of ADP-glucose pyrophosphorylase and vacuolar invertase genes indicated the presence of cis-regulatory elements that supported their responsiveness to defoliation. HD and MD had differential effects on transcripts, enzyme activities and metabolites. However, the correlation between transcript abundance and enzymatic activities was very limited. A better correlation was found between enzymes, metabolite levels and growth and reproductive parameters. Conclusions It is concluded that a rapid reduction of NSC reserves in leaves, stems and roots followed by their long-term recovery underlies tolerance to defoliation in grain amaranth. This requires the

  3. The intrinsically disordered protein LEA7 from Arabidopsis thaliana protects the isolated enzyme lactate dehydrogenase and enzymes in a soluble leaf proteome during freezing and drying.

    Science.gov (United States)

    Popova, Antoaneta V; Rausch, Saskia; Hundertmark, Michaela; Gibon, Yves; Hincha, Dirk K

    2015-10-01

    The accumulation of Late Embryogenesis Abundant (LEA) proteins in plants is associated with tolerance against stresses such as freezing and desiccation. Two main functions have been attributed to LEA proteins: membrane stabilization and enzyme protection. We have hypothesized previously that LEA7 from Arabidopsis thaliana may stabilize membranes because it interacts with liposomes in the dry state. Here we show that LEA7, contrary to this expectation, did not stabilize liposomes during drying and rehydration. Instead, it partially preserved the activity of the enzyme lactate dehydrogenase (LDH) during drying and freezing. Fourier-transform infrared (FTIR) spectroscopy showed no evidence of aggregation of LDH in the dry or rehydrated state under conditions that lead to complete loss of activity. To approximate the complex influence of intracellular conditions on the protective effects of a LEA protein in a convenient in-vitro assay, we measured the activity of two Arabidopsis enzymes (glucose-6-P dehydrogenase and ADP-glucose pyrophosphorylase) in total soluble leaf protein extract (Arabidopsis soluble proteome, ASP) after drying and rehydration or freezing and thawing. LEA7 partially preserved the activity of both enzymes under these conditions, suggesting its role as an enzyme protectant in vivo. Further FTIR analyses indicated the partial reversibility of protein aggregation in the dry ASP during rehydration. Similarly, aggregation in the dry ASP was strongly reduced by LEA7. In addition, mixtures of LEA7 with sucrose or verbascose reduced aggregation more than the single additives, presumably through the effects of the protein on the H-bonding network of the sugar glasses. PMID:25988244

  4. Lauric acid production in a glycogen-less Synechococcus sp. PCC 7002 mutant

    Directory of Open Access Journals (Sweden)

    Victoria H. Work

    2015-04-01

    Full Text Available The cyanobacterium Synechococcus sp. PCC 7002 was genetically engineered to synthesize biofuel compatible medium-chain fatty acids during photoautotrophic growth. Expression of a heterologous lauroyl-acyl carrier protein (C12:0-ACP thioesterase with concurrent deletion of the endogenous putative acyl-ACP synthetase led to secretion of transesterifiable C12:0 fatty acid in CO2-supplemented batch cultures. When grown at steady state over a range of light intensities in an LED turbidostat photobioreactor, the C12-secreting mutant exhibited a modest reduction in growth rate and increased O2 evolution relative to the wildtype. Inhibition of i glycogen synthesis by deletion of the glgC-encoded ADP-glucose pyrophosphorylase (AGPase, and ii protein synthesis by nitrogen deprivation were investigated as potential mechanisms for metabolite redistribution to increase fatty acid synthesis. Deletion of AGPase led to a ten-fold decrease in reducing carbohydrates and secretion of organic acids during nitrogen deprivation consistent with an energy spilling phenotype. When the carbohydrate-deficient background (∆glgC was modified for C12 secretion, no increase in C12 was achieved during nutrient replete growth, and no C12 was recovered from any strain upon nitrogen deprivation under the conditions used. At steady state, the growth rate of the ∆glgC strain saturated at a lower light intensity than the wildtype, but O2 evolution was not compromised and became increasingly decoupled from growth rate with rising irradiance. Photophysiological properties of the ∆glgC strain suggest energy dissipation from photosystem II and reconfiguration of electron flow at the level of the plastoquinone pool.

  5. Photosynthesis down-regulation precedes carbohydrate accumulation under sink limitation in Citrus.

    Science.gov (United States)

    Nebauer, Sergio G; Renau-Morata, Begoña; Guardiola, José Luis; Molina, Rosa-Victoria

    2011-02-01

    Photosynthesis down-regulation due to an imbalance between sources and sinks in Citrus leaves could be mediated by excessive accumulation of carbohydrates. However, there is limited understanding of the physiological role of soluble and insoluble carbohydrates in photosynthesis regulation and the elements triggering the down-regulation process. In this work, the role of non-structural carbohydrates in the regulation of photosynthesis under a broad spectrum of source-sink relationships has been investigated in the Salustiana sweet orange. Soluble sugar and starch accumulation in leaves, induced by girdling experiments, did not induce down-regulation of the photosynthetic rate in the presence of sinks (fruits). The leaf-to-fruit ratio did not modulate photosynthesis but allocation of photoassimilates to the fruits. The lack of strong sink activity led to a decrease in the photosynthetic rate and starch accumulation in leaves. However, photosynthesis down-regulation due to an excess of total soluble sugars or starch was discarded because photosynthesis and stomatal conductance reduction occurred prior to any significant accumulation of these carbohydrates. Gas exchange and fluorescence parameters suggested biochemical limitations to photosynthesis. In addition, the expression of carbon metabolism-related genes was altered within 24 h when strong sinks were removed. Sucrose synthesis and export genes were inhibited, whereas the expression of ADP-glucose pyrophosphorylase was increased to cope with the excess of assimilates. In conclusion, changes in starch and soluble sugar turnover, but not sugar content per se, could provide the signal for photosynthesis regulation. In these conditions, non-stomatal limitations strongly inhibited the photosynthetic rate prior to any significant increase in carbohydrate levels. PMID:21367744

  6. The evolution of contact-dependent inhibition in non-growing populations of Escherichia coli.

    Science.gov (United States)

    Lemonnier, Marc; Levin, Bruce R; Romeo, Tony; Garner, Kim; Baquero, María-Rosario; Mercante, Jeff; Lemichez, Emmanuel; Baquero, Fernando; Blázquez, Jesús

    2008-01-01

    In the course of liquid culture, serial passage experiments with Escherichia coli K-12 bearing a mutator gene deletion (DeltamutS) we observed the evolution of strains that appeared to kill or inhibit the growth of the bacteria from where they were derived, their ancestors. We demonstrate that this inhibition occurs after the cells stop growing and requires physical contact between the evolved and ancestral bacteria. Thereby, it is referred to as stationary phase contact-dependent inhibition (SCDI). The evolution of this antagonistic relationship is not anticipated from existing theory and experiments of competition in mass (liquid) culture. Nevertheless, it occurred in the same way (parallel evolution) in the eight independent serial transfer cultures, through different single base substitutions in a gene in the glycogen synthesis pathway, glgC. We demonstrate that the observed mutations in glgC, which codes for ADP-glucose pyrophosphorylase, are responsible for both the ability of the evolved bacteria to inhibit or kill their ancestors and their immunity to that inhibition or killing. We present evidence that without additional evolution, mutator genes, or known mutations in glgC, other strains of E. coli K-12 are also capable of SCDI or sensitive to this inhibition. We interpret this, in part, as support for the generality of SCDI and also as suggesting that the glgC mutations responsible for the SCDI, which evolved in our experiments, may suppress the action of one or more genes responsible for the sensitivity of E. coli to SCDI. Using numerical solutions to a mathematical model and in vitro experiments, we explore the population dynamics of SCDI and postulate the conditions responsible for its evolution in mass culture. We conclude with a brief discussion of the potential ecological significance of SCDI and its possible utility for the development of antimicrobial agents, which unlike existing antibiotics, can kill or inhibit the growth of bacteria that are

  7. Photosynthesis Activates Plasma Membrane H+-ATPase via Sugar Accumulation.

    Science.gov (United States)

    Okumura, Masaki; Inoue, Shin-Ichiro; Kuwata, Keiko; Kinoshita, Toshinori

    2016-05-01

    Plant plasma membrane H(+)-ATPase acts as a primary transporter via proton pumping and regulates diverse physiological responses by controlling secondary solute transport, pH homeostasis, and membrane potential. Phosphorylation of the penultimate threonine and the subsequent binding of 14-3-3 proteins in the carboxyl terminus of the enzyme are required for H(+)-ATPase activation. We showed previously that photosynthesis induces phosphorylation of the penultimate threonine in the nonvascular bryophyte Marchantia polymorpha However, (1) whether this response is conserved in vascular plants and (2) the process by which photosynthesis regulates H(+)-ATPase phosphorylation at the plasma membrane remain unresolved issues. Here, we report that photosynthesis induced the phosphorylation and activation of H(+)-ATPase in Arabidopsis (Arabidopsis thaliana) leaves via sugar accumulation. Light reversibly phosphorylated leaf H(+)-ATPase, and this process was inhibited by pharmacological and genetic suppression of photosynthesis. Immunohistochemical and biochemical analyses indicated that light-induced phosphorylation of H(+)-ATPase occurred autonomously in mesophyll cells. We also show that the phosphorylation status of H(+)-ATPase and photosynthetic sugar accumulation in leaves were positively correlated and that sugar treatment promoted phosphorylation. Furthermore, light-induced phosphorylation of H(+)-ATPase was strongly suppressed in a double mutant defective in ADP-glucose pyrophosphorylase and triose phosphate/phosphate translocator (adg1-1 tpt-2); these mutations strongly inhibited endogenous sugar accumulation. Overall, we show that photosynthesis activated H(+)-ATPase via sugar production in the mesophyll cells of vascular plants. Our work provides new insight into signaling from chloroplasts to the plasma membrane ion transport mechanism. PMID:27016447

  8. A suite of Lotus japonicus starch mutants reveals both conserved and novel features of starch metabolism.

    Science.gov (United States)

    Vriet, Cécile; Welham, Tracey; Brachmann, Andreas; Pike, Marilyn; Pike, Jodie; Perry, Jillian; Parniske, Martin; Sato, Shusei; Tabata, Satoshi; Smith, Alison M; Wang, Trevor L

    2010-10-01

    The metabolism of starch is of central importance for many aspects of plant growth and development. Information on leaf starch metabolism other than in Arabidopsis (Arabidopsis thaliana) is scarce. Furthermore, its importance in several agronomically important traits exemplified by legumes remains to be investigated. To address this issue, we have provided detailed information on the genes involved in starch metabolism in Lotus japonicus and have characterized a comprehensive collection of forward and TILLING (for Targeting Induced Local Lesions IN Genomes) reverse genetics mutants affecting five enzymes of starch synthesis and two enzymes of starch degradation. The mutants provide new insights into the structure-function relationships of ADP-glucose pyrophosphorylase and glucan, water dikinase1 in particular. Analyses of the mutant phenotypes indicate that the pathways of leaf starch metabolism in L. japonicus and Arabidopsis are largely conserved. However, the importance of these pathways for plant growth and development differs substantially between the two species. Whereas essentially starchless Arabidopsis plants lacking plastidial phosphoglucomutase grow slowly relative to wild-type plants, the equivalent mutant of L. japonicus grows normally even in a 12-h photoperiod. In contrast, the loss of GLUCAN, WATER DIKINASE1, required for starch degradation, has a far greater effect on plant growth and fertility in L. japonicus than in Arabidopsis. Moreover, we have also identified several mutants likely to be affected in new components or regulators of the pathways of starch metabolism. This suite of mutants provides a substantial new resource for further investigations of the partitioning of carbon and its importance for symbiotic nitrogen fixation, legume seed development, and perenniality and vegetative regrowth.

  9. Starch Accumulation and Enzyme Activities Associated with Starch Synthesis in Maize Kernels

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hai-yan; DONG Shu-ting; GAO Rong-qi; SUN Qing-quan

    2007-01-01

    The filling rate and the starch accumulation in developing maize kernel were analyzed. The changes of enzyme activities associated with sucrose metabolism and starch biosynthesis were investigated. The purpose is to discuss the enzymatic mechanisms responsible for starch synthesis. Two types of maize cultivars (Zea mays), high starch maize (Feiyu 3) and normal maize (Yuyu 22), were grown in a corn field. The factors involved in starch synthesis were performed during the growth period. The kernel filling rate, the sucrose content, the starch accumulating rates and the activities of SS (sucrose synthase), GBSS (granule-bound starch synthase), SBE (starch branching enzyme) of Feiyu 3, which has high starch content, were significantly higher than those of Yuyu 22, which has low starch content, after 10 DAP (days after pollination).Correlation analysis indicated that ADPGPPase (ADP-glucose pyrophosphorylase) and DBE (starch debranching enzyme)were not correlated with the starch accumulating rates and the kernel filling rate, but the SS activity at the middle and late period were highly significantly correlated with the starch accumulating rates and the kernel filling rate. The GBSS activity was highly significantly correlated with the amylose accumulating rate, but not correlated with the kernel filling rate. The SBE activity was highly significantly correlated with the amylopectin accumulating rate and the kernel filling rate. It was not ADPGPPase and DBE, but SS was the rate-limiting factor of starch biosynthesis in developing maize kernels. GBSS had an important effect on amylose accumulation, and SBE had a significant effect on amylopectin accumulation.

  10. Glycogen synthase isoforms in Synechocystis sp. PCC6803: identification of different roles to produce glycogen by targeted mutagenesis.

    Directory of Open Access Journals (Sweden)

    Sang-Ho Yoo

    Full Text Available Synechocystis sp. PCC6803 belongs to cyanobacteria which carry out photosynthesis and has recently become of interest due to the evolutionary link between bacteria and plant species. Similar to other bacteria, the primary carbohydrate storage source of Synechocystis sp. PCC6803 is glycogen. While most bacteria are not known to have any isoforms of glycogen synthase, analysis of the genomic DNA sequence of Synechocystis sp. PCC6803 predicts that this strain encodes two isoforms of glycogen synthase (GS for synthesizing glycogen structure. To examine the functions of the putative GS genes, each gene (sll1393 or sll0945 was disrupted by double cross-over homologous recombination. Zymogram analysis of the two GS disruption mutants allowed the identification of a protein band corresponding to each GS isoform. Results showed that two GS isoforms (GSI and GSII are present in Synechocystis sp. PCC6803, and both are involved in glycogen biosynthesis with different elongation properties: GSI is processive and GSII is distributive. Total GS activities in the mutant strains were not affected and were compensated by the remaining isoform. Analysis of the branch-structure of glycogen revealed that the sll1393- mutant (GSI- produced glycogen containing more intermediate-length chains (DP 8-18 at the expense of shorter and longer chains compared with the wild-type strain. The sll0945- mutant (GSII- produced glycogen similar to the wild-type, with only a slightly higher proportion of short chains (DP 4-11. The current study suggests that GS isoforms in Synechocystis sp. PCC6803 have different elongation specificities in the biosynthesis of glycogen, combined with ADP-glucose pyrophosphorylase and glycogen branching enzyme.

  11. Leaf Responses of Micropropagated Apple Plants to Water Stress: Changes in Endogenous Hormones and Their Influence on Carbohydrate Metabolism

    Institute of Scientific and Technical Information of China (English)

    LI Tian-hong; LI Shao-hua

    2007-01-01

    The changes in the concentrations of endogenous hormones and their influence on carbohydrate metabolism in leaves of micropropagated Fuji apple plants were studied under water deficiency stress. The results showed that water stress induced a rapid increase in the concentration of abscisic acid (ABA) and led to a decrease in concentrations of both zeatin and gibberellins (GAs). The concentration of indole-3-acetic acid (IAA) changed in an independent manner, which was not correlated with the different levels of water stress. With regard to the carbohydrates, the contents of sorbitol and sucrose increased, whereas the content of starch decreased. The increase in the concentration of ABA was significantly correlated with both the increase in the activity of aldose-6-phosphate reductase (A6PR) and the decrease in the activity of sorbitol dehydrogenase (SDH), indicating that ABA played a regulatory role in sorbitol metabolism. The concentration of ABA was positively correlated to the activity of sucrose-phosphate synthase (SPS) but negatively correlated to the activities of acid invertase (AI) and ADP-glucose-pyrophosphorylase (ADPGppase) in water-stressed plants, which indicated that ABA promoted sucrose synthesis and inhibited sucrose degradation and starch synthesis at the same time. Under conditions of water stress, the decrease in the level of zeatin was accompanied by a decrease in the activities of SDH and ADPGPPase. GAs concentration showed positive correlation with ADPGPPase activity. IAA showed no significant correlation with any of the enzymes tested in this study. The results of this study suggested that ABA might be one of the key factors regulating the distribution of carbohydrates under water stress. The metabolism of sorbitol and starch under conditions of water stress might be regulated by the combined action of many plant hormones.

  12. Impeded Carbohydrate Metabolism in Rice Plants under Submergence Stress

    Institute of Scientific and Technical Information of China (English)

    Malay Kumar ADAK; Nirmalya GHOSH; Dilip Kumar DASGUPTA; Sudha GUPTA

    2011-01-01

    The detrimental effects of submergence on physiological performances of some rice varieties with special references to carbohydrate metabolisms and their allied enzymes during post-flowering stages have been documented and clarified in the present investigation.It was found that photosynthetic rate and concomitant translocation of sugars into the panicles were both related to the yield.The detrimental effects of the complete submergence were recorded in generation of sucrose,starch,sucrose phosphate synthase and phosphorylase activity in the developing panicles of the plants as compared to those under normal or control (i.e.non-submerged) condition.The accumulation of starch was significantly lower in plants under submergence and that was correlated with ADP-glucose pyrophosphorylase activity.Photosynthetic rate was most affected under submergence in varying days of post-flowering and was also related to the down regulation of Ribulose bisphosphate carboxylase activity.However,under normal or control condition,there recorded a steady maintenance of photosynthetic rate at the post-flowering stages and significantly higher values of Ribulose bisphosphate carboxylase activity.Still,photosynthetic rate of the plants under both control and submerged conditions had hardly any significant correlation with sugar accumulation and other enzymes of carbohydrate metabolism like invertase with grain yield.Finally,plants under submergence suffered significant loss of yield by poor grain filling which was related to impeded carbohydrate metabolism in the tissues.It is evident that loss of yield under submergence is attributed both by lower sink size or sink capacity (number of panicles,in this case) as well as subdued carbohydrate metabolism in plants and its subsequent partitioning into the grains.

  13. Responses of ethylene and ACC in rice grains to soil moisture and their relations to grain filling

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The objectives of this study were to-investigate ethylene and 1-aminocylopropane-1-carboxylic acid (ACC) in rice grains and root bleeding sap during the grain filling period and their relationship to the grain filling rate.Two high lodging-resistant rice (Oryza sativa L.) cultivars were grown in pots or tanks.Three treatments,including well watered (WW),moderate soil-drying (MD) and severe soil-drying (SD),were conducted from 9 days of post-anthesis until maturity.The effects of chemical regulators on the concentrations of ethylene and ACC in the grains were also studied.The results show that MD significantly increased the grainfilling rate and grain weight,whereas SD significantly reduced the grain-filling rate and grain weight.Concentrations of ethylene and ACC in the grains were very high at the early grain filling stage and then sharply decreased during the linear period of grain growth.MD reduced the ACC concentrations and ethylene evolution rate,whereas SD remarkably increased the ACC concentrations and ethylene evolution rate.Both the ethylene evolution rate in rice grains and the ACC concentrations in the root-bleeding sap were significantly and positively correlated with the ACC concentrations in rice grains.The ethylene evolution rate was significantly and negatively correlated with the grain-filling rate.The application of amino-ethoxyvinylglycine (AVG),an inhibitor of ethylene synthesis,at 9-13 days of postanthesis significantly reduced the ACC concentrations and ethylene evolution rate of grains,but significantly enhanced the activities of sucrose synthase,ADP glucose pyrophosphorylase and soluble starch synthase.The results were reversed when ethephon,an ethylenereleasing agent,was applied.The results suggest that moderate soil drying during the grain-filling period in rice could inhibit the production of ethylene and ACC and therefore accelerate grain filling and increase grain weight.

  14. Quantitative Multilevel Analysis of Central Metabolism in Developing Oilseeds of Oilseed Rape during in Vitro Culture.

    Science.gov (United States)

    Schwender, Jörg; Hebbelmann, Inga; Heinzel, Nicolas; Hildebrandt, Tatjana; Rogers, Alistair; Naik, Dhiraj; Klapperstück, Matthias; Braun, Hans-Peter; Schreiber, Falk; Denolf, Peter; Borisjuk, Ljudmilla; Rolletschek, Hardy

    2015-07-01

    Seeds provide the basis for many food, feed, and fuel products. Continued increases in seed yield, composition, and quality require an improved understanding of how the developing seed converts carbon and nitrogen supplies into storage. Current knowledge of this process is often based on the premise that transcriptional regulation directly translates via enzyme concentration into flux. In an attempt to highlight metabolic control, we explore genotypic differences in carbon partitioning for in vitro cultured developing embryos of oilseed rape (Brassica napus). We determined biomass composition as well as 79 net fluxes, the levels of 77 metabolites, and 26 enzyme activities with specific focus on central metabolism in nine selected germplasm accessions. Overall, we observed a tradeoff between the biomass component fractions of lipid and starch. With increasing lipid content over the spectrum of genotypes, plastidic fatty acid synthesis and glycolytic flux increased concomitantly, while glycolytic intermediates decreased. The lipid/starch tradeoff was not reflected at the proteome level, pointing to the significance of (posttranslational) metabolic control. Enzyme activity/flux and metabolite/flux correlations suggest that plastidic pyruvate kinase exerts flux control and that the lipid/starch tradeoff is most likely mediated by allosteric feedback regulation of phosphofructokinase and ADP-glucose pyrophosphorylase. Quantitative data were also used to calculate in vivo mass action ratios, reaction equilibria, and metabolite turnover times. Compounds like cyclic 3',5'-AMP and sucrose-6-phosphate were identified to potentially be involved in so far unknown mechanisms of metabolic control. This study provides a rich source of quantitative data for those studying central metabolism. PMID:25944824

  15. Factors Altering Pyruvate Excretion in a Glycogen Storage Mutant of the Cyanobacterium, Synechococcus PCC7942.

    Science.gov (United States)

    Benson, Phoebe J; Purcell-Meyerink, Diane; Hocart, Charles H; Truong, Thy T; James, Gabriel O; Rourke, Loraine; Djordjevic, Michael A; Blackburn, Susan I; Price, G D

    2016-01-01

    Interest in the production of carbon commodities from photosynthetically fixed CO2 has focused attention on cyanobacteria as a target for metabolic engineering and pathway investigation. We investigated the redirection of carbon flux in the model cyanobacterial species, Synechococcus elongatus PCC 7942, under nitrogen deprivation, for optimized production of the industrially desirable compound, pyruvate. Under nitrogen limited conditions, excess carbon is naturally stored as the multi-branched polysaccharide, glycogen, but a block in glycogen synthesis, via knockout mutation in the gene encoding ADP-glucose pyrophosphorylase (glgC), results in the accumulation of the organic acids, pyruvate and 2-oxoglutarate, as overflow excretions into the extracellular media. The ΔglgC strain, under 48 h of N-deprivation was shown to excrete pyruvate for the first time in this strain. Additionally, by increasing culture pH, to pH 10, it was possible to substantially elevate excretion of pyruvate, suggesting the involvement of an unknown substrate/proton symporter for export. The ΔglgC mutant was also engineered to express foreign transporters for glucose and sucrose, and then grown photomixotrophically with exogenous organic carbon supply, as added 5 mM glucose or sucrose during N- deprivation. Under these conditions we observed a fourfold increase in extracellular pyruvate excretion when glucose was added, and a smaller increase with added sucrose. Although the magnitude of pyruvate excretion did not correlate with the capacity of the ΔglgC strain for bicarbonate-dependent photosynthetic O2 evolution, or with light intensity, there was, however, a positive correlation observed between the density of the starter culture prior to N-deprivation and the final extracellular pyruvate concentration. The factors that contribute to enhancement of pyruvate excretion are discussed, as well as consideration of whether the source of carbon for pyruvate excretion might be derived from

  16. Quantitative Multilevel Analysis of Central Metabolism in Developing Oilseeds of Oilseed Rape During In Vitro Culture

    Energy Technology Data Exchange (ETDEWEB)

    Schwender, Jorg [Brookhaven National Lab. (BNL), Upton, NY (United States); Hebbelmann, Inga [Brookhaven National Lab. (BNL), Upton, NY (United States); Heinzel, Nicholas [Leibniz Inst. of Plant Genetics and Crop Plant Research, Gatersleben (Germany); Hildebrandt, Tatjana [Univ. of Hannover (Germany); Rogers, Alistair [Brookhaven National Lab. (BNL), Upton, NY (United States); Naik, Dhiraj [Brookhaven National Lab. (BNL), Upton, NY (United States); Indian Inst. of Advanced Research Koba, Gujarat (India); Klapperstuck, Matthias [Monash Univ., Melbourne, VIC (Australia); Braun, Hans -Peter [Univ. of Hannover (Germany); Schreiber, Falk [Monash Univ., Melbourne, VIC (Australia); Univ. Halle-Wittenberg, Melbourne (Australia); Denolf, Peter [Bayer CropScience (Belgium); Borisjuk, Ljudmilla [Leibniz Inst. of Plant Genetics and Crop Plant Research, Gatersleben (Germany); Rolletschek, Hardy [Leibniz Inst. of Plant Genetics and Crop Plant Research, Gatersleben (Germany)

    2015-07-01

    Seeds provide the basis for many food, feed, and fuel products. Continued increases in seed yield, composition, and quality require an improved understanding of how the developing seed converts carbon and nitrogen supplies into storage. Current knowledge of this process is often based on the premise that transcriptional regulation directly translates via enzyme concentration into flux. In an attempt to highlight metabolic control, we explore genotypic differences in carbon partitioning for in vitro cultured developing embryos of oilseed rape (Brassica napus). We determined biomass composition as well as 79 net fluxes, the levels of 77 metabolites, and 26 enzyme activities with specific focus on central metabolism in nine selected germplasm accessions. We observed a tradeoff between the biomass component fractions of lipid and starch. With increasing lipid content over the spectrum of genotypes, plastidic fatty acid synthesis and glycolytic flux increased concomitantly, while glycolytic intermediates decreased. The lipid/starch tradeoff was not reflected at the proteome level, pointing to the significance of (posttranslational) metabolic control. Enzyme activity/flux and metabolite/flux correlations suggest that plastidic pyruvate kinase exerts flux control and that the lipid/starch tradeoff is most likely mediated by allosteric feedback regulation of phosphofructokinase and ADP-glucose pyrophosphorylase. Also, quantitative data were used to calculate in vivo mass action ratios, reaction equilibria, and metabolite turnover times. Compounds like cyclic 3',5'-AMP and sucrose-6-phosphate were identified to potentially be involved in so far unknown mechanisms of metabolic control. This study provides a rich source of quantitative data for those studying central metabolism..

  17. Cumulative effect of heterologous AtWRI1 gene expression and endogenous BjAGPase gene silencing increases seed lipid content in Indian mustard Brassica juncea.

    Science.gov (United States)

    Bhattacharya, Surajit; Das, Natasha; Maiti, Mrinal K

    2016-10-01

    The production of vegetable oil in many countries of the world, including India has not been able to keep pace with the increasing requirement, leading to a very large gap in the demand-supply chain. Thus, there is an urgent need to increase the yield potential of the oilseed crops so as to enhance the storage lipid productivity. The present study describes a novel metabolic engineering ploy involving the constitutive down-regulation of endogenous ADP-glucose pyrophosphorylase (BjAGPase) enzyme and the seed-specific expression of WRINKLED1 transcription factor (AtWRI1) from Arabidopsis thaliana in Indian mustard (Brassica juncea) with an aim to divert the photosynthetically fixed carbon pool from starch to lipid synthesis in the seeds for the enhanced production of storage lipids in the seeds of transgenic mustard plants. The starch content, in both the vegetative leaf and developing seed tissues of the transgenic B. juncea lines exhibited a reduction by about 45-53% compared to the untransformed control, whereas the soluble sugar content was increased by 2.4 and 1.3-fold in the leaf and developing seed tissues, respectively. Consequently, the transgenic lines showed a significant enhancement in total seed lipid content ranging between 7.5 and 16.9%. The results indicate that the adopted metabolic engineering strategy was successful in significantly increasing the seed oil content. Therefore, findings of our research suggest that the metabolic engineering strategy adopted in this study for shifting the anabolic carbon flux from starch synthesis to lipid biosynthesis can be employed for increasing the storage lipid content of seeds in other plant species. PMID:27314514

  18. 石门揭露突出煤层冻结温度场数值模拟研究%Research on numerical simulation of freezing temperature field in uncovering outburst coal seam in cross-cut

    Institute of Scientific and Technical Information of China (English)

    谢雄刚; 冯涛

    2011-01-01

    Aiming at a new-presented outburst-proof method by injecting liquid and freezing in uncovering coal seam in cross-cut in this paper,with the ANSYS numerical simulation software,according to the operation parameters in the work face of uncovering coal seam at No.2 cross-cut of-400 m level in Longjiashan Mine,the authors established the numerical simulation calculation model of the temperature field in freezing section,analyzed its expand nephogram in different period,decided the effective range,average temperature,closure time of ice zone and expand velocity.The simulation shows that the more near to the freezing center,the more fast the temperature of the No.6 coal seam will decline.At the same time,the temperature in coal seam of frozen tubes in center cross-section and vertical-section is lowest.After 35~40 days,reached the frozen control temperature of-15 ℃ for outburst-proof.The No.6 coal in freezing zone is strong enough to prevent coal and gas outburst.The feasibility of injecting liquid and freezing as a new outburst-proof method was proved.%针对新提出的石门揭煤注液冻结防突方法,根据龙家山煤矿-400 m水平2号石门揭煤工作面施工参数,应用ANSYS数值模拟软件,建立了石门揭煤冻结温度场数值模拟计算模型,分析了不同时期冻结区温度扩展云图,得出不同冻结时间冻结区有效范围、平均温度、交圈时间及温度扩展速度。数值模拟表明:距离中心越近,冻结区煤层温度下降越快;相同冻结时间,竖向中排冻结管断面和横向中排冻结管断面处煤层温度最低。该石门揭煤工作面需要35~40 d冻结时间来满足-15℃煤层控制温度的防突工程要求。证明石门揭煤注液冻结防突技术是可行性的。

  19. Potato guard cells respond to drying soil by a complex change in the expression of genes related to carbon metabolism and turgor regulation.

    Science.gov (United States)

    Kopka, J; Provart, N J; Müller-Röber, B

    1997-04-01

    Altering stomatal function by a guard cell-targeted transgenic approach with the aim of increased stress tolerance and crop yield requires knowledge of the natural fluctuations of stomatal gene expression under stress conditions. We developed a fast method for the isolation of RNA from epidermal fragments of potato leaves (Solanum tuberosum L. cv. Désirée), demonstrated that this RNA preparation is highly enriched in guard cell transcripts and used this method to investigate the response of gene expression in guard cells to mild drought stress. Drought was applied in planta by withholding water over a period of 2-4 days. In the following work responses observed under these conditions are called 'long-term' in contrast to immediate (short-term) stomatal opening and closing responses to environmental stress. We observed both gene-specific increases and decreases of steady-state transcript levels. In particular, the mRNA levels of sucrose synthase and sucrose-phosphate synthase were elevated 5.5-fold and 1.4-fold, respectively. In contrast, expression of an inwardly rectifying K+ channel from guard cells (kst1) and of a plasma membrane H(+)-ATPase (pha2) was reduced to 26% and 36%, respectively, of the expression in watered controls. In addition, expression of vacuolar invertase, UDP-glucose pyrophosphorylase, ADP-glucose pyrophosphorylase (large subunit), cytosolic glyceraldehyde-3-phosphate dehydrogenase, a sucrose/H+ cotransporter, and a novel isoform of phosphoenolpyruvate carboxylase were also reduced. Other genes exhibited unaltered expression. Compared with the response in whole leaves, the transcript levels of phosphoenolpyruvate carboxylase, vacuolar invertase, and cytosolic glyceraldehyde-3-phosphate dehydrogenase were regulated guard cell specifically. Most importantly, changes in steady-state transcript levels were complete before the onset of a decrease in leaf water potential, when drought-induced stomatal closure was already obvious. These data

  20. 大型露天停车场雷电灾害分析与防护措施的研究%Lightning Hazard Analysis and Protective Measures of Large Uncovered Parking

    Institute of Scientific and Technical Information of China (English)

    赵涛; 李斐

    2014-01-01

    近年来,由于气候变化使强对流性天气不断增多,雷击事件频发。特别是空旷地区防雷设施不完善,防雷设施的缺乏,致使雷击造成人员伤亡和经济损失的事故时有发生。通过武汉经济技术开发区神龙汽车公司的露天停车场两次成品车遭受雷击事故的实地调查,就该村地理位置、气象资料、雷灾产生的原因进行了分析,提出了相应的雷电防护对策及建议。%In recent years, the climate change makes strong convective weather increasing and frequent lightning events. Especially in open areas, the lightning protection facilities in open areas are imperfect, even lack of lightning protection facilities, so the lightning casualties and economic losses occurred often. Through the fieldwork of the two lightning accident of finished car in uncovered parking of Shenlong Car company in Wuhan Economic and Technological Development Zone, the paper analyzes the location, meteorological data and the reasons of lightning disaster, and puts forward the corresponding countermeasures and suggestions for lightning protection.

  1. Uncovering the nutritional landscape of food

    CERN Document Server

    Kim, Seunghyeon; Foo, Mathias; Jin, Yong-Su; Kim, Pan-Jun

    2014-01-01

    The study of foods and nutrients is essential for designing healthy diets. This can be facilitated through quantitative, data-driven approaches that utilize massive nutritional information collected for many different foods. Using information from over 1,000 raw foods, we systematically evaluated the nutrient composition of each food in regards to satisfying daily nutritional requirements. Such nutrient balance within a food was quantified herein as nutritional fitness, using the food's frequency of occurrence in nutritionally-adequate food combinations. Nutritional fitness offers prioritization of recommendable foods within a food network, in which foods are connected based on similarities of nutrient compositions. We found a number of key nutrients, such as choline and \\alpha-linolenic acid, whose levels in foods can critically affect the foods' nutritional fitness. Analogously, pairs of nutrients can have the same effect. In fact, two nutrients can impact nutritional fitness synergistically, although the i...

  2. Islands uncovered by melting polar ice

    Science.gov (United States)

    Kumar, Mohi

    Thawing glaciers north of Norway's Svalbard archipelago have revealed at least two unmapped and unclaimed islands, one roughly the size of a basketball court, according to a 20 August Reuters report. In addition, information released in August by the U.S. National Snow and Ice Data Center indicated that with one month left in the melting season, Arctic sea ice is already below the record minimum. "Reductions of snow and ice are happening at an alarming rate," said Norwegian Environment Minister Helen Bjoernoy. She suggested that these observations may indicate that the loss of sea ice is perhaps accelerating faster than predicted by the Intergovernmental Panel on Climate Change, which warned in February that summer sea ice could almost vanish by the end of this century.

  3. The Great 1787 Corralero, Oaxaca, Tsunami Uncovered

    Science.gov (United States)

    Ramirez-Herrera, M.; Lagos, M.; Goguitchaichrili, A.; Aguilar, B.; Machain-Castillo, M. L.; Caballero, M.; Ruíz-Fernández, A. C.; Suarez, G.; Ortuño, M.

    2013-05-01

    In 28th March 1787, more than two centuries ago, a deadly tsunami (related to the the San Sixto earthquake) poured over the coast of Oaxaca, Guerrero, and Chiapas, along more than 500 km of the Mexican Pacific coast and up to 6 km inland, the tsunami destroyed mostly farmlands, and livestock and few villages since the density of population was sparse at the time, according to known historical accounts. We report the first geological evidence from the Corralero (Alotengo) lagoon coastal area to support these historical accounts. A transect was made with coring and test pits every 100 m from the coastline and up to 1.6 km inland. The test pits showed an anomalous sand layer that had been deposited in a single event in the swales of a series of beach ridges. The anomalous layer is continuous along the transect, about a 1000 m-long, and is formed of coarse to medium sand, at about 36 to 64 cm depth. It thickness varies, averaging 28 cm in the middle of a swale. Based on the accounts of the 1787 earthquake (M 8.6) and tsunami, we deduced that this might be the evidence of its existence. As the only major tsunami described at that time, the San Sixto earthquake-triggered tsunami. We used the stratigraphy, grain size, microfossils (foraminifera and diatoms), magnetic properties such as magnetic susceptibility, remanent magnetization analyses to reveal the nature of this anomalous sand layer. These proxies support a sudden and rapid event, consisting of sands transported by an extreme sea-wave inland. Further analysis will confirm the estimated age of this event.

  4. Uncovering Randomness and Success in Society

    OpenAIRE

    Sarika Jalan; Camellia Sarkar; Anagha Madhusudanan; Sanjiv Kumar Dwivedi

    2014-01-01

    An understanding of how individuals shape and impact the evolution of society is vastly limited due to the unavailability of large-scale reliable datasets that can simultaneously capture information regarding individual movements and social interactions. We believe that the popular Indian film industry, "Bollywood", can provide a social network apt for such a study. Bollywood provides massive amounts of real, unbiased data that spans more than 100 years, and hence this network has been used a...

  5. Uncovering randomness and success in society.

    Directory of Open Access Journals (Sweden)

    Sarika Jalan

    Full Text Available An understanding of how individuals shape and impact the evolution of society is vastly limited due to the unavailability of large-scale reliable datasets that can simultaneously capture information regarding individual movements and social interactions. We believe that the popular Indian film industry, "Bollywood", can provide a social network apt for such a study. Bollywood provides massive amounts of real, unbiased data that spans more than 100 years, and hence this network has been used as a model for the present paper. The nodes which maintain a moderate degree or widely cooperate with the other nodes of the network tend to be more fit (measured as the success of the node in the industry in comparison to the other nodes. The analysis carried forth in the current work, using a conjoined framework of complex network theory and random matrix theory, aims to quantify the elements that determine the fitness of an individual node and the factors that contribute to the robustness of a network. The authors of this paper believe that the method of study used in the current paper can be extended to study various other industries and organizations.

  6. Uncovering the Secrets: Homophobia in Physical Education

    Science.gov (United States)

    Ayvazo, Shiri; Sutherland, Sue

    2009-01-01

    Studies examining the discourse on issues related to sexual orientation in physical education reveal that the physical education setting is an environment where heterosexism, heteronormativity, and homophobia subsist fervently. The purpose of this article is to review the growing research that has been conducted on homophobia in physical education…

  7. Seduction without cause: uncovering explanatory neurophilia.

    Science.gov (United States)

    Trout, J D

    2008-08-01

    Credibility is a cherished currency in science, but its cues can be counterfeit. A novel series of experiments by Weisberg and her colleagues show that non-expert consumers of behavioral explanations assign greater standing to explanations that contain neuroscientific details, even if these details provide no additional explanatory value. Here, we discuss the part that this 'placebic' information might play in producing a potentially misleading sense of intellectual fluency and, consequently, an unreliable sense of understanding.

  8. Cobalamins uncovered by modern electronic structure calculations

    DEFF Research Database (Denmark)

    Kepp, Kasper Planeta; Ryde, Ulf

    2009-01-01

    these are cis-steric distortions, electrostatic stabilization of radical products, the realization that nucleotide units can serve as polar handles, and the careful design of the active sites, with polar residues in the radical enzymes and non-polar residues in the transferases. Together, these strategies...

  9. Uncovering the white place: whitewashing at work

    OpenAIRE

    Reitman, Meredith

    2006-01-01

    Recent work exploring the racialization of place tends to focus on the racialization of marginalized group space. This paper shifts attention toward the racialization of dominant group space, namely, the creation and maintenance of white places. Using the case study of the software workplace, I argue that white places are formed through a process of whitewashing, which simultaneously denies race and superimposes white culture. Whitewashing wields language and invisibility to deny race and pro...

  10. The crisis has uncovered the Slovak helplessness

    International Nuclear Information System (INIS)

    In this paper author deals with problems connected with close of transport of nature gas through the gas pipeline from Russia via Ukraine to the Slovak Republic. Russia-Ukraine gas dispute fully revealed as unreliable suppliers Moscow and Kiev as the carrier gas. Slovakia for the worse, imports it from Russia a long time covering almost a hundred percent of domestic consumption. From mouth of politicians and representatives of the Slovak Gas Industry (SPP) has repeatedly resounded that Gazprom is a reliable partner who offers the best conditions including prices. Events of other days reliability refuted the argument. A theory of the best terms and the lowest prices are valid until there are not empty tubes.

  11. Uncovering dengue in India: morbidity estimates

    Directory of Open Access Journals (Sweden)

    Ananda Amarasinghe

    2014-05-01

    Full Text Available Over the last few decades, reporting of dengue cases has dramatically spread over almost entire India but the disease burden is grossly under-estimated under the current surveillance system. This review based on literature searches in PubMed and Medline for the period 1961-2012 describes changing epidemiological patterns, emerging challenges to public health intervention for control of dengue transmission in India and estimates magnitude of under-reporting. The annual reported numbers in 10 selected states/Union Territories with the highest number of cases during the years 2008-2012 and the surveillance system estimated expansion factor of 8.9-9.6 derived from Thailand and Cambodia data respectively were used for new estimates of dengue morbidity in India. The reporting incidence of dengue is as low as 4/100,000 in 2012. The estimated crude incidence of dengue for 2012 is 53/100,000 to 58.83/100,000 and the country annual health care facility based case load would be around 700,000. India needs to expand surveillance activities to non-hospitalized cases and to the distribution and abundance of Aedes aegypti throughout country and review state and local vector control activities for Aedes aegypti and Aedes albopictus. Knowledge of vector prevalence is essential to estimate the geographical distribution of dengue infection and associated disease.

  12. Uncovering the Costs of the Iraq War

    OpenAIRE

    Fred E. Foldvary

    2008-01-01

    Fred Foldvary reviews the recent book by Joseph Stiglitz and Linda Bilmes, The Three Trillion Dollar War: The True Cost of the Iraq Conflict. Foldvary commends the book for its assembly of both the budgeted and implicit costs of the war, and its analysis of the economic impact of the war. The review posits that the better knowledge and accounting of the war costs as provided by this work will aid in establishing a more coherent dialog on policy for dealing with this and future conflicts abroad.

  13. Mathematicians in Schools: Uncovering Maths' Beautiful Secrets

    Science.gov (United States)

    Welch, Bronwyn

    2016-01-01

    Mathematics professionals are working with teachers revealing the reality and beauty that happens in the world of math and to show that this is essentially a "human endeavour," embedded in much of what people do and the ways in which they think. In this article, the author shares vignettes of primary classes working with mathematicians…

  14. Uncovering Mass Generation Through Higgs Flavor Violation

    CERN Document Server

    Altmannshofer, Wolfgang; Kagan, Alexander L; Silvestrini, Luca; Zupan, Jure

    2015-01-01

    If the flavor violating decay h --> tau mu is observed at the LHC, extra sources of electroweak symmetry breaking (EWSB) beyond the Higgs would be required in order to reconcile it with the bounds from tau --> mu gamma, barring fine-tuned cancellations. In fact, an h --> tau mu decay rate at a level indicated by the CMS measurement is easily realized if the muon and electron masses are due to a new source of EWSB, while the tau mass is due to the Higgs. We illustrate this with two examples: a two Higgs doublet model, and a model in which the Higgs is partially composite, with EWSB triggered by a technicolor sector. The 1st and 2nd generation quark masses and CKM mixing can also be assigned to the new EWSB source. Large deviations in the flavor diagonal lepton and quark Higgs Yukawa couplings are generic. If m_mu is due to a rank 1 mass matrix contribution, a novel Yukawa coupling sum rule holds, providing a precision test of our framework. Flavor violating quark and lepton (pseudo)scalar couplings combine to ...

  15. UNCOVERING THE NUCLEUS CANDIDATE FOR NGC 253

    Energy Technology Data Exchange (ETDEWEB)

    Günthardt, G. I.; Camperi, J. A. [Observatorio Astronómico, Universidad Nacional de Córdoba (Argentina); Agüero, M. P. [Observatorio Astronómico, Universidad Nacional de Córdoba, and CONICET (Argentina); Díaz, R. J.; Gomez, P. L.; Schirmer, M. [Gemini Observatory, AURA (United States); Bosch, G., E-mail: gunth@oac.uncor.edu, E-mail: camperi@oac.uncor.edu, E-mail: mpaguero@oac.uncor.edu, E-mail: rdiaz@gemini.edu, E-mail: pgomez@gemini.edu, E-mail: mschirmer@gemini.edu, E-mail: guille@fcaglp.unlp.edu.ar [Instituto de Astrofísica de La Plata (CONICET-UNLP) (Argentina)

    2015-11-15

    NGC 253 is the nearest spiral galaxy with a nuclear starburst that becomes the best candidate for studying the relationship between starburst and active galactic nucleus activity. However, this central region is veiled by large amounts of dust, and it has been so far unclear which is the true dynamical nucleus to the point that there is no strong evidence that the galaxy harbors a supermassive black hole co-evolving with the starburst as was supposed earlier. Near-infrared (NIR) spectroscopy, especially NIR emission line analysis, could be advantageous in shedding light on the true nucleus identity. Using Flamingos-2 at Gemini South we have taken deep K-band spectra along the major axis of the central structure and through the brightest infrared source. In this work, we present evidence showing that the brightest NIR and mid-infrared source in the central region, already known as radio source TH7 and so far considered just a large stellar supercluster, in fact presents various symptoms of a genuine galactic nucleus. Therefore, it should be considered a valid nucleus candidate. Mentioning some distinctive aspects, it is the most massive compact infrared object in the central region, located at 2.″0 of the symmetry center of the galactic bar, as measured in the K-band emission. Moreover, our data indicate that this object is surrounded by a large circumnuclear stellar disk and it is also located at the rotation center of the large molecular gas disk of NGC 253. Furthermore, a kinematic residual appears in the H{sub 2} rotation curve with a sinusoidal shape consistent with an outflow centered in the candidate nucleus position. The maximum outflow velocity is located about 14 pc from TH7, which is consistent with the radius of a shell detected around the nucleus candidate, observed at 18.3 μm (Qa) and 12.8 μm ([Ne ii]) with T-ReCS. Also, the Brγ emission line profile shows a pronounced blueshift and this emission line also has the highest equivalent width at this position. All this evidence points to TH7 as the best candidate for the galactic nucleus of NGC 253.

  16. Uncovering History for Future History Teachers

    Science.gov (United States)

    Fischer, Fritz

    2010-01-01

    The art of history teaching is at a crossroads. Recent scholarship focuses on the need to change the teaching of history so students can better learn history, and insists that history teachers must move beyond traditional structures and methods of teaching in order to improve their students' abilities to think with history. This article presents…

  17. Uncovering the 2010 Haiti earthquake death toll

    Directory of Open Access Journals (Sweden)

    J. E. Daniell

    2013-05-01

    Full Text Available Casualties are estimated for the 12 January 2010 earthquake in Haiti using various reports calibrated by observed building damage states from satellite imagery and reconnaissance reports on the ground. By investigating various damage reports, casualty estimates and burial figures, for a one year period from 12 January 2010 until 12 January 2011, there is also strong evidence that the official government figures of 316 000 total dead and missing, reported to have been caused by the earthquake, are significantly overestimated. The authors have examined damage and casualties report to arrive at their estimation that the median death toll is less than half of this value (±137 000$. The authors show through a study of historical earthquake death tolls, that overestimates of earthquake death tolls occur in many cases, and is not unique to Haiti. As death toll is one of the key elements for determining the amount of aid and reconstruction funds that will be mobilized, scientific means to estimate death tolls should be applied. Studies of international aid in recent natural disasters reveal that large distributions of aid which do not match the respective needs may cause oversupply of help, aggravate corruption and social disruption rather than reduce them, and lead to distrust within the donor community.

  18. Skin tumors Rb(eing uncovered

    Directory of Open Access Journals (Sweden)

    CLOTILDE eCOSTA

    2013-12-01

    Full Text Available The Rb1 gene was the first bona fide tumor suppressor identified and cloned more than 25 years ago. Since then, a plethora of studies have revealed the functions of pRb and the existence of a sophisticated and strictly regulated pathway that modulates such functional roles. An emerging paradox affecting Rb1 in cancer connects the relatively low number of mutations affecting Rb1 gene in specific human tumors, compared with the widely functional inactivation of pRb in most, if not in all, human cancers. The existence of a retinoblastoma family of proteins pRb, p107 and p130 and their potential unique and overlapping functions as master regulators of cell cycle progression and transcriptional modulation by similar processes, may provide potential clues to explain such conundrum. Here, we will review the development of different genetically engineered mouse models, in particular those affecting stratified epithelia, and how they have offered new avenues to understand the roles of the Rb family members and their targets in the context of tumor development and progression.

  19. Uncovering Racial Bias in Nursing Fundamentals Textbooks.

    Science.gov (United States)

    Byrne, Michelle M.

    2001-01-01

    The portrayal of African Americans in nursing fundamentals textbooks was analyzed, resulting in 11 themes in the areas of history, culture, and physical assessment. Few African American leaders were included, and racial bias and stereotyping were apparent. Differences were often discussed using Eurocentric norms, and language tended to minimize…

  20. Tracing lineages to uncover neuronal identity

    OpenAIRE

    Perlmann Thomas; Panman Lia

    2011-01-01

    Abstract Many previous studies have focused on understanding how midbrain dopamine neurons, which are implicated in many neurological conditions, are generated during embryogenesis. One of the remaining questions concerns how different dopamine neuron subtypes are specified. A recent paper in Neural Development has revealed features of a spatial and temporal lineage map that, together with other studies, begins to elucidate the developmental origin of distinct neuronal subtypes within the dev...

  1. Comet mission hopes to uncover Earth's origins

    CERN Multimedia

    Henderson, M

    2004-01-01

    "A European spacecraft that will hunt down a comet in search of clues to the origin of life on Earth will blast off tomorrow from the Kourou spaceport in French Guiana. The Rosetta probe will take 12 years to catch up with Churyumov-Gerasimenko before becoming the first spacecraft to make a soft, controlled landing on a comet's nucleus" (1 page).

  2. Uncovering the spatial structure of mobility networks

    CERN Document Server

    Louail, Thomas; Picornell, Miguel; Cantú, Oliva García; Herranz, Ricardo; Frias-Martinez, Enrique; Ramasco, José J; Barthelemy, Marc

    2015-01-01

    The extraction of a clear and simple footprint of the structure of large, weighted and directed networks is a general problem that has many applications. An important example is given by origin-destination matrices which contain the complete information on commuting flows, but are difficult to analyze and compare. We propose here a versatile method which extracts a coarse-grained signature of mobility networks, under the form of a $2\\times 2$ matrix that separates the flows into four categories. We apply this method to origin-destination matrices extracted from mobile phone data recorded in thirty-one Spanish cities. We show that these cities essentially differ by their proportion of two types of flows: integrated (between residential and employment hotspots) and random flows, whose importance increases with city size. Finally the method allows to determine categories of networks, and in the mobility case to classify cities according to their commuting structure.

  3. Uncovering ecosystem service bundles through social preferences.

    Directory of Open Access Journals (Sweden)

    Berta Martín-López

    Full Text Available Ecosystem service assessments have increasingly been used to support environmental management policies, mainly based on biophysical and economic indicators. However, few studies have coped with the social-cultural dimension of ecosystem services, despite being considered a research priority. We examined how ecosystem service bundles and trade-offs emerge from diverging social preferences toward ecosystem services delivered by various types of ecosystems in Spain. We conducted 3,379 direct face-to-face questionnaires in eight different case study sites from 2007 to 2011. Overall, 90.5% of the sampled population recognized the ecosystem's capacity to deliver services. Formal studies, environmental behavior, and gender variables influenced the probability of people recognizing the ecosystem's capacity to provide services. The ecosystem services most frequently perceived by people were regulating services; of those, air purification held the greatest importance. However, statistical analysis showed that socio-cultural factors and the conservation management strategy of ecosystems (i.e., National Park, Natural Park, or a non-protected area have an effect on social preferences toward ecosystem services. Ecosystem service trade-offs and bundles were identified by analyzing social preferences through multivariate analysis (redundancy analysis and hierarchical cluster analysis. We found a clear trade-off among provisioning services (and recreational hunting versus regulating services and almost all cultural services. We identified three ecosystem service bundles associated with the conservation management strategy and the rural-urban gradient. We conclude that socio-cultural preferences toward ecosystem services can serve as a tool to identify relevant services for people, the factors underlying these social preferences, and emerging ecosystem service bundles and trade-offs.

  4. Uncovering the 2010 Haiti earthquake death toll

    Science.gov (United States)

    Daniell, J. E.; Khazai, B.; Wenzel, F.

    2013-05-01

    Casualties are estimated for the 12 January 2010 earthquake in Haiti using various reports calibrated by observed building damage states from satellite imagery and reconnaissance reports on the ground. By investigating various damage reports, casualty estimates and burial figures, for a one year period from 12 January 2010 until 12 January 2011, there is also strong evidence that the official government figures of 316 000 total dead and missing, reported to have been caused by the earthquake, are significantly overestimated. The authors have examined damage and casualties report to arrive at their estimation that the median death toll is less than half of this value (±137 000). The authors show through a study of historical earthquake death tolls, that overestimates of earthquake death tolls occur in many cases, and is not unique to Haiti. As death toll is one of the key elements for determining the amount of aid and reconstruction funds that will be mobilized, scientific means to estimate death tolls should be applied. Studies of international aid in recent natural disasters reveal that large distributions of aid which do not match the respective needs may cause oversupply of help, aggravate corruption and social disruption rather than reduce them, and lead to distrust within the donor community.

  5. Tracing lineages to uncover neuronal identity

    Directory of Open Access Journals (Sweden)

    Perlmann Thomas

    2011-07-01

    Full Text Available Abstract Many previous studies have focused on understanding how midbrain dopamine neurons, which are implicated in many neurological conditions, are generated during embryogenesis. One of the remaining questions concerns how different dopamine neuron subtypes are specified. A recent paper in Neural Development has revealed features of a spatial and temporal lineage map that, together with other studies, begins to elucidate the developmental origin of distinct neuronal subtypes within the developing midbrain. See research article http://www.neuraldevelopment.com/content/6/1/29

  6. $\\eta$ Carinae Baby Homunculus Uncovered by ALMA

    CERN Document Server

    Abraham, Zulema; Beaklini, Pedro P B

    2014-01-01

    We report observations of $\\eta$ Carinae obtained with ALMA in the continuum of 100, 230, 280 and 660 GHz in 2012 November, with a resolution that varied from 2.88" to 0.45" for the lower and higher frequencies respectively. The source is not resolved, even at the highest frequency; its spectrum is characteristic of thermal bremsstrahlung of a compact source, but different from the spectrum of optically thin wind. The recombination lines H42$\\alpha$, He42$\\alpha$, H40$\\alpha$, He40$\\alpha$, H50$\\beta$, H28$\\alpha$, He28$\\alpha$, H21$\\alpha$ and He21$\\alpha$ were also detected and their intensities reveal non local thermodynamic equilibrium (NLTE) effects. We found that the line profiles could only be fit by an expanding shell of dense and ionized gas, which produces a slow shock in the surroundings of $\\eta$ Carinae. Combined with fittings to the continuum, we were able to constrain the shell size, radius, density, temperature and velocity. The detection of the He recombination lines is compatible with the hi...

  7. Uncovering the Hidden Costs of Offshoring

    DEFF Research Database (Denmark)

    Larsen, Marcus M.; Manning, Stephan; Pedersen, Torben

    2013-01-01

    -estimation errors given increasing configuration and task complexity in captive offshoring and offshore outsourcing, respectively. Moreover, we show that experience and a strong orientation toward organizational design in the offshoring strategy reduce the cost-estimation errors that follow from complexity. Our......This study investigates estimation errors due to hidden costs—the costs of implementation that are neglected in strategic decision-making processes—in the context of services offshoring. Based on data from the Offshoring Research Network, we find that decision makers are more likely to make cost...... findings contribute to research on the effectiveness of sourcing and global strategies by stressing the importance of organizational design and experience in dealing with increasing complexity....

  8. uncovering the everyday moral knowledge of nurses

    Directory of Open Access Journals (Sweden)

    Elizabeth Peter

    2007-01-01

    Full Text Available En el presente artículo exploramos el uso de la perspectiva metafísica de Margaret Urban Walter, particularmente el uso de narrativas, para informar sobre el desarrollo de un abordaje de investigación que revela el conocimiento moral cotidiano de las enfermeras. Un método basado en el trabajo de Walter permite analizar las dimensiones de poder inherentes en la experiencia moral de las enfermeras, así como fundamentar con una moral epistemológica robusta, el abordaje narrativo ético de la enfermería, y distinguir los diferentes tipos de narrativas. Un número de cuestiones analíticas basadas en el trabajo de Walker son aquí presentadas y empleadas para analizar la práctica narrativa e ilustrar cómo las narrativas pueden ser usadas para delinear el conocimiento moral de las enfermeras dentro del contexto de su trabajo real.

  9. Transcriptional profiling of C. elegans DAF-19 uncovers a ciliary base-associated protein and a CDK/CCRK/LF2p-related kinase required for intraflagellar transport.

    Science.gov (United States)

    Phirke, Prasad; Efimenko, Evgeni; Mohan, Swetha; Burghoorn, Jan; Crona, Filip; Bakhoum, Mathieu W; Trieb, Maria; Schuske, Kim; Jorgensen, Erik M; Piasecki, Brian P; Leroux, Michel R; Swoboda, Peter

    2011-09-01

    Cilia are ubiquitous cell surface projections that mediate various sensory- and motility-based processes and are implicated in a growing number of multi-organ genetic disorders termed ciliopathies. To identify new components required for cilium biogenesis and function, we sought to further define and validate the transcriptional targets of DAF-19, the ciliogenic C. elegans RFX transcription factor. Transcriptional profiling of daf-19 mutants (which do not form cilia) and wild-type animals was performed using embryos staged to when the cell types developing cilia in the worm, the ciliated sensory neurons (CSNs), still differentiate. Comparisons between the two populations revealed 881 differentially regulated genes with greater than a 1.5-fold increase or decrease in expression. A subset of these was confirmed by quantitative RT-PCR. Transgenic worms expressing transcriptional GFP fusions revealed CSN-specific expression patterns for 11 of 14 candidate genes. We show that two uncharacterized candidate genes, termed dyf-17 and dyf-18 because their corresponding mutants display dye-filling (Dyf) defects, are important for ciliogenesis. DYF-17 localizes at the base of cilia and is specifically required for building the distal segment of sensory cilia. DYF-18 is an evolutionarily conserved CDK7/CCRK/LF2p-related serine/threonine kinase that is necessary for the proper function of intraflagellar transport, a process critical for cilium biogenesis. Together, our microarray study identifies targets of the evolutionarily conserved RFX transcription factor, DAF-19, providing a rich dataset from which to uncover-in addition to DYF-17 and DYF-18-cellular components important for cilium formation and function. PMID:21740898

  10. Uncovering a Nuisance Influence of a Phenological Trait of Plants Using a Nonlinear Structural Equation: Application to Days to Heading and Culm Length in Asian Cultivated Rice (Oryza Sativa L.).

    Science.gov (United States)

    Onogi, Akio; Ideta, Osamu; Yoshioka, Takuma; Ebana, Kaworu; Yamasaki, Masanori; Iwata, Hiroyoshi

    2016-01-01

    Phenological traits of plants, such as flowering time, are linked to growth phase transition. Thus, phenological traits often influence other traits through the modification of the duration of growth period. This influence is a nuisance in plant breeding because it hampers genetic evaluation of the influenced traits. Genetic effects on the influenced traits have two components, one that directly affects the traits and one that indirectly affects the traits via the phenological trait. These cannot be distinguished by phenotypic evaluation and ordinary linear regression models. Consequently, if a phenological trait is modified by introgression or editing of the responsible genes, the phenotypes of the influenced traits can change unexpectedly. To uncover the influence of the phenological trait and evaluate the direct genetic effects on the influenced traits, we developed a nonlinear structural equation (NSE) incorporating a nonlinear influence of the phenological trait. We applied the NSE to real data for cultivated rice (Oryza sativa L.): days to heading (DH) as a phenological trait and culm length (CL) as the influenced trait. This showed that CL of the cultivars that showed extremely early heading was shortened by the strong influence of DH. In a simulation study, it was shown that the NSE was able to infer the nonlinear influence and direct genetic effects with reasonable accuracy. However, the NSE failed to infer the linear influence in this study. When no influence was simulated, an ordinary bi-trait linear model (OLM) tended to infer the genetic effects more accurately. In such cases, however, by comparing the NSE and OLM using an information criterion, we could assess whether the nonlinear assumption of the NSE was appropriate for the data analyzed. This study demonstrates the usefulness of the NSE in revealing the phenotypic influence of phenological traits.

  11. The SSR-based molecular profile of 1005 grapevine (Vitis vinifera L.) accessions uncovers new synonymy and parentages, and reveals a large admixture amongst varieties of different geographic origin.

    Science.gov (United States)

    Cipriani, Guido; Spadotto, Alessandro; Jurman, Irena; Di Gaspero, Gabriele; Crespan, Manna; Meneghetti, Stefano; Frare, Enrica; Vignani, Rita; Cresti, Mauro; Morgante, Michele; Pezzotti, Mario; Pe, Enrico; Policriti, Alberto; Testolin, Raffaele

    2010-11-01

    A collection of 1005 grapevine accessions was genotyped at 34 microsatellite loci (SSR) with the aim of analysing genetic diversity and exploring parentages. The comparison of molecular profiles revealed 200 groups of synonymy. The removal of perfect synonyms reduced the database to 745 unique genotypes, on which population genetic parameters were calculated. The analysis of kinship uncovered 74 complete pedigrees, with both parents identified. Many of these parentages were not previously known and are of considerable historical interest, e.g. Chenin blanc (Sauvignon × Traminer rot), Covè (Harslevelu selfed), Incrocio Manzoni 2-14 and 2-15 (Cabernet franc × Prosecco), Lagrein (Schiava gentile × Teroldego), Malvasia nera of Bolzano (Perera × Schiava gentile), Manzoni moscato (Raboso veronese × Moscato d'Amburgo), Moscato violetto (Moscato bianco × Duraguzza), Muscat of Alexandria (Muscat blanc à petit grain × Axina de tres bias) and others. Statistical robustness of unexpected pedigrees was reinforced with the analysis of an additional 7-30 SSRs. Grouping the accessions by profile resulted in a weak correlation with their geographical origin and/or current area of cultivation, revealing a large admixture of local varieties with those most widely cultivated, as a result of ancient commerce and population flow. The SSRs with tri- to penta-nucleotide repeats adopted for the present study showed a great capacity for discriminating amongst accessions, with probabilities of identity by chance as low as 1.45 × 10(-27) and 9.35 × 10(-12) for unrelated and full sib individuals, respectively. A database of allele frequencies and SSR profiles of 32 reference cultivars are provided. PMID:20689905

  12. Revelando sentidos na prática docente: a abordagem de corpus na análise do discurso Uncovering meanings in pedagogical practice: the corpus approach in discourse analysis

    Directory of Open Access Journals (Sweden)

    Vander Viana

    2011-01-01

    Full Text Available Este artigo discute a viabilidade da utilização de ferramentas da Linguística de Corpus na análise do discurso pedagógico. Para tanto, são apresentados dois estudos de caso. O primeiro focaliza o discurso de professores de língua inglesa de um renomado curso de idiomas do Rio de Janeiro acerca da implementação de recursos tecnológicos na sala de aula. O segundo estudo, por sua vez, busca perceber qual é o posicionamento de professores universitários de literaturas em língua inglesa sobre literatura e seu ensino. Os resultados apontam para a riqueza dos dados contextuais que podem ser depreendidos a partir de uma análise linguística de base empírica. Em última análise, o artigo revela a importância e a flexibilidade da abordagem de corpus na análise do discurso, que pode ser aplicada a inúmeros contextos.This paper discusses the feasibility of using Corpus Linguistics tools in the analysis of pedagogic discourse. For doing this, two case studies are presented. The first one focuses on the discourse of English language teachers of a well-known languages course in Rio de Janeiro about the implementation of technological resources in the classroom. The second study, in its turn, seeks to realize the position held by university professors of literatures in English language with regard to literature and its teaching. The results point out to the richness of contextual data which can be inferred from a linguistic analysis with an empirical basis. All in all, the paper uncovers the importance and flexibility of the corpus approach in discourse analysis, which may be applied to several contexts.

  13. Tensor GSVD of patient- and platform-matched tumor and normal DNA copy-number profiles uncovers chromosome arm-wide patterns of tumor-exclusive platform-consistent alterations encoding for cell transformation and predicting ovarian cancer survival.

    Science.gov (United States)

    Sankaranarayanan, Preethi; Schomay, Theodore E; Aiello, Katherine A; Alter, Orly

    2015-01-01

    The number of large-scale high-dimensional datasets recording different aspects of a single disease is growing, accompanied by a need for frameworks that can create one coherent model from multiple tensors of matched columns, e.g., patients and platforms, but independent rows, e.g., probes. We define and prove the mathematical properties of a novel tensor generalized singular value decomposition (GSVD), which can simultaneously find the similarities and dissimilarities, i.e., patterns of varying relative significance, between any two such tensors. We demonstrate the tensor GSVD in comparative modeling of patient- and platform-matched but probe-independent ovarian serous cystadenocarcinoma (OV) tumor, mostly high-grade, and normal DNA copy-number profiles, across each chromosome arm, and combination of two arms, separately. The modeling uncovers previously unrecognized patterns of tumor-exclusive platform-consistent co-occurring copy-number alterations (CNAs). We find, first, and validate that each of the patterns across only 7p and Xq, and the combination of 6p+12p, is correlated with a patient's prognosis, is independent of the tumor's stage, the best predictor of OV survival to date, and together with stage makes a better predictor than stage alone. Second, these patterns include most known OV-associated CNAs that map to these chromosome arms, as well as several previously unreported, yet frequent focal CNAs. Third, differential mRNA, microRNA, and protein expression consistently map to the DNA CNAs. A coherent picture emerges for each pattern, suggesting roles for the CNAs in OV pathogenesis and personalized therapy. In 6p+12p, deletion of the p21-encoding CDKN1A and p38-encoding MAPK14 and amplification of RAD51AP1 and KRAS encode for human cell transformation, and are correlated with a cell's immortality, and a patient's shorter survival time. In 7p, RPA3 deletion and POLD2 amplification are correlated with DNA stability, and a longer survival. In Xq, PABPC5

  14. Tensor GSVD of patient- and platform-matched tumor and normal DNA copy-number profiles uncovers chromosome arm-wide patterns of tumor-exclusive platform-consistent alterations encoding for cell transformation and predicting ovarian cancer survival.

    Directory of Open Access Journals (Sweden)

    Preethi Sankaranarayanan

    Full Text Available The number of large-scale high-dimensional datasets recording different aspects of a single disease is growing, accompanied by a need for frameworks that can create one coherent model from multiple tensors of matched columns, e.g., patients and platforms, but independent rows, e.g., probes. We define and prove the mathematical properties of a novel tensor generalized singular value decomposition (GSVD, which can simultaneously find the similarities and dissimilarities, i.e., patterns of varying relative significance, between any two such tensors. We demonstrate the tensor GSVD in comparative modeling of patient- and platform-matched but probe-independent ovarian serous cystadenocarcinoma (OV tumor, mostly high-grade, and normal DNA copy-number profiles, across each chromosome arm, and combination of two arms, separately. The modeling uncovers previously unrecognized patterns of tumor-exclusive platform-consistent co-occurring copy-number alterations (CNAs. We find, first, and validate that each of the patterns across only 7p and Xq, and the combination of 6p+12p, is correlated with a patient's prognosis, is independent of the tumor's stage, the best predictor of OV survival to date, and together with stage makes a better predictor than stage alone. Second, these patterns include most known OV-associated CNAs that map to these chromosome arms, as well as several previously unreported, yet frequent focal CNAs. Third, differential mRNA, microRNA, and protein expression consistently map to the DNA CNAs. A coherent picture emerges for each pattern, suggesting roles for the CNAs in OV pathogenesis and personalized therapy. In 6p+12p, deletion of the p21-encoding CDKN1A and p38-encoding MAPK14 and amplification of RAD51AP1 and KRAS encode for human cell transformation, and are correlated with a cell's immortality, and a patient's shorter survival time. In 7p, RPA3 deletion and POLD2 amplification are correlated with DNA stability, and a longer survival

  15. 石门揭露突出煤层冻结温度场的实验研究%Experimental study of freezing temperature field in uncovering outburst coal seam in cross-cut

    Institute of Scientific and Technical Information of China (English)

    冯涛; 谢雄刚; 刘河清

    2011-01-01

    针对新提出的石门揭煤注液冻结防突方法,设计了室内水泥槽模型煤体冻结实验,分析了注液冻结后水泥槽中煤体温度、物理力学性能与冻结时间的关系。实验表明:槽中煤体形成以冻结管中心为圆心、半径为R沿径向随时间扩展的冻煤圆柱。槽中煤、瓦斯和水三相体最终变成坚硬冻结体,极大提高了其抗压强度和弹性模量等力学性能。实验论证了注液冻结石门揭煤工作面冻结区的形成,距离冻结管越近,煤体温度越低,最终能降到石门揭煤防突工程所需的-15℃煤层控制温度。%Aiming at a new-presented proof-outburst method by injecting liquid and freezing in uncovering coal seam in cross-cut,designed the coal freezing experimentation in cement trough model,analyzed the relation between the coal temperature,mechanical property and freezing time.Through the coal freezing experimentation in cement trough model,it shows that the freezing section,whose radius is R,is revolved around the freezing tube centre.The formed frozen coal column is patulous with the freezing time.The coal,gas,and water in the trough is frozen into the firm freezing structure finally,so the uniaxial compression strengths and elastic modulus of coal models and the other mechanical property are greatly increased.Through the experiment it proved the formation of freezing area in the cross-cut working face.The more near to the freezing tube,the more low the coal temperature is,reaching to the frozen control temperature of-15 ℃ for proof-outburst.

  16. Tensor GSVD of Patient- and Platform-Matched Tumor and Normal DNA Copy-Number Profiles Uncovers Chromosome Arm-Wide Patterns of Tumor-Exclusive Platform-Consistent Alterations Encoding for Cell Transformation and Predicting Ovarian Cancer Survival

    Science.gov (United States)

    Sankaranarayanan, Preethi; Schomay, Theodore E.; Aiello, Katherine A.; Alter, Orly

    2015-01-01

    The number of large-scale high-dimensional datasets recording different aspects of a single disease is growing, accompanied by a need for frameworks that can create one coherent model from multiple tensors of matched columns, e.g., patients and platforms, but independent rows, e.g., probes. We define and prove the mathematical properties of a novel tensor generalized singular value decomposition (GSVD), which can simultaneously find the similarities and dissimilarities, i.e., patterns of varying relative significance, between any two such tensors. We demonstrate the tensor GSVD in comparative modeling of patient- and platform-matched but probe-independent ovarian serous cystadenocarcinoma (OV) tumor, mostly high-grade, and normal DNA copy-number profiles, across each chromosome arm, and combination of two arms, separately. The modeling uncovers previously unrecognized patterns of tumor-exclusive platform-consistent co-occurring copy-number alterations (CNAs). We find, first, and validate that each of the patterns across only 7p and Xq, and the combination of 6p+12p, is correlated with a patient’s prognosis, is independent of the tumor’s stage, the best predictor of OV survival to date, and together with stage makes a better predictor than stage alone. Second, these patterns include most known OV-associated CNAs that map to these chromosome arms, as well as several previously unreported, yet frequent focal CNAs. Third, differential mRNA, microRNA, and protein expression consistently map to the DNA CNAs. A coherent picture emerges for each pattern, suggesting roles for the CNAs in OV pathogenesis and personalized therapy. In 6p+12p, deletion of the p21-encoding CDKN1A and p38-encoding MAPK14 and amplification of RAD51AP1 and KRAS encode for human cell transformation, and are correlated with a cell’s immortality, and a patient’s shorter survival time. In 7p, RPA3 deletion and POLD2 amplification are correlated with DNA stability, and a longer survival. In Xq

  17. 全覆膜与非覆膜金属支架治疗胆道恶性梗阻随机对照研究%Covered versus uncovered self-expandable metal stents for malignant biliary obstruction: a randomized, controlled study

    Institute of Scientific and Technical Information of China (English)

    冀明; 王拥军; 李鹏; 吕富靖; 李巍; 张澍田

    2012-01-01

    目的 比较全覆膜金属支架与非覆膜金属支架治疗胆道恶性梗阻的有效性和安全性.方法 2010年10月至2012年8月无法手术根治性切除胆道恶性梗阻病例,随机分为两组,A组置入全覆膜金属支架,B组置入非覆膜金属支架,观察治疗效果及并发症情况.结果 共入组81例患者,其中A组41例,B组40例,两组均成功置入支架,达到有效引流目的.A组支架开放中位时间182.5 d,B组支架开放中位时间195.0 d,两组间支架开放时间差异无统计学意义(P=0.616).A组发生并发症3例(7.3%),B组发生4例(10%).结论 全覆膜金属支架与非覆膜金属支架治疗胆道恶性梗阻均安全有效,通畅时间相似.%Objective To compare therapeutic efficacy and safety of covered and uncovered self-expandable metal stents for malignant biliary obstruction.Methods From October 2010 to August 2012,patients with unresectable malignant biliary obstruction were recruited and divided into 2 groups to receive covered metal stents (group A) or uncovered metal stents (group B).Efficacy and complication of the procedure were compared.Results A total of 81 patients were recruited,with 41 in group A and 40 in group B.Stents were placed successfully in all patients.The median patency time of stent in group A was 182.5 d,which was not significantly different from that of group B (195.0 d,P =0.616).Complications occurred in 3 patients of group A (7.3%) and 4 of group B (10%).Conclusion Covered and uncovered metal stents are both safe and effective for treatment of malignant biliary obstruction with same patency time.

  18. [Studies on the initiation of glycogen metabolism in Escherichia coli (author's transl)].

    Science.gov (United States)

    Barengo, R; Krisman, C R

    1976-01-01

    Glycogen biosynthesis was studied in Escherichia coli. An enzyme complex composed of UDP-glucose; protein glucosyltransferase, ADP-glucose: protein glucosyltransferase and ADP-glucose: alpha-1,4 glucan alpha-4-glucosyltransferase was found. Further results revealed that while glycogen concentration remained unchanged, the specific activity of the glucosyltransferase complex increased during the growth phase of the culture. The detergents Lubrol and Brij provoked a decrease of 80% and 20% in the glucose transfer to protein from ADP-glucose and UDP-glucose, respectively. These detergents did not inhibit the glucose incorporation into glycogen by ADP-glucose: alpha-1,4-glucosyltransferase. We postulated that the biosynthesis of glycogen in Escherichia coli could be initiated by two different enzymes which catalyze the transfer of glucose from UDP-glucose or ADP-glucose to an acceptor protien. In a second step, the glucan protein formed is used as primer by the ADP-glucose: alpha-1,4 glucan alpha-1-glucosyltransferase for glycogen formation.

  19. GlgS, described previously as a glycogen synthesis control protein, negatively regulates motility and biofilm formation in Escherichia coli.

    Science.gov (United States)

    Rahimpour, Mehdi; Montero, Manuel; Almagro, Goizeder; Viale, Alejandro M; Sevilla, Ángel; Cánovas, Manuel; Muñoz, Francisco J; Baroja-Fernández, Edurne; Bahaji, Abdellatif; Eydallin, Gustavo; Dose, Hitomi; Takeuchi, Rikiya; Mori, Hirotada; Pozueta-Romero, Javier

    2013-06-15

    Escherichia coli glycogen metabolism involves the regulation of glgBXCAP operon expression and allosteric control of the GlgC [ADPG (ADP-glucose) pyrophosphorylase]-mediated catalysis of ATP and G1P (glucose-1-phosphate) to ADPG linked to glycogen biosynthesis. E. coli glycogen metabolism is also affected by glgS. Though the precise function of the protein it encodes is unknown, its deficiency causes both reduced glycogen content and enhanced levels of the GlgC-negative allosteric regulator AMP. The transcriptomic analyses carried out in the present study revealed that, compared with their isogenic BW25113 wild-type strain, glgS-null (ΔglgS) mutants have increased expression of the operons involved in the synthesis of type 1 fimbriae adhesins, flagella and nucleotides. In agreement, ΔglgS cells were hyperflagellated and hyperfimbriated, and displayed elevated swarming motility; these phenotypes all reverted to the wild-type by ectopic glgS expression. Also, ΔglgS cells accumulated high colanic acid content and displayed increased ability to form biofilms on polystyrene surfaces. F-driven conjugation based on large-scale interaction studies of glgS with all the non-essential genes of E. coli showed that deletion of purine biosynthesis genes complement the glycogen-deficient, high motility and high biofilm content phenotypes of ΔglgS cells. Overall the results of the present study indicate that glycogen deficiency in ΔglgS cells can be ascribed to high flagellar propulsion and high exopolysaccharide and purine nucleotides biosynthetic activities competing with GlgC for the same ATP and G1P pools. Supporting this proposal, glycogen-less ΔglgC cells displayed an elevated swarming motility, and accumulated high levels of colanic acid and biofilm. Furthermore, glgC overexpression reverted the glycogen-deficient, high swarming motility, high colanic acid and high biofilm content phenotypes of ΔglgS cells to the wild-type. As on the basis of the present study Glg

  20. Defects in leaf carbohydrate metabolism compromise acclimation to high light and lead to a high chlorophyll fluorescence phenotype in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Schmitz Jessica

    2012-01-01

    Full Text Available Abstract Background We have studied the impact of carbohydrate-starvation on the acclimation response to high light using Arabidopsis thaliana double mutants strongly impaired in the day- and night path of photoassimilate export from the chloroplast. A complete knock-out mutant of the triose phosphate/phosphate translocator (TPT; tpt-2 mutant was crossed to mutants defective in (i starch biosynthesis (adg1-1, pgm1 and pgi1-1; knock-outs of ADP-glucose pyrophosphorylase, plastidial phosphoglucomutase and phosphoglucose isomerase or (ii starch mobilization (sex1-3, knock-out of glucan water dikinase as well as in (iii maltose export from the chloroplast (mex1-2. Results All double mutants were viable and indistinguishable from the wild type when grown under low light conditions, but - except for sex1-3/tpt-2 - developed a high chlorophyll fluorescence (HCF phenotype and growth retardation when grown in high light. Immunoblots of thylakoid proteins, Blue-Native gel electrophoresis and chlorophyll fluorescence emission analyses at 77 Kelvin with the adg1-1/tpt-2 double mutant revealed that HCF was linked to a specific decrease in plastome-encoded core proteins of both photosystems (with the exception of the PSII component cytochrome b559, whereas nuclear-encoded antennae (LHCs accumulated normally, but were predominantly not attached to their photosystems. Uncoupled antennae are the major cause for HCF of dark-adapted plants. Feeding of sucrose or glucose to high light-grown adg1-1/tpt-2 plants rescued the HCF- and growth phenotypes. Elevated sugar levels induce the expression of the glucose-6-phosphate/phosphate translocator2 (GPT2, which in principle could compensate for the deficiency in the TPT. A triple mutant with an additional defect in GPT2 (adg1-1/tpt-2/gpt2-1 exhibited an identical rescue of the HCF- and growth phenotype in response to sugar feeding as the adg1-1/tpt-2 double mutant, indicating that this rescue is independent from the

  1. A diagnostic trap potentially lethal: chordomas uncovered by C3 large osseous destruction inconspicuous on bis-phosphonates-({sup 99}Tc) bone scintigraphy; Un piege diagnostique potentiellement letal: chordome revele par une vaste lesion lytique de C3 normofixante a la scintigraphie osseuse aux bisphosphonates-({sup 99}Tc)

    Energy Technology Data Exchange (ETDEWEB)

    Paycha, F.; Ramadan, A.; Akrout, L. [Hopital Louis Mourier, Unite de Medecine Nucleaire, 92 - Colombes (France); Dion, E. [Hopital Louis Mourier, Service de Radiologie, 92 - Colombes (France); Grossin, M. [Hopital Louis Mourier, Service d' Anatomie Pathologique, 92 - Colombes (France); Gazals-Hatem, D. [Hopital Beaujon, Service d' Anatomie Pathologique, 92 - Clichy (France)

    2006-07-15

    The authors describe a case report of a brachialgy uncovering a solitary bone destruction of C3 associated with epidural involvement. CT and MRI properly depicted the lesion and the loco-regional extension but failed to entertain the diagnosis of the causative tumor, a chordoma. Bis-phosphonates-({sup 99m}Tc) bone scintigraphy proved unconspicuous. Diagnosis was eventually established from the resection specimen, after decision of C3 spondyl-ectomy, C4 hemi-superior spondyl-ectomy and epidural extension excision. Immunohistochemistry study of the material was decisive in identifying the tumor. Cervical chordoma is a tricky diagnosis. Discussion underscores that the crux of diagnostic process is the double discrepancy firstly between extra-osseous and intra-osseous tumoral expansion, secondly between large tumoral mass obvious on multi-slice morphological imaging and negativity of bone scintigraphy, SPECT study included. Among the armamentarium of conventional scintigraphies and PET studies, methionine-({sup 11}C) PET emerges as the most promising anatomo-metabolic procedure to assess loco-regional tumoral expansion, tumoral viability, therapy efficiency, and, potentially, to search for metastases in chordoma. (author)

  2. Uncovering the roles of PINK1 and parkin in mitophagy

    OpenAIRE

    Matsuda, Noriyuki; Tanaka, Keiji

    2010-01-01

    Parkinson disease (PD) is the second most prevalent neurodegenerative disorder, and thus elucidation of the pathogenic mechanism and establishment of a fundamental cure is essential in terms of public welfare. Fortunately, our understanding of the pathogenesis of two types of recessive familial PDs—early-onset familial PD caused by dysfunction of the PTEN-induced putative kinase 1 (PINK1) gene and autosomal recessive juvenile Parkinsonism (ARJP) caused by a mutation in the Parkin gene—has evo...

  3. Temperature stress and plant sexual reproduction: uncovering the weakest links.

    Science.gov (United States)

    Zinn, Kelly E; Tunc-Ozdemir, Meral; Harper, Jeffrey F

    2010-04-01

    The reproductive (gametophytic) phase in flowering plants is often highly sensitive to hot or cold temperature stresses, with even a single hot day or cold night sometimes being fatal to reproductive success. This review describes studies of temperature stress on several crop plants, which suggest that pollen development and fertilization may often be the most sensitive reproductive stage. Transcriptome and proteomic studies on several plant species are beginning to identify stress response pathways that function during pollen development. An example is provided here of genotypic differences in the reproductive stress tolerance between two ecotypes of Arabidopsis thaliana Columbia (Col) and Hilversum (Hi-0), when reproducing under conditions of hot days and cold nights. Hi-0 exhibited a more severe reduction in seed set, correlated with a reduction in pollen tube growth potential and tropism defects. Hi-0 thus provides an Arabidopsis model to investigate strategies for improved stress tolerance in pollen. Understanding how different plants cope with stress during reproductive development offers the potential to identify genetic traits that could be manipulated to improve temperature tolerance in selected crop species being cultivated in marginal climates.

  4. Uncovering the essential links in online commercial networks

    Science.gov (United States)

    Zeng, Wei; Fang, Meiling; Shao, Junming; Shang, Mingsheng

    2016-09-01

    Recommender systems are designed to effectively support individuals' decision-making process on various web sites. It can be naturally represented by a user-object bipartite network, where a link indicates that a user has collected an object. Recently, research on the information backbone has attracted researchers' interests, which is a sub-network with fewer nodes and links but carrying most of the relevant information. With the backbone, a system can generate satisfactory recommenda- tions while saving much computing resource. In this paper, we propose an enhanced topology-aware method to extract the information backbone in the bipartite network mainly based on the information of neighboring users and objects. Our backbone extraction method enables the recommender systems achieve more than 90% of the accuracy of the top-L recommendation, however, consuming only 20% links. The experimental results show that our method outperforms the alternative backbone extraction methods. Moreover, the structure of the information backbone is studied in detail. Finally, we highlight that the information backbone is one of the most important properties of the bipartite network, with which one can significantly improve the efficiency of the recommender system.

  5. Uncovering MIT wind myths through micro-climatological CFD analysis

    CERN Document Server

    Kalmikov, Alexander

    2013-01-01

    Popular campus myths of unusually strong pedestrian level winds are investigated with a Computational Fluid Dynamics (CFD) approach. The numerical simulations confirm the existence of the reported phenomena and provide a qualitative explanation of their physical mechanisms.

  6. Book Review, Waste: Uncovering the Global Food Scandal

    Science.gov (United States)

    Could curbing food waste significantly reduce world hunger and environmental pressures? Tristram Stuart argues cogently that it could in his book Waste, which details the global food-waste scandal and delves into questions such as how much food is available globally? How much is needed and used, a...

  7. Scratching below the surface to uncover HRM practices in Denmark

    DEFF Research Database (Denmark)

    Jørgensen, Frances; Ulhøi, John Parm

    2010-01-01

    Is HRM in Denmark behind the times and only now beginning to be prioritized by Danish firms? Or is it possible that managers are successfully capitalizing on characteristics of the Danish society and the Danish workforce? We propose quite adamantly that HRM practices indeed are alive in Danish fi...

  8. Uncovering Portuguese teachers’ difficulties in implementing sciences curriculum

    Directory of Open Access Journals (Sweden)

    Clara Vasconcelos

    2015-12-01

    Full Text Available Many countries recognize the positive and effective results of improving science education through the introduction of reforms in the sciences curriculum. However, some important issues are generally neglected like, for example, the involvement of the teachers in the reform process. Taking the sciences curriculum reform under analysis and benefitting from 10 years of teachers’ experiences in teaching sciences based on this curriculum, 19 semi-structure interviews were applied so as to identify the major difficulties felt by science teachers when implementing the Portuguese sciences curriculum in the third cycle of middle school (pupils’ age range of 12–15. Some of the difficulties depicted by the data analysis include: length of the curriculum, lack of time, unsuitable laboratory facilities, insufficient means and materials for experimental work, pupils’ indiscipline and little interest in learning sciences. Although less frequently mentioned, the lack of professional development was also referred to as a constraint that seems to play an essential role in this process. Some recommendations for improving the success of sciences curriculum reforms’ implementation are given: defining and conceptualizing curricular policies by relating the reality of both the schools and the science classrooms; reorganizing and restructuring pre-service teachers’ courses; organizing professional development courses for in-service teachers.

  9. Ellis-van Creveld Syndrome: Mutations Uncovered in Lebanese Families

    Directory of Open Access Journals (Sweden)

    Maria Valencia

    2015-01-01

    Full Text Available Background. Ellis-van Creveld (EvC syndrome is a rare, autosomal recessive disorder characterized by short stature, short limbs, growth retardation, polydactyly, and ectodermal defects with cardiac anomalies occurring in around 60% of cases. EVC syndrome has been linked to mutations in EVC and EVC2 genes. Case Presentation. We report EvC syndrome in two unrelated Lebanese families both having homozygous mutations in the EVC2 gene, c.2653C>T (p.(Arg885* and c.2012_2015del (p.(Leu671* in exons 15 and 13, respectively, with the latter being reported for the first time. Conclusion. Although EvC has been largely described in the medical literature, clinical features of this syndrome vary. While more research is required to explore other genes involved in EvC, early diagnosis and therapeutic care are important to achieve a better quality of life.

  10. Ellis-van Creveld Syndrome: Mutations Uncovered in Lebanese Families.

    Science.gov (United States)

    Valencia, Maria; Tabet, Lara; Yazbeck, Nadine; Araj, Alia; Ruiz-Perez, Victor L; Charaffedine, Khalil; Fares, Farah; Badra, Rebecca; Farra, Chantal

    2015-01-01

    Background. Ellis-van Creveld (EvC) syndrome is a rare, autosomal recessive disorder characterized by short stature, short limbs, growth retardation, polydactyly, and ectodermal defects with cardiac anomalies occurring in around 60% of cases. EVC syndrome has been linked to mutations in EVC and EVC2 genes. Case Presentation. We report EvC syndrome in two unrelated Lebanese families both having homozygous mutations in the EVC2 gene, c.2653C>T (p.(Arg885(*))) and c.2012_2015del (p.(Leu671(*))) in exons 15 and 13, respectively, with the latter being reported for the first time. Conclusion. Although EvC has been largely described in the medical literature, clinical features of this syndrome vary. While more research is required to explore other genes involved in EvC, early diagnosis and therapeutic care are important to achieve a better quality of life.

  11. Uncovering attribute-based determinants of loyalty in cigarette brands

    DEFF Research Database (Denmark)

    Krystallis Krontalis, Athanasios

    2013-01-01

    . Originality/value – Not much research has been done on loyalty within the tobacco category, possibly due to the ethical considerations accompanying managerial suggestions about smoking. The contribution of the present work lies in the provisions of evidence-based insights to help brand managers and other...

  12. Fast and frugal food choices: uncovering individual decision heuristics

    OpenAIRE

    Scheibehenne, Benjamin; Todd, Peter M.; Miesler, Linda

    2007-01-01

    Research on food decision making is often based on the assumption that people take many different aspects into account and weight and add them according to their personally assessed importance. Yet there is a growing body of research suggesting that people's decisions can often be better described by simple heuristics—rules of thumb that people use to make choices based on only a few important pieces of information. To test empirically whether a simple heuristic is able to account for individ...

  13. Laryngopharyngeal reflux COPD to uncover reflux and columnar lined esophagus

    OpenAIRE

    Kristo I; Riegler M; Schoppmann SF

    2015-01-01

    Ivan Kristo, Martin Riegler, Sebastian F Schoppmann Upper-GI-Service, Gastroesophageal Tumor Unit, Department of Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, AustriaWith interest we read the article by Jung et al1 published in the recent issue of the International Journal of Chronic Obstructive Pulmonary Disease. An important finding of the study was the positive correlation between symptoms of gastroesophageal reflux disease (GERD), endoscopic signs for laryng...

  14. Bird embryos uncover homology and evolution of the dinosaur ankle.

    Science.gov (United States)

    Ossa-Fuentes, Luis; Mpodozis, Jorge; Vargas, Alexander O

    2015-11-13

    The anklebone (astragalus) of dinosaurs presents a characteristic upward projection, the 'ascending process' (ASC). The ASC is present in modern birds, but develops a separate ossification centre, and projects from the calcaneum in most species. These differences have been argued to make it non-comparable to dinosaurs. We studied ASC development in six different orders of birds using traditional techniques and spin-disc microscopy for whole-mount immunofluorescence. Unexpectedly, we found the ASC derives from the embryonic intermedium, an ancient element of the tetrapod ankle. In some birds it comes in contact with the astragalus, and, in others, with the calcaneum. The fact that the intermedium fails to fuse early with the tibiale and develops an ossification centre is unlike any other amniotes, yet resembles basal, amphibian-grade tetrapods. The ASC originated in early dinosaurs along changes to upright posture and locomotion, revealing an intriguing combination of functional innovation and reversion in its evolution.

  15. Uncovering the Role of the Methylome in Dementia and Neurodegeneration.

    Science.gov (United States)

    Klein, Hans-Ulrich; De Jager, Philip L

    2016-08-01

    Our understanding of the epigenome has advanced dramatically over the past decade, particularly in terms of DNA methylation, a modification found throughout the genome. Studies of the brain and neurons have outlined an increasingly complex architecture involving not just CG dinucleotide methylation but also methylation of other dinucleotides, and modifications of methylated bases such as 5-hydroxymethylcytosine. Different modifications may play an important role in brain development, function and decline; recent descriptions of the effects of aging and neurodegenerative processes such as Alzheimer disease on methylation profiles have ushered in an era of DNA methylome-wide association studies. Rapidly improving technologies and study designs are returning robust results, and investigations of the human brain's epigenome are increasingly feasible, complementing insights gained from genetic studies. PMID:27423266

  16. Uncovering the dynamics of interaction in development cooperation

    DEFF Research Database (Denmark)

    Fejerskov, Adam Moe; Lundsgaarde, Erik; Cold-Ravnkilde, Signe

    The rising prominence of new state and non-state actors in international politics has stimulated extensive discussion in the social sciences over the last decade and development cooperation has been a central arena for conceptualising the encounter between old and new powers. This working paper...... critically reflects on the substantial body of scholarship that seeks to document the characteristics of new actors in international development and chart the consequences of their engagement for global development governance. This review underlines the importance of questioning the homogeneity of actor...... constellations, relationships and ideas. Specifically, it addresses the extent to which the commonly-used binary concepts of development cooperation provider groups adequately capture relevant distinctions among the actors and add analytical value to research on development cooperation. The paper advocates...

  17. Uncovering spatio-temporal patterns in environmental data

    NARCIS (Netherlands)

    Wachowicz, M.

    2002-01-01

    The integration of data mining and geographic visualization techniques facilitates the identification and the interpretation of spatio-temporal patterns – a process recognized as knowledge construction. Knowledge construction is a dynamic process of manipulating `data' to find, relate, and interpret

  18. HIDDEN WEB EXTRACTOR DYNAMIC WAY TO UNCOVER THE DEEP WEB

    OpenAIRE

    DR. ANURADHA; BABITA AHUJA

    2012-01-01

    In this era of digital tsunami of information on the web, everyone is completely dependent on the WWW for information retrieval. This has posed a challenging problem in extracting relevant data. Traditional web crawlers focus only on the surface web while the deep web keeps expanding behind the scene. The web databases are hidden behind the query interfaces. In this paper, we propose a Hidden Web Extractor (HWE) that can automatically discover and download data from the Hidden Web databases. ...

  19. Uncovering the Genetic Landscape for Multiple Sleep-Wake Traits

    OpenAIRE

    Winrow, Christopher J.; Deanna L Williams; Andrew Kasarskis; Joshua Millstein; Laposky, Aaron D.; Yang, He S.; Karrie Mrazek; Lili Zhou; Owens, Joseph R.; Daniel Radzicki; Fabian Preuss; Schadt, Eric E.; Kazuhiro Shimomura; Martha H Vitaterna; Chunsheng Zhang

    2009-01-01

    Despite decades of research in defining sleep-wake properties in mammals, little is known about the nature or identity of genes that regulate sleep, a fundamental behaviour that in humans occupies about one-third of the entire lifespan. While genome-wide association studies in humans and quantitative trait loci (QTL) analyses in mice have identified candidate genes for an increasing number of complex traits and genetic diseases, the resources and time-consuming process necessary for obtaining...

  20. [Calcium supplementation uncovering lactose intolerance - a case report].

    Science.gov (United States)

    Trifina, Eva; Geissler, Dietmar; Zwettler, Elisabeth; Klaushofer, Klaus; Mikosch, Peter

    2012-03-01

    A 44 yr-old female with osteoporosis had no relevant gastrointestinal symptoms and did not avoid any specific food. However, after prescription of a lactose-rich calcium supplementation, clinical symptoms suspicious for lactose intolerance occurred, which were thereafter confirmed by a lactose tolerance test. Lactose intolerance may present with only slight or subtle symptoms. Drugs containing lactose may induce or increase gastrointestinal symptoms in patients with lactose intolerance. In case of gastrointestinal symptoms occurring after the initiation of drugs containing lactose, the possibility of lactose intolerance should be considered and tested by lactose tolerance test or genetic testing for the LCT (-13910) polymorphism. Due to the prevalence of about 15-25% lactose intolerance in the Austrian population, lactose free drugs should be prescribed as widely as possible.

  1. An improvement of the fast uncovering community algorithm

    International Nuclear Information System (INIS)

    Community detection methods have been used in computer, sociology, physics, biology, and brain information science areas. Many methods are based on the optimization of modularity. The algorithm proposed by Blondel et al. (Blondel V D, Guillaume J L, Lambiotte R and Lefebvre E 2008 J. Stat. Mech. 10 10008) is one of the most widely used methods because of its good performance, especially in the big data era. In this paper we make some improvements to this algorithm in correctness and performance. By tests we see that different node orders bring different performances and different community structures. We find some node swings in different communities that influence the performance. So we design some strategies on the sweeping order of node to reduce the computing cost made by repetition swing. We introduce a new concept of overlapping degree (OV) that shows the strength of connection between nodes. Three improvement strategies are proposed that are based on constant OV, adaptive OV, and adaptive weighted OV, respectively. Experiments on synthetic datasets and real datasets are made, showing that our improved strategies can improve the performance and correctness. (interdisciplinary physics and related areas of science and technology)

  2. Uncovering the Recycling Potential of "New" WEEE in China.

    Science.gov (United States)

    Zeng, Xianlai; Gong, Ruying; Chen, Wei-Qiang; Li, Jinhui

    2016-02-01

    Newly defined categories of WEEE have increased the types of China's regulated WEEE from 5 to 14. Identification of the amounts and valuable-resource components of the "new" WEEE generated is critical to solving the e-waste problem, for both governmental policy decisions and recycling enterprise expansions. This study first estimates and predicts China's new WEEE generation for the period of 2010-2030 using material flow analysis and the lifespan model of the Weibull distribution, then determines the amounts of valuable resources (e.g., base materials, precious metals, and rare-earth minerals) encased annually in WEEE, and their dynamic transfer from in-use stock to waste. Main findings include the following: (i) China will generate 15.5 and 28.4 million tons WEEE in 2020 and 2030, respectively, and has already overtaken the U.S. to become the world's leading producer of e-waste; (ii) among all the types of WEEE, air conditioners, desktop personal computers, refrigerators, and washing machines contribute over 70% of total WEEE by weight. The two categories of EEE-electronic devices and electrical appliances-each contribute about half of total WEEE by weight; (iii) more and more valuable resources have been transferred from in-use products to WEEE, significantly enhancing the recycling potential of WEEE from an economic perspective; and (iv) WEEE recycling potential has been evolving from ∼16 (10-22) billion US$ in 2010, to an anticipated ∼42 (26-58) billion US$ in 2020 and ∼73.4 (44.5-103.4) billion US$ by 2030. All the obtained results can improve the knowledge base for closing the loop of WEEE recycling, and contribute to governmental policy making and the recycling industry's business development.

  3. Uncovering Mass Segregation with Galaxy Analogues in Dark Matter Simulations

    CERN Document Server

    Joshi, Gandhali D; Wadsley, James

    2016-01-01

    We investigate mass segregation in group and cluster environments by identifying galaxy analogues in high-resolution dark matter simulations. Subhalos identified by the AHF and ROCKSTAR halo finders have similar mass functions, independent of resolution, but different radial distributions due to significantly different subhalo hierarchies. We propose a simple way to classify subhalos as galaxy analogues. The radial distributions of galaxy analogues agree well at large halo-centric radii for both AHF and ROCKSTAR but disagree near parent halo centres where the phase-space information used by ROCKSTAR is essential. We see clear mass segregation at small radii (within $0.5\\,r_{vir}$) with average galaxy analogue mass decreasing with radius. Beyond the virial radius, we find a mild trend where the average galaxy analogue mass increases with radius. These mass segregation trends are strongest in small groups and dominated by the segregation of low mass analogues. The lack of mass segregation in massive galaxy anal...

  4. From cellular characteristics to disease diagnosis: uncovering phenotypes with supercells.

    Directory of Open Access Journals (Sweden)

    Julián Candia

    Full Text Available Cell heterogeneity and the inherent complexity due to the interplay of multiple molecular processes within the cell pose difficult challenges for current single-cell biology. We introduce an approach that identifies a disease phenotype from multiparameter single-cell measurements, which is based on the concept of "supercell statistics", a single-cell-based averaging procedure followed by a machine learning classification scheme. We are able to assess the optimal tradeoff between the number of single cells averaged and the number of measurements needed to capture phenotypic differences between healthy and diseased patients, as well as between different diseases that are difficult to diagnose otherwise. We apply our approach to two kinds of single-cell datasets, addressing the diagnosis of a premature aging disorder using images of cell nuclei, as well as the phenotypes of two non-infectious uveitides (the ocular manifestations of Behçet's disease and sarcoidosis based on multicolor flow cytometry. In the former case, one nuclear shape measurement taken over a group of 30 cells is sufficient to classify samples as healthy or diseased, in agreement with usual laboratory practice. In the latter, our method is able to identify a minimal set of 5 markers that accurately predict Behçet's disease and sarcoidosis. This is the first time that a quantitative phenotypic distinction between these two diseases has been achieved. To obtain this clear phenotypic signature, about one hundred CD8(+ T cells need to be measured. Although the molecular markers identified have been reported to be important players in autoimmune disorders, this is the first report pointing out that CD8(+ T cells can be used to distinguish two systemic inflammatory diseases. Beyond these specific cases, the approach proposed here is applicable to datasets generated by other kinds of state-of-the-art and forthcoming single-cell technologies, such as multidimensional mass cytometry, single-cell gene expression, and single-cell full genome sequencing techniques.

  5. Uncovering oral Neisseria tropism and persistence using metagenomic sequencing.

    Science.gov (United States)

    Donati, Claudio; Zolfo, Moreno; Albanese, Davide; Tin Truong, Duy; Asnicar, Francesco; Iebba, Valerio; Cavalieri, Duccio; Jousson, Olivier; De Filippo, Carlotta; Huttenhower, Curtis; Segata, Nicola

    2016-01-01

    Microbial epidemiology and population genomics have previously been carried out near-exclusively for organisms grown in vitro. Metagenomics helps to overcome this limitation, but it is still challenging to achieve strain-level characterization of microorganisms from culture-independent data with sufficient resolution for epidemiological modelling. Here, we have developed multiple complementary approaches that can be combined to profile and track individual microbial strains. To specifically profile highly recombinant neisseriae from oral metagenomes, we integrated four metagenomic analysis techniques: single nucleotide polymorphisms in the clade's core genome, DNA uptake sequence signatures, metagenomic multilocus sequence typing and strain-specific marker genes. We applied these tools to 520 oral metagenomes from the Human Microbiome Project, finding evidence of site tropism and temporal intra-subject strain retention. Although the opportunistic pathogen Neisseria meningitidis is enriched for colonization in the throat, N. flavescens and N. subflava populate the tongue dorsum, and N. sicca, N. mucosa and N. elongata the gingival plaque. The buccal mucosa appeared as an intermediate ecological niche between the plaque and the tongue. The resulting approaches to metagenomic strain profiling are generalizable and can be extended to other organisms and microbiomes across environments. PMID:27572971

  6. Connectionist neuropsychology: uncovering ultimate causes of acquired dyslexia.

    Science.gov (United States)

    Woollams, Anna M

    2014-01-01

    Acquired dyslexia offers a unique window on to the nature of the cognitive and neural architecture supporting skilled reading. This paper provides an integrative overview of recent empirical and computational work on acquired dyslexia within the context of the primary systems framework as implemented in connectionist neuropsychological models. This view proposes that damage to general visual, phonological or semantic processing abilities are the root causes of different forms of acquired dyslexia. Recent case-series behavioural evidence concerning pure alexia, phonological dyslexia and surface dyslexia that supports this perspective is presented. Lesion simulations of these findings within connectionist models of reading demonstrate the viability of this approach. The commitment of such models to learnt representations allows them to capture key aspects of performance in each type of acquired dyslexia, particularly the associated non-reading deficits, the role of relearning and the influence of individual differences in the premorbid state of the reading system. Identification of these factors not only advances our understanding of acquired dyslexia and the mechanisms of normal reading but they are also relevant to the complex interactions underpinning developmental reading disorders.

  7. High-Throughput Screening Uncovers Novel Botulinum Neurotoxin Inhibitor Chemotypes.

    Science.gov (United States)

    Bompiani, Kristin M; Caglič, Dejan; Krutein, Michelle C; Benoni, Galit; Hrones, Morgan; Lairson, Luke L; Bian, Haiyan; Smith, Garry R; Dickerson, Tobin J

    2016-08-01

    Botulism is caused by potent and specific bacterial neurotoxins that infect host neurons and block neurotransmitter release. Treatment for botulism is limited to administration of an antitoxin within a short time window, before the toxin enters neurons. Alternatively, current botulism drug development targets the toxin light chain, which is a zinc-dependent metalloprotease that is delivered into neurons and mediates long-term pathology. Several groups have identified inhibitory small molecules, peptides, or aptamers, although no molecule has advanced to the clinic due to a lack of efficacy in advanced models. Here we used a homogeneous high-throughput enzyme assay to screen three libraries of drug-like small molecules for new chemotypes that modulate recombinant botulinum neurotoxin light chain activity. High-throughput screening of 97088 compounds identified numerous small molecules that activate or inhibit metalloprotease activity. We describe four major classes of inhibitory compounds identified, detail their structure-activity relationships, and assess their relative inhibitory potency. A previously unreported chemotype in any context of enzyme inhibition is described with potent submicromolar inhibition (Ki = 200-300 nM). Additional detailed kinetic analyses and cellular cytotoxicity assays indicate the best compound from this series is a competitive inhibitor with cytotoxicity values around 4-5 μM. Given the potency and drug-like character of these lead compounds, further studies, including cellular activity assays and DMPK analysis, are justified. PMID:27314875

  8. Uncovering Substance: Teaching Revision in High School Classrooms

    Science.gov (United States)

    Early, Jessica Singer; Saidy, Christina

    2014-01-01

    This article shares the process and outcomes from a three-day revision workshop designed and implemented in a diverse high school language arts classroom. The revision workshop included: direct instruction, self-reflection, and peer feedback to provide struggling writers with opportunities to take part in substantive revision. The authors examine…

  9. Quantitative approaches to uncover physical mechanisms of tissue morphogenesis

    Science.gov (United States)

    Gleghorn, Jason P.; Manivannan, Sriram; Nelson, Celeste M.

    2013-01-01

    Morphogenesis, the creation of tissue and organ architecture, is a series of complex and dynamic processes driven by genetic programs, microenvironmental cues, and intercellular interactions. Elucidating the physical mechanisms that generate tissue form is key to understanding development, disease, and the strategies needed for regenerative therapies. Advancements in imaging technologies, genetic recombination techniques, laser ablation, and microfabricated tissue models have enabled quantitative descriptions of the cellular motions and tissue deformations and stresses with unprecedented temporal and spatial resolution. Using these data synergistically with increasingly more sophisticated physical, mathematical, and computational models will unveil the physical mechanisms that drive morphogenesis. PMID:23647971

  10. Diabetes insipidus uncovered during conservative management of complicated acute appendicitis

    OpenAIRE

    Mamtani, Anita; Odom, Stephen R.; Butler, Kathryn L.

    2016-01-01

    Key Clinical Message Diabetes insipidus (DI) arises from impaired function of antidiuretic hormone, characterized by hypovolemia, hypernatremia, polyuria, and polydipsia. This case is a reminder of the rare but challenging obstacle that undiagnosed DI poses in fasting surgical patients, requiring prompt recognition and vigilant management of marked homeostatic imbalances.

  11. Diabetes insipidus uncovered during conservative management of complicated acute appendicitis.

    Science.gov (United States)

    Mamtani, Anita; Odom, Stephen R; Butler, Kathryn L

    2016-05-01

    Diabetes insipidus (DI) arises from impaired function of antidiuretic hormone, characterized by hypovolemia, hypernatremia, polyuria, and polydipsia. This case is a reminder of the rare but challenging obstacle that undiagnosed DI poses in fasting surgical patients, requiring prompt recognition and vigilant management of marked homeostatic imbalances. PMID:27190614

  12. Unique small RNA signatures uncovered in the tammar wallaby genome

    Directory of Open Access Journals (Sweden)

    Lindsay James

    2012-10-01

    Full Text Available Abstract Background Small RNAs have proven to be essential regulatory molecules encoded within eukaryotic genomes. These short RNAs participate in a diverse array of cellular processes including gene regulation, chromatin dynamics and genome defense. The tammar wallaby, a marsupial mammal, is a powerful comparative model for studying the evolution of regulatory networks. As part of the genome sequencing initiative for the tammar, we have explored the evolution of each of the major classes of mammalian small RNAs in an Australian marsupial for the first time, including the first genome-scale analysis of the newest class of small RNAs, centromere repeat associated short interacting RNAs (crasiRNAs. Results Using next generation sequencing, we have characterized the major classes of small RNAs, micro (mi RNAs, piwi interacting (pi RNAs, and the centromere repeat associated short interacting (crasi RNAs in the tammar. We examined each of these small RNA classes with respect to the newly assembled tammar wallaby genome for gene and repeat features, salient features that define their canonical sequences, and the constitution of both highly conserved and species-specific members. Using a combination of miRNA hairpin predictions and co-mapping with miRBase entries, we identified a highly conserved cluster of miRNA genes on the X chromosome in the tammar and a total of 94 other predicted miRNA producing genes. Mapping all miRNAs to the tammar genome and comparing target genes among tammar, mouse and human, we identified 163 conserved target genes. An additional nine genes were identified in tammar that do not have an orthologous miRNA target in human and likely represent novel miRNA-regulated genes in the tammar. A survey of the tammar gonadal piRNAs shows that these small RNAs are enriched in retroelements and carry members from both marsupial and tammar-specific repeat classes. Lastly, this study includes the first in-depth analyses of the newly discovered crasiRNAs. These small RNAs are derived largely from centromere-enriched retroelements, including a novel SINE. Conclusions This study encompasses the first analyses of the major classes of small RNAs for the newly completed tammar genome, validates preliminary annotations using deep sequencing and computational approaches, and provides a foundation for future work on tammar-specific as well as conserved, but previously unknown small RNA progenitors and targets identified herein. The characterization of new miRNA target genes and a unique profile for crasiRNAs has allowed for insight into multiple RNA mediated processes in the tammar, including gene regulation, species incompatibilities, centromere and chromosome function.

  13. Uncovering light scalars with exotic Higgs decays to bbmumu

    CERN Document Server

    Curtin, David; Zhong, Yi-Ming

    2014-01-01

    The search for exotic Higgs decays are an essential probe of new physics. In particular, the small width of the Higgs boson makes its decay uniquely sensitive to the existence of light hidden sectors. Here we assess the potential of an exotic Higgs decay search for h -> 2X -> bbmumu to constrain theories with light CP-even (X = s) and CP-odd (X = a) singlet scalars in the mass range of 15 to 60 GeV. This decay channel arises naturally in many scenarios, such as the Standard Model augmented with a singlet, the two-Higgs-doublet model with a singlet (2HDM+S) -- which includes the Next-to-Minimal Supersymmetric Standard Model (NMSSM) -- and in hidden valley models. The 2b2mu channel may represent the best discovery avenue for many models. It has competitive reach, and is less reliant on low-pT b- and tau-reconstruction compared to other channels like 4b, 4tau, and 2tau2mu. We analyze the sensitivity of a 2b2mu search for the 8 and 14 TeV LHC, including the HL-LHC. We consider three types of analyses, employing c...

  14. Organisational change: a methodology to uncover the business idea.

    Science.gov (United States)

    Barker, J; Anderson, P

    2001-01-01

    A study was undertaken to identify the "Business Idea", as defined by van der Heijden (1996), in The Family Planning Association of WA Inc (FPWA) which is a Non-Government Organisation (NGO) in Perth, Western Australia. This organisation was chosen as, along with many other NGOs, it was undergoing major changes in its funding, role and required outcomes. A qualitative interpretivist single case study methodology employing grounded theory research principles and methods was used to study the Business Idea framework in this setting. Thirty-four members of FPWA's staff were interviewed and data was managed using NUD*IST4 and Decision Explorer data storage, data retrieval and graphical reproduction facilities. Results indicated that images of the Business Idea model within FPWA were largely consistent across all staff levels excepting members of the Board of Management. Changes within the organisation were impacting heavily on staff, who needed to be assisted over the transitional phase. Strong leadership and corporate direction were identified as essential if the FPWA was to balance the strongly held sense of social justice amongst its staff with a need for greater productivity efficiency and accountability across the organisation. PMID:11496471

  15. Vaporous Marketing: Uncovering Pervasive Electronic Cigarette Advertisements on Twitter.

    Directory of Open Access Journals (Sweden)

    Eric M Clark

    Full Text Available Twitter has become the "wild-west" of marketing and promotional strategies for advertisement agencies. Electronic cigarettes have been heavily marketed across Twitter feeds, offering discounts, "kid-friendly" flavors, algorithmically generated false testimonials, and free samples.All electronic cigarette keyword related tweets from a 10% sample of Twitter spanning January 2012 through December 2014 (approximately 850,000 total tweets were identified and categorized as Automated or Organic by combining a keyword classification and a machine trained Human Detection algorithm. A sentiment analysis using Hedonometrics was performed on Organic tweets to quantify the change in consumer sentiments over time. Commercialized tweets were topically categorized with key phrasal pattern matching.The overwhelming majority (80% of tweets were classified as automated or promotional in nature. The majority of these tweets were coded as commercialized (83.65% in 2013, up to 33% of which offered discounts or free samples and appeared on over a billion twitter feeds as impressions. The positivity of Organic (human classified tweets has decreased over time (5.84 in 2013 to 5.77 in 2014 due to a relative increase in the negative words 'ban', 'tobacco', 'doesn't', 'drug', 'against', 'poison', 'tax' and a relative decrease in the positive words like 'haha', 'good', 'cool'. Automated tweets are more positive than organic (6.17 versus 5.84 due to a relative increase in the marketing words like 'best', 'win', 'buy', 'sale', 'health', 'discount' and a relative decrease in negative words like 'bad', 'hate', 'stupid', 'don't'.Due to the youth presence on Twitter and the clinical uncertainty of the long term health complications of electronic cigarette consumption, the protection of public health warrants scrutiny and potential regulation of social media marketing.

  16. New incompatibilities uncovered using the Promega DNA IQ™ chemistry.

    Science.gov (United States)

    Laurin, Nancy; Célestin, Florence; Clark, Meagan; Wilkinson, Della; Yamashita, Brian; Frégeau, Chantal

    2015-12-01

    Over the years, the Promega DNA IQ™ System was proven an effective technology for the production of clean DNA from a wide variety of casework specimens. The capture of DNA using the DNA IQ™ paramagnetic beads, however, was shown to be affected by a few specific chemicals that could be present on exhibits submitted to the laboratory. In this study, various blood and latent fingerprint enhancement reagents/methods, marker pens and adhesive tapes, applied at the crime scene or in the forensic laboratory on casework exhibits or used to collect biological material, were tested for their compatibility with the DNA IQ™ technology. Although no impact on DNA recovery was observed for most reagents, the MAGNA™ Jet Black fingerprint powder and three 3M Scotch(®) adhesive tapes were shown to severely or completely inhibit DNA binding onto the DNA IQ™ beads. The effect of MAGNA™ Jet Black on DNA recovery could be counteracted by separating the magnetic powder from the lysates by centrifugation or filtration, prior to DNA extraction. High quality STR profiles were obtained from samples subjected to MAGNA™ Jet Black suggesting it does not impact DNA integrity.

  17. Uncovering the Connections Among Sustainability,Governance and GDP

    Institute of Scientific and Technical Information of China (English)

    Tan Xiaomei; Brett Rose

    2007-01-01

    This paper examines the connections among sustainability, governance and GDP, using the data from 123 countries.Sustainability is found to be related with GDP in two contradictory ways. On the one hand, growth in GDP strengthens a nation's ability to maintain favorable environmental conditions into the future. On the other hand, GDP growth is built on more consumption of natural resources, and therefore generates a larger "footprint" on the Earth. Governance plays a key role in sustainable development. However, it is not helping to reduce our footprint on the Earth. In fact, good governance is linked to a larger footprint.This reflects our materialist value and human impulse. When a society prefers the comfort and well-being of human beings to the welfare of its environment, democratic governance might be used as an effective tool against nature.

  18. Bird embryos uncover homology and evolution of the dinosaur ankle

    Science.gov (United States)

    Ossa-Fuentes, Luis; Mpodozis, Jorge; Vargas, Alexander O

    2015-01-01

    The anklebone (astragalus) of dinosaurs presents a characteristic upward projection, the ‘ascending process' (ASC). The ASC is present in modern birds, but develops a separate ossification centre, and projects from the calcaneum in most species. These differences have been argued to make it non-comparable to dinosaurs. We studied ASC development in six different orders of birds using traditional techniques and spin–disc microscopy for whole-mount immunofluorescence. Unexpectedly, we found the ASC derives from the embryonic intermedium, an ancient element of the tetrapod ankle. In some birds it comes in contact with the astragalus, and, in others, with the calcaneum. The fact that the intermedium fails to fuse early with the tibiale and develops an ossification centre is unlike any other amniotes, yet resembles basal, amphibian-grade tetrapods. The ASC originated in early dinosaurs along changes to upright posture and locomotion, revealing an intriguing combination of functional innovation and reversion in its evolution. PMID:26563435

  19. Uncovering the Secret: Medieval Women, Magic and the Other

    Directory of Open Access Journals (Sweden)

    Ludwikowska Joanna

    2015-01-01

    Full Text Available For medieval audiences women occupied a specific, designated cultural area which, while they could freely form it according to their will and nature, was in fact imaginary and immaterial. Women in social, legal, and religious contexts were mostly counted among the receptive, inactive, and non-ruling groups. On both levels, there was a group of features universally defining all women: the strong, virtuous and independent model Aquinas lamented was replaced in real life by the sinful, carnal and weak stereotype, and the erotic, emotional, mysterious, and often wild type present predominantly in literature. Indeed, women were a source of scientific, theological, and cultural fascination because of their uncanny and complex nature, producing both fear and desire of the source and nature of the unattainable and inaccessible femininity. In social contexts, however, the enchantress seems to lose that veil of allure and, instead, is forced to re-define her identity by suppressing, denying, or losing her supernatural features. With the example of Saint Agnes from the South English Legendary Life of Saint Agnes, and Melior from Partonope of Blois (ca. 1450, the article will explore how medieval texts dealt with the complex and unruly female supernatural, and how its neutralization and subduing fitted into the moral, scientific, and cultural norms of medieval society.

  20. Uncovering of melanin fluorescence in human skin tissue

    Science.gov (United States)

    Scholz, Matthias; Stankovic, Goran; Seewald, Gunter; Leupold, Dieter

    2007-07-01

    Due to its extremely low fluorescence quantum yield, in the conventionally (one-photon) excited autofluorescence of skin tissue, melanin fluorescence is masked by several other endogenous and possibly also exogenous fluorophores (e.g. NADH, FAD, Porphyrins). A first step to enhance the melanin contribution had been realized by two-photon fs-pulse excitation in the red/near IR, based on the fact that melanin can be excited by stepwise two-photon absorption, whereas all other fluorophores in this spectral region allow only simultaneous two-photon excitation. Now, the next and decisive step has been realized: Using an extremely sensitive detection system, for the first time twophoton fluorescence of skin tissue excited with pulses in the ns-range could be measured. The motivation for this step was based on the fact that the population density of the fluorescent level resulting from a stepwise excitation has a different dependence of the pulse duration than that from a simultaneous excitation (Δt2 vs. Δt). Due to this strong discrimination between the fluorophores, practically pure melanin fluorescence can be obtained. Examples for in-vivo, ex-vivo as well as paraffin embedded skin tissue will be shown. The content of information with respect to early diagnosis of skin deseases will be discussed.

  1. Uncovering collective listening habits and music genres in bipartite networks

    CERN Document Server

    Lambiotte, R

    2005-01-01

    In this paper, we analyze web-downloaded data on people sharing their music library, that we use as their individual musical signatures (IMS). The system is represented by a bipartite network, nodes being the music groups and the listeners. Music groups audience size behaves like a power law, but the individual music library size is an exponential with deviations at small values. In order to extract structures from the network, we focus on correlation matrices, that we filter by removing the least correlated links. This percolation idea-based method reveals the emergence of social communities and music genres, that are visualised by a branching representation. Evidence of collective listening habits that do not fit the neat usual genres defined by the music industry indicates an alternative way of classifying listeners/music groups. The structure of the network is also studied by a more refined method, based upon a random walk exploration of its properties. Finally, a personal identification - community imita...

  2. Uncovering Cultural Prototypes : Old Men in Japanese Folktales and Culture

    OpenAIRE

    ニコリッチ細中, ネベンカ; ニコリッチホソナカ, ネベンカ; Nevenka, Nikolic Hosonaka

    2004-01-01

    This paper is a progress report on the preliminary stages of a larger project that aims to find out if Japanese children's concepts of old men would change through exposure to the images of old men in Western folktales. It is the old men's characterization that differs most in the two cultures, as seen in traditional folktales. Research showed both Japanese adults' and the 2-3^ graders' familiarity with the folktales representative of the Japanese culture. Their concepts of old men were compa...

  3. Uncovering "Threshold Concepts" in Web Development: An Instructor Perspective

    Science.gov (United States)

    Alston, Peter; Walsh, David; Westhead, Gary

    2015-01-01

    The field of Web development has evolved and diversified significantly in recent years, and narrowing the gap between the requirements of academia and the demands of industry remains a challenge. Moreover, many faculty members often struggle with knowing "how much" of a particular subject they should teach to their students and at what…

  4. Uncovered secret of a Vasseur-Tramond wax model.

    Science.gov (United States)

    Pastor, J F; Gutiérrez, B; Montes, J M; Ballestriero, R

    2016-01-01

    The technique of anatomical wax modelling reached its heyday in Italy during the 18th century, through a fruitful collaboration between sculptors and anatomists. It soon spread to other countries, and prestigious schools were created in England, France, Spain and Austria. Paris subsequently replaced Italy as the major centre of manufacture, and anatomical waxes were created there from the mid-19th century in workshops such as that of Vasseur-Tramond. This workshop began to sell waxes to European Faculties of Medicine and Schools of Surgery around 1880. Little is known of the technique employed in the creation of such artefacts as this was deemed a professional secret. To gain some insight into the methods of construction, we have studied a Vasseur-Tramond wax model in the Valladolid University Anatomy Museum, Spain, by means of multi-slice computerised tomography and X-ray analysis by means of environmental scanning electron microscopy. Scanning electron microscopy was used to examine the hair. These results have revealed some of the methods used to make these anatomical models and the materials employed.

  5. Uncovering the magnetic environment of our solar system

    CERN Document Server

    Ben-Jaffel, Lotfi

    2012-01-01

    Since its formation 4.6 billion years ago, our solar system has most likely crossed numerous magnetized interstellar clouds and bubbles of different sizes and contents on its path through the Milky Way. Having a reference model for how the heliosphere and interstellar winds interact is critical for understanding our current Galactic environment, and it requires untangling the roles of two major actors: the time-variable solar wind and the local interstellar magnetic field. Numerical simulations predict a distortion of the heliosphere caused by both solar wind anisotropy and interstellar magnetic field orientation. However, model comparison to deep space probes' measurements led to contradictory reports by Voyager 1 and Voyager 2 of both several crossings of the solar wind's termination shock and of the strength of the local interstellar field, with values ranging from 1.8 to 5.7 {\\mu}G. Here, we show that Voyager 1 & 2 plasma, fields, and Lyman-{\\alpha} sky background measurements, as well as space observ...

  6. Uncovering the dynamics of interaction in development cooperation

    DEFF Research Database (Denmark)

    Fejerskov, Adam Moe; Lundsgaarde, Erik; Cold-Ravnkilde, Signe

    critically reflects on the substantial body of scholarship that seeks to document the characteristics of new actors in international development and chart the consequences of their engagement for global development governance. This review underlines the importance of questioning the homogeneity of actor......The rising prominence of new state and non-state actors in international politics has stimulated extensive discussion in the social sciences over the last decade and development cooperation has been a central arena for conceptualising the encounter between old and new powers. This working paper...... constellations, relationships and ideas. Specifically, it addresses the extent to which the commonly-used binary concepts of development cooperation provider groups adequately capture relevant distinctions among the actors and add analytical value to research on development cooperation. The paper advocates...

  7. Simplivariate Models: Uncovering the Underlying Biology in Functional Genomics Data

    OpenAIRE

    Edoardo Saccenti; Westerhuis, Johan A.; Smilde, Age K.; van der Werf, Mariët J; Jos A Hageman; Hendriks, Margriet M. W. B.

    2011-01-01

    One of the first steps in analyzing high-dimensional functional genomics data is an exploratory analysis of such data. Cluster Analysis and Principal Component Analysis are then usually the method of choice. Despite their versatility they also have a severe drawback: they do not always generate simple and interpretable solutions. On the basis of the observation that functional genomics data often contain both informative and non-informative variation, we propose a method that finds sets of va...

  8. Uncovering the foundational heritage of Irish occupational therapy

    OpenAIRE

    O'Riordan, Yvonne

    2013-01-01

    non-peer-reviewed Background: This study arose from a wider University of Limerick, Clinical Therapies Departmental project, seeking to plot Irish occupational therapy history. Dr. Eamonn O???Sullivan???s, ??? A Textbook of Occupational Therapy with Chief Reference to Psychological Medicine??? emerged as a primary document outlining occupational therapy in Ireland at the beginning of the 20th Century. Objective: The study aims to identify the philosophical assumptions of occ...

  9. Uncovering Biological Network Function via Graphlet Degree Signatures

    Directory of Open Access Journals (Sweden)

    Nataša Pržulj

    2008-01-01

    Full Text Available Motivation: Proteins are essential macromolecules of life and thus understanding their function is of great importance. The number of functionally unclassified proteins is large even for simple and well studied organisms such as baker’s yeast. Methods for determining protein function have shifted their focus from targeting specific proteins based solely on sequence homology to analyses of the entire proteome based on protein-protein interaction (PPI networks. Since proteins interact to perform a certain function, analyzing structural properties of PPI networks may provide useful clues about the biological function of individual proteins, protein complexes they participate in, and even larger subcellular machines.Results: We design a sensitive graph theoretic method for comparing local structures of node neighborhoods that demonstrates that in PPI networks, biological function of a node and its local network structure are closely related. The method summarizes a protein’s local topology in a PPI network into the vector of graphlet degrees called the signature of the protein and computes the signature similarities between all protein pairs. We group topologically similar proteins under this measure in a PPI network and show that these protein groups belong to the same protein complexes, perform the same biological functions, are localized in the same subcellular compartments, and have the same tissue expressions. Moreover, we apply our technique on a proteome-scale network data and infer biological function of yet unclassified proteins demonstrating that our method can provide valuable guidelines for future experimental research such as disease protein prediction.Availability: Data is available upon request.

  10. Uncovering Concerns with Developing a Scoring System at ETS.

    Science.gov (United States)

    Stires, Susan

    1995-01-01

    Describes an expert panel member's experiences in working with Educational Testing Service to redesign the scoring for the National Board for Professional Teaching Standards Early Adolescence/English Language Arts Assessment. Maintains that a less mechanistic and more valid scoring system could have been developed if criticism and open discussion…

  11. Uncovering urban human mobility from large scale taxi GPS data

    Science.gov (United States)

    Tang, Jinjun; Liu, Fang; Wang, Yinhai; Wang, Hua

    2015-11-01

    Taxi GPS trajectories data contain massive spatial and temporal information of urban human activity and mobility. Taking taxi as mobile sensors, the information derived from taxi trips benefits the city and transportation planning. The original data used in study are collected from more than 1100 taxi drivers in Harbin city. We firstly divide the city area into 400 different transportation districts and analyze the origin and destination distribution in urban area on weekday and weekend. The Density-Based Spatial Clustering of Applications with Noise (DBSCAN) algorithm is used to cluster pick-up and drop-off locations. Furthermore, four spatial interaction models are calibrated and compared based on trajectories in shopping center of Harbin city to study the pick-up location searching behavior. By extracting taxi trips from GPS data, travel distance, time and average speed in occupied and non-occupied status are then used to investigate human mobility. Finally, we use observed OD matrix of center area in Harbin city to model the traffic distribution patterns based on entropy-maximizing method, and the estimation performance verify its effectiveness in case study.

  12. Uncovering the components of the Francisella tularensis Virulence stealth strategy

    Directory of Open Access Journals (Sweden)

    Bradley D Jones

    2014-03-01

    Full Text Available Over the last decade, studies on the virulence of the highly pathogenic intracellular bacterial pathogen Francisella tularensis have increased dramatically. The organism produces an inert LPS, a capsule, escapes the phagosome to grow in the cytosol (encoded by the FPI genes of a variety of host cell types that include epithelial, endothelial, dendritic, macrophage and neutrophil. This review focuses on the work that has identified and characterized individual virulence factors of this organism and we hope to highlight how these factors collectively function to produce the pathogenic strategy of this pathogen. In addition, several recent studies have been published characterizing F. tularensis mutants that induce host immune responses not observed in wild type F. tularensis strains that can induce protection against challenge with virulent F. tularensis. As more detailed studies with attenuated strains are performed, it will be possible to see how host models develop acquired immunity to Francisella. Collectively, detailed insights into the mechanisms of virulence of this pathogen are emerging that will allow the design of anti-infective strategies.

  13. Uncovering Our Feminist Pedagogy: A Co/Autoethnography

    Science.gov (United States)

    Coia, Lesley; Taylor, Monica

    2013-01-01

    What does it mean to be a feminist educator? How would we know if we were? We call ourselves feminist teachers and yet we have not focused on this identification and its influence on our teaching in some time. In this self-study, we set out to look at our practice-using co/autoethnography. As our study progressed, we began to realize that our…

  14. Uncovering Spatial Variation in Acoustic Environments Using Sound Mapping.

    Science.gov (United States)

    Job, Jacob R; Myers, Kyle; Naghshineh, Koorosh; Gill, Sharon A

    2016-01-01

    Animals select and use habitats based on environmental features relevant to their ecology and behavior. For animals that use acoustic communication, the sound environment itself may be a critical feature, yet acoustic characteristics are not commonly measured when describing habitats and as a result, how habitats vary acoustically over space and time is poorly known. Such considerations are timely, given worldwide increases in anthropogenic noise combined with rapidly accumulating evidence that noise hampers the ability of animals to detect and interpret natural sounds. Here, we used microphone arrays to record the sound environment in three terrestrial habitats (forest, prairie, and urban) under ambient conditions and during experimental noise introductions. We mapped sound pressure levels (SPLs) over spatial scales relevant to diverse taxa to explore spatial variation in acoustic habitats and to evaluate the number of microphones needed within arrays to capture this variation under both ambient and noisy conditions. Even at small spatial scales and over relatively short time spans, SPLs varied considerably, especially in forest and urban habitats, suggesting that quantifying and mapping acoustic features could improve habitat descriptions. Subset maps based on input from 4, 8, 12 and 16 microphones differed slightly ( 4 dBA/pixel) from full maps than the remaining subset maps, but maps with input from eight microphones resulted in smaller differences. Thus, acoustic environments varied over small spatial scales and variation could be mapped with input from 4-8 microphones. Mapping sound in different environments will improve understanding of acoustic environments and allow us to explore the influence of spatial variation in sound on animal ecology and behavior. PMID:27467503

  15. A spiral galaxy's mass distribution uncovered through lensing and dynamics

    CERN Document Server

    Trick, Wilma H; Dutton, Aaron A

    2016-01-01

    We investigate the matter distribution of a spiral galaxy with a counter-rotating stellar core, SDSS J1331+3628 (J1331), independently with gravitational lensing and stellar dynamical modelling. By fitting a gravitational potential model to a quadruplet of lensing images around J1331's bulge, we tightly constrain the mass inside the Einstein radius R_ein = (0.91 +/- 0.02)'' (~= 1.83 +/- 0.04 kpc) to within 4%: M_ein = (7.8 +/- 0.3) x 10^10 M_Sun. We model observed long-slit major axis stellar kinematics in J1331's central regions by finding Multi-Gaussian Expansion (MGE) models for the stellar and dark matter distribution that solve the axisymmetric Jeans equations. The lens and dynamical model are independently derived, but in very good agreement with each other around ~R_ein. We find that J1331's center requires a steep total mass-to-light ratio gradient. A dynamical model including an NFW halo (with virial velocity v_200 ~= 240 +/- 40 km/s and concentration c_200 ~= 8 +/- 2) and moderate tangential velocit...

  16. Autism Spectrum Disorder: Uncovering Clues to a Complicated Condition

    Science.gov (United States)

    ... autism. One NIH-funded team found that the brain waves of some 2-year-olds with autism can have a distinctive pattern when they listen to familiar words. The children with ... in the brain region that processes language. Follow-up studies showed ...

  17. Uncovering the Chemistry of Earth-like Planets

    Science.gov (United States)

    Zeng, L.; Jacobsen, S. B.; Sasselov, D. D.

    2015-12-01

    We propose to use the evidence from our solar system to understand exoplanets, and in particular, to predict their surface chemistry and thereby the possibility of life. An Earth-like planet, born from the same nebula as its host star, is composed primarily of silicate rocks and an iron-nickel metal core, and depleted in volatile content in a systematic manner. The more volatile (easier to vaporize or dissociate into gas form) an element is in an Earth-like planet, the more depleted the element is compared to its host star. After depletion, an Earth-like planet would go through the process of core formation due to heat from radioactive decay and collisions. Core formation depletes a planet's rocky mantle of siderophile (iron-loving) elements, in addition to the volatile depletion. After that, Earth-like planets likely accrete some volatile-rich materials, called "late veneer". The late veneer could be essential to the origins of life on Earth and Earth-like planets, as it also delivers the volatiles such as nitrogen, sulfur, carbon and water to the planet's surface, which are crucial for life to occur. Here we build an integrative model of Earth-like planets from the bottom up. Thus the chemical compositions of Earth-like planets could be inferred from their mass-radius relations and their host stars' elemental abundances, and the origins of volatile contents (especially water) on their surfaces could be understood, and thereby shed light on the origins of life on them. This elemental abundance model could be applied to other rocky exoplanets in exoplanet systems.

  18. Hidden Stories: Uncovering the Visual Metaphor for Education and Communication

    Science.gov (United States)

    Hube, Amy M.; Tremblay, Kenneth R., Jr.; Leigh, Katharine E.

    2015-01-01

    Design solutions have become increasingly complex and based on a rapidly growing body of knowledge. In order to articulate a design solution to a client, the graphic use of the design narrative can effectively communicate complex ideas. Two case study interventions were conducted in an interior design program in which students were introduced to…

  19. In the minds of OSCE examiners: uncovering hidden assumptions.

    Science.gov (United States)

    Chahine, Saad; Holmes, Bruce; Kowalewski, Zbigniew

    2016-08-01

    The Objective Structured Clinical Exam (OSCE) is a widely used method of assessment in medical education. Rater cognition has become an important area of inquiry in the medical education assessment literature generally, and in the OSCE literature specifically, because of concerns about potential compromises of validity. In this study, a novel approach to mixed methods that combined Ordinal Logistic Hierarchical Linear Modeling and cognitive interviews was used to gain insights about what examiners were thinking during an OSCE. This study is based on data from the 2010 to 2014 administrations of the Clinician Assessment for Practice Program OSCE for International Medical Graduates (IMGs) in Nova Scotia. An IMG is a physician trained outside of Canada who was a licensed practitioner in a different country. The quantitative data were examined alongside four follow-up cognitive interviews of examiners conducted after the 2014 administration. The quantitative results show that competencies of (1) Investigation and Management and (2) Counseling were highly predictive of the Overall Global score. These competencies were also described in the cognitive interviews as the most salient parts of OSCE. Examiners also found Communication Skills and Professional Behavior to be relevant but the quantitative results revealed these to be less predictive of the Overall Global score. The interviews also reveal that there is a tacit sequence by which IMGs are expected to proceed in an OSCE, starting with more basic competencies such as History Taking and building up to Investigation Management and Counseling. The combined results confirm that a hidden pattern exists with respect to how examiners rate candidates. This study has potential implications for research into rater cognition, and the design and scoring of practice-ready OSCEs. PMID:26661783

  20. Uncovering Metaethical Assumptions in Bioethical Discourse across Cultures.

    Science.gov (United States)

    Sullivan, Laura Specker

    2016-03-01

    Much of bioethical discourse now takes place across cultures. This does not mean that cross-cultural understanding has increased. Many cross-cultural bioethical discussions are marked by entrenched disagreement about whether and why local practices are justified. In this paper, I argue that a major reason for these entrenched disagreements is that problematic metaethical commitments are hidden in these cross-cultural discourses. Using the issue of informed consent in East Asia as an example of one such discourse, I analyze two representative positions in the discussion and identify their metaethical commitments. I suggest that the metaethical assumptions of these positions result from their shared method of ethical justification: moral principlism. I then show why moral principlism is problematic in cross-cultural analyses and propose a more useful method for pursuing ethical justification across cultures.

  1. Uncovering the etiology of conversion disorder: insights from functional neuroimaging

    Directory of Open Access Journals (Sweden)

    Ejareh dar M

    2016-01-01

    Full Text Available Maryam Ejareh dar, Richard AA Kanaan Department of Psychiatry, University of Melbourne, Austin Health, Heidelberg, VIC, Australia Abstract: Conversion disorder (CD is a syndrome of neurological symptoms arising without organic cause, arguably in response to emotional stress, but the exact neural substrates of these symptoms and the underlying mechanisms remain poorly understood with the hunt for a biological basis afoot for centuries. In the past 15 years, novel insights have been gained with the advent of functional neuroimaging studies in patients suffering from CDs in both motor and nonmotor domains. This review summarizes recent functional neuroimaging studies including functional magnetic resonance imaging (fMRI, single photon emission computerized tomography (SPECT, and positron emission tomography (PET to see whether they bring us closer to understanding the etiology of CD. Convergent functional neuroimaging findings suggest alterations in brain circuits that could point to different mechanisms for manifesting functional neurological symptoms, in contrast with feigning or healthy controls. Abnormalities in emotion processing and in emotion-motor processing suggest a diathesis, while differential reactions to certain stressors implicate a specific response to trauma. No comprehensive theory emerges from these clues, and all results remain preliminary, but functional neuroimaging has at least given grounds for hope that a model for CD may soon be found. Keywords: conversion disorder, neuroimaging, functional neurology, hysteria, mechanisms 

  2. Uncovering the etiology of conversion disorder: insights from functional neuroimaging.

    Science.gov (United States)

    Ejareh Dar, Maryam; Kanaan, Richard Aa

    2016-01-01

    Conversion disorder (CD) is a syndrome of neurological symptoms arising without organic cause, arguably in response to emotional stress, but the exact neural substrates of these symptoms and the underlying mechanisms remain poorly understood with the hunt for a biological basis afoot for centuries. In the past 15 years, novel insights have been gained with the advent of functional neuroimaging studies in patients suffering from CDs in both motor and nonmotor domains. This review summarizes recent functional neuroimaging studies including functional magnetic resonance imaging (fMRI), single photon emission computerized tomography (SPECT), and positron emission tomography (PET) to see whether they bring us closer to understanding the etiology of CD. Convergent functional neuroimaging findings suggest alterations in brain circuits that could point to different mechanisms for manifesting functional neurological symptoms, in contrast with feigning or healthy controls. Abnormalities in emotion processing and in emotion-motor processing suggest a diathesis, while differential reactions to certain stressors implicate a specific response to trauma. No comprehensive theory emerges from these clues, and all results remain preliminary, but functional neuroimaging has at least given grounds for hope that a model for CD may soon be found. PMID:26834476

  3. Uncovering the etiology of conversion disorder: insights from functional neuroimaging

    OpenAIRE

    Ejareh dar M; Kanaan RAA

    2016-01-01

    Maryam Ejareh dar, Richard AA Kanaan Department of Psychiatry, University of Melbourne, Austin Health, Heidelberg, VIC, Australia Abstract: Conversion disorder (CD) is a syndrome of neurological symptoms arising without organic cause, arguably in response to emotional stress, but the exact neural substrates of these symptoms and the underlying mechanisms remain poorly understood with the hunt for a biological basis afoot for centuries. In the past 15 years, novel insights have been gained wit...

  4. Uncovering Spatial Variation in Acoustic Environments Using Sound Mapping

    Science.gov (United States)

    Job, Jacob R.; Myers, Kyle; Naghshineh, Koorosh; Gill, Sharon A.

    2016-01-01

    Animals select and use habitats based on environmental features relevant to their ecology and behavior. For animals that use acoustic communication, the sound environment itself may be a critical feature, yet acoustic characteristics are not commonly measured when describing habitats and as a result, how habitats vary acoustically over space and time is poorly known. Such considerations are timely, given worldwide increases in anthropogenic noise combined with rapidly accumulating evidence that noise hampers the ability of animals to detect and interpret natural sounds. Here, we used microphone arrays to record the sound environment in three terrestrial habitats (forest, prairie, and urban) under ambient conditions and during experimental noise introductions. We mapped sound pressure levels (SPLs) over spatial scales relevant to diverse taxa to explore spatial variation in acoustic habitats and to evaluate the number of microphones needed within arrays to capture this variation under both ambient and noisy conditions. Even at small spatial scales and over relatively short time spans, SPLs varied considerably, especially in forest and urban habitats, suggesting that quantifying and mapping acoustic features could improve habitat descriptions. Subset maps based on input from 4, 8, 12 and 16 microphones differed slightly ( 4 dBA/pixel) from full maps than the remaining subset maps, but maps with input from eight microphones resulted in smaller differences. Thus, acoustic environments varied over small spatial scales and variation could be mapped with input from 4–8 microphones. Mapping sound in different environments will improve understanding of acoustic environments and allow us to explore the influence of spatial variation in sound on animal ecology and behavior. PMID:27467503

  5. Uncovering Embedded Face Threat Mitigation in Landscape Architecture Critique Feedback

    Science.gov (United States)

    Housley Gaffney, Amy L.

    2015-01-01

    Receiving public feedback on academic work may threaten students' face, particularly when such feedback is critical. One way that feedback may be cushioned is through face-threat mitigation techniques. I analyzed the use of such techniques in the feedback given by faculty and professionals to landscape architecture students as preparation for…

  6. Uncovering growth-suppressive MicroRNAs in lung cancer

    DEFF Research Database (Denmark)

    Liu, Xi; Sempere, Lorenzo F; Galimberti, Fabrizio;

    2009-01-01

    transgenic line (designated as ED-1 and ED-2 cells, respectively). Each highlighted miRNA was independently transfected into these cells. Growth-suppressive mechanisms were explored. Expression of a computationally predicted miRNA target was examined. These miRNAs were studied in a paired normal...... tissues. Individual overexpression of miR-34c, miR-145, and miR-142-5p in ED-1 and ED-2 cells markedly repressed cell growth. Anti-miR cotransfections antagonized this inhibition. The miR-34c target, cyclin E, was repressed by miR-34c transfection and provided a mechanism for observed growth suppression...

  7. Uncovering the features of spin dynamics in hadronic physics

    International Nuclear Information System (INIS)

    We summarize the program pursued by Michael J. Moravicsik and the authors on spin amplitude analyses and interpretation. We present the recent observations that 'phase histograms' reveal striking peaks corresponding to spin amplitudes that tend to have definite simple phase relations. An interpretation is proposed in which the spin amplitudes receive a coherent and an incoherent contribution over large ranges of energies and angles. Continuing research directions are reported. (Authors)

  8. Uncovering the features of spin dynamics in hadronic physics

    Science.gov (United States)

    Goldstein, G. R.; Arash, F.

    1990-06-01

    We summarize the program pursued by Michael J. Moravcsik and the authors on spin amplitude analyses and interpretation. We present the recent observations that “phase histograms” reveal striking peaks corresponding to spin amplitudes that tend to have definite simple phase relations. An interpretation is proposed in which the spin amplitudes receive a coherent and an incoherent contribution over large ranges of energies and angles. Continuing research directions are reported.

  9. Uncovering forbidden optical transitions in PbSe nanocrystals.

    Science.gov (United States)

    Peterson, Jeffrey J; Huang, Libai; Delerue, Christophe; Allan, Guy; Krauss, Todd D

    2007-12-01

    The 1S(h,e)-1P(e,h) exciton transition energy of PbSe nanocrystals was determined via two-photon photoluminescence excitation spectroscopy and was found to be in good agreement with predictions from a tight-binding calculation. The two-photon excitation peak occurs at energies very close to a strong feature in the one-photon absorption spectrum and suggests that it should be assigned as a formally forbidden S-P transition. Leading explanations for the unusual strength of the forbidden transition are discussed.

  10. Uncovering the Recycling Potential of "New" WEEE in China.

    Science.gov (United States)

    Zeng, Xianlai; Gong, Ruying; Chen, Wei-Qiang; Li, Jinhui

    2016-02-01

    Newly defined categories of WEEE have increased the types of China's regulated WEEE from 5 to 14. Identification of the amounts and valuable-resource components of the "new" WEEE generated is critical to solving the e-waste problem, for both governmental policy decisions and recycling enterprise expansions. This study first estimates and predicts China's new WEEE generation for the period of 2010-2030 using material flow analysis and the lifespan model of the Weibull distribution, then determines the amounts of valuable resources (e.g., base materials, precious metals, and rare-earth minerals) encased annually in WEEE, and their dynamic transfer from in-use stock to waste. Main findings include the following: (i) China will generate 15.5 and 28.4 million tons WEEE in 2020 and 2030, respectively, and has already overtaken the U.S. to become the world's leading producer of e-waste; (ii) among all the types of WEEE, air conditioners, desktop personal computers, refrigerators, and washing machines contribute over 70% of total WEEE by weight. The two categories of EEE-electronic devices and electrical appliances-each contribute about half of total WEEE by weight; (iii) more and more valuable resources have been transferred from in-use products to WEEE, significantly enhancing the recycling potential of WEEE from an economic perspective; and (iv) WEEE recycling potential has been evolving from ∼16 (10-22) billion US$ in 2010, to an anticipated ∼42 (26-58) billion US$ in 2020 and ∼73.4 (44.5-103.4) billion US$ by 2030. All the obtained results can improve the knowledge base for closing the loop of WEEE recycling, and contribute to governmental policy making and the recycling industry's business development. PMID:26709550

  11. Uncovering product development competence by applying the laddering technique

    DEFF Research Database (Denmark)

    Jensen, Bjarne; Harmsen, Hanne

    This paper addresses companies' lack of implementation of success factors in new product development. Drawing on theories in the competence perspective and an exploratory empirical study, the paper points to two major areas that have not been covered by previous studies on new product development...

  12. Uncovering the footprints of malicious traffic in cellular data networks

    OpenAIRE

    Raghuramu, A; Zang, H.; Chuah, CN

    2015-01-01

    © Springer International Publishing Switzerland 2015. In this paper, we present a comprehensive characterization of malicious traffic generated by mobile devices using Deep Packet Inspection (DPI) records and security event logs from a large US based cellular provider network. Our analysis reveals that 0.17% of mobile devices in the cellular network are affected by security threats. This proportion, while small, is orders of magnitude higher than the last reported (in 2013) infection rate of ...

  13. Uncovering Oscillations, Complexity, and Chaos in Chemical Kinetics Using Mathematica

    Science.gov (United States)

    Ferreira, M. M. C.; Ferreira, W. C., Jr.; Lino, A. C. S.; Porto, M. E. G.

    1999-06-01

    Unlike reactions with no peculiar temporal behavior, in oscillatory reactions concentrations can rise and fall spontaneously in a cyclic or disorganized fashion. In this article, the software Mathematica is used for a theoretical study of kinetic mechanisms of oscillating and chaotic reactions. A first simple example is introduced through a three-step reaction, called the Lotka model, which exhibits a temporal behavior characterized by damped oscillations. The phase plane method of dynamic systems theory is introduced for a geometric interpretation of the reaction kinetics without solving the differential rate equations. The equations are later numerically solved using the built-in routine NDSolve and the results are plotted. The next example, still with a very simple mechanism, is the Lotka-Volterra model reaction, which oscillates indefinitely. The kinetic process and rate equations are also represented by a three-step reaction mechanism. The most important difference between this and the former reaction is that the undamped oscillation has two autocatalytic steps instead of one. The periods of oscillations are obtained by using the discrete Fourier transform (DFT)-a well-known tool in spectroscopy, although not so common in this context. In the last section, it is shown how a simple model of biochemical interactions can be useful to understand the complex behavior of important biological systems. The model consists of two allosteric enzymes coupled in series and activated by its own products. This reaction scheme is important for explaining many metabolic mechanisms, such as the glycolytic oscillations in muscles, yeast glycolysis, and the periodic synthesis of cyclic AMP. A few of many possible dynamic behaviors are exemplified through a prototype glycolytic enzymatic reaction proposed by Decroly and Goldbeter. By simply modifying the initial concentrations, limit cycles, chaos, and birhythmicity are computationally obtained and visualized.

  14. Beyond the power law: Uncovering stylized facts in interbank networks

    Science.gov (United States)

    Vandermarliere, Benjamin; Karas, Alexei; Ryckebusch, Jan; Schoors, Koen

    2015-06-01

    We use daily data on bilateral interbank exposures and monthly bank balance sheets to study network characteristics of the Russian interbank market over August 1998-October 2004. Specifically, we examine the distributions of (un)directed (un)weighted degree, nodal attributes (bank assets, capital and capital-to-assets ratio) and edge weights (loan size and counterparty exposure). We search for the theoretical distribution that fits the data best and report the "best" fit parameters. We observe that all studied distributions are heavy tailed. The fat tail typically contains 20% of the data and can be mostly described well by a truncated power law. Also the power law, stretched exponential and log-normal provide reasonably good fits to the tails of the data. In most cases, however, separating the bulk and tail parts of the data is hard, so we proceed to study the full range of the events. We find that the stretched exponential and the log-normal distributions fit the full range of the data best. These conclusions are robust to (1) whether we aggregate the data over a week, month, quarter or year; (2) whether we look at the "growth" versus "maturity" phases of interbank market development; and (3) with minor exceptions, whether we look at the "normal" versus "crisis" operation periods. In line with prior research, we find that the network topology changes greatly as the interbank market moves from a "normal" to a "crisis" operation period.

  15. Uncovering Interaction Structures in a Brief Psychodynamic Psychotherapy

    Directory of Open Access Journals (Sweden)

    Fernanda Barcellos Serralta

    2016-08-01

    Full Text Available Abstract Interaction structures refers to the repetitive ways of interaction between the patient-therapist dyad over the course of treatment. This construct is operationalized by the repeated application of the Psychotherapy Process Q-Set (PQS to psychotherapy sessions. Studies in this line of research have so far focused only on long-term treatment. The present study examines whether interaction structures can be detected empirically in short-term psychotherapies. All sessions (N = 31 of a successful case of brief psychodynamic psychotherapy were coded with the Psychotherapy Process Q-Set (PQS. The application of Q type factor analysis procedures with varimax rotation revealed five interaction structures: resistance, alliance, facing depression, expectation of change, and introspection and hearing. The analysis of variation of these structures over the course of the treatment showed that these interactions are nonlinear, may be positively or negatively protruding in different sessions, or be predominant at some treatment phase.

  16. Uncovering the Complex Behavior of Hydrogen in Cu2O

    OpenAIRE

    Scanlon, D. O.; Watson, G. W.

    2011-01-01

    The behavior of hydrogen in p-type Cu(2)O has been reported to be quite unusual. Muon experiments have been unable to ascertain the preferential hydrogen site within the Cu(2)O lattice, and indicate that hydrogen causes an electrically active level near the middle of the band gap, whose nature, whether accepting or donating, is not known. In this Letter, we use screened hybrid-density-functional theory to study the nature of hydrogen in Cu(2)O, and identify for the first time the "quasiatomic...

  17. Uncovering the complex behavior of hydrogen in Cu2O.

    Science.gov (United States)

    Scanlon, David O; Watson, Graeme W

    2011-05-01

    The behavior of hydrogen in p-type Cu(2)O has been reported to be quite unusual. Muon experiments have been unable to ascertain the preferential hydrogen site within the Cu(2)O lattice, and indicate that hydrogen causes an electrically active level near the middle of the band gap, whose nature, whether accepting or donating, is not known. In this Letter, we use screened hybrid-density-functional theory to study the nature of hydrogen in Cu(2)O, and identify for the first time the "quasiatomic" site adopted by hydrogen in Cu(2)O. We show that hydrogen will always act as a hole killer in p-type Cu(2)O, and is one likely cause of the low performance of Cu(2)O solar cell devices. PMID:21635109

  18. Uncovering Recovery: The Resistible Rise of Recovery and Resilience

    Directory of Open Access Journals (Sweden)

    David Harper

    2012-10-01

    Full Text Available Discourses of recovery and resilience have risen to positions of dominance in the mental health field. Models of recovery and resilience enjoy purchase, in both policy and practice, across a range of settings from self-described psychiatric survivors through to mental health charities through to statutory mental health service providers. Despite this ubiquity, there is confusion about what recovery means. In this article we problematize notions of recovery and resilience, and consider what, if anything, should be recovered from these concepts. We focus on three key issues, i individualization, ii the persistence of a deficit model, and iii collective approaches to recovery. Through documentary analysis we consider these issues across third sector organizations, and public and mental health policy. Firstly, definitional debates about recovery reflect wider ideological debates about the nature of mental health. The vagueness of these concepts and implicit assumptions inherent in dominant recovery and resilience discourses render them problematic because they individualize what are social problems. Secondly, these discourses, despite being seen as inherently liberatory are conceptually dependent on a notion of deficit in that talk of “positives” and “strengths” requires the existence of “negatives” and “weaknesses” for these concepts to make sense.  We argue that this does little to substantially transform dominant understandings of psychological distress. Thirdly, these issues combine to impact upon the progressive potential of recovery. It comes to be seen as an individualistic experiential narrative accompaniment to medical understandings where the structural causes of distress are obscured. This in turn impacts upon the potential for recovery to be used to explore more collective, political aspects of emotional distress. Drawing on the work of Fraser, we use this critique to characterize “recovery” as a “struggle for recognition,” founded on a model of identity politics which displaces and marginalizes the need for social, political and economic redistribution to address many of the underlying causes of emotional distress. We conclude by stating that it is only when the collective, structural experiences of inequality and injustice are explicitly linked to processes of emotional distress that recovery will be possible. 

  19. A unique chromatin signature uncovers early developmental enhancers in humans.

    Science.gov (United States)

    Rada-Iglesias, Alvaro; Bajpai, Ruchi; Swigut, Tomek; Brugmann, Samantha A; Flynn, Ryan A; Wysocka, Joanna

    2011-02-10

    Cell-fate transitions involve the integration of genomic information encoded by regulatory elements, such as enhancers, with the cellular environment. However, identification of genomic sequences that control human embryonic development represents a formidable challenge. Here we show that in human embryonic stem cells (hESCs), unique chromatin signatures identify two distinct classes of genomic elements, both of which are marked by the presence of chromatin regulators p300 and BRG1, monomethylation of histone H3 at lysine 4 (H3K4me1), and low nucleosomal density. In addition, elements of the first class are distinguished by the acetylation of histone H3 at lysine 27 (H3K27ac), overlap with previously characterized hESC enhancers, and are located proximally to genes expressed in hESCs and the epiblast. In contrast, elements of the second class, which we term 'poised enhancers', are distinguished by the absence of H3K27ac, enrichment of histone H3 lysine 27 trimethylation (H3K27me3), and are linked to genes inactive in hESCs and instead are involved in orchestrating early steps in embryogenesis, such as gastrulation, mesoderm formation and neurulation. Consistent with the poised identity, during differentiation of hESCs to neuroepithelium, a neuroectoderm-specific subset of poised enhancers acquires a chromatin signature associated with active enhancers. When assayed in zebrafish embryos, poised enhancers are able to direct cell-type and stage-specific expression characteristic of their proximal developmental gene, even in the absence of sequence conservation in the fish genome. Our data demonstrate that early developmental enhancers are epigenetically pre-marked in hESCs and indicate an unappreciated role of H3K27me3 at distal regulatory elements. Moreover, the wealth of new regulatory sequences identified here provides an invaluable resource for studies and isolation of transient, rare cell populations representing early stages of human embryogenesis.

  20. Superior photoprotective motifs and mechanisms in eumelanins uncovered

    NARCIS (Netherlands)

    Corani, Alice; Huijser, Annemarie; Gustavsson, Thomas; Markovitsi, Dimitra; Malmqvist, Per-Ake; Pezzella, Alessandro; D'Ischia, Marco; Sundström, Villy

    2014-01-01

    Human pigmentation is a complex phenomenon commonly believed to serve a photoprotective function through the generation and strategic localization of black insoluble eumelanin biopolymers in sun exposed areas of the body. Despite compelling biomedical relevance to skin cancer and melanoma, eumelanin

  1. UNCOVERING FACTORS INFLUENCING PUBLIC PERCEPTIONS OF FOOD BIOTECHNOLOGY

    OpenAIRE

    Hossain, Ferdaus; Onyango, Benjamin M.; Adelaja, Adesoji O.; Schilling, Brian J.; Hallman, William K.

    2002-01-01

    Significant divergence exists in public opinions about biotechnology. Although there is broad support for plant biotechnology for health benefits, opinions differ on the issue of animal genetics for pure economic benefits. While some are opposed to it, many are undecided about genetically modified foods. Considerable skepticism exists about scientists, corporations and government which have negative influence on public acceptance of food biotechnology. Consumers' personal attributes have sign...

  2. The Rosenberg Trial: Uncovering the Layers of History

    Science.gov (United States)

    Ragsdale, Bruce A.

    2013-01-01

    The trial of Julius and Ethel Rosenberg on charges of conspiring to spy for the Soviet Union remains one of the defining moments of the Cold War era. The dramatic allegations of stolen atomic secrets and networks of Communist spies riveted the public's attention. The determination of government prosecutors reflected a widely shared belief…

  3. Uncovering what lies beneath a Salmonella enterica empyema.

    Science.gov (United States)

    Woo, Jia Wei; Tam, John Kit Chung; Chan, Douglas Su Gin; Wang, Shi; Ying, Lee Shir

    2015-01-01

    A 67-year-old woman with myelodysplastic syndrome (MDS) and transfusional haemosiderosis developed Salmonella empyema caused by direct extension from splenic abscesses. She was successfully treated with antibiotics, pleural decortication and splenectomy. She had presented with fever after being treated for presumed pneumonia and parapneumonic effusion 2 months prior. CT scan showed splenic abscesses eroding through the diaphragm causing a left pleural empyema. Pleural fluid and spleen bacterial cultures grew Salmonella enterica. She was treated with 4 weeks of antibiotics and underwent surgical pleural decortication and splenectomy in the same sitting. She made a good postoperative recovery. Patients with severe iron overload are susceptible to various types of bacterial sepsis, including salmonellosis. It is unusual for enteric bacterial such as Salmonella to present with empyema, and should prompt a search for intra-abdominal infection. Pleural decortication and splenectomy can be performed during the same surgical sitting and can lead to good surgical outcomes. PMID:26336186

  4. Uncovering Circumbinary Planetary Architectural Properties from Selection Biases

    CERN Document Server

    Li, Gongjie; Tao, Molei

    2016-01-01

    The new discoveries of circumbinary planetary systems shed light on the understanding of planetary system formation. Learning the architectural properties of these systems is essential for constraining the different formation mechanisms. We first revisit the stability limit of circumbinary planets. Next, we focus on eclipsing stellar binaries and obtain an analytical expression for the transit probability in a realistic setting, where finite observation period and planetary orbital precession are included. Then, understanding of the architectural properties of the currently observed transiting systems is refined, based on Bayesian analysis and a series of hypothesis tests. We find 1) it is not a selection bias that the innermost planets reside near the stability limit for eight of the nine observed systems, and this is consistent with a log uniform distribution of the planetary semi-major axis; 2) it is not a selection bias that the planetary and stellar orbits are nearly coplanar ($\\lesssim 3^\\circ$), and th...

  5. HIDDEN WEB EXTRACTOR DYNAMIC WAY TO UNCOVER THE DEEP WEB

    Directory of Open Access Journals (Sweden)

    DR. ANURADHA

    2012-06-01

    Full Text Available In this era of digital tsunami of information on the web, everyone is completely dependent on the WWW for information retrieval. This has posed a challenging problem in extracting relevant data. Traditional web crawlers focus only on the surface web while the deep web keeps expanding behind the scene. The web databases are hidden behind the query interfaces. In this paper, we propose a Hidden Web Extractor (HWE that can automatically discover and download data from the Hidden Web databases. Since the only “entry point” to a Hidden Web site is a query interface, the main challenge that a Hidden WebExtractor has to face is how to automatically generate meaningful queries for the unlimited number of website pages.

  6. Stars Just Got Bigger - A 300 Solar Mass Star Uncovered

    Science.gov (United States)

    2010-07-01

    Using a combination of instruments on ESO's Very Large Telescope, astronomers have discovered the most massive stars to date, one weighing at birth more than 300 times the mass of the Sun, or twice as much as the currently accepted limit of 150 solar masses. The existence of these monsters - millions of times more luminous than the Sun, losing weight through very powerful winds - may provide an answer to the question "how massive can stars be?" A team of astronomers led by Paul Crowther, Professor of Astrophysics at the University of Sheffield, has used ESO's Very Large Telescope (VLT), as well as archival data from the NASA/ESA Hubble Space Telescope, to study two young clusters of stars, NGC 3603 and RMC 136a in detail. NGC 3603 is a cosmic factory where stars form frantically from the nebula's extended clouds of gas and dust, located 22 000 light-years away from the Sun (eso1005). RMC 136a (more often known as R136) is another cluster of young, massive and hot stars, which is located inside the Tarantula Nebula, in one of our neighbouring galaxies, the Large Magellanic Cloud, 165 000 light-years away (eso0613). The team found several stars with surface temperatures over 40 000 degrees, more than seven times hotter than our Sun, and a few tens of times larger and several million times brighter. Comparisons with models imply that several of these stars were born with masses in excess of 150 solar masses. The star R136a1, found in the R136 cluster, is the most massive star ever found, with a current mass of about 265 solar masses and with a birthweight of as much as 320 times that of the Sun. In NGC 3603, the astronomers could also directly measure the masses of two stars that belong to a double star system [1], as a validation of the models used. The stars A1, B and C in this cluster have estimated masses at birth above or close to 150 solar masses. Very massive stars produce very powerful outflows. "Unlike humans, these stars are born heavy and lose weight as they age," says Paul Crowther. "Being a little over a million years old, the most extreme star R136a1 is already 'middle-aged' and has undergone an intense weight loss programme, shedding a fifth of its initial mass over that time, or more than fifty solar masses." If R136a1 replaced the Sun in our Solar System, it would outshine the Sun by as much as the Sun currently outshines the full Moon. "Its high mass would reduce the length of the Earth's year to three weeks, and it would bathe the Earth in incredibly intense ultraviolet radiation, rendering life on our planet impossible," says Raphael Hirschi from Keele University, who belongs to the team. These super heavyweight stars are extremely rare, forming solely within the densest star clusters. Distinguishing the individual stars - which has now been achieved for the first time - requires the exquisite resolving power of the VLT's infrared instruments [2]. The team also estimated the maximum possible mass for the stars within these clusters and the relative number of the most massive ones. "The smallest stars are limited to more than about eighty times more than Jupiter, below which they are 'failed stars' or brown dwarfs," says team member Olivier Schnurr from the Astrophysikalisches Institut Potsdam. "Our new finding supports the previous view that there is also an upper limit to how big stars can get, although it raises the limit by a factor of two, to about 300 solar masses." Within R136, only four stars weighed more than 150 solar masses at birth, yet they account for nearly half of the wind and radiation power of the entire cluster, comprising approximately 100 000 stars in total. R136a1 alone energises its surroundings by more than a factor of fifty compared to the Orion Nebula cluster, the closest region of massive star formation to Earth. Understanding how high mass stars form is puzzling enough, due to their very short lives and powerful winds, so that the identification of such extreme cases as R136a1 raises the challenge to theorists still further. "Either they were born so big or smaller stars merged together to produce them," explains Crowther. Stars between about 8 and 150 solar masses explode at the end of their short lives as supernovae, leaving behind exotic remnants, either neutron stars or black holes. Having now established the existence of stars weighing between 150 and 300 solar masses, the astronomers' findings raise the prospect of the existence of exceptionally bright, "pair instability supernovae" that completely blow themselves apart, failing to leave behind any remnant and dispersing up to ten solar masses of iron into their surroundings. A few candidates for such explosions have already been proposed in recent years. Not only is R136a1 the most massive star ever found, but it also has the highest luminosity too, close to 10 million times greater than the Sun. "Owing to the rarity of these monsters, I think it is unlikely that this new record will be broken any time soon," concludes Crowther. Notes [1] The star A1 in NGC 3603 is a double star, with an orbital period of 3.77 days. The two stars in the system have, respectively, 120 and 92 times the mass of the Sun, which means that they have formed as stars weighing, respectively, 148 and 106 solar masses. [2] The team used the SINFONI, ISAAC and MAD instruments, all attached to ESO's Very Large Telescope at Paranal, Chile. [3] (note added on 26 July 2010) The "bigger" in the title does not imply that these stars are the biggest observed. Such stars, called red supergiants, can have radii up to about a thousand solar radii, while R136a1, which is blue, is about 35 times as large as the Sun. However, R136a1 is the star with the greatest mass known to date. More information This work is presented in an article published in the Monthly Notices of the Royal Astronomical Society ("The R136 star cluster hosts several stars whose individual masses greatly exceed the accepted 150 Msun stellar mass limit", by P. Crowther et al.). The team is composed of Paul A. Crowther, Richard J. Parker, and Simon P. Goodwin (University of Sheffield, UK), Olivier Schnurr (University of Sheffield and Astrophysikalisches Institut Potsdam, Germany), Raphael Hirschi (Keele University, UK), and Norhasliza Yusof and Hasan Abu Kassim (University of Malaya, Malaysia). ESO, the European Southern Observatory, is the foremost intergovernmental astronomy organisation in Europe and the world's most productive astronomical observatory. It is supported by 14 countries: Austria, Belgium, the Czech Republic, Denmark, France, Finland, Germany, Italy, the Netherlands, Portugal, Spain, Sweden, Switzerland and the United Kingdom. ESO carries out an ambitious programme focused on the design, construction and operation of powerful ground-based observing facilities enabling astronomers to make important scientific discoveries. ESO also plays a leading role in promoting and organising cooperation in astronomical research. ESO operates three unique world-class observing sites in Chile: La Silla, Paranal and Chajnantor. At Paranal, ESO operates the Very Large Telescope, the world's most advanced visible-light astronomical observatory and VISTA, the world's largest survey telescope. ESO is the European partner of a revolutionary astronomical telescope ALMA, the largest astronomical project in existence. ESO is currently planning a 42-metre European Extremely Large optical/near-infrared Telescope, the E-ELT, which will become "the world's biggest eye on the sky".

  7. Vaporous Marketing: Uncovering Pervasive Electronic Cigarette Advertisements on Twitter

    Science.gov (United States)

    Jones, Chris A.; Williams, Jake Ryland; Kurti, Allison N.; Norotsky, Mitchell Craig; Danforth, Christopher M.; Dodds, Peter Sheridan

    2016-01-01

    Background Twitter has become the “wild-west” of marketing and promotional strategies for advertisement agencies. Electronic cigarettes have been heavily marketed across Twitter feeds, offering discounts, “kid-friendly” flavors, algorithmically generated false testimonials, and free samples. Methods All electronic cigarette keyword related tweets from a 10% sample of Twitter spanning January 2012 through December 2014 (approximately 850,000 total tweets) were identified and categorized as Automated or Organic by combining a keyword classification and a machine trained Human Detection algorithm. A sentiment analysis using Hedonometrics was performed on Organic tweets to quantify the change in consumer sentiments over time. Commercialized tweets were topically categorized with key phrasal pattern matching. Results The overwhelming majority (80%) of tweets were classified as automated or promotional in nature. The majority of these tweets were coded as commercialized (83.65% in 2013), up to 33% of which offered discounts or free samples and appeared on over a billion twitter feeds as impressions. The positivity of Organic (human) classified tweets has decreased over time (5.84 in 2013 to 5.77 in 2014) due to a relative increase in the negative words ‘ban’, ‘tobacco’, ‘doesn’t’, ‘drug’, ‘against’, ‘poison’, ‘tax’ and a relative decrease in the positive words like ‘haha’, ‘good’, ‘cool’. Automated tweets are more positive than organic (6.17 versus 5.84) due to a relative increase in the marketing words like ‘best’, ‘win’, ‘buy’, ‘sale’, ‘health’, ‘discount’ and a relative decrease in negative words like ‘bad’, ‘hate’, ‘stupid’, ‘don’t’. Conclusions Due to the youth presence on Twitter and the clinical uncertainty of the long term health complications of electronic cigarette consumption, the protection of public health warrants scrutiny and potential regulation of social media marketing. PMID:27410031

  8. Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide

    Science.gov (United States)

    Freudenthal, Bret D.; Beard, William A.; Perera, Lalith; Shock, David D.; Kim, Taejin; Schlick, Tamar; Wilson, Samuel H.

    2015-01-01

    Oxidative stress promotes genomic instability and human diseases. A common oxidized nucleoside is 8-oxo-7,8-dihydro-2'-deoxyguanosine, which is found both in DNA (8-oxo-G) and as a free nucleotide (8-oxo-dGTP). Nucleotide pools are especially vulnerable to oxidative damage. Therefore cells encode an enzyme (MutT/MTH1) that removes free oxidized nucleotides. This cleansing function is required for cancer cell survival and to modulate Escherichia coli antibiotic sensitivity in a DNA polymerase (pol)-dependent manner. How polymerases discriminate between damaged and non-damaged nucleotides is not well understood. This analysis is essential given the role of oxidized nucleotides in mutagenesis, cancer therapeutics, and bacterial antibiotics. Even with cellular sanitizing activities, nucleotide pools contain enough 8-oxo-dGTP to promote mutagenesis. This arises from the dual coding potential where 8-oxo-dGTP(anti) base pairs with cytosine and 8-oxo-dGTP(syn) uses its Hoogsteen edge to base pair with adenine. Here we use time-lapse crystallography to follow 8-oxo-dGTP insertion opposite adenine or cytosine with human pol β, to reveal that insertion is accommodated in either the syn- or anti-conformation, respectively. For 8-oxo-dGTP(anti) insertion, a novel divalent metal relieves repulsive interactions between the adducted guanine base and the triphosphate of the oxidized nucleotide. With either templating base, hydrogen-bonding interactions between the bases are lost as the enzyme reopens after catalysis, leading to a cytotoxic nicked DNA repair intermediate. Combining structural snapshots with kinetic and computational analysis reveals how 8-oxo-dGTP uses charge modulation during insertion that can lead to a blocked DNA repair intermediate.

  9. Interactome map uncovers phosphatidylserine transport by oxysterol-binding proteins.

    Science.gov (United States)

    Maeda, Kenji; Anand, Kanchan; Chiapparino, Antonella; Kumar, Arun; Poletto, Mattia; Kaksonen, Marko; Gavin, Anne-Claude

    2013-09-12

    The internal organization of eukaryotic cells into functionally specialized, membrane-delimited organelles of unique composition implies a need for active, regulated lipid transport. Phosphatidylserine (PS), for example, is synthesized in the endoplasmic reticulum and then preferentially associates--through mechanisms not fully elucidated--with the inner leaflet of the plasma membrane. Lipids can travel via transport vesicles. Alternatively, several protein families known as lipid-transfer proteins (LTPs) can extract a variety of specific lipids from biological membranes and transport them, within a hydrophobic pocket, through aqueous phases. Here we report the development of an integrated approach that combines protein fractionation and lipidomics to characterize the LTP-lipid complexes formed in vivo. We applied the procedure to 13 LTPs in the yeast Saccharomyces cerevisiae: the six Sec14 homology (Sfh) proteins and the seven oxysterol-binding homology (Osh) proteins. We found that Osh6 and Osh7 have an unexpected specificity for PS. In vivo, they participate in PS homeostasis and the transport of this lipid to the plasma membrane. The structure of Osh6 bound to PS reveals unique features that are conserved among other metazoan oxysterol-binding proteins (OSBPs) and are required for PS recognition. Our findings represent the first direct evidence, to our knowledge, for the non-vesicular transfer of PS from its site of biosynthesis (the endoplasmic reticulum) to its site of biological activity (the plasma membrane). We describe a new subfamily of OSBPs, including human ORP5 and ORP10, that transfer PS and propose new mechanisms of action for a protein family that is involved in several human pathologies such as cancer, dyslipidaemia and metabolic syndrome. PMID:23934110

  10. Uncovering Students' Incorrect Ideas about Foundational Concepts for Biochemistry

    Science.gov (United States)

    Villafane, Sachel M.; Loertscher, Jennifer; Minderhout, Vicky; Lewis, Jennifer E.

    2011-01-01

    This paper presents preliminary data on how an assessment instrument with a unique structure can be used to identify common incorrect ideas from prior coursework at the beginning of a biochemistry course, and to determine whether these ideas have changed by the end of the course. The twenty-one multiple-choice items address seven different…

  11. Starting to Uncover the Mystery of Interdisciplinary Research in Kinesiology

    Science.gov (United States)

    Schary, David P.; Cardinal, Bradley J.

    2016-01-01

    The multidisciplinary nature of kinesiology seems to be an ideal configuration for conducting interdisciplinary research. Proposed as a potential solution to overcome fragmentation, interdisciplinary research has a role within kinesiology that remains unknown. In this study, we explored kinesiologists' perceptions of interdisciplinary research,…

  12. Uncovering the single top: observation of electroweak top quark production

    Energy Technology Data Exchange (ETDEWEB)

    Benitez, Jorge Armando; /Michigan State U.

    2009-08-01

    The top quark is generally produced in quark and anti-quark pairs. However, the Standard Model also predicts the production of only one top quark which is mediated by the electroweak interaction, known as 'Single Top'. Single Top quark production is important because it provides a unique and direct way to measure the CKM matrix element V{sub tb}, and can be used to explore physics possibilities beyond the Standard Model predictions. This dissertation presents the results of the observation of Single Top using 2.3 fb{sup -1} of Data collected with the D0 detector at the Fermilab Tevatron collider. The analysis includes the Single Top muon+jets and electron+jets final states and employs Boosted Decision Tress as a method to separate the signal from the background. The resulting Single Top cross section measurement is: (1) {sigma}(p{bar p} {yields} tb + X, tqb + X) = 3.74{sub -0.74}{sup +0.95} pb, where the errors include both statistical and systematic uncertainties. The probability to measure a cross section at this value or higher in the absence of signal is p = 1.9 x 10{sup -6}. This corresponds to a standard deviation Gaussian equivalence of 4.6. When combining this result with two other analysis methods, the resulting cross section measurement is: (2) {sigma}(p{bar p} {yields} tb + X, tqb + X) = 3.94 {+-} 0.88 pb, and the corresponding measurement significance is 5.0 standard deviations.

  13. HSPG-Deficient Zebrafish Uncovers Dental Aspect of Multiple Osteochondromas

    OpenAIRE

    Wiweger, Malgorzata I; Zhao, Zhe; van Merkesteyn, Richard J. P.; Roehl, Henry H.; Hogendoorn, Pancras C. W.

    2012-01-01

    Multiple Osteochondromas (MO; previously known as multiple hereditary exostosis) is an autosomal dominant genetic condition that is characterized by the formation of cartilaginous bone tumours (osteochondromas) at multiple sites in the skeleton, secondary bursa formation and impingement of nerves, tendons and vessels, bone curving, and short stature. MO is also known to be associated with arthritis, general pain, scarring and occasional malignant transformation of osteochondroma into secondar...

  14. HSPG-deficient zebrafish uncovers dental aspect of multiple osteochondromas.

    Directory of Open Access Journals (Sweden)

    Malgorzata I Wiweger

    Full Text Available Multiple Osteochondromas (MO; previously known as multiple hereditary exostosis is an autosomal dominant genetic condition that is characterized by the formation of cartilaginous bone tumours (osteochondromas at multiple sites in the skeleton, secondary bursa formation and impingement of nerves, tendons and vessels, bone curving, and short stature. MO is also known to be associated with arthritis, general pain, scarring and occasional malignant transformation of osteochondroma into secondary peripheral chondrosarcoma. MO patients present additional complains but the relevance of those in relation to the syndromal background needs validation. Mutations in two enzymes that are required during heparan sulphate synthesis (EXT1 or EXT2 are known to cause MO. Previously, we have used zebrafish which harbour mutations in ext2 as a model for MO and shown that ext2⁻/⁻ fish have skeletal defects that resemble those seen in osteochondromas. Here we analyse dental defects present in ext2⁻/⁻ fish. Histological analysis reveals that ext2⁻/⁻ fish have very severe defects associated with the formation and the morphology of teeth. At 5 days post fertilization 100% of ext2⁻/⁻ fish have a single tooth at the end of the 5(th pharyngeal arch, whereas wild-type fish develop three teeth, located in the middle of the pharyngeal arch. ext2⁻/⁻ teeth have abnormal morphology (they were shorter and thicker than in the WT and patchy ossification at the tooth base. Deformities such as split crowns and enamel lesions were found in 20% of ext2⁺/⁻ adults. The tooth morphology in ext2⁻/⁻ was partially rescued by FGF8 administered locally (bead implants. Our findings from zebrafish model were validated in a dental survey that was conducted with assistance of the MHE Research Foundation. The presence of the malformed and/or displaced teeth with abnormal enamel was declared by half of the respondents indicating that MO might indeed be also associated with dental problems.

  15. Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Tyler, Brett M.; Tripathy, Sucheta; Zhang, Xuemin; Dehal, Paramvir; Jiang, Rays H. Y.; Aerts, Andrea; Arredondo, Felipe D.; Baxter, Laura; Bensasson, Douda; Beynon, JIm L.; Chapman, Jarrod; Damasceno, Cynthia M. B.; Dorrance, Anne E.; Dou, Daolong; Dickerman, Allan W.; Dubchak, Inna L.; Garbelotto, Matteo; Gijzen, Mark; Gordon, Stuart G.; Govers, Francine; Grunwald, NIklaus J.; Huang, Wayne; Ivors, Kelly L.; Jones, Richard W.; Kamoun, Sophien; Krampis, Konstantinos; Lamour, Kurt H.; Lee, Mi-Kyung; McDonald, W. Hayes; Medina, Monica; Meijer, Harold J. G.; Nordberg, Erik K.; Maclean, Donald J.; Ospina-Giraldo, Manuel D.; Morris, Paul F.; Phuntumart, Vipaporn; Putnam, Nicholas J.; Rash, Sam; Rose, Jocelyn K. C.; Sakihama, Yasuko; Salamov, Asaf A.; Savidor, Alon; Scheuring, Chantel F.; Smith, Brian M.; Sobral, Bruno W. S.; Terry, Astrid; Torto-Alalibo, Trudy A.; Win, Joe; Xu, Zhanyou; Zhang, Hongbin; Grigoriev, Igor V.; Rokhsar, Daniel S.; Boore, Jeffrey L.

    2006-04-17

    Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oömycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oömycete avirulence genes.

  16. Uncovering a Role for SK2 in Angelman Syndrome

    Directory of Open Access Journals (Sweden)

    Sofia B. Lizarraga

    2015-07-01

    Full Text Available Angelman syndrome is a severe neurodevelopmental disorder caused by mutations in UBE3A. Sun et al. (2015 report SK2 as a UBE3A substrate and provide insight into the molecular mechanisms that might underlie impaired neuronal function in individuals affected by Angelman syndrome.

  17. Multicolored words: Uncovering the relationship between reading mechanisms and synesthesia.

    Science.gov (United States)

    Blazej, Laura J; Cohen-Goldberg, Ariel M

    2016-02-01

    Grapheme-color and lexical-color synesthesia, the association of colors with letters and words, respectively, are some of the most commonly studied forms of synesthesia, yet relatively little is known about how synesthesia arises from and interfaces with the reading process. To date, synesthetic experiences in reading have only been reported in relation to a word's graphemes and meaning. We present a case study of WBL, a 21-year old male who experiences synesthetic colors for letters and words. Over 3 months, we obtained nearly 3000 color judgments for visually presented monomorphemic, prefixed, suffixed, and compound words as well as judgments for pseudocompound words (e.g., carpet), and nonwords. In Experiment 1, we show that word color is nearly always determined by the color of the first letter. Furthermore, WBL reported two separate colors for prefixed and compound words approximately 14% of the time, with the additional color determined by the first letter of the second morpheme. In Experiment 2, we further investigated how various morphological factors influenced WBL's percepts using the compound norms of Juhasz, Lai, and Woodcock (2014). In a logistic regression analysis of color judgments for nearly 400 compounds, we observed that the likelihood that WBL would perceive a compound as bearing 1 lexical color or 2 lexical colors was influenced by a variety of factors including stem frequency, compound frequency, and the relationship between the meaning of the compound and the meaning of its stems. This constitutes the first study reporting an effect of morphological structure in synesthesia and demonstrates that synesthetic colors result from a complex interaction of perceptual, graphemic, morphological, and semantic factors. PMID:26794531

  18. A spiral galaxy's mass distribution uncovered through lensing and dynamics

    Science.gov (United States)

    Trick, Wilma H.; van de Ven, Glenn; Dutton, Aaron A.

    2016-09-01

    We investigate the matter distribution of a spiral galaxy with a counter-rotating stellar core, SDSS J1331+3628 (J1331), independently with gravitational lensing and stellar dynamical modelling. By fitting a gravitational potential model to a quadruplet of lensing images around J1331's bulge, we tightly constrain the mass inside the Einstein radius Rein = (0.91 ± 0.02)″( ≃ 1.83 ± 0.04~kpc) to within 4%: Mein = (7.8 ± 0.3) × 1010M⊙. We model observed long-slit major axis stellar kinematics in J1331's central regions by finding Multi-Gaussian Expansion (MGE) models for the stellar and dark matter distribution that solve the axisymmetric Jeans equations. The lens and dynamical model are independently derived, but in very good agreement with each other around ˜Rein. We find that J1331's center requires a steep total mass-to-light ratio gradient. A dynamical model including a NFW halo (with virial velocity v200 ≃ 240 ± 40~kms-1 and concentration c200 ≃ 8 ± 2) and moderate tangential velocity anisotropy (βz ≃ -0.4 ± 0.1) can reproduce the signatures of J1331's counter-rotating core and predict the stellar and gas rotation curve at larger radii. However, our models do not agree with the observed velocity dispersion at large radii. We speculate that the reason could be a non-trivial change in structure and kinematics due to a possible merger event in J1331's recent past.

  19. An improvement of the fast uncovering community algorithm

    Science.gov (United States)

    Wang, Li; Wang, Jiang; Shen, Hua-Wei; Cheng, Xue-Qi

    2013-10-01

    Community detection methods have been used in computer, sociology, physics, biology, and brain information science areas. Many methods are based on the optimization of modularity. The algorithm proposed by Blondel et al. (Blondel V D, Guillaume J L, Lambiotte R and Lefebvre E 2008 J. Stat. Mech. 10 10008) is one of the most widely used methods because of its good performance, especially in the big data era. In this paper we make some improvements to this algorithm in correctness and performance. By tests we see that different node orders bring different performances and different community structures. We find some node swings in different communities that influence the performance. So we design some strategies on the sweeping order of node to reduce the computing cost made by repetition swing. We introduce a new concept of overlapping degree (OV) that shows the strength of connection between nodes. Three improvement strategies are proposed that are based on constant OV, adaptive OV, and adaptive weighted OV, respectively. Experiments on synthetic datasets and real datasets are made, showing that our improved strategies can improve the performance and correctness.

  20. Biological Ferroelectricity Uncovered in Aortic Walls by Piezoresponse Force Microscopy

    OpenAIRE

    Liu, Yuanming; Zhang, Yanhang; Chow, Ming-Jay; Chen, Qian Nataly; Li, Jiangyu

    2012-01-01

    Many biological tissues are piezoelectric and pyroelectric with spontaneous polarization. Ferroelectricity, however, has not been reported in soft biological tissues yet. Using piezoresponse force microscopy, we discover that the porcine aortic walls are not only piezoelectric, but also ferroelectric, with the piezoelectric coefficient in the order of 1 pm/V and coercive voltage approximately 10 V. Through detailed switching spectroscopy mapping and relaxation studies, we also find that the p...

  1. New incompatibilities uncovered using the Promega DNA IQ™ chemistry.

    Science.gov (United States)

    Laurin, Nancy; Célestin, Florence; Clark, Meagan; Wilkinson, Della; Yamashita, Brian; Frégeau, Chantal

    2015-12-01

    Over the years, the Promega DNA IQ™ System was proven an effective technology for the production of clean DNA from a wide variety of casework specimens. The capture of DNA using the DNA IQ™ paramagnetic beads, however, was shown to be affected by a few specific chemicals that could be present on exhibits submitted to the laboratory. In this study, various blood and latent fingerprint enhancement reagents/methods, marker pens and adhesive tapes, applied at the crime scene or in the forensic laboratory on casework exhibits or used to collect biological material, were tested for their compatibility with the DNA IQ™ technology. Although no impact on DNA recovery was observed for most reagents, the MAGNA™ Jet Black fingerprint powder and three 3M Scotch(®) adhesive tapes were shown to severely or completely inhibit DNA binding onto the DNA IQ™ beads. The effect of MAGNA™ Jet Black on DNA recovery could be counteracted by separating the magnetic powder from the lysates by centrifugation or filtration, prior to DNA extraction. High quality STR profiles were obtained from samples subjected to MAGNA™ Jet Black suggesting it does not impact DNA integrity. PMID:26295931

  2. Uncovering the true identity of naive pluripotent stem cells

    NARCIS (Netherlands)

    Welling, M.; Geijsen, N.

    2013-01-01

    Embryonic stem cells (ESCs) are pluripotent stem cells derived from the inner cell mass (ICM) of blastocyst embryos. Although first characterized over 30 years ago, the ontology of these cells remains elusive. Identifying the in vivo counterpart of murine ESCs will be essential for the derivation of

  3. Uncovering the single top: observation of electroweak top quark production

    Energy Technology Data Exchange (ETDEWEB)

    Benitez, Jorge Armando [Michigan State Univ., East Lansing, MI (United States)

    2009-01-01

    The top quark is generally produced in quark and anti-quark pairs. However, the Standard Model also predicts the production of only one top quark which is mediated by the electroweak interaction, known as 'Single Top'. Single Top quark production is important because it provides a unique and direct way to measure the CKM matrix element Vtb, and can be used to explore physics possibilities beyond the Standard Model predictions. This dissertation presents the results of the observation of Single Top using 2.3 fb-1 of Data collected with the D0 detector at the Fermilab Tevatron collider. The analysis includes the Single Top muon+jets and electron+jets final states and employs Boosted Decision Tress as a method to separate the signal from the background. The resulting Single Top cross section measurement is: (1) σ(p$\\bar{p}$→ tb + X, tqb + X) = 3.74-0.74+0.95 pb, where the errors include both statistical and systematic uncertainties. The probability to measure a cross section at this value or higher in the absence of signal is p = 1.9 x 10-6. This corresponds to a standard deviation Gaussian equivalence of 4.6. When combining this result with two other analysis methods, the resulting cross section measurement is: (2) σ(p$\\bar{p}$ → tb + X, tqb + X) = 3.94 ± 0.88 pb, and the corresponding measurement significance is 5.0 standard deviations.

  4. Uncovering layers of human RNA polymerase II transcription

    DEFF Research Database (Denmark)

    Jensen, Torben Heick

    In recent years DNA microarray and high-throughput sequencing technologies have challenged the “gene-centric” view that pre-mRNA is the only RNA species transcribed off protein-coding genes. Instead unorthodox transcription from within genic- and intergenic regions has been demonstrated to occur...

  5. Uncovering Web search tactics in South African higher education

    Directory of Open Access Journals (Sweden)

    Surika Civilcharran

    2015-02-01

    Full Text Available Background: The potential of the World Wide Web (‘the Web’ as a tool for information retrieval in higher education is beyond question. Harnessing this potential, however, remains a challenge, particularly in the context of developing countries, where students are drawn from diverse socio-economic, educational and technological backgrounds. Objectives: The purpose of this study is to identify the Web search tactics used by postgraduate students in order to address the weaknesses of undergraduate students with regard to their Web searching tactics. This article forms part of a wider study into postgraduate students’ information retrieval strategies at the University of KwaZulu-Natal, Pietermaritzburg campus, South Africa. Method: The study utilised the mixed methods approach, employing both questionnaires (Phase 1 and structured interviews (Phase 2, and was largely underpinned by Bates’s model of information search tactics. This article reports and reflects on the findings of Phase 1, which focused on identifying the Web search tactics employed by postgraduate students. Results: Findings indicated a preference for lower-level Web search tactics, despite respondents largely self-reporting as intermediate or expert users. Moreover, the majority of respondents gained their knowledge on Web searching through experience and only a quarter of respondents have been given formal training on Web searching. Conclusion: In addition to contributing to theory, it is envisaged that this article will contribute to practice by informing the design of undergraduate training interventions to proactively address the information retrieval challenges faced by novice users. Subsequent papers will report on Phase 2 of the study.

  6. Uncovering a Role for SK2 in Angelman Syndrome.

    Science.gov (United States)

    Lizarraga, Sofia B; Morrow, Eric M

    2015-07-21

    Angelman syndrome is a severe neurodevelopmental disorder caused by mutations in UBE3A. Sun et al. (2015) report SK2 as a UBE3A substrate and provide insight into the molecular mechanisms that might underlie impaired neuronal function in individuals affected by Angelman syndrome. PMID:26200312

  7. Uncovering the multiple objectives behind national energy efficiency planning

    International Nuclear Information System (INIS)

    This work seeks to identify the fundamental objectives behind the development of energy efficiency (EE) plans for countries. It also presents a method to quantify the degree of achievement of each objective, through the identification and operationalization of attributes. This was achieved by applying Keeney's value-focused thinking approach. For that purpose, three key decision makers in EE planning were interviewed along with a bibliographic review on the subject. From this process six fundamental objectives were identified formalizing the problem as a multi-objective one: (i) to minimize the influence of energy use on climate change; (ii) to minimize the financial risk from the investment; (iii) to maximize the security of energy supply; (iv) to minimize investment costs; (v) to minimize the impacts of building new power plants and transmission infrastructures and (vi) to maximize the local air quality. The respective attributes were: (i) CO2 emissions savings; (ii) payback; (iii) imported energy savings; (iv) investment cost; (v) electricity savings; and (vi) total suspended particles savings. To show the usefulness of the work, the objectives and attributes identified were used to show the possible outcomes from five hypothetical EE plans for Portugal

  8. Uncovering the transcriptional control of "Bartonella henselae" host adaptation factors

    OpenAIRE

    Québatte, Maxime

    2014-01-01

    A recurrent theme in bacterial pathogenicity is the understanding of the regulatory events necessary for a given pathogen to progress through its infection cycle while resisting the host defense mechanisms. This progression typically requires the coordinated expression of defined sub-portions of the virulence repertoire at the same time as others need to be tightly repressed or degraded. This so-called adaptive response is ultimately linked to the ability of the pathogen to sense its direct e...

  9. Uncovering the genetic landscape for multiple sleep-wake traits.

    Directory of Open Access Journals (Sweden)

    Christopher J Winrow

    Full Text Available Despite decades of research in defining sleep-wake properties in mammals, little is known about the nature or identity of genes that regulate sleep, a fundamental behaviour that in humans occupies about one-third of the entire lifespan. While genome-wide association studies in humans and quantitative trait loci (QTL analyses in mice have identified candidate genes for an increasing number of complex traits and genetic diseases, the resources and time-consuming process necessary for obtaining detailed quantitative data have made sleep seemingly intractable to similar large-scale genomic approaches. Here we describe analysis of 20 sleep-wake traits from 269 mice from a genetically segregating population that reveals 52 significant QTL representing a minimum of 20 genomic loci. While many (28 QTL affected a particular sleep-wake trait (e.g., amount of wake across the full 24-hr day, other loci only affected a trait in the light or dark period while some loci had opposite effects on the trait during the light vs. dark. Analysis of a dataset for multiple sleep-wake traits led to previously undetected interactions (including the differential genetic control of number and duration of REM bouts, as well as possible shared genetic regulatory mechanisms for seemingly different unrelated sleep-wake traits (e.g., number of arousals and REM latency. Construction of a Bayesian network for sleep-wake traits and loci led to the identification of sub-networks of linkage not detectable in smaller data sets or limited single-trait analyses. For example, the network analyses revealed a novel chain of causal relationships between the chromosome 17@29cM QTL, total amount of wake, and duration of wake bouts in both light and dark periods that implies a mechanism whereby overall sleep need, mediated by this locus, in turn determines the length of each wake bout. Taken together, the present results reveal a complex genetic landscape underlying multiple sleep-wake traits and emphasize the need for a systems biology approach for elucidating the full extent of the genetic regulatory mechanisms of this complex and universal behavior.

  10. Obesity and psychotic disorders: uncovering common mechanisms through metabolomics

    Directory of Open Access Journals (Sweden)

    Matej Orešič

    2012-09-01

    Full Text Available Primary obesity and psychotic disorders are similar with respect to the associated changes in energy balance and co-morbidities, including metabolic syndrome. Such similarities do not necessarily demonstrate causal links, but instead suggest that specific causes of and metabolic disturbances associated with obesity play a pathogenic role in the development of co-morbid disorders, potentially even before obesity develops. Metabolomics – the systematic study of metabolites, which are small molecules generated by the process of metabolism – has been important in elucidating the pathways underlying obesity-associated co-morbidities. This review covers how recent metabolomic studies have advanced biomarker discovery and the elucidation of mechanisms underlying obesity and its co-morbidities, with a specific focus on metabolic syndrome and psychotic disorders. The importance of identifying metabolic markers of disease-associated intermediate phenotypes – traits modulated but not encoded by the DNA sequence – is emphasized. Such markers would be applicable as diagnostic tools in a personalized healthcare setting and might also open up novel therapeutic avenues.

  11. Emperical Laws in Economics Uncovered Using Methods in Statistical Mechanics

    Science.gov (United States)

    Stanley, H. Eugene

    2001-06-01

    In recent years, statistical physicists and computational physicists have determined that physical systems which consist of a large number of interacting particles obey universal "scaling laws" that serve to demonstrate an intrinsic self-similarity operating in such systems. Further, the parameters appearing in these scaling laws appear to be largely independent of the microscopic details. Since economic systems also consist of a large number of interacting units, it is plausible that scaling theory can be usefully applied to economics. To test this possibility using realistic data sets, a number of scientists have begun analyzing economic data using methods of statistical physics [1]. We have found evidence for scaling (and data collapse), as well as universality, in various quantities, and these recent results will be reviewed in this talk--starting with the most recent study [2]. We also propose models that may lead to some insight into these phenomena. These results will be discussed, as well as the overall rationale for why one might expect scaling principles to hold for complex economic systems. This work on which this talk is based is supported by BP, and was carried out in collaboration with L. A. N. Amaral S. V. Buldyrev, D. Canning, P. Cizeau, X. Gabaix, P. Gopikrishnan, S. Havlin, Y. Lee, Y. Liu, R. N. Mantegna, K. Matia, M. Meyer, C.-K. Peng, V. Plerou, M. A. Salinger, and M. H. R. Stanley. [1.] See, e.g., R. N. Mantegna and H. E. Stanley, Introduction to Econophysics: Correlations & Complexity in Finance (Cambridge University Press, Cambridge, 1999). [2.] P. Gopikrishnan, B. Rosenow, V. Plerou, and H. E. Stanley, "Identifying Business Sectors from Stock Price Fluctuations," e-print cond-mat/0011145; V. Plerou, P. Gopikrishnan, L. A. N. Amaral, X. Gabaix, and H. E. Stanley, "Diffusion and Economic Fluctuations," Phys. Rev. E (Rapid Communications) 62, 3023-3026 (2000); P. Gopikrishnan, V. Plerou, X. Gabaix, and H. E. Stanley, "Statistical Properties of Share Volume Traded in Financial Markets," Phys. Rev. E (Rapid Communications) 62, 4493-4496 (2000).

  12. Uncovering middle managers' role in healthcare innovation implementation

    Directory of Open Access Journals (Sweden)

    Birken Sarah A

    2012-04-01

    Full Text Available Abstract Background Middle managers have received little attention in extant health services research, yet they may have a key role in healthcare innovation implementation. The gap between evidence of effective care and practice may be attributed in part to poor healthcare innovation implementation. Investigating middle managers' role in healthcare innovation implementation may reveal an opportunity for improvement. In this paper, we present a theory of middle managers' role in healthcare innovation implementation to fill the gap in the literature and to stimulate research that empirically examines middle managers' influence on innovation implementation in healthcare organizations. Discussion Extant healthcare innovation implementation research has primarily focused on the roles of physicians and top managers. Largely overlooked is the role of middle managers. We suggest that middle managers influence healthcare innovation implementation by diffusing information, synthesizing information, mediating between strategy and day-to-day activities, and selling innovation implementation. Summary Teamwork designs have become popular in healthcare organizations. Because middle managers oversee these team initiatives, their potential to influence innovation implementation has grown. Future research should investigate middle managers' role in healthcare innovation implementation. Findings may aid top managers in leveraging middle managers' influence to improve the effectiveness of healthcare innovation implementation.

  13. Correlation of Activities of the Enzymes α-Phosphoglucomutase, UDP-Galactose 4-Epimerase, and UDP-Glucose Pyrophosphorylase with Exopolysaccharide Biosynthesis by Streptococcus thermophilus LY03

    OpenAIRE

    Degeest, Bart; De Vuyst, Luc

    2000-01-01

    The effects of different carbohydrates or mixtures of carbohydrates as substrates on bacterial growth and exopolysaccharide (EPS) production were studied for the yoghurt starter culture Streptococcus thermophilus LY03. This strain produces two heteropolysaccharides with the same monomeric composition (galactose and glucose in the ratio 4:1) but with different molecular masses. Lactose and glucose were fermented by S. thermophilus LY03 only when they were used as sole energy and carbohydrate s...

  14. Yeast Interacting Proteins Database: YML064C, YKL035W [Yeast Interacting Proteins Database

    Lifescience Database Archive (English)

    Full Text Available th this bait as prey (0) YKL035W UGP1 UDP-glucose pyrophosphorylase (UGPase), catalyses the reversible forma... gene name UGP1 Prey description UDP-glucose pyrophosphorylase (UGPase), catalyses the reversible

  15. Efeitos a curto prazo de "stents" não recobertos e recobertos com politetrafluoroetileno em aorta de suínos: um modelo experimental Short-term effects of polytetrafluoroethylene covered and uncovered metallic "stents" in pig aorta: an experimental model

    Directory of Open Access Journals (Sweden)

    Marco Aurélio Grüdtner

    2004-04-01

    -expandable uncovered metallic stent. On group III animals (n=10 an auto-expandable stent covered with PTFE was inserted. After four weeks the animals were killed, the specimens were harvested and the intimal thickening was quantified by morphometric analysis. RESULTS: In the comparison among groups I, II and III referring to intimal, medial area and intimal index, it was not observed statistically significant variation. Differences were identified among groups referring to luminal proximal (p=0,036 and distal areas (p=0,044. Through multiple comparison tests for Kruskal-Wallis it was identified a difference between groups I and II. However, when these variables were controlled by weigh factor (luminal area/weigh relation, this difference was not observed anymore. CONCLUSION: In this short term study, the PTFE covering is not associated to further intimal thickening besides that promoted by the metallic mesh in large arteries and in high flow conditions.

  16. Comparison of Starch Synthesis and Related Enzyme Activities in Developing Grains among Different Types of Maize%不同类型玉米发育籽粒中淀粉合成及相关酶活性比较

    Institute of Scientific and Technical Information of China (English)

    张海艳; 董树亭; 高荣岐; 李玉全

    2007-01-01

    period.SBE activity of waxy corn was significantly higher than other lines after 10 DAP.DBE activity of sweet corn was extremely lOW and completely lost at 40 DAP.The rates of starch synthesis had some correlation with the activities of SS,SSS,GBSS and SBE during the grain filling process.No correlation was found between the rates of starch synthesis and the activities of ADP-glucose pyrophosphorylase(AGPase)and DBE.SS activity appears to play a major role in starch biosynthesis in maize.GBSS is responsible for amylose synthesis especially in the later period.SSS and SBE are associated with amylopectin biosynthesis.

  17. 水稻淀粉合成相关基因SSⅠ、SSⅢ-1和PUL对稻米品质的影响%Effects of the Starch-synthesizing Genes SSⅠ, SSⅢ-1 and PUL on Rice (Oryza sativa L.) Quality

    Institute of Scientific and Technical Information of China (English)

    康翠芳; 向珣朝; 龙小林; 苏文丽; 许顺菊

    2015-01-01

    可溶性淀粉合成酶基因(soluble starch synthase Ⅰ gene,SSⅠ)和SSⅢ-1以及极限糊精酶基因(pullulanase,PUL)是淀粉合成过程中参与支链淀粉合成的关键基因.为了研究SS Ⅰ、SSⅢ-1和PUL对稻米(Oryza sativa L.)品质的影响,本研究以颗粒结合淀粉合成酶基因(granule bound starch synthas,Wx)与SSⅡ-3均相同的籼型(indica)光温敏核不育系广占63S与潜力三系恢复系CG173R为亲本构建的B1C1F9株系作为供试材料,分析回交重组自交系(backcross inbred lines,BILs)各株系的蒸煮食味品质.结果表明,双亲仅在焦磷酸化酶基因大亚基基因(ADP-glucose pyrophos-phorylase large subunit ADPG,AGPlar)、分支酶3基因(starch branching enzymeⅢgene,SBE3)、PUL、SSⅠ和SSⅢ-1基因位点存在差异;SS Ⅰ、SSⅢ-1和PUL基因在B1C1F9株系中分离对蒸煮品质指标具有显著影响.SSⅢ-1基因在后代分离过程中,不同基因型之间碱消值(alkaline spreading value,ASV)、峰值粘度(peak viscosity,PKV)、崩解值(breakdown value,BDV)和峰值时间(peak time,PeT)4个指标具有显著性差异;PUL基因在后代分离过程中,不同基因型之间,胶稠度(gel consistency,GC)和回复值(consistence value,CSV)具有显著性差异(P<0.05);在SSⅢ-1和SSⅠ基因同时分离的株系中,裂区试验分析表明,SSⅢ-1和SSⅠ基因的互作效应对糊化温度(gelatinization temperature,GT)的效应达极显著水平(P<0.01),对表观直链淀粉含量(apparent amylose content,AAC)、GC、PKV和ASV的效应达显著水平(P<0.05).说明SSⅢ-1和PUL基因对稻米蒸煮食味品质的部分理化指标有显著影响,且SSⅢ-1和SSⅠ基因之间存在显著的互作效应.在相同Wx和SSⅡ-3基因基因背景下,研究稻米淀粉合成途径效应较小的基因对稻米食味品质的影响,对改良稻米蒸煮食味品质和加快稻米品质育种研究具有重要意义.

  18. 番木瓜GDP-D-甘露糖焦磷酸化酶基因的克隆及分析%Cloning and analysis of GDP-D-mannose pyrophosphorylase gene from papaya

    Institute of Scientific and Technical Information of China (English)

    申艳红; 陈晓静; 卢秉国; 何玮毅

    2011-01-01

    The full-length GMP cDNA was cloned by RACE-PCR from papaya and the gene was designated as CpGMP ( C enBank accession No. FJ4896.52). Open reading frame which encoded 361 amino acids was cloned from cDNA. DNA sequence including4extrons and 3 introns was cloned from genomic DNA. Sequencing analysis showed that the amino acid sequence was 90.30%,89.47%, 88.92%, 88.09%, 85.87% homologous with GMP from Malpighia glabra, peach, tomato, Arabidopsis thaliana and rice, respectively. Semi-quantitative RT-PCR analysis showed that the expression of CpGMP increased gradually with papaya fruit maturating and decreased when fruit began to soften.%采用cDNA末端快速扩增方法,获得了番木瓜果实GDP-D-甘露糖焦磷酸化酶(GMP)基因的cDNA全长序列,将其命名为CpGMP,GenBank登录号为FJ489652.然后,根据拼接序列设计开放性阅读框上、下游引物,扩增得到了CpGMP基因的开放性阅读框序列和DNA序列.ORF序列编码361个氨基酸,DNA序列包含4个外显子和3个内含子.序列分析表明,番木瓜GMP与大果黄褥花、桃、番茄、拟南芥、水稻GMP的同源性分别为90.30%、89.47%、88.92%、88.09%、85.87%.半定量RT-PCR分析表明,CpGMP基因随着番木瓜果实的成熟表达量逐渐增加,软化时又逐渐降低.

  19. "The Teacher Is an Octopus": Uncovering Preservice English Language Teachers' Prior Beliefs through Metaphor Analysis

    Science.gov (United States)

    Farrell, Thomas S. C.

    2006-01-01

    Preservice teachers come to any teacher education course with prior experiences, knowledge and beliefs about learning and teaching. Additionally, the belief systems of preservice teachers often serve as a lens through which they view the content of the teacher education program. Consequently, it is essential that teacher educators take these prior…

  20. Genetic architecture of vitamin B12 and folate levels uncovered applying deeply sequenced large datasets.

    Science.gov (United States)

    Grarup, Niels; Sulem, Patrick; Sandholt, Camilla H; Thorleifsson, Gudmar; Ahluwalia, Tarunveer S; Steinthorsdottir, Valgerdur; Bjarnason, Helgi; Gudbjartsson, Daniel F; Magnusson, Olafur T; Sparsø, Thomas; Albrechtsen, Anders; Kong, Augustine; Masson, Gisli; Tian, Geng; Cao, Hongzhi; Nie, Chao; Kristiansen, Karsten; Husemoen, Lise Lotte; Thuesen, Betina; Li, Yingrui; Nielsen, Rasmus; Linneberg, Allan; Olafsson, Isleifur; Eyjolfsson, Gudmundur I; Jørgensen, Torben; Wang, Jun; Hansen, Torben; Thorsteinsdottir, Unnur; Stefánsson, Kari; Pedersen, Oluf

    2013-06-01

    Genome-wide association studies have mainly relied on common HapMap sequence variations. Recently, sequencing approaches have allowed analysis of low frequency and rare variants in conjunction with common variants, thereby improving the search for functional variants and thus the understanding of the underlying biology of human traits and diseases. Here, we used a large Icelandic whole genome sequence dataset combined with Danish exome sequence data to gain insight into the genetic architecture of serum levels of vitamin B(12) (B12) and folate. Up to 22.9 million sequence variants were analyzed in combined samples of 45,576 and 37,341 individuals with serum B(12) and folate measurements, respectively. We found six novel loci associating with serum B(12) (CD320, TCN2, ABCD4, MMAA, MMACHC) or folate levels (FOLR3) and confirmed seven loci for these traits (TCN1, FUT6, FUT2, CUBN, CLYBL, MUT, MTHFR). Conditional analyses established that four loci contain additional independent signals. Interestingly, 13 of the 18 identified variants were coding and 11 of the 13 target genes have known functions related to B(12) and folate pathways. Contrary to epidemiological studies we did not find consistent association of the variants with cardiovascular diseases, cancers or Alzheimer's disease although some variants demonstrated pleiotropic effects. Although to some degree impeded by low statistical power for some of these conditions, these data suggest that sequence variants that contribute to the population diversity in serum B(12) or folate levels do not modify the risk of developing these conditions. Yet, the study demonstrates the value of combining whole genome and exome sequencing approaches to ascertain the genetic and molecular architectures underlying quantitative trait associations. PMID:23754956

  1. Using giant scarlet runner bean embryos to uncover regulatory networks controlling suspensor gene activity

    Directory of Open Access Journals (Sweden)

    Kelli F. Henry

    2015-02-01

    Full Text Available One of the major unsolved issues in plant development is understanding the regulatory networks that control the differential gene activity that is required for the specification and development of the two major embryonic regions, the embryo proper and suspensor. Historically, the giant embryo of scarlet runner bean (SRB, Phaseolus coccineus, has been used as a model system to investigate the physiological events that occur early in embryogenesis – focusing on the question of what role the suspensor region plays. A major feature distinguishing SRB embryos from those of other plants is a highly enlarged suspensor containing at least 200 cells that synthesize growth regulators required for subsequent embryonic development. Recent studies have exploited the giant size of the SRB embryo to micro-dissect the embryo proper and suspensor regions in order to use genomics-based approaches to identify regulatory genes that may be involved in controlling suspensor and embryo proper differentiation, as well as the cellular processes that may be unique to each embryonic region. Here we review the current genomics resources that make SRB embryos a compelling model system for studying the early events required to program embryo development.

  2. Uncovering the Ancestry of B Chromosomes in Moenkhausia sanctaefilomenae (Teleostei, Characidae.

    Directory of Open Access Journals (Sweden)

    Ricardo Utsunomia

    Full Text Available B chromosomes constitute a heterogeneous mixture of genomic parasites that are sometimes derived intraspecifically from the standard genome of the host species, but result from interspecific hybridization in other cases. The mode of origin determines the DNA content, with the B chromosomes showing high similarity with the A genome in the first case, but presenting higher similarity with a different species in the second. The characid fish Moenkhausia sanctaefilomenae harbours highly invasive B chromosomes, which are present in all populations analyzed to date in the Parana and Tietê rivers. To investigate the origin of these B chromosomes, we analyzed two natural populations: one carrying B chromosomes and the other lacking them, using a combination of molecular cytogenetic techniques, nucleotide sequence analysis and high-throughput sequencing (Illumina HiSeq2000. Our results showed that i B chromosomes have not yet reached the Paranapanema River basin; ii B chromosomes are mitotically unstable; iii there are two types of B chromosomes, the most frequent of which is lightly C-banded (similar to euchromatin in A chromosomes (B1, while the other is darkly C-banded (heterochromatin-like (B2; iv the two B types contain the same tandem repeat DNA sequences (18S ribosomal DNA, H3 histone genes, MS3 and MS7 satellite DNA, with a higher content of 18S rDNA in the heterochromatic variant; v all of these repetitive DNAs are present together only in the paracentromeric region of autosome pair no. 6, suggesting that the B chromosomes are derived from this A chromosome; vi the two B chromosome variants show MS3 sequences that are highly divergent from each other and from the 0B genome, although the B2-derived sequences exhibit higher similarity with the 0B genome (this suggests an independent origin of the two B variants, with the less frequent, B2 type presumably being younger; and vii the dN/dS ratio for the H3.2 histone gene is almost 4-6 times higher for B chromosomes than for A chromosome sequences, suggesting that purifying selection is relaxed for the DNA sequences located on the B chromosomes, presumably because they are mostly inactive.

  3. Uncovering the Ancestry of B Chromosomes in Moenkhausia sanctaefilomenae (Teleostei, Characidae).

    Science.gov (United States)

    Utsunomia, Ricardo; Silva, Duílio Mazzoni Zerbinato de Andrade; Ruiz-Ruano, Francisco J; Araya-Jaime, Cristian; Pansonato-Alves, José Carlos; Scacchetti, Priscilla Cardim; Hashimoto, Diogo Teruo; Oliveira, Claudio; Trifonov, Vladmir A; Porto-Foresti, Fábio; Camacho, Juan Pedro M; Foresti, Fausto

    2016-01-01

    B chromosomes constitute a heterogeneous mixture of genomic parasites that are sometimes derived intraspecifically from the standard genome of the host species, but result from interspecific hybridization in other cases. The mode of origin determines the DNA content, with the B chromosomes showing high similarity with the A genome in the first case, but presenting higher similarity with a different species in the second. The characid fish Moenkhausia sanctaefilomenae harbours highly invasive B chromosomes, which are present in all populations analyzed to date in the Parana and Tietê rivers. To investigate the origin of these B chromosomes, we analyzed two natural populations: one carrying B chromosomes and the other lacking them, using a combination of molecular cytogenetic techniques, nucleotide sequence analysis and high-throughput sequencing (Illumina HiSeq2000). Our results showed that i) B chromosomes have not yet reached the Paranapanema River basin; ii) B chromosomes are mitotically unstable; iii) there are two types of B chromosomes, the most frequent of which is lightly C-banded (similar to euchromatin in A chromosomes) (B1), while the other is darkly C-banded (heterochromatin-like) (B2); iv) the two B types contain the same tandem repeat DNA sequences (18S ribosomal DNA, H3 histone genes, MS3 and MS7 satellite DNA), with a higher content of 18S rDNA in the heterochromatic variant; v) all of these repetitive DNAs are present together only in the paracentromeric region of autosome pair no. 6, suggesting that the B chromosomes are derived from this A chromosome; vi) the two B chromosome variants show MS3 sequences that are highly divergent from each other and from the 0B genome, although the B2-derived sequences exhibit higher similarity with the 0B genome (this suggests an independent origin of the two B variants, with the less frequent, B2 type presumably being younger); and vii) the dN/dS ratio for the H3.2 histone gene is almost 4-6 times higher for B chromosomes than for A chromosome sequences, suggesting that purifying selection is relaxed for the DNA sequences located on the B chromosomes, presumably because they are mostly inactive. PMID:26934481

  4. Uncovering Undergraduate English-as-a-Foreign-Language Learners’ Perceptions of Reticence

    Directory of Open Access Journals (Sweden)

    Abbas Zare-ee

    2014-10-01

    Full Text Available The study of factors influencing undergraduate learners’ participation and/or reticence in second/foreign language classrooms, a relatively recent line of research, can contribute to the betterment of language teaching and learning practices. In this work, we attempt to investigate the causes of a population of undergraduate English as a foreign language (EFL learners’ reticence by focusing on their own perceptions and by seeing the problem from their perspective. 201 male and female undergraduate Iranian EFL learners selected randomly based on Krejcie and Morgan’s formula for determining sample size served as the participants of the study. The data were collected through interviews, observations and a five-point Likert-scale researcher-made questionnaire. The results of the analyses of the data through qualitative content-based coding of the transcripts, frequency counts, and factorial analysis of the questionnaire responses revealed the following: a based on systematic class observations, most students appeared to understand teachers’ instruction, took notes, and spoke when addressed; however, they rarely asked questions or volunteered responses; b unfriendly and competitive class atmosphere, boring and useless topics and materials, and having unmotivated and serious teachers were among the most  frequent  learner-perceived factors causing reticence; c based on the results of exploratory factorial analysis, 12 factors including  learner anxiety,  poor class management, peer/ teacher correction,  background knowledge, grouping learners, and self-image were reported as the main causes of reticence. Based on these findings, we make suggestions for EFL teachers about how to consider students’ concerns and to promote class participation.

  5. Uncovering the Stabilization Mechanism in Bimetallic Ruthenium-Iridium Anodes for Proton Exchange Membrane Electrolyzers.

    Science.gov (United States)

    Saveleva, Viktoriia A; Wang, Li; Luo, Wen; Zafeiratos, Spyridon; Ulhaq-Bouillet, Corinne; Gago, Aldo S; Friedrich, K Andreas; Savinova, Elena R

    2016-08-18

    Proton exchange membrane (PEM) electrolyzers are attracting an increasing attention as a promising technology for the renewable electricity storage. In this work, near ambient pressure X-ray photoelectron spectroscopy (NAP-XPS) is applied for in situ monitoring of the surface state of membrane electrode assemblies with RuO2 and bimetallic Ir0.7Ru0.3O2 anodes during water splitting. We demonstrate that Ir protects Ru from the formation of an unstable hydrous Ru(IV) oxide thereby rendering bimetallic Ru-Ir oxide electrodes with higher corrosion resistance. We further show that the water splitting occurs through a surface Ru(VIII) intermediate, and, contrary to common opinion, the presence of Ir does not hinder its formation. PMID:27477824

  6. Uncovering Critical Research Agendas for School Psychology: Conceptual Dimensions and Future Directions.

    Science.gov (United States)

    Kratochwill, Thomas R.; Stoiber, Karen Callan

    2000-01-01

    Considers research agendas for moving the school psychology profession forward by yielding unique contributions in the millennium, while enabling school psychologists to enhance outcomes for children and families with greater precision and effectiveness. Specifically examines some research agendas in the areas of diagnosis and assessment,…

  7. Uncovering Trophic Interactions in Arthropod Predators through DNA Shotgun-Sequencing of Gut Contents.

    Science.gov (United States)

    Paula, Débora P; Linard, Benjamin; Crampton-Platt, Alex; Srivathsan, Amrita; Timmermans, Martijn J T N; Sujii, Edison R; Pires, Carmen S S; Souza, Lucas M; Andow, David A; Vogler, Alfried P

    2016-01-01

    Characterizing trophic networks is fundamental to many questions in ecology, but this typically requires painstaking efforts, especially to identify the diet of small generalist predators. Several attempts have been devoted to develop suitable molecular tools to determine predatory trophic interactions through gut content analysis, and the challenge has been to achieve simultaneously high taxonomic breadth and resolution. General and practical methods are still needed, preferably independent of PCR amplification of barcodes, to recover a broader range of interactions. Here we applied shotgun-sequencing of the DNA from arthropod predator gut contents, extracted from four common coccinellid and dermapteran predators co-occurring in an agroecosystem in Brazil. By matching unassembled reads against six DNA reference databases obtained from public databases and newly assembled mitogenomes, and filtering for high overlap length and identity, we identified prey and other foreign DNA in the predator guts. Good taxonomic breadth and resolution was achieved (93% of prey identified to species or genus), but with low recovery of matching reads. Two to nine trophic interactions were found for these predators, some of which were only inferred by the presence of parasitoids and components of the microbiome known to be associated with aphid prey. Intraguild predation was also found, including among closely related ladybird species. Uncertainty arises from the lack of comprehensive reference databases and reliance on low numbers of matching reads accentuating the risk of false positives. We discuss caveats and some future prospects that could improve the use of direct DNA shotgun-sequencing to characterize arthropod trophic networks. PMID:27622637

  8. Congenital Heart Disease Genetics Uncovers Context-Dependent Organization and Function of Nucleoporins at Cilia.

    Science.gov (United States)

    Del Viso, Florencia; Huang, Fang; Myers, Jordan; Chalfant, Madeleine; Zhang, Yongdeng; Reza, Nooreen; Bewersdorf, Joerg; Lusk, C Patrick; Khokha, Mustafa K

    2016-09-12

    Human genomics is identifying candidate genes for congenital heart disease (CHD), but discovering the underlying mechanisms remains challenging. In a patient with CHD and heterotaxy (Htx), a disorder of left-right patterning, we previously identified a duplication in Nup188. However, a mechanism to explain how a component of the nuclear pore complex (NPC) could cause Htx/CHD was undefined. Here, we show that knockdown of Nup188 or its binding partner Nup93 leads to a loss of cilia during embryonic development while leaving NPC function largely intact. Many data, including the localization of endogenous Nup188/93 at cilia bases, support their direct role at cilia. Super-resolution imaging of Nup188 shows two barrel-like structures with dimensions and organization incompatible with an NPC-like ring, arguing against a proposed "ciliary pore complex." We suggest that the nanoscale organization and function of nucleoporins are context dependent in a way that is required for the structure of the heart. PMID:27593162

  9. Self-Efficacy Beliefs and Mental Time Travel Ability: Uncovering a Hidden Relationship in Educational Settings

    Science.gov (United States)

    Eren, Altay

    2009-01-01

    The aim of this study was threefold: first, it was to explore the profiles of student teachers' mental time travel ability; second, it was to examine the relationship between student teachers' mental time travel ability and self-efficacy beliefs; and third, it was to investigate the role of self-efficacy beliefs in relationship between the past…

  10. Uncovering China’s greenhouse gas emission from regional and sectoral perspectives

    International Nuclear Information System (INIS)

    Understanding China’s GHG (greenhouse gas) emission status is critical for achieving the national mitigation plan. While much attention has addressed China’s national level GHG emission, less is known about its regional and sectoral emission features. In this paper China’s regional and sectoral GHG emission patterns and their driving forces were explored by using upgraded energy consumption data. We constructed a detailed GHG inventory for each province in the year 2009 which covering 28 sectors and further expanded time-serious inventories during 1997–2009. We then conducted variation and index decomposition analysis to explore its sectoral/regional disparity and features. Results showed significant differences of sectoral emission intensity among different provinces, implying a huge disparity of technology level. Since less developed provinces still apply energy intensive technologies, they had contributed to most of national emission increment during 1997–2009 and made the whole country towards carbon intensive direction. Our research outcomes indicate that the inequity of technology level among regions has already become a main barrier for China’s CO2 mitigation. Such a reality deserves more attention from both researchers and policy makers so that appropriate carbon reduction policies can be raised. -- Highlights: ► We present spacial and sectoral disparity and drivers on green house gas (GHG) emission in 30 Chinese provinces. ► We indicated a huge difference of technology level among regions. ► Different industrial structure and development stage further result in GHG intensive in China's poor regions. ► Inequity of technology level among regions has already become a main barrier for China's GHG mitigation.

  11. The next generation of metastatic melanoma: uncovering the genetic variants for anti-BRAF therapy response.

    Science.gov (United States)

    Pinto, Rosamaria; De Summa, Simona; Strippoli, Sabino; Pilato, Brunella; Azzariti, Amalia; Guida, Gabriella; Guida, Michele; Tommasi, Stefania

    2016-05-01

    Metastatic melanoma (MM) is a highly aggressive cancer with a median overall survival of 6-9 months, notwithstanding the numerous efforts in development of new therapeutic approaches. To this aim we tested the clinical applicability of the Ion Torrent Personal Genome Machine to simultaneously screen MM patients in order to individuate new or already known SNPs and mutations able to predict the duration of response to BRAF inhibitors. An Ampliseq Custom Panel, including 11 crucial full length genes involved in melanoma carcinogenesis and therapy response pathways, was created and used to analyze 25 MM patients. We reported BRAFV600 and NRASQ61 mutations in 68% and 24% of samples, respectively. Moreover, we more frequently identified the following alterations related to BRAF status: PIK3CAI391M (44%) and KITD737N (36%) mutations, CTLA4T17A (52%), MC1RV60L (32%) and MITFS473A (60%) polymorphisms. Considering the progression free survival (PFS), statistical analyses showed that BRAFV600 patients without any of these more frequent alterations had a higher median PFS. Protein structure changes seem to be due to these variants by in silico analysis. In conclusion, a Next-Generation Sequencing approach with custom panel may provide new information to evaluate tumor-specific therapeutic susceptibility and individual prognosis to improve the care of MM patients.

  12. Recharging or retiring older workers? Uncovering age-based strategies of European employers

    NARCIS (Netherlands)

    H.P. van Dalen; K. Henkens; M. Wang

    2014-01-01

    Purpose of the Study: We offer an empirically based taxonomy of the human resource policies of European employers in relation to older workers. In particular, 3 age-based strategies are discussed and analyzed in a simultaneous fashion: a focus on exit through retirement, workplace accommodation meas

  13. An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits.

    Directory of Open Access Journals (Sweden)

    Yang Liu

    2006-11-01

    Full Text Available With mounting availability of genomic and phenotypic databases, data integration and mining become increasingly challenging. While efforts have been put forward to analyze prokaryotic phenotypes, current computational technologies either lack high throughput capacity for genomic scale analysis, or are limited in their capability to integrate and mine data across different scales of biology. Consequently, simultaneous analysis of associations among genomes, phenotypes, and gene functions is prohibited. Here, we developed a high throughput computational approach, and demonstrated for the first time the feasibility of integrating large quantities of prokaryotic phenotypes along with genomic datasets for mining across multiple scales of biology (protein domains, pathways, molecular functions, and cellular processes. Applying this method over 59 fully sequenced prokaryotic species, we identified genetic basis and molecular mechanisms underlying the phenotypes in bacteria. We identified 3,711 significant correlations between 1,499 distinct Pfam and 63 phenotypes, with 2,650 correlations and 1,061 anti-correlations. Manual evaluation of a random sample of these significant correlations showed a minimal precision of 30% (95% confidence interval: 20%-42%; n = 50. We stratified the most significant 478 predictions and subjected 100 to manual evaluation, of which 60 were corroborated in the literature. We furthermore unveiled 10 significant correlations between phenotypes and KEGG pathways, eight of which were corroborated in the evaluation, and 309 significant correlations between phenotypes and 166 GO concepts evaluated using a random sample (minimal precision = 72%; 95% confidence interval: 60%-80%; n = 50. Additionally, we conducted a novel large-scale phenomic visualization analysis to provide insight into the modular nature of common molecular mechanisms spanning multiple biological scales and reused by related phenotypes (metaphenotypes. We propose that this method elucidates which classes of molecular mechanisms are associated with phenotypes or metaphenotypes and holds promise in facilitating a computable systems biology approach to genomic and biomedical research.

  14. The Correspondence Analysis Platform for Uncovering Deep Structure in Data and Information

    CERN Document Server

    Murtagh, Fionn

    2008-01-01

    We study two aspects of information semantics: (i) the collection of all relationships, (ii) tracking and spotting anomaly and change. The first is implemented by endowing all relevant information spaces with a Euclidean metric in a common projected space. The second is modelled by an induced ultrametric. A very general way to achieve a Euclidean embedding of different information spaces based on cross-tabulation counts (and from other input data formats) is provided by Correspondence Analysis. From there, the induced ultrametric that we are particularly interested in takes a sequential - e.g. temporal - ordering of the data into account. We employ such a perspective to look at narrative, "the flow of thought and the flow of language" (Chafe). In application to policy decision making, we show how we can focus analysis in a small number of dimensions.

  15. Uncovering the prevalence and diversity of integrating conjugative elements in actinobacteria.

    Directory of Open Access Journals (Sweden)

    Mariana Gabriela Ghinet

    Full Text Available Horizontal gene transfer greatly facilitates rapid genetic adaptation of bacteria to shifts in environmental conditions and colonization of new niches by allowing one-step acquisition of novel functions. Conjugation is a major mechanism of horizontal gene transfer mediated by conjugative plasmids and integrating conjugative elements (ICEs. While in most bacterial conjugative systems DNA translocation requires the assembly of a complex type IV secretion system (T4SS, in Actinobacteria a single DNA FtsK/SpoIIIE-like translocation protein is required. To date, the role and diversity of ICEs in Actinobacteria have received little attention. Putative ICEs were searched for in 275 genomes of Actinobacteria using HMM-profiles of proteins involved in ICE maintenance and transfer. These exhaustive analyses revealed 144 putative FtsK/SpoIIIE-type ICEs and 17 putative T4SS-type ICEs. Grouping of the ICEs based on the phylogenetic analyses of maintenance and transfer proteins revealed extensive exchanges between different sub-families of ICEs. 17 ICEs were found in Actinobacteria from the genus Frankia, globally important nitrogen-fixing microorganisms that establish root nodule symbioses with actinorhizal plants. Structural analysis of ICEs from Frankia revealed their unexpected diversity and a vast array of predicted adaptive functions. Frankia ICEs were found to excise by site-specific recombination from their host's chromosome in vitro and in planta suggesting that they are functional mobile elements whether Frankiae live as soil saprophytes or plant endosymbionts. Phylogenetic analyses of proteins involved in ICEs maintenance and transfer suggests that active exchange between ICEs cargo-borne and chromosomal genes took place within the Actinomycetales order. Functionality of Frankia ICEs in vitro as well as in planta lets us anticipate that conjugation and ICEs could allow the development of genetic manipulation tools for this challenging microorganism and for many other Actinobacteria.

  16. Uncovering the Prevalence and Diversity of Integrating Conjugative Elements in Actinobacteria

    OpenAIRE

    Mariana Gabriela Ghinet; Eric Bordeleau; Julie Beaudin; Ryszard Brzezinski; Sébastien Roy; Vincent Burrus

    2011-01-01

    Horizontal gene transfer greatly facilitates rapid genetic adaptation of bacteria to shifts in environmental conditions and colonization of new niches by allowing one-step acquisition of novel functions. Conjugation is a major mechanism of horizontal gene transfer mediated by conjugative plasmids and integrating conjugative elements (ICEs). While in most bacterial conjugative systems DNA translocation requires the assembly of a complex type IV secretion system (T4SS), in Actinobacteria a sing...

  17. Using Caenorhabditis elegans to Uncover Conserved Functions of Omega-3 and Omega-6 Fatty Acids

    Directory of Open Access Journals (Sweden)

    Jennifer L. Watts

    2016-02-01

    Full Text Available The nematode Caenorhabditis elegans is a powerful model organism to study functions of polyunsaturated fatty acids. The ability to alter fatty acid composition with genetic manipulation and dietary supplementation permits the dissection of the roles of omega-3 and omega-6 fatty acids in many biological process including reproduction, aging and neurobiology. Studies in C. elegans to date have mostly identified overlapping functions of 20-carbon omega-6 and omega-3 fatty acids in reproduction and in neurons, however, specific roles for either omega-3 or omega-6 fatty acids are beginning to emerge. Recent findings with importance to human health include the identification of a conserved Cox-independent prostaglandin synthesis pathway, critical functions for cytochrome P450 derivatives of polyunsaturated fatty acids, the requirements for omega-6 and omega-3 fatty acids in sensory neurons, and the importance of fatty acid desaturation for long lifespan. Furthermore, the ability of C. elegans to interconvert omega-6 to omega-3 fatty acids using the FAT-1 omega-3 desaturase has been exploited in mammalian studies and biotechnology approaches to generate mammals capable of exogenous generation of omega-3 fatty acids.

  18. Recharging or Retiring Older Workers? Uncovering the Age-Based Strategies of European Employers

    NARCIS (Netherlands)

    van Dalen, Hendrik P.; Henkens, Kene; Wang, Mo

    2015-01-01

    Purpose of the Study: We offer an empirically based taxonomy of the human resource policies of European employers in relation to older workers. In particular, 3 age-based strategies are discussed and analyzed in a simultaneous fashion: a focus on exit through retirement, workplace accommodation meas

  19. Using earthquakes to uncover the Earth's inner secrets: interactive exhibits for geophysical education

    Directory of Open Access Journals (Sweden)

    C. Nostro

    2005-01-01

    Full Text Available The Educational & Outreach Group (E&O Group of the Istituto Nazionale di Geofisica e Vulcanologia (INGV designed a portable museum to bring on the road educational activities focused on seismology, seismic hazard and Earth science. This project was developed for the first edition of the Science Festival organized in Genoa, Italy, in 2003. The museum has been mainly focused to school students of all ages and explains the main topics of geophysics through posters, movie and slide presentations, and exciting interactive experiments. This new INGV museum has been remarkably successful, being visited by more than 8000 children and adults during the 10 days of the Science Festival. It is now installed at the INGV headquarters in Rome and represents the main attraction during the visits of the schools all year round.

  20. Uncovering molecular structural mechanisms of signaling mediated by the prion protein

    International Nuclear Information System (INIS)

    The glycosyl phosphatidylinositol (GPI) - anchored prion protein (PrPc), usually associated with neurodegenerative diseases, modulates various cellular responses and may scaffold multiprotein cell surface signaling complexes. Engagement of PrPc with the secretable cochaperone hop/STI 1 induces neurotrophic transmembrane signals through unknown molecular mechanisms. We addressed whether interaction of Pr Pc and hop STI 1 entails structural rearrangements relevant for signaling. Circular dichroism and fluorescence spectroscopy showed that PrPc:hop/STI 1 interaction triggers loss of PrP helical structures, involving at least a perturbation of the Pr Pc143-153 beta-helix. Novel SAXS models revealed a significant C-terminal compaction of hop/STI 1 when bound to PrPc. Differing from a recent dimeric model of human hop/STI 1, both size exclusion chromatography and SAXS data support a monomeric form of free murine hop/STI 1. Changes in the Pr Pc143-153 beta-helix may engage the transmembrane signaling protein laminin receptor precursor and neural cell adhesion molecule, both of which bind that domain of Pr Pc, and further ligands may be engaged by the tertiary structural changes of hop/STI 1. These reciprocal structural modifications indicate a versatile mechanism for signaling mediated by Pr Pc:hop/STI 1 interaction, consistent with the hypothesis that Pr Pc scaffolds multiprotein signaling complexes at the cell surface. (author)

  1. Transcriptional Profiles Uncover Aspergillus flavus-Induced Resistance in Maize Kernels

    Science.gov (United States)

    Luo, Meng; Brown, Robert L.; Chen, Zhi-Yuan; Menkir, Abebe; Yu, Jiujiang; Bhatnagar, Deepak

    2011-01-01

    Aflatoxin contamination caused by the opportunistic pathogen A. flavus is a major concern in maize production prior to harvest and through storage. Previous studies have highlighted the constitutive production of proteins involved in maize kernel resistance against A. flavus’ infection. However, little is known about induced resistance nor about defense gene expression and regulation in kernels. In this study, maize oligonucleotide arrays and a pair of closely-related maize lines varying in aflatoxin accumulation were used to reveal the gene expression network in imbibed mature kernels in response to A. flavus’ challenge. Inoculated kernels were incubated 72 h via the laboratory-based Kernel Screening Assay (KSA), which highlights kernel responses to fungal challenge. Gene expression profiling detected 6955 genes in resistant and 6565 genes in susceptible controls; 214 genes induced in resistant and 2159 genes induced in susceptible inoculated kernels. Defense related and regulation related genes were identified in both treatments. Comparisons between the resistant and susceptible lines indicate differences in the gene expression network which may enhance our understanding of the maize-A. flavus interaction. PMID:22069739

  2. Fysieke belasting bij verschillende kuilblootmethoden = Physical load during different methods to uncover silage pits

    NARCIS (Netherlands)

    Roelofs, P.F.M.M.; Berg, van den G.; Dooren, van H.J.C.

    2006-01-01

    In 2006 is in het kader van het Arboconvenant Agrarische sectoren onderzoek uitgevoerd naar mogelijkheden om de fysieke belasting bij het bloten van voerkuilen te verminderen. Het onderzoek was gericht op afdekkingmethoden van voerkuilen en op hulpmiddelen bij het bloten die men op praktijkbedrijven

  3. Uncovering document fraud in maritime freight transport based on probabilistic classification

    NARCIS (Netherlands)

    Triepels, Ron; Feelders, A. F.; Daniels, Hennie

    2015-01-01

    Deficient visibility in global supply chains causes significant risks for the customs brokerage practices of freight forwarders. One of the risks that freight forwarders face is that shipping documentation might contain document fraud and is used to declare a shipment. Traditional risk controls are

  4. Uncovering microRNA-mediated response to SO2 stress in Arabidopsis thaliana by deep sequencing.

    Science.gov (United States)

    Li, Lihong; Xue, Meizhao; Yi, Huilan

    2016-10-01

    Sulfur dioxide (SO2) is a major air pollutant and has significant impacts on plants. MicroRNAs (miRNAs) are a class of gene expression regulators that play important roles in response to environmental stresses. In this study, deep sequencing was used for genome-wide identification of miRNAs and their expression profiles in response to SO2 stress in Arabidopsis thaliana shoots. A total of 27 conserved miRNAs and 5 novel miRNAs were found to be differentially expressed under SO2 stress. qRT-PCR analysis showed mostly negative correlation between miRNA accumulation and target gene mRNA abundance, suggesting regulatory roles of these miRNAs during SO2 exposure. The target genes of SO2-responsive miRNAs encode transcription factors and proteins that regulate auxin signaling and stress response, and the miRNAs-mediated suppression of these genes could improve plant resistance to SO2 stress. Promoter sequence analysis of genes encoding SO2-responsive miRNAs showed that stress-responsive and phytohormone-related cis-regulatory elements occurred frequently, providing additional evidence of the involvement of miRNAs in adaption to SO2 stress. This study represents a comprehensive expression profiling of SO2-responsive miRNAs in Arabidopsis and broads our perspective on the ubiquitous regulatory roles of miRNAs under stress conditions. PMID:27232729

  5. A dynamical network approach to uncovering hidden causality relationships in collective neuron firings

    CERN Document Server

    Ruszczycki, Bła\\ zej; Johnson, Neil F

    2009-01-01

    We analyze the synchronous firings of the salamander ganglion cells from the perspective of the complex network viewpoint where the network's links reflect the correlated behavior of firings. We study the time-aggregated properties of the resulting network focusing on its topological features. The behavior of pairwise correlations has been inspected in order to construct an appropriate measure that will serve as a weight of network connection.

  6. The next generation of metastatic melanoma: uncovering the genetic variants for anti-BRAF therapy response

    Science.gov (United States)

    Pinto, Rosamaria; De Summa, Simona; Strippoli, Sabino; Pilato, Brunella; Azzariti, Amalia; Guida, Gabriella; Guida, Michele; Tommasi, Stefania

    2016-01-01

    Metastatic melanoma (MM) is a highly aggressive cancer with a median overall survival of 6–9 months, notwithstanding the numerous efforts in development of new therapeutic approaches. To this aim we tested the clinical applicability of the Ion Torrent Personal Genome Machine to simultaneously screen MM patients in order to individuate new or already known SNPs and mutations able to predict the duration of response to BRAF inhibitors. An Ampliseq Custom Panel, including 11 crucial full length genes involved in melanoma carcinogenesis and therapy response pathways, was created and used to analyze 25 MM patients. We reported BRAFV600 and NRASQ61 mutations in 68% and 24% of samples, respectively. Moreover, we more frequently identified the following alterations related to BRAF status: PIK3CAI391M (44%) and KITD737N (36%) mutations, CTLA4T17A (52%), MC1RV60L (32%) and MITFS473A (60%) polymorphisms. Considering the progression free survival (PFS), statistical analyses showed that BRAFV600 patients without any of these more frequent alterations had a higher median PFS. Protein structure changes seem to be due to these variants by in silico analysis. In conclusion, a Next-Generation Sequencing approach with custom panel may provide new information to evaluate tumor-specific therapeutic susceptibility and individual prognosis to improve the care of MM patients. PMID:26863566

  7. Cryptic speciation patterns in Iranian rock lizards uncovered by integrative taxonomy.

    Directory of Open Access Journals (Sweden)

    Faraham Ahmadzadeh

    Full Text Available While traditionally species recognition has been based solely on morphological differences either typological or quantitative, several newly developed methods can be used for a more objective and integrative approach on species delimitation. This may be especially relevant when dealing with cryptic species or species complexes, where high overall resemblance between species is coupled with comparatively high morphological variation within populations. Rock lizards, genus Darevskia, are such an example, as many of its members offer few diagnostic morphological features. Herein, we use a combination of genetic, morphological and ecological criteria to delimit cryptic species within two species complexes, D. chlorogaster and D. defilippii, both distributed in northern Iran. Our analyses are based on molecular information from two nuclear and two mitochondrial genes, morphological data (15 morphometric, 16 meristic and four categorical characters and eleven newly calculated spatial environmental predictors. The phylogeny inferred for Darevskia confirmed monophyly of each species complex, with each of them comprising several highly divergent clades, especially when compared to other congeners. We identified seven candidate species within each complex, of which three and four species were supported by Bayesian species delimitation within D. chlorogaster and D. defilippii, respectively. Trained with genetically determined clades, Ecological Niche Modeling provided additional support for these cryptic species. Especially those within the D. defilippii-complex exhibit well-differentiated niches. Due to overall morphological resemblance, in a first approach PCA with mixed variables only showed the separation between the two complexes. However, MANCOVA and subsequent Discriminant Analysis performed separately for both complexes allowed for distinction of the species when sample size was large enough, namely within the D. chlorogaster-complex. In conclusion, the results support four new species, which are described herein.

  8. Buffering mechanisms in aging: a systems approach toward uncovering the genetic component of aging.

    Directory of Open Access Journals (Sweden)

    Aviv Bergman

    2007-08-01

    Full Text Available An unrealized potential to understand the genetic basis of aging in humans, is to consider the immense survival advantage of the rare individuals who live 100 years or more. The Longevity Gene Study was initiated in 1998 at the Albert Einstein College of Medicine to investigate longevity genes in a selected population: the "oldest old" Ashkenazi Jews, 95 years of age and older, and their children. The study proved the principle that some of these subjects are endowed with longevity-promoting genotypes. Here we reason that some of the favorable genotypes act as mechanisms that buffer the deleterious effect of age-related disease genes. As a result, the frequency of deleterious genotypes may increase among individuals with extreme lifespan because their protective genotype allows disease-related genes to accumulate. Thus, studies of genotypic frequencies among different age groups can elucidate the genetic determinants and pathways responsible for longevity. Borrowing from evolutionary theory, we present arguments regarding the differential survival via buffering mechanisms and their target age-related disease genes in searching for aging and longevity genes. Using more than 1,200 subjects between the sixth and eleventh decades of life (at least 140 subjects in each group, we corroborate our hypotheses experimentally. We study 66 common allelic site polymorphism in 36 candidate genes on the basis of their phenotype. Among them we have identified a candidate-buffering mechanism and its candidate age-related disease gene target. Previously, the beneficial effect of an advantageous cholesteryl ester transfer protein (CETP-VV genotype on lipoprotein particle size in association with decreased metabolic and cardiovascular diseases, as well as with better cognitive function, have been demonstrated. We report an additional advantageous effect of the CETP-VV (favorable genotype in neutralizing the deleterious effects of the lipoprotein(a (LPA gene. Finally, using literature-based interaction discovery methods, we use the set of longevity genes, buffering genes, and their age-related target disease genes to construct the underlying subnetwork of interacting genes that is expected to be responsible for longevity. Genome wide, high-throughput hypothesis-free analyses are currently being utilized to elucidate unknown genetic pathways in many model organisms, linking observed phenotypes to their underlying genetic mechanisms. The longevity phenotype and its genetic mechanisms, such as our buffering hypothesis, are similar; thus, the experimental corroboration of our hypothesis provides a proof of concept for the utility of high-throughput methods for elucidating such mechanisms. It also provides a framework for developing strategies to prevent some age-related diseases by intervention at the appropriate level.

  9. Uncovering mass segregation with galaxy analogues in dark-matter simulations

    Science.gov (United States)

    Joshi, Gandhali D.; Parker, Laura C.; Wadsley, James

    2016-10-01

    We investigate mass segregation in group and cluster environments by identifying galaxy analogues in high-resolution dark-matter simulations. Subhaloes identified by the Amiga's Halo Finder (AHF) and ROCKSTAR halo finders have similar mass functions, independent of resolution, but different radial distributions due to significantly different subhalo hierarchies. We propose a simple way to classify subhaloes as galaxy analogues. The radial distributions of galaxy analogues agree well at large halocentric radii for both AHF and ROCKSTAR but disagree near parent halo centres where the phase-space information used by ROCKSTAR is essential. We see clear mass segregation at small radii (within 0.5 rvir) with average galaxy analogue mass decreasing with radius. Beyond the virial radius, we find a mild trend where the average galaxy analogue mass increases with radius. These mass segregation trends are strongest in small groups and dominated by the segregation of low-mass analogues. The lack of mass segregation in massive galaxy analogues suggests that the observed trends are driven by the complex accretion histories of the parent haloes rather than dynamical friction.

  10. Contract Faculty in Canada: Using Access to Information Requests to Uncover Hidden Academics in Canadian Universities

    Science.gov (United States)

    Brownlee, Jamie

    2015-01-01

    In Canada, universities are undergoing a process of corporatization where business interests, values and practices are assuming a more prominent place in higher education. A key feature of this process has been the changing composition of academic labor. While it is generally accepted that universities are relying more heavily on contract faculty,…

  11. Connectivity mapping uncovers small molecules that modulate neurodegeneration in Huntington’s disease models

    OpenAIRE

    Joshua L Smalley; Breda, Carlo; Mason, Robert P.; Kooner, Gurdeep; Luthi-Carter, Ruth; Gant, Timothy W.; Giorgini, Flaviano

    2015-01-01

    Abstract Huntington’s disease (HD) is a genetic disease caused by a CAG trinucleotide repeat expansion encoding a polyglutamine tract in the huntingtin (HTT) protein, ultimately leading to neuronal loss and consequent cognitive decline and death. As no treatments for HD currently exist, several chemical screens have been performed using cell-based models of mutant HTT toxicity. These screens measured single disease-related endpoints, such as cell death, but had low ‘hit rates’ and limited dim...

  12. Uncovering Norway’s regional disparities with respect to natural riches

    Directory of Open Access Journals (Sweden)

    Sevil Acar

    2015-03-01

    Full Text Available This study aims at unveiling regional development differences in Norway with respect to various natural resource-based activities that take place in the NUTS 3 regions. Norway’s natural riches range from agricultural and forest resources to fisheries, mines, petroleum and gas. Considering the possible spatial links for various regional characteristics of the Norwegian economy, this study does not only reveal the wide-ranging distribution of resource-based activities, but also sheds light on divergent income and population patterns in the Norwegian regions. Besides, these patterns are investigated through a number of models that test the impact of employment, investment and value added in natural resource sectors on regional differences. The main findings suggest that mining and quarrying as well as oil and gas extraction activities generate significant advantages for regional income generation whereas each resource type affects the distribution of population in a different way.

  13. Uncovering Local Trends in Genetic Effects of Multiple Phenotypes via Functional Linear Models.

    Science.gov (United States)

    Vsevolozhskaya, Olga A; Zaykin, Dmitri V; Barondess, David A; Tong, Xiaoren; Jadhav, Sneha; Lu, Qing

    2016-04-01

    Recent technological advances equipped researchers with capabilities that go beyond traditional genotyping of loci known to be polymorphic in a general population. Genetic sequences of study participants can now be assessed directly. This capability removed technology-driven bias toward scoring predominantly common polymorphisms and let researchers reveal a wealth of rare and sample-specific variants. Although the relative contributions of rare and common polymorphisms to trait variation are being debated, researchers are faced with the need for new statistical tools for simultaneous evaluation of all variants within a region. Several research groups demonstrated flexibility and good statistical power of the functional linear model approach. In this work we extend previous developments to allow inclusion of multiple traits and adjustment for additional covariates. Our functional approach is unique in that it provides a nuanced depiction of effects and interactions for the variables in the model by representing them as curves varying over a genetic region. We demonstrate flexibility and competitive power of our approach by contrasting its performance with commonly used statistical tools and illustrate its potential for discovery and characterization of genetic architecture of complex traits using sequencing data from the Dallas Heart Study. PMID:27027515

  14. SNP and Mutation Data on the Web – Hidden Treasures for Uncovering

    OpenAIRE

    Barnes, Michael R.

    2002-01-01

    SNP data has grown exponentially over the last two years, SNP database evolution has matched this growth, as initial development of several independent SNP databases has given way to one central SNP database, dbSNP. Other SNP databases have instead evolved to complement this central database by providing gene specific focus and an increased level of curation and analysis on subsets of data, derived from the central data set. By contrast, human mutation data, which has been collected over many...

  15. Transcriptional profiles uncover Aspergillus flavus-induced resistance in maize kernels.

    Science.gov (United States)

    Luo, Meng; Brown, Robert L; Chen, Zhi-Yuan; Menkir, Abebe; Yu, Jiujiang; Bhatnagar, Deepak

    2011-07-01

    Aflatoxin contamination caused by the opportunistic pathogen A. flavus is a major concern in maize production prior to harvest and through storage. Previous studies have highlighted the constitutive production of proteins involved in maize kernel resistance against A. flavus' infection. However, little is known about induced resistance nor about defense gene expression and regulation in kernels. In this study, maize oligonucleotide arrays and a pair of closely-related maize lines varying in aflatoxin accumulation were used to reveal the gene expression network in imbibed mature kernels in response to A. flavus' challenge. Inoculated kernels were incubated 72 h via the laboratory-based Kernel Screening Assay (KSA), which highlights kernel responses to fungal challenge. Gene expression profiling detected 6955 genes in resistant and 6565 genes in susceptible controls; 214 genes induced in resistant and 2159 genes induced in susceptible inoculated kernels. Defense related and regulation related genes were identified in both treatments. Comparisons between the resistant and susceptible lines indicate differences in the gene expression network which may enhance our understanding of the maize-A. flavus interaction. PMID:22069739

  16. 9 Sgr: uncovering an O-type spectroscopic binary with an 8.6 year period

    OpenAIRE

    Rauw, G.; Sana, H.; Spano, M; Gosset, E.; Mahy, L.; Becker, M.; Eenens, P.

    2012-01-01

    The O-type object 9 Sgr is a well-known synchrotron radio emitter. This feature is usually attributed to colliding-wind binary systems, but 9 Sgr was long considered a single star. We have conducted a long-term spectroscopic monitoring of this star to investigate its multiplicity and search for evidence for wind-wind interactions. Radial velocities are determined and analysed using various period search methods. Spectral disentangling is applied to separate the spectra of the components of th...

  17. Yeast as a Heterologous Model System to Uncover Type III Effector Function

    Science.gov (United States)

    Popa, Crina; Coll, Núria S.; Valls, Marc; Sessa, Guido

    2016-01-01

    Type III effectors (T3E) are key virulence proteins that are injected by bacterial pathogens inside the cells of their host to subvert cellular processes and contribute to disease. The budding yeast Saccharomyces cerevisiae represents an important heterologous system for the functional characterisation of T3E proteins in a eukaryotic environment. Importantly, yeast contains eukaryotic processes with low redundancy and are devoid of immunity mechanisms that counteract T3Es and mask their function. Expression in yeast of effectors from both plant and animal pathogens that perturb conserved cellular processes often resulted in robust phenotypes that were exploited to elucidate effector functions, biochemical properties, and host targets. The genetic tractability of yeast and its amenability for high-throughput functional studies contributed to the success of this system that, in recent years, has been used to study over 100 effectors. Here, we provide a critical view on this body of work and describe advantages and limitations inherent to the use of yeast in T3E research. “Favourite” targets of T3Es in yeast are cytoskeleton components and small GTPases of the Rho family. We describe how mitogen-activated protein kinase (MAPK) signalling, vesicle trafficking, membrane structures, and programmed cell death are also often altered by T3Es in yeast and how this reflects their function in the natural host. We describe how effector structure–function studies and analysis of candidate targeted processes or pathways can be carried out in yeast. We critically analyse technologies that have been used in yeast to assign biochemical functions to T3Es, including transcriptomics and proteomics, as well as suppressor, gain-of-function, or synthetic lethality screens. We also describe how yeast can be used to select for molecules that block T3E function in search of new antibacterial drugs with medical applications. Finally, we provide our opinion on the limitations of S. cerevisiae as a model system and its most promising future applications. PMID:26914889

  18. Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens.

    Science.gov (United States)

    Wilms, Ina; Overlöper, Aaron; Nowrousian, Minou; Sharma, Cynthia M; Narberhaus, Franz

    2012-04-01

    Agrobacterium species are capable of interkingdom gene transfer between bacteria and plants. The genome of Agrobacterium tumefaciens consists of a circular and a linear chromosome, the At-plasmid and the Ti-plasmid, which harbors bacterial virulence genes required for tumor formation in plants. Little is known about promoter sequences and the small RNA (sRNA) repertoire of this and other α-proteobacteria. We used a differential RNA sequencing (dRNA-seq) approach to map transcriptional start sites of 388 annotated genes and operons. In addition, a total number of 228 sRNAs was revealed from all four Agrobacterium replicons. Twenty-two of these were confirmed by independent RNA gel blot analysis and several sRNAs were differentially expressed in response to growth media, growth phase, temperature or pH. One sRNA from the Ti-plasmid was massively induced under virulence conditions. The presence of 76 cis-antisense sRNAs, two of them on the reverse strand of virulence genes, suggests considerable antisense transcription in Agrobacterium. The information gained from this study provides a valuable reservoir for an in-depth understanding of sRNA-mediated regulation of the complex physiology and infection process of Agrobacterium.

  19. Functional genomics of the brain: uncovering networks in the CNS using a systems approach.

    Science.gov (United States)

    Konopka, Genevieve

    2011-01-01

    The central nervous system (CNS) is undoubtedly the most complex human organ system in terms of its diverse functions, cellular composition, and connections. Attempts to capture this diversity experimentally were the foundation on which the field of neurobiology was built. Until now though, techniques were either painstakingly slow or insufficient in capturing this heterogeneity. In addition, the combination of multiple layers of information needed for a complete picture of neuronal diversity from the epigenome to the proteome requires an even more complex compilation of data. In this era of high-throughput genomics though, the ability to isolate and profile neurons and brain tissue has increased tremendously and now requires less effort. Both microarrays and next-generation sequencing have identified neuronal transcriptomes and signaling networks involved in normal brain development, as well as in disease. However, the expertise needed to organize and prioritize the resultant data remains substantial. A combination of supervised organization and unsupervised analyses are needed to fully appreciate the underlying structure in these datasets. When utilized effectively, these analyses have yielded striking insights into a number of fundamental questions in neuroscience on topics ranging from the evolution of the human brain to neuropsychiatric and neurodegenerative disorders. Future studies will incorporate these analyses with behavioral and physiological data from patients to more efficiently move toward personalized therapeutics.

  20. Uncovering the secrets of a productive environment, A journey through the impact of plants and colour

    NARCIS (Netherlands)

    Bakker, I.C.

    2014-01-01

    This PhD concerns the relationship between the physical environment and knowledge productivity. To create an optimal environment it is important to study the needs of knowledge workers in connection to the characteristics of the physical environment. Two components of the physical environment have b

  1. Searching for behavioral indicators of welfare in zoos: uncovering anticipatory behavior.

    Science.gov (United States)

    Watters, Jason V

    2014-01-01

    A current focus of zoo-based research aims to identify indicators of animal welfare. Reliable behavioral indicators of welfare are highly desirable as behavioral observation is non invasive and requires little in the way of specialized equipment and other costly resources-save for observer time. Anticipatory behavior is an indicator of an animal's sensitivity to reward and as such, it is a real-time indicator of animals' own perceptions of their well-being. In fact, anticipatory behavior may generate a positive affective state and thus be at least a brief manifestation of good welfare itself. The husbandry conditions of most captive animals are such that food acquisition and other positive outcomes are highly scheduled and easily signaled. These conditions promote the development of anticipatory behavior, yet little research has either documented or interpreted this behavior in zoo and aquarium animals. This commentary suggests that anticipatory behavior could be a useful tool for assessing welfare and calls upon zoo and aquarium researchers to begin to develop this tool by describing the behavior and the circumstances that lead to its modulation. PMID:25042907

  2. Life-Metaphors among Colombian Medical Students: Uncovering Core Values and Educational Implications

    Science.gov (United States)

    Hoffman, Edward; Acosta-Orozco, Catalina; Compton, William C.

    2015-01-01

    The present study utilized metaphor analysis to examine the core values of Colombian medical students. The entire 9th semester medical class of 60 students was invited to respond to a structured questionnaire. It asked participants to state their preferred life-metaphor, whether they had always preferred this metaphor since childhood or…

  3. Uncovering blind spots in education and practice leadership: towards a collaborative response to the nurse shortage.

    Science.gov (United States)

    Regan, Sandra; Thorne, Sally; Mildon, Barbara

    2009-01-01

    As the nursing shortage becomes an increasingly prominent everyday pressure for practice leaders, the search for quick solutions has intensified. A widespread perception has emerged within the service sector that nursing education is failing to fulfill its responsibility to prepare the next generation of nurses. This perception is escalating tensions between leaders in the education and practice sectors, and creating new barriers towards finding collaborative solutions. Although the "job ready/practice ready" debate between practice and education has been a long-standing undercurrent within nursing, extreme shortages affecting practice sector performance across the country create conditions that fuel heightened distrust and division. In this context, it becomes increasingly important that nursing leaders in education and practice engage in thoughtful and respectful dialogue to ensure that tensions between the two sectors are managed and counterproductive schisms prevented. In this paper, we deconstruct some of the current thinking regarding responsibility for the current problem by describing differences in the distinct cultures and contexts of the practice and education sectors, noting potential "blind spots" that interfere with our mutual understanding and encouraging a better-informed, shared responsibility to promote constructive engagement in preparing tomorrow's nursing workforce. PMID:19521159

  4. An Integrated Metabolomic and Genomic Mining Workflow to Uncover the Biosynthetic Potential of Bacteria

    DEFF Research Database (Denmark)

    Månsson, Maria; Vynne, Nikolaj Grønnegaard; Klitgaard, Andreas;

    2016-01-01

    in bacteria and mine the associated chemical diversity. Thirteen strains closely related to Pseudoalteromonas luteoviolacea isolated from all over the Earth were analyzed using an untargeted metabolomics strategy, and metabolomic profiles were correlated with whole-genome sequences of the strains. We found...... considerable diversity: only 2% of the chemical features and 7% of the biosynthetic genes were common to all strains, while 30% of all features and 24% of the genes were unique to single strains. The list of chemical features was reduced to 50 discriminating features using a genetic algorithm and support......, integrative strategy for elucidating the chemical richness of a given set of bacteria and link the chemistry to biosynthetic genes....

  5. An orphan gyrB in the Mycobacterium smegmatis genome uncovered by comparative genomics

    Indian Academy of Sciences (India)

    P. Jain; V. Nagaraja

    2002-11-01

    DNA gyrase is an essential topoisomerase found in all bacteria. It is encoded by gyrB and gyrA genes. These genes are organized differently in different bacteria. Direct comparison of Mycobacterium tuberculosis and Mycobacterium smegmatis genomes reveals presence of an additional gyrB in M. smegmatis flanked by novel genes. Analysis of the amino acid sequence of GyrB from different organisms suggests that the orphan GyrB in M. smegmatis may have an important cellular role.

  6. Early changes in gene expression profiles of hepatic GVHD uncovered by oligonucleotide microarrays.

    Science.gov (United States)

    Ichiba, Tamotsu; Teshima, Takanori; Kuick, Rork; Misek, David E; Liu, Chen; Takada, Yuichiro; Maeda, Yoshinobu; Reddy, Pavan; Williams, Debra L; Hanash, Samir M; Ferrara, James L M

    2003-07-15

    The liver, skin, and gastrointestinal tract are major target organs of acute graft-versus-host disease (GVHD), the major complication of allogeneic bone marrow transplantation (BMT). In order to gain a better understanding of acute GVHD in the liver, we compared the gene expression profiles of livers after experimental allogeneic and syngeneic BMT using oligonucleotide microarray. At 35 days after allogeneic BMT when hepatic GVHD was histologically evident, genes related to cellular effectors and acute-phase proteins were up-regulated, whereas genes largely related to metabolism and endocrine function were down-regulated. At day 7 after BMT before the development of histologic changes in the liver, interferon gamma (IFN-gamma)-inducible genes, major histocompatibility (MHC) class II molecules, and genes related to leukocyte trafficking had been up-regulated. Immunohistochemistry demonstrated that expression of IFN-gamma protein itself was increased in the spleen but not in hepatic tissue. These results suggest that the increased expression of genes associated with the attraction and activation of donor T cells induced by IFN-gamma early after BMT is important in the initiation of hepatic GVHD in this model and provide new potential molecular targets for early detection and intervention of acute GVHD.

  7. Uncovering the social deficits in the autistic brain.A Source-Based Morphometric study

    Directory of Open Access Journals (Sweden)

    Alessandro Grecucci

    2016-08-01

    Full Text Available Autism is a neurodevelopmental disorder that mainly affects social interaction and communication. Evidence from behavioral and functional MRI studies supports the hypothesis that dysfunctional mechanisms involving social brain structures play a major role in autistic symptomatology. However, the investigation of anatomical abnormalities in the brain of people with autism has led to inconsistent results. We investigated whether specific brain regions, known to display functional abnormalities in autism, may exhibit mutual and peculiar patterns of covariance in their grey-matter concentrations. We analyzed structural MRI images of 32 young men affected by autistic disorder (AD and 50 healthy controls. Controls were matched for sex, age, handedness. IQ scores were also monitored to avoid confounding. A multivariate Source-Based Morphometry (SBM was applied for the first time on AD and controls to detect maximally independent networks of gray matter. Group comparison revealed a gray-matter source that showed differences in AD compared to controls. This network includes broad temporal regions involved in social cognition and high-level visual processing, but also motor and executive areas of the frontal lobe. Notably, we found that gray matter differences, as reflected by SBM, significantly correlated with social and behavioral deficits displayed by AD individuals and encoded via the Autism Diagnostic Observation Schedule scores. These findings provide support for current hypotheses about the neural basis of atypical social and mental states information processing in autism.

  8. Observing the observers - uncovering the role of values in research assessments of organic food systems

    DEFF Research Database (Denmark)

    Thorsøe, Martin Hermansen; Alrøe, Hugo Fjelsted; Noe, Egon

    2014-01-01

    Assessing the overall effects of organic food systems is important, but also a challenge because organic food systems cannot be fully assessed from one single research perspective. The aim of our research was to determine the role of values in assessments of organic food systems as a basis...... for discussing the implications of combining multiple perspectives in overall sustainability assessments of the food system. We explored how values were embedded in five research perspectives: (1) food science, (2) discourse analysis, (3) phenomenology, (4) neoclassical welfare economics, and (5) actor......-network theory. Value has various meanings according to different scientific perspectives. A strategy for including and balancing different forms of knowledge in overall assessments of the effects of food systems is needed. Based on the analysis, we recommend four courses of action: (1) elucidate values...

  9. Uncovering homo-and hetero-interactions on the cell membrane using single particle tracking approaches

    Science.gov (United States)

    Torreno-Pina, Juan A.; Manzo, Carlo; Garcia-Parajo, Maria F.

    2016-03-01

    The plasma membrane of eukaryotic cells is responsible for a myriad of functions that regulate cell physiology and plays a crucial role in a multitude of processes that include adhesion, migration, signaling recognition and cell-cell communication. This is accomplished by specific interactions between different membrane components such as lipids and proteins on the lipid bilayer but also through interactions with the underlying cortical actin cytoskeleton on the intracellular side and the glycocalyx matrix in close proximity to the extracellular side. Advanced biophysical techniques, including single particle tracking (SPT) have revealed that the lateral diffusion of molecular components on the plasma membrane represents a landmark manifestation of such interactions. Indeed, by studying changes in the diffusivity of individual membrane molecules, including sub-diffusion, confined diffusion and/or transient arrest of molecules in membrane compartments, it has been possible to gain insight on the nature of molecular interactions and to infer on its functional role for cell response. In this review, we will revise some exciting results where SPT has been crucial to reveal homo- and hetero-interactions on the cell membrane.

  10. Metabolic profiling uncovers a phenotypic signature of small for gestational age in early pregnancy.

    LENUS (Irish Health Repository)

    Horgan, Richard P

    2012-01-31

    Being born small for gestational age (SGA) confers increased risks of perinatal morbidity and mortality and increases the risk of cardiovascular complications and diabetes in later life. Accumulating evidence suggests that the etiology of SGA is usually associated with poor placental vascular development in early pregnancy. We examined metabolomic profiles using ultra performance liquid chromatography-mass spectrometry (UPLC-MS) in three independent studies: (a) venous cord plasma from normal and SGA babies, (b) plasma from a rat model of placental insufficiency and controls, and (c) early pregnancy peripheral plasma samples from women who subsequently delivered a SGA baby and controls. Multivariate analysis by cross-validated Partial Least Squares Discriminant Analysis (PLS-DA) of all 3 studies showed a comprehensive and similar disruption of plasma metabolism. A multivariate predictive model combining 19 metabolites produced by a Genetic Algorithm-based search program gave an Odds Ratio for developing SGA of 44, with an area under the Receiver Operator Characteristic curve of 0.9. Sphingolipids, phospholipids, carnitines, and fatty acids were among this panel of metabolites. The finding of a consistent discriminatory metabolite signature in early pregnancy plasma preceding the onset of SGA offers insight into disease pathogenesis and offers the promise of a robust presymptomatic screening test.

  11. Health Econometric: Uncovering the Anthropometric Behavior on the Women's Labor Market

    OpenAIRE

    Lopez-Pablos, Rodrigo A.

    2007-01-01

    Exploring current literature which assess relations between cognitive ability and height, obesity, and its productivity-employability effect on women's labor market, we appraised the Argentine case to quantify for social-physical interactions which involve anthropometric and traditional economic variables. Hence, an anthropometric Mincer approach has been adapted by using probabilistic and censured econometric models which were developed for it. There has been found evidence that could be ...

  12. Simultaneously uncovering the patterns of brain regions involved in different story reading subprocesses.

    Directory of Open Access Journals (Sweden)

    Leila Wehbe

    Full Text Available Story understanding involves many perceptual and cognitive subprocesses, from perceiving individual words, to parsing sentences, to understanding the relationships among the story characters. We present an integrated computational model of reading that incorporates these and additional subprocesses, simultaneously discovering their fMRI signatures. Our model predicts the fMRI activity associated with reading arbitrary text passages, well enough to distinguish which of two story segments is being read with 74% accuracy. This approach is the first to simultaneously track diverse reading subprocesses during complex story processing and predict the detailed neural representation of diverse story features, ranging from visual word properties to the mention of different story characters and different actions they perform. We construct brain representation maps that replicate many results from a wide range of classical studies that focus each on one aspect of language processing and offer new insights on which type of information is processed by different areas involved in language processing. Additionally, this approach is promising for studying individual differences: it can be used to create single subject maps that may potentially be used to measure reading comprehension and diagnose reading disorders.

  13. Leadership skills teaching in Yorkshire & the Humber - a survey: uncovering, sharing, developing, embedding.

    Science.gov (United States)

    Fowler, Iolanthe; Gill, Andy

    2015-09-01

    Medical leadership is a hot topic, but it is not known yet how to teach this most effectively. A working party of educators in Yorkshire and the Humber (Y&H) studied the leadership domains, as set out in the Medical Leadership Competency Framework and from this distilled a set of 'trainable' leadership skills, which were felt to be important to teach during general practitioner (GP) training. A questionnaire was sent out to a large GP educational community (educators and trainees) within Y&H to establish the following: (i) whether the distilled skills were thought to have face validity when applied to the concept of leadership, (ii) what was the relative importance of these skills in relation to each other and (iii) the degree to which these skills were already being taught in practice placements and at General Practice Specialty Training Programme (GPSTP) teaching sessions.Educators reported more teaching and training occurring than trainees reported receiving, and the relative importance of the skills sets were different between educators and trainees. It was evident that leadership skills are currently being taught, but that making training explicitly 'leadership', and raising the importance of leadership skills in GP, may address some of these imbalances. Educators requested guidance on how to teach these skills effectively and commented that many existing opportunities for leadership teaching and training are not well recognised or used. Routinely and regularly offering the chance for trainees at all levels to be exposed to leadership skills by role modelling, making use of everyday opportunities in practice to teach and encouraging trainee involvement in projects and opportunities to practice new skills can facilitate the acquisition and celebration of mastery of generic leadership skills. PMID:26808794

  14. The relationship between DTCA, drug requests, and prescriptions: Uncovering variation in specialty and space

    NARCIS (Netherlands)

    S. Stremersch (Stefan); V. Schwartz-Landsman (Vardit); S. Venkataraman (Sriram)

    2013-01-01

    textabstractPatients increasingly request their physicians to prescribe specific brands of pharmaceutical drugs. A popular belief is that requests are triggered by direct-to-consumer advertising (DTCA). We examine the relationship between DTCA, patient requests, and prescriptions for statins. We fin

  15. Uncovering the differences in linguistic network dynamics of book and social media texts.

    Science.gov (United States)

    Türker, İlker; Şehirli, Eftal; Demiral, Emrullah

    2016-01-01

    Complex network studies span a large variety of applications including linguistic networks. To investigate the differences in book and social media texts in terms of linguistic typology, we constructed both sequential and sentence collocation networks of book, Facebook and Twitter texts with undirected and weighted edges. The comparisons are performed using the basic parameters like average degree, modularity, average clustering coefficient, average path length, diameter, average link weight etc. We also presented the distribution graphs for node degrees, edge weights and maximum degree differences of the pairing nodes. The degree difference occurrences are furtherly detailed with the grayscale percentile plots with respect to the edge weights. We linked the network analysis with linguistic aspects like word and sentence length distributions. We concluded that linguistic typology demonstrates a formal usage in book that slightly deviates to informal in Twitter. Facebook interpolates between these media by the means of network parameters, while the informality of Twitter is mostly influenced by the character limitations. PMID:27386313

  16. Interdimensional interference in the Stroop effect: uncovering the cognitive and neural anatomy of attention.

    Science.gov (United States)

    MacLeod; MacDonald

    2000-10-01

    In the classic Stroop effect, naming the color of an incompatible color word (e.g. the word RED printed in green ink; say, 'green') is much slower and more error-prone than is naming the color of a control item (e.g. XXX or CAT printed in green; say 'green'). This seemingly simple interference phenomenon has long provided a fertile testing ground for theories of the cognitive and neural components of selective attention. We present a sketch of the behavioral phenomenon, focusing on the idea that the relative automaticity of the two dimensions determines the direction and the degree of interdimensional interference between them. We then present an outline of current parallel processing explanations that instantiate this automaticity account, and we show how existing interference data are captured by such models. We also consider how Stroop facilitation (faster response of 'red' to RED printed in red) can be understood. Along the way, we describe research on two tasks that have emerged from the basic Stroop phenomenon - negative priming and the emotional Stroop task. Finally, we provide a survey of brain imaging research, highlighting the possible roles of the anterior cingulate in maintaining attentional set and in processing conflict or competition situations.

  17. Uncovering the genetic history of the present-day Greenlandic population.

    Science.gov (United States)

    Moltke, Ida; Fumagalli, Matteo; Korneliussen, Thorfinn S; Crawford, Jacob E; Bjerregaard, Peter; Jørgensen, Marit E; Grarup, Niels; Gulløv, Hans Christian; Linneberg, Allan; Pedersen, Oluf; Hansen, Torben; Nielsen, Rasmus; Albrechtsen, Anders

    2015-01-01

    Because of past limitations in samples and genotyping technologies, important questions about the history of the present-day Greenlandic population remain unanswered. In an effort to answer these questions and in general investigate the genetic history of the Greenlandic population, we analyzed ∼200,000 SNPs from more than 10% of the adult Greenlandic population (n = 4,674). We found that recent gene flow from Europe has had a substantial impact on the population: more than 80% of the Greenlanders have some European ancestry (on average ∼25% of their genome). However, we also found that the amount of recent European gene flow varies across Greenland and is far smaller in the more historically isolated areas in the north and east and in the small villages in the south. Furthermore, we found that there is substantial population structure in the Inuit genetic component of the Greenlanders and that individuals from the east, west, and north can be distinguished from each other. Moreover, the genetic differences in the Inuit ancestry are consistent with a single colonization wave of the island from north to west to south to east. Although it has been speculated that there has been historical admixture between the Norse Vikings who lived in Greenland for a limited period ∼600-1,000 years ago and the Inuit, we found no evidence supporting this hypothesis. Similarly, we found no evidence supporting a previously hypothesized admixture event between the Inuit in East Greenland and the Dorset people, who lived in Greenland before the Inuit.

  18. Transcriptome sequencing uncovers the Avr5 avirulence gene of the tomato leaf mold pathogen Cladosporium fulvum.

    Science.gov (United States)

    Mesarich, Carl H; Griffiths, Scott A; van der Burgt, Ate; Okmen, Bilal; Beenen, Henriek G; Etalo, Desalegn W; Joosten, Matthieu H A J; de Wit, Pierre J G M

    2014-08-01

    The Cf-5 gene of tomato confers resistance to strains of the fungal pathogen Cladosporium fulvum carrying the avirulence gene Avr5. Although Cf-5 has been cloned, Avr5 has remained elusive. We report the cloning of Avr5 using a combined bioinformatic and transcriptome sequencing approach. RNA-Seq was performed on the sequenced race 0 strain (0WU; carrying Avr5), as well as a race 5 strain (IPO 1979; lacking a functional Avr5 gene) during infection of susceptible tomato. Forty-four in planta-induced C. fulvum candidate effector (CfCE) genes of 0WU were identified that putatively encode a secreted, small cysteine-rich protein. An expressed transcript sequence comparison between strains revealed two polymorphic CfCE genes in IPO 1979. One of these conferred avirulence to IPO 1979 on Cf-5 tomato following complementation with the corresponding 0WU allele, confirming identification of Avr5. Complementation also led to increased fungal biomass during infection of susceptible tomato, signifying a role for Avr5 in virulence. Seven of eight race 5 strains investigated escape Cf-5-mediated resistance through deletion of the Avr5 gene. Avr5 is heavily flanked by repetitive elements, suggesting that repeat instability, in combination with Cf-5-mediated selection pressure, has led to the emergence of race 5 strains deleted for the Avr5 gene.

  19. Metagenomics uncovers gaps in amplicon-based detection of microbial diversity.

    Science.gov (United States)

    Eloe-Fadrosh, Emiley A; Ivanova, Natalia N; Woyke, Tanja; Kyrpides, Nikos C

    2016-01-01

    Our view of microbial diversity has expanded greatly over the past 40 years, primarily through the wide application of PCR-based surveys of the small-subunit ribosomal RNA (SSU rRNA) gene. Yet significant gaps in knowledge remain due to well-recognized limitations of this method. Here, we systematically survey primer fidelity in SSU rRNA gene sequences recovered from over 6,000 assembled metagenomes sampled globally. Our findings show that approximately 10% of environmental microbial sequences might be missed from classical PCR-based SSU rRNA gene surveys, mostly members of the Candidate Phyla Radiation (CPR) and as yet uncharacterized Archaea. These results underscore the extent of uncharacterized microbial diversity and provide fruitful avenues for describing additional phylogenetic lineages. PMID:27572438

  20. Thyroid-Specific Genes Expression Uncovered Age-Related Differences in Pediatric Thyroid Carcinomas

    Directory of Open Access Journals (Sweden)

    Maria Isabel Cunha Vieira Cordioli

    2016-01-01

    Full Text Available Despite a more advanced stage of disease at presentation, a better response to radioiodine (RAI therapy and a reduced overall mortality have been reported in pediatric differentiated thyroid cancer (DTC in comparison to adult DTC. Few studies suggested that the better response to RAI therapy in pediatric patients might be associated with an increased expression of NIS. However, a marked heterogeneity within the pediatric group has been recognized. Children (<10 years old usually present a more aggressive disease than adolescents (≥10–18 years old. By analyzing the expression of thyroid-specific genes in 38 sporadic pediatric tumors, we show that the expression of NIS, PDS, and TSHR was lower in children than adolescents (P<0.05. A linear regression confirmed the association between NIS expression and age. Most significantly, NIS was expressed at similar levels in DTC from children and adults, whereas PDS and TSHR expression was even lower in DTC from children, compared to adolescents and adults. Our data suggest that biological behaviors of DTC in adolescents might differ from those in children and adults. Therefore, the premise that the expression of thyroid-specific genes is higher in tumors from pediatric patients than in adults is not entirely true and might be too oversimplified.