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Sample records for adp-glucose pyrophosphorylase uncovered

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  4. Aspartic acid 413 is important for the normal allosteric functioning of ADP-glucose pyrophosphorylase

    Energy Technology Data Exchange (ETDEWEB)

    Greene, T.W.; Woodbury, R.L.; Okita, T.W. [Washington State Univ., Pullman, WA (United States)

    1996-11-01

    As part of a structure-function analysis of the higher-plant ADP-glucose pyrophosphorylase (AGP), we used a random mutagenesis approach in combination with a novel bacterial complementation system to isolate over 100 mutants that were defective in glycogen production. One mutant of the large subunit M27 was identified by its capacity to only partially complement a mutation in the structural gene for the bacterial AGP (glg C), as determined by its light-staining phenotype when cells were exposed to I{sub 2} vapors. Enzyme-linked immunosorbent assay and enzymatic pyrophosphorylysis assays of M27 cell extracts showed that the level of expression and AGP activity was comparable to those of cells that expressed the wildtype recombinant enzyme. Kinetic analysis indicated that the M27 AGP displays normal Michaelis constant values for the substrates glucose-1-phosphate and ATP but requires 6- to 10-fold greater levels of 3-phosphoglycerate (3-PGA) than the wild-type recombinant enzyme for maximum activation. DNA sequence analysis showed that M27 contains a single point mutation that resulted in the replacement of aspartic acid 413 to alanine. Substitution of a lysine residue at this site almost completely abolished activation by 3-PGA. Aspartic acid 413 is adjacent to a lysine residue that was previously identified by chemical modification studies to be important in the binding of 3-PGA. The kinetic properties of M27 corroborate the importance of this region in the allosteric regulation of a higher-plant AGP. 28 refs., 3 figs., 1 tab.

  5. Aspartic acid 413 is important for the normal allosteric functioning of ADP-glucose pyrophosphorylase.

    Science.gov (United States)

    Greene, T W; Woodbury, R L; Okita, T W

    1996-01-01

    As part of a structure-function analysis of the higher-plant ADP-glucose pyrophosphorylase (AGP), we used a random mutagenesis approach in combination with a novel bacterial complementation system to isolate over 100 mutants that were defective in glycogen production (T.W. Greene, S.E. Chantler, M.L. Khan, G.F. Barry, J. Preiss, T.W. Okita [1996] Proc Natl Acad Sci USA 93: 1509-1513). One mutant of the large subunit M27 was identified by its capacity to only partially complement a mutation in the structural gene for the bacterial AGP (glg C), as determined by its light-staining phenotype when cells were exposed to l3 vapors. Enzyme-linked immunosorbent assay and enzymatic pyrophosphorylysis assays of M27 cell extracts showed that the level of expression and AGP activity was comparable to those of cells that expressed the wild-type recombinant enzyme. Kinetic analysis indicated that the M27 AGP displays normal Michaelis constant values for the substrates glucose-1-phosphate and ATP but requires 6- to 10-fold greater levels of 3-phosphoglycerate (3-PGA) than the wild-type recombinant enzyme for maximum activation. DNA sequence analysis showed that M27 contains a single point mutation that resulted in the replacement of aspartic acid 413 to alanine. Substitution of a lysine residue at this site almost completely abolished activation by 3-PGA. Aspartic acid 413 is adjacent to a lysine residue that was previously identified by chemical modification studies to be important in the binding of 3-PGA (K. Ball, J. Preiss [1994] J Biol Chem 269: 24706-24711). The kinetic properties of M27 corroborate the importance of this region in the allosteric regulation of a higher-plant AGP. PMID:8938421

  6. 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.

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

    Science.gov (United States)

    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.

  8. Structure and expression analysis of genes encoding ADP-glucose pyrophosphorylase large subunit in wheat and its relatives.

    Science.gov (United States)

    Zhang, Xiao-Wei; Li, Si-Yu; Zhang, Ling-Ling; Yang, Qiang; Jiang, Qian-Tao; Ma, Jian; Qi, Peng-Fei; Li, Wei; Chen, Guo-Yue; Lan, Xiu-Jin; Deng, Mei; Lu, Zhen-Xiang; Liu, Chunji; Wei, Yu-Ming; Zheng, You-Liang

    2016-07-01

    ADP-glucose pyrophosphorylase (AGP), which consists of two large subunits (AGP-L) and two small subunits (AGP-S), controls the rate-limiting step in the starch biosynthetic pathway. In this study, a full-length open reading frame (ORF) of AGP-L gene (named as Agp2) in wheat and a series of Agp2 gene sequences in wheat relatives were isolated. The coding region of Agp2 contained 15 exons and 14 introns including a full-length ORF of 1566 nucleotides, and the deduced protein contained 522 amino acids (57.8 kDa). Generally, the phylogenetic tree of Agp2 indicated that sequences from A- and D-genome donor species were most similar to each other and sequences from B-genome donor species contained more variation. Starch accumulation and Agp2 expression in wheat grains reached their peak at 21 and 15 days post anthesis (DPA), respectively.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  10. Plastidic phosphoglucomutase and ADP-glucose pyrophosphorylase mutants impair starch synthesis in rice pollen grains and cause male sterility.

    Science.gov (United States)

    Lee, Sang-Kyu; Eom, Joon-Seob; Hwang, Seon-Kap; Shin, Dongjin; An, Gynheung; Okita, Thomas W; Jeon, Jong-Seong

    2016-10-01

    To elucidate the starch synthesis pathway and the role of this reserve in rice pollen, we characterized mutations in the plastidic phosphoglucomutase, OspPGM, and the plastidic large subunit of ADP-glucose (ADP-Glc) pyrophosphorylase, OsAGPL4 Both genes were up-regulated in maturing pollen, a stage when starch begins to accumulate. Progeny analysis of self-pollinated heterozygous lines carrying the OspPGM mutant alleles, osppgm-1 and osppgm-2, or the OsAGPL4 mutant allele, osagpl4-1, as well as reciprocal crosses between the wild type (WT) and heterozygotes revealed that loss of OspPGM or OsAGPL4 caused male sterility, with the former condition rescued by the introduction of the WT OspPGM gene. While iodine staining and transmission electron microscopy analyses of pollen grains from homozygous osppgm-1 lines produced by anther culture confirmed the starch null phenotype, pollen from homozygous osagpl4 mutant lines, osagpl4-2 and osagpl4-3, generated by the CRISPR/Cas system, accumulated small amounts of starch which were sufficient to produce viable seed. Such osagpl4 mutant pollen, however, was unable to compete against WT pollen successfully, validating the important role of this reserve in fertilization. Our results demonstrate that starch is mainly polymerized from ADP-Glc synthesized from plastidic hexose phosphates in rice pollen and that starch is an essential requirement for successful fertilization in rice.

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

    Science.gov (United States)

    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.

  12. ADP-glucose pyrophosphorylase in shrunken-2 and brittle-2 mutants of maize.

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    Giroux, M J; Hannah, L C

    1994-05-25

    The Shrunken-2 (Sh2) and Brittle-2 (Bt2) genes of maize encode subunits of the tetrameric maize endosperm ADPglucose pyrophosphorylase. However, in all sh2 and bt2 mutants so far examined, measurable ADPglucose pyrophosphorylase activity remains. We have investigated the origin of the residual activity found in various sh2 and bt2 mutants as well as tissue specific expression and post-translational modification of the Sh2 and Bt2 proteins. Sh2 and Bt2 cDNAs were expressed in Escherichia coli and antibodies were prepared against the resulting proteins SH2 and BT2 specific antibodies were used to demonstrate that SH2 and BT2 are endosperm specific, are altered or missing in various sh2 or bt2 mutants, and have a mol. wt. of 54 and 51 kDa respectively in the wild type. The Sh2 and Bt2 transcripts are also endosperm specific. Ten sh2 and eight bt2 mutants show varying severity of phenotypes expressed at transcript, protein subunit and kernel level. Synthesis of multiple transcripts and proteins commonly occurs as a result of sh2 or bt2 mutation. While all mutants produce detectable enzymic activity, not all produce detectable transcripts and proteins. To examine the origin of the apparent non-SH2/BT2 endosperm enzymic activity, homologs of Sh2 and Bt2, designated Agp1 and Agp2 respectively, were isolated from an embryo cDNA library and found to hybridize to endosperm transcripts distinct from those of Sh2 and Bt2. Thus Agp1 and Agp2 or closely related genes may be responsible for the residual activity in some sh2 and bt2 mutants. Surprisingly, no evidence of post-translational modification of the SH2 and BT2 protein subunits was detected.

  13. Expression of fission yeast cdc25 driven by the wheat ADP-glucose pyrophosphorylase large subunit promoter reduces pollen viability and prevents transmission of the transgene in wheat.

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    Chrimes, D; Rogers, H J; Francis, D; Jones, H D; Ainsworth, C

    2005-04-01

    Cell number was to be measured in wheat (Triticum aestivum) endosperm expressing Spcdc25 (a fission yeast cell-cycle regulator) controlled by a supposedly endosperm-specific promoter, AGP2 (from the large subunit of ADP glucose pyrophosphorylase). Wheat was transformed by biolistics either with AGP2::GUS or AGP2::Spcdc25. PCR and RT-PCR checked integration and expression of the transgene, respectively. In cv. Chinese Spring, AGP2::GUS was unexpectedly expressed in carpels and pollen, as well as endosperm. In cv. Cadenza, three AGP2::Spcdc25 plants, AGP2::Spcdc25.1, .2 and .3, were generated. Spcdc25 expression was detected in mature leaves of AGP2::Spcdc25.1/.3 which exhibited abnormal spikes, 50% pollen viability and low seed set per plant; both were small compared with the nonexpressing and normal AGP2::Spcdc25.2. Spcdc25 was not transmitted to the T(1) in AGP2::Spcdc25.1 or .3, which developed normally. Spcdc25 was PCR-positive in AGP2::Spcdc25.2, using primers for a central portion, but not with primers for the 5' end, of the ORF, indicating a rearrangement; Spcdc25 was not expressed in either T(0) or T(1). The AGP2 promoter is not tissue-specific and Spcdc25 expression disrupted reproduction.

  14. 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

  15. 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.

  16. 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.

  17. Adenosine diphosphate glucose pyrophosphorylase genes in wheat: differential expression and gene mapping.

    Science.gov (United States)

    Ainsworth, C; Hosein, F; Tarvis, M; Weir, F; Burrell, M; Devos, K M; Gale, M D

    1995-01-01

    A full-length cDNA clone representing the large (shrunken-2) subunit of ADP-glucose pyrophosphorylase (AGP; EC 2.7.7.27) has been isolated from a cDNA library prepared from developing grain of hexaploid wheat (Triticum aestivum L., cv. Chinese Spring). The 2084-bp cDNA insert contains an open reading frame of 1566 nucleotides and primer-extension analysis indicated that the 5' end is 10 nucleotides shorter than the mRNA. The deduced protein contains 522 amino acids (57.8 kDa) and includes a putative transit peptide of 62 amino acids (6.5 kDa). The similarity of the deduced protein to the small subunit of AGP and to other AGP genes from plants and microorganisms is discussed. Northern hybridisation shows that the Agp1 genes (encoding the small subunit in the wheat endosperm) and the Agp2 genes (encoding the large subunit in the wheat endosperm) are differentially expressed in the wheat grain. Transcripts from both gene sets accumulate to high levels in the endosperm during grain development with the majority of the expression in the endopsperm rather than the embryo and pericarp layers. Although enzyme activity is detected in developing grains prior to 10 d post anthesis, only the Agp1 genes are active at this time (the Agp2 genes are not expressed until 10 d post anthesis). The possibility that the enzyme expressed during early grain development is a homotetramer of small subunits is discussed. The Agp1 and Agp2 genes are arranged as triplicate sets of single-copy homoeoloci in wheat. The Agp2 genes are located on the long arms of chromosomes 1A, 1B and 1D, about 80 cM from the centromere. The Agp1 genes have been mapped to a position just distal to the centromere on the long arms of chromosomes 7A, 7B and 7D.

  18. Decreasing the mitochondrial synthesis of malate in potato tubers does not affect plastidial starch synthesis, suggesting that the physiological regulation of ADPglucose pyrophosphorylase is context dependent.

    Science.gov (United States)

    Szecowka, Marek; Osorio, Sonia; Obata, Toshihiro; Araújo, Wagner L; Rohrmann, Johannes; Nunes-Nesi, Adriano; Fernie, Alisdair R

    2012-12-01

    Modulation of the malate content of tomato (Solanum lycopersicum) fruit by altering the expression of mitochondrially localized enzymes of the tricarboxylic acid cycle resulted in enhanced transitory starch accumulation and subsequent effects on postharvest fruit physiology. In this study, we assessed whether such a manipulation would similarly affect starch biosynthesis in an organ that displays a linear, as opposed to a transient, kinetic of starch accumulation. For this purpose, we used RNA interference to down-regulate the expression of fumarase in potato (Solanum tuberosum) under the control of the tuber-specific B33 promoter. Despite displaying similar reductions in both fumarase activity and malate content as observed in tomato fruit expressing the same construct, the resultant transformants were neither characterized by an increased flux to, or accumulation of, starch, nor by alteration in yield parameters. Since the effect in tomato was mechanistically linked to derepression of the reaction catalyzed by ADP-glucose pyrophosphorylase, we evaluated whether the lack of effect on starch biosynthesis was due to differences in enzymatic properties of the enzyme from potato and tomato or rather due to differential subcellular compartmentation of reductant in the different organs. The results are discussed in the context both of current models of metabolic compartmentation and engineering.

  19. Uncovering the Math Curriculum

    Science.gov (United States)

    Burns, Marilyn

    2014-01-01

    Teachers often express to Marulyn Burns their worry about the need to "cover the curriculum." In response, she draws on one of her favorite quotes: "You don't want to cover a subject; you want to uncover it." This quote is from "The Having of Wonderful Ideas and Other Essays on Teaching and Learning" by Eleanor…

  20. 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 ...

  1. [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.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. Structural basis for the reaction mechanism of UDP-glucose pyrophosphorylase.

    Science.gov (United States)

    Kim, Hun; Choi, Jongkeun; Kim, Truc; Lokanath, Neratur K; Ha, Sung Chul; Suh, Se Won; Hwang, Hye-Yeon; Kim, Kyeong Kyu

    2010-04-01

    UDP-glucose pyrophosphorylases (UGPase; EC 2.7.7.9) catalyze the conversion of UTP and glucose-1-phosphate to UDP-glucose and pyrophosphate and vice versa. Prokaryotic UGPases are distinct from their eukaryotic counterparts and are considered appropriate targets for the development of novel antibacterial agents since their product, UDP-glucose, is indispensable for the biosynthesis of virulence factors such as lipopolysaccharides and capsular polysaccharides. In this study, the crystal structures of UGPase from Helicobacter pylori (HpUGPase) were determined in apo- and UDP-glucose/Mg(2+)-bound forms at 2.9 A and 2.3 A resolutions, respectively. HpUGPase is a homotetramer and its active site is located in a deep pocket of each subunit. Magnesium ion is coordinated by Asp130, two oxygen atoms of phosphoryl groups, and three water molecules with octahedral geometry. Isothermal titration calorimetry analyses demonstrated that Mg(2+) ion plays a key role in the enzymatic activity of UGPase by enhancing the binding of UGPase to UTP or UDP-glucose, suggesting that this reaction is catalyzed by an ordered sequential Bi Bi mechanism. Furthermore, the crystal structure explains the specificity for uracil bases. The current structural study combined with functional analyses provides essential information for understanding the reaction mechanism of bacterial UGPases, as well as a platform for the development of novel antibacterial agents.

  7. 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.

  8. 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.

  9. 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.

  10. Up-regulation of sucrose synthase and UDP-glucose pyrophosphorylase impacts plant growth and metabolism.

    Science.gov (United States)

    Coleman, Heather D; Ellis, Dave D; Gilbert, Margarita; Mansfield, Shawn D

    2006-01-01

    The effects of the overexpression of sucrose synthase (SuSy) and UDP-glucose pyrophosphorylase (UGPase) on plant growth and metabolism were evaluated in tobacco (Nicotiana tabacum cv. Xanthi). T(1) transgenic plants expressing either gene under the control of a tandem repeat cauliflower mosaic virus 35S promoter (2x35S) or a xylem-localized 4CL promoter (4-coumarate:CoA ligase; 4CL) were generated, and reciprocally crossed to generate plants expressing both genes. Transcript levels, enzyme activity, growth parameters, fibre properties and carbohydrate content of stem tissue were quantified. The expression profiles of both genes confirmed the expression pattern of the promoters: 2x35S expressed more strongly in leaves, while 4CL expression was highest in stem tissue. In-depth plant characterization revealed that the single-transgene lines showed significant increases in the height growth compared with corresponding control lines. The double-transgene plants demonstrated an additive effect, proving to be even taller than the single-transgene parents. Several of these lines had associated increases in soluble sugar content. Although partitioning of storage carbohydrates into starch or cellulose was not observed, the increased height growth and increases in soluble carbohydrates suggest a role for SuSy as a marker in sink strength and lend credit to the function of UGPase in a similar role. The up-regulation of these two genes, although not increasing the percentage cellulose content, was effective in increasing the total biomass, and thus the overall cellulose yield, from a given plant.

  11. Octamerization is essential for enzymatic function of human UDP-glucose pyrophosphorylase.

    Science.gov (United States)

    Führing, Jana; Damerow, Sebastian; Fedorov, Roman; Schneider, Julia; Münster-Kühnel, Anja-Katharina; Gerardy-Schahn, Rita

    2013-04-01

    Uridine diphosphate-glucose pyrophosphorylase (UGP) occupies a central position in carbohydrate metabolism in all kingdoms of life, since its product uridine diphosphate-glucose (UDP-glucose) is essential in a number of anabolic and catabolic pathways and is a precursor for other sugar nucleotides. Its significance as a virulence factor in protists and bacteria has given momentum to the search for species-specific inhibitors. These attempts are, however, hampered by high structural conservation of the active site architecture. A feature that discriminates UGPs of different species is the quaternary organization. While UGPs in protists are monomers, di- and tetrameric forms exist in bacteria, and crystal structures obtained for the enzyme from yeast and human identified octameric UGPs. These octamers are formed by contacts between highly conserved amino acids in the C-terminal β-helix. Still under debate is the question whether octamerization is required for the functionality of the human enzyme. Here, we used single amino acid replacements in the C-terminal β-helix to interrogate the impact of highly conserved residues on octamer formation and functional activity of human UGP (hUGP). Replacements were guided by the sequence of Arabidopsis thaliana UGP, known to be active as a monomer. Correlating the data obtained in blue native PAGE, size exclusion chromatography and enzymatic activity testing, we prove that the octamer is the active enzyme form. This new insight into structure-function relationships in hUGP does not only improve the understanding of the catalysis of this important enzyme, but in addition broadens the basis for studies aimed at designing drugs that selectively inhibit UGPs from pathogens.

  12. Improving starch yield in cereals by over-expression of ADPglucose pyrophosphorylase: expectations and unanticipated outcomes.

    Science.gov (United States)

    Tuncel, Aytug; Okita, Thomas W

    2013-10-01

    Significant improvements in crop productivity are required to meet the nutritional requirements of a growing world population. This challenge is magnified by an increased demand for bioenergy as a means to mitigate carbon inputs into the environment. Starch is a major component of the harvestable organs of many crop plants, and various endeavors have been taken to improve the yields of starchy organs through the manipulation of starch synthesis. Substantial efforts have centered on the starch regulatory enzyme ADPglucose pyrophosphorylase (AGPase) due to its pivotal role in starch biosynthesis. These efforts include over-expression of this enzyme in cereal plants such as maize, rice and wheat as well as potato and cassava, as they supply the bulk of the staple food worldwide. In this perspective, we describe efforts to increase starch yields in cereal grains by first providing an introduction about the importance of source-sink relationship and the motives behind the efforts to alter starch biosynthesis and turnover in leaves. We then discuss the catalytic and regulatory properties of AGPase and the molecular approaches used to enhance starch synthesis by manipulation of this process during grain filling using seed-specific promoters. Several studies have demonstrated increases in starch content per seed using endosperm-specific promoters, but other studies have demonstrated an increase in seed number with only marginal impact on seed weight. Potential mechanisms that may be responsible for this paradoxical increase in seed number will also be discussed. Finally, we describe current efforts and future prospects to improve starch yield in cereals. These efforts include further enhancement of starch yield in rice by augmenting the process of ADPglucose transport into amyloplast as well as other enzymes involved in photoassimilate partitioning in seeds.

  13. Molecular and functional analysis of UDP-N-acetylglucosamine Pyrophosphorylases from the Migratory Locust, Locusta migratoria.

    Science.gov (United States)

    Liu, Xiaojian; Li, Feng; Li, Daqi; Ma, Enbo; Zhang, Wenqing; Zhu, Kun Yan; Zhang, Jianzhen

    2013-01-01

    UDP-N-acetylglucosamine pyrophosphorylases (UAP) function in the formation of extracellular matrix by producing N-acetylglucosamine (GlcNAc) residues needed for chitin biosynthesis and protein glycosylation. Herein, we report two UAP cDNA's derived from two different genes (LmUAP1 and LmUAP2) in the migratory locust Locusta migratoria. Both the cDNA and their deduced amino acid sequences showed about 70% identities between the two genes. Phylogenetic analysis suggests that LmUAP1 and LmUAP2 derive from a relatively recent gene duplication event. Both LmUAP1 and LmUAP2 were widely expressed in all the major tissues besides chitin-containing tissues. However, the two genes exhibited different developmental expression patterns. High expression of LmUAP1 was detected during early embryogenesis, then decreased greatly, and slowly increased before egg hatch. During nymphal development, the highest expression of LmUAP1 appeared just after molting but declined in each inter-molting period and then increased before molting to the next stage, whereas LmUAP2 was more consistently expressed throughout all these stages. When the early second- and fifth-instar nymphs (1-day-old) were injected with LmUAP1 double-stranded RNA (dsRNA), 100% mortality was observed 2 days after the injection. When the middle second- and fifth-instar nymphs (3- to 4-day-old) were injected with LmUAP1 dsRNA, 100% mortality was observed during their next molting process. In contrast, when the insects at the same stages were injected with LmUAP2 dsRNA, these insects were able to develop normally and molt to the next stage successfully. It is presumed that the lethality caused by RNAi of LmUAP1 is due to reduced chitin biosynthesis of the integument and midgut, whereas LmUAP2 is not essential for locust development at least in nymph stage. This study is expected to help better understand different functions of UAP1 and UAP2 in the locust and other insect species.

  14. Molecular and functional analysis of UDP-N-acetylglucosamine Pyrophosphorylases from the Migratory Locust, Locusta migratoria.

    Directory of Open Access Journals (Sweden)

    Xiaojian Liu

    Full Text Available UDP-N-acetylglucosamine pyrophosphorylases (UAP function in the formation of extracellular matrix by producing N-acetylglucosamine (GlcNAc residues needed for chitin biosynthesis and protein glycosylation. Herein, we report two UAP cDNA's derived from two different genes (LmUAP1 and LmUAP2 in the migratory locust Locusta migratoria. Both the cDNA and their deduced amino acid sequences showed about 70% identities between the two genes. Phylogenetic analysis suggests that LmUAP1 and LmUAP2 derive from a relatively recent gene duplication event. Both LmUAP1 and LmUAP2 were widely expressed in all the major tissues besides chitin-containing tissues. However, the two genes exhibited different developmental expression patterns. High expression of LmUAP1 was detected during early embryogenesis, then decreased greatly, and slowly increased before egg hatch. During nymphal development, the highest expression of LmUAP1 appeared just after molting but declined in each inter-molting period and then increased before molting to the next stage, whereas LmUAP2 was more consistently expressed throughout all these stages. When the early second- and fifth-instar nymphs (1-day-old were injected with LmUAP1 double-stranded RNA (dsRNA, 100% mortality was observed 2 days after the injection. When the middle second- and fifth-instar nymphs (3- to 4-day-old were injected with LmUAP1 dsRNA, 100% mortality was observed during their next molting process. In contrast, when the insects at the same stages were injected with LmUAP2 dsRNA, these insects were able to develop normally and molt to the next stage successfully. It is presumed that the lethality caused by RNAi of LmUAP1 is due to reduced chitin biosynthesis of the integument and midgut, whereas LmUAP2 is not essential for locust development at least in nymph stage. This study is expected to help better understand different functions of UAP1 and UAP2 in the locust and other insect species.

  15. 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.

  16. 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.

  17. 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.

  18. Uncovering Topological Structures in Unstructured Data

    Science.gov (United States)

    2015-04-20

    AFRL-OSR-VA-TR-2015-0091 Uncovering Topological Structures in Unstructured Data Keith Bowman ILLINOIS INSTITUTE OF TECHNOLOGY Final Report 04/20/2015...COVERED (From - To)      01-05-2012 to 30-04-2015 4.  TITLE AND SUBTITLE Uncovering Topological Structures in Unstructured Data 5a.  CONTRACT NUMBER 5b...scanned point-cloud data . It has two stages. In the first stage, we analyzed scan data and extracted topologically critical points. We used these critical

  19. A Brassica cDNA clone encoding a bifunctional hydroxymethylpyrimidine kinase/thiamin-phosphate pyrophosphorylase involved in thiamin biosynthesis.

    Science.gov (United States)

    Kim, Y S; Nosaka, K; Downs, D M; Kwak, J M; Park, D; Chung, I K; Nam, H G

    1998-08-01

    We report the characterization of a Brassica napus cDNA clone (pBTHI) encoding a protein (BTHI) with two enzymatic activities in the thiamin biosynthetic pathway, thiamin-phosphate pyrophosphorylase (TMP-PPase) and 2-methyl-4-amino-5-hydroxymethylpyrimidine-monophosphate kinase (HMP-P kinase). The cDNA clone was isolated by a novel functional complementation strategy employing an Escherichia coli mutant deficient in the TMP-PPase activity. A biochemical assay showed the clone to confer recovery of TMP-PPase activity in the E. coli mutant strain. The cDNA clone is 1746 bp long and contains an open reading frame encoding a peptide of 524 amino acids. The C-terminal part of BTH1 showed 53% and 59% sequence similarity to the N-terminal TMP-PPase region of the bifunctional yeast proteins Saccharomyces THI6 and Schizosaccharomyces pombe THI4, respectively. The N-terminal part of BTH1 showed 58% sequence similarity to HMP-P kinase of Salmonella typhimurium. The cDNA clone functionally complemented the S. typhimurium and E. coli thiD mutants deficient in the HMP-P kinase activity. These results show that the clone encodes a bifunctional protein with TMP-PPase at the C-terminus and HMP-P kinase at the N-terminus. This is in contrast to the yeast bifunctional proteins that encode TMP-PPase at the N-terminus and 4-methyl-5-(2-hydroxyethyl)thiazole kinase at the C-terminus. Expression of the BTH1 gene is negatively regulated by thiamin, as in the cases for the thiamin biosynthetic genes of microorganisms. This is the first report of a plant thiamin biosynthetic gene on which a specific biochemical activity is assigned. The Brassica BTH1 gene may correspond to the Arabidopsis TH-1 gene.

  20. Sinorhizobium meliloti low molecular mass phosphotyrosine phosphatase SMc02309 modifies activity of the UDP-glucose pyrophosphorylase ExoN involved in succinoglycan biosynthesis.

    Science.gov (United States)

    Medeot, Daniela B; Romina Rivero, María; Cendoya, Eugenia; Contreras-Moreira, Bruno; Rossi, Fernando A; Fischer, Sonia E; Becker, Anke; Jofré, Edgardo

    2016-03-01

    In Gram-negative bacteria, tyrosine phosphorylation has been shown to play a role in the control of exopolysaccharide (EPS) production. This study demonstrated that the chromosomal ORF SMc02309 from Sinorhizobium meliloti 2011 encodes a protein with significant sequence similarity to low molecular mass protein-tyrosine phosphatases (LMW-PTPs), such as the Escherichia coli Wzb. Unlike other well-characterized EPS biosynthesis gene clusters, which contain neighbouring LMW-PTPs and kinase, the S. meliloti succinoglycan (EPS I) gene cluster located on megaplasmid pSymB does not encode a phosphatase. Biochemical assays revealed that the SMc02309 protein hydrolyses p-nitrophenyl phosphate (p-NPP) with kinetic parameters similar to other bacterial LMW-PTPs. Furthermore, we show evidence that SMc02309 is not the LMW-PTP of the bacterial tyrosine-kinase (BY-kinase) ExoP. Nevertheless, ExoN, a UDP-glucose pyrophosphorylase involved in the first stages of EPS I biosynthesis, is phosphorylated at tyrosine residues and constitutes an endogenous substrate of the SMc02309 protein. Additionally, we show that the UDP-glucose pyrophosphorylase activity is modulated by SMc02309-mediated tyrosine dephosphorylation. Moreover, a mutation in the SMc02309 gene decreases EPS I production and delays nodulation on Medicago sativa roots.

  1. 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.

  2. Enhanced Production of Polysaccharide Through the Overexpression of Homologous Uridine Diphosphate Glucose Pyrophosphorylase Gene in a Submerged Culture of Lingzhi or Reishi Medicinal Mushroom, Ganoderma lucidum (Higher Basidiomycetes).

    Science.gov (United States)

    Ji, Sen-Lin; Liu, Rui; Ren, Meng-Fei; Li, Huan-Jun; Xu, Jun-Wei

    2015-01-01

    This study aimed to improve polysaccharide production by engineering the biosynthetic pathway in Ganoderma lucidum through the overexpression of the homologous UDP glucose pyrophosphorylase (UGP) gene. The effects of UGP gene overexpression on intracellular polysaccharide (IPS) content, extracellular polysaccharide (EPS) production, and transcription levels of 3 genes encoding the enzymes involved in polysaccharide biosynthesis, including phosphoglucomutase (PGM), UGP, and α-1,3-glucan synthase (GLS), were investigated. The maximum IPS content and EPS production in G. lucidum overexpressing the UGP gene were 24.32 mg/100 mg dry weight and 1.66 g/L, respectively, which were higher by 42% and 36% than those of the wild-type strain. The transcription levels of PGM, UGP, and GLS were up-regulated by 1.6, 2.6, and 2.4-fold, respectively, in the engineered strain, suggesting that increased polysaccharide biosynthesis may result from a higher expression of those genes.

  3. 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.

  4. 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...... million individuals worldwide, causing chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. The only approved treatment, combination therapy with IFN- and ribavirin, targets cellular pathways (2); however, a sustained virologic response is achieved only in approximately half of the patients...... 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...

  5. Uncovering the Hidden Decisions that Shape Curricula

    Science.gov (United States)

    Harlow, Danielle Boyd

    2010-10-01

    Developing explanatory models is a central practice to scientific inquiry. When students create and test explanatory models for scientific phenomenon, they develop content knowledge, knowledge of the nature of science, and creative thinking skills. Unfortunately, such instruction rarely occurs in K-12 science. This is, in part, because teachers do not have the opportunity to develop sophisticated understandings of the process of modeling, but also because teaching in this way requires teachers to make real-time instructional decisions that are responsive to students' ideas. This is challenging for teachers, especially because this decision process is often invisible. In this talk, I will highlight the importance of providing opportunities for sophisticated science thinking for our youngest learners and consider how uncovering the decisions that shape physics courses for teachers may benefit their future students.

  6. 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.

  7. Uncovering Wolbachia diversity upon artificial host transfer.

    Directory of Open Access Journals (Sweden)

    Daniela I Schneider

    Full Text Available The common endosymbiotic Wolbachia bacteria influence arthropod hosts in multiple ways. They are mostly recognized for their manipulations of host reproduction, yet, more recent studies demonstrate that Wolbachia also impact host behavior, metabolic pathways and immunity. Besides their biological and evolutionary roles, Wolbachia are new potential biological control agents for pest and vector management. Importantly, Wolbachia-based control strategies require controlled symbiont transfer between host species and predictable outcomes of novel Wolbachia-host associations. Theoretically, this artificial horizontal transfer could inflict genetic changes within transferred Wolbachia populations. This could be facilitated through de novo mutations in the novel recipient host or changes of haplotype frequencies of polymorphic Wolbachia populations when transferred from donor to recipient hosts. Here we show that Wolbachia resident in the European cherry fruit fly, Rhagoletis cerasi, exhibit ancestral and cryptic sequence polymorphism in three symbiont genes, which are exposed upon microinjection into the new hosts Drosophila simulans and Ceratitis capitata. Our analyses of Wolbachia in microinjected D. simulans over 150 generations after microinjection uncovered infections with multiple Wolbachia strains in trans-infected lines that had previously been typed as single infections. This confirms the persistence of low-titer Wolbachia strains in microinjection experiments that had previously escaped standard detection techniques. Our study demonstrates that infections by multiple Wolbachia strains can shift in prevalence after artificial host transfer driven by either stochastic or selective processes. Trans-infection of Wolbachia can claim fitness costs in new hosts and we speculate that these costs may have driven the shifts of Wolbachia strains that we saw in our model system.

  8. NLM Grantee's "HealthMap" Helps Uncover Measles Vaccination Gap

    Science.gov (United States)

    ... courtesy of NLM NLM Grantee's "HealthMap" Helps Uncover Measles Vaccination Gap Inadequate vaccine coverage is likely a driving force behind the ongoing Disneyland measles outbreak, according to calculations by a research team ...

  9. 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.

  10. 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.

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

    DEFF Research Database (Denmark)

    Jørgensen, Frances; Ulhøi, John Parm

    2010-01-01

    firms. The empirical part of this research stems from an ongoing in-depth study aimed at uncovering and describing the relationship between HRM and innovation, highlighting possible areas for misinterpretations that have contributed to the assumption that Danish firms do not prioritize HRM....

  12. Weaving Social Foundations through Dance Pedagogy: A Pedagogy of Uncovering

    Science.gov (United States)

    Barr, Sherrie; Risner, Doug

    2014-01-01

    Today's dance educators enter classrooms populated by increasingly diverse students in which teachers' pedagogical knowledge necessitates heightened understandings of race, ethnicity, social class, gender, and sexuality. Uncovering taken-for-granted assumptions, dominant stereotypes, and educational structures that reproduce social…

  13. Uncovering Students' Thinking about Thinking Using Concept Maps

    Science.gov (United States)

    Ritchhart, Ron; Turner, Terri; Hadar, Linor

    2009-01-01

    A method for uncovering students' thinking about thinking, specifically their meta-strategic knowledge, is explored within the context of an ongoing, multi-year intervention designed to promote the development of students' thinking dispositions. The development of a concept-map instrument that classroom teachers can use and an analytic framework…

  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. Uncovering introductory astronomy students' conceptual modules of lunar phases

    Science.gov (United States)

    Lindell, Rebecca; Traxler, Adrienne

    2017-01-01

    Brewe, Bruun and Bearden developed Module Analysis of Multiple Choice Responses (MAMCR) methodology for using network analysis to uncover the underlying conceptual modules of student performance on multiple-choice assessments. The Lunar Phases Concept Inventory (LPCI) assesses students understanding of lunar phases across 8 separate dimensions of understanding based on the results of a detailed qualitative phenomenology of college students' understanding of lunar phases. Unlike many concept inventories, the LPCI has multiple items for each dimension of understanding and each response corresponds to either the scientifically correct answer or to an alternative idea uncovered from the qualitative investigation. In this study, we have combined MAMCR with the database of nearly 2000 LPCI pre-test results. We will report on the preliminary different conceptual modules of lunar phases and the relationship of these modules to previous qualitative research.

  16. 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.

  17. 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

  18. 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

  19. Uncovering growth-suppressive MicroRNAs in lung cancer

    DEFF Research Database (Denmark)

    Liu, Xi; Sempere, Lorenzo F; Galimberti, Fabrizio

    2009-01-01

    PURPOSE: MicroRNA (miRNA) expression profiles improve classification, diagnosis, and prognostic information of malignancies, including lung cancer. This study uncovered unique growth-suppressive miRNAs in lung cancer. EXPERIMENTAL DESIGN: miRNA arrays were done on normal lung tissues...... and adenocarcinomas from wild-type and proteasome degradation-resistant cyclin E transgenic mice to reveal repressed miRNAs in lung cancer. Real-time and semiquantitative reverse transcription-PCR as well as in situ hybridization assays validated these findings. Lung cancer cell lines were derived from each...... 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...

  20. 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.

  1. DOES UNCOVERED INTEREST RATE PARITY HOLD IN TURKEY?

    Directory of Open Access Journals (Sweden)

    Ozcan Karahan

    2012-01-01

    Full Text Available Most of the earlier empirical studies focusing on developed countries failed to give evidence in favor of the Uncovered Interest Rate Parity (UIP. After intensive financial liberalization processes and mostly preferred free exchange rate regimes, a new area of research starts to involve the investigation whether UIP holds for developing economies differently. Accordingly, we tested the UIP for Turkey’s monthly interest rate and exchange rate data between 2002 and 2011. We run conventional regressions in the form of Ordinary Least Squares (OLS and used a simple Generalized Autoregressive Conditional Heteroskedasticity (GARCH analysis. The empirical results of both methods do not support the validity of UIP for Turkey. Thus, together with most of the earlier empirical studies focusing on developed countries and detecting the invalidity of UIP, we can argue that the experience of Turkey and developed economies are not different.

  2. 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.

  3. Charge uncovering effects on flute instabilities in hot electron plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Spong, D.A.

    1985-01-01

    Recent measurements and concurrent theoretical equilibrium models of the ELMO Bumpy Torus (EBT) edge plasma region (as described by E. F. Jaeger et al. in Magnetic Well Depth in EBT and Sensitivity to Hot Electron Ring Geometry, ORNL/TM-9185 (1984)) have indicated that the hot electron ring beta ..beta../sub hot/ at the C-T transition may not always be sufficient to produce the local minimum in the magnetic field thought to be necessary for MHD stability. This has led to the examination of other mechanisms that could account for the observed stability of the T-mode. In this report, an effect known as charge uncovering, which depends not on the value of ..beta../sub hot/ but rather on the ratio n/sub hot//n/sub core/, is studied.

  4. 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.

  5. 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.

  6. Uncovering transcriptional regulation of metabolism by using metabolic network topology

    DEFF Research Database (Denmark)

    Patil, Kiran Raosaheb; Nielsen, Jens

    2005-01-01

    therefore developed an algorithm that is based on hypothesis-driven data analysis to uncover the transcriptional regulatory architecture of metabolic networks. By using information on the metabolic network topology from genome-scale metabolic reconstruction, we show that it is possible to reveal patterns...... in the metabolic network that follow a common transcriptional response. Thus, the algorithm enables identification of so-called reporter metabolites (metabolites around which the most significant transcriptional changes occur) and a set of connected genes with significant and coordinated response to genetic...... changes induced by complex regulatory mechanisms coordinating the activity of different metabolic pathways. It is difficult to map such global transcriptional responses by using traditional methods, because many genes in the metabolic network have relatively small changes at their transcription level. We...

  7. TIME HORIZON AND UNCOVERED INTEREST PARITY IN EMERGING ECONOMIES

    Directory of Open Access Journals (Sweden)

    Norlida Hanim Mohd Salleh

    2011-07-01

    Full Text Available The aim of this study is to re-examine the well-known empirical puzzle of uncovered interest parity (UIP for emerging market economies with different prediction time horizons. The empirical results obtained using dynamic panel and time series techniques for monthly data from January 1995 to December 2009 eventually show that the panel data estimates are more powerful than those obtained by applying individual time series estimations and the significant contribution of the exchange rate prediction horizons in determining the status of UIP. This finding reveals that at the longer time horizon, the model has better econometric specification and thus more predictive power for exchange rate movements compared to the shorter time period. The findings can also be a signalling of well-integrated currency markets and a reliable guide to international investors as well as for the orderly conduct of monetary authorities.

  8. Consolidity: Mystery of inner property of systems uncovered

    Directory of Open Access Journals (Sweden)

    Hassen T. Dorrah

    2012-10-01

    Full Text Available This paper uncovers the mystery of consolidity, an inner property of systems that was amazingly hidden. Consolidity also reveals the secrecy of why strong stable and highly controllable systems are not invulnerable of falling and collapsing. Consolidity is measured by its Consolidity Index, defined as the ratio of overall changes of output parameters over combined changes of input and system parameters, all operating in fully fuzzy environment. Under this notion, systems are classified into consolidated, quasi-consolidated, neutrally consolidated, unconsolidated, quasi-unconsolidated and mixed types. The strategy for the implementation of consolidity is elaborated for both natural and man-made existing systems as well as the new developed ones. An important critique arises that the by-product consolidity of natural or built-as-usual system could lead to trapping such systems into a completely undesired unconsolidity. This suggests that the ample number of conventional techniques that do not take system consolidity into account should gradually be changed, and adjusted with improved consolidity-based techniques. Four Golden Rules are highlighted for handling system consolidity, and applied to several illustrative case studies. These case studies cover the consolidity analysis of the Drug Concentration problem, Predator-Prey Population problem, Spread of Infectious Disease problem, AIDS Epidemic problem and Arm Race model. It is demonstrated that consolidity changes are contrary (opposite in sign to changes of both stability and controllability. This is a very significant result showing that our present practice of stressing on building strong stable and highly controllable systems could have already jeopardized the consolidity behavior of an ample family of existing real life systems. It is strongly recommended that the four Golden Rules of consolidity should be enforced as future strict regulations of systems modeling, analysis, design and

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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...

  14. 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.

  15. Uncovering disassortativity in large scale-free networks

    Science.gov (United States)

    Litvak, Nelly; van der Hofstad, Remco

    2013-02-01

    Mixing patterns in large self-organizing networks, such as the Internet, the World Wide Web, and social and biological networks, are often characterized by degree-degree dependencies between neighboring nodes. In this paper, we propose a new way of measuring degree-degree dependencies. One of the problems with the commonly used assortativity coefficient is that in disassortative networks its magnitude decreases with the network size. We mathematically explain this phenomenon and validate the results on synthetic graphs and real-world network data. As an alternative, we suggest to use rank correlation measures such as Spearman's ρ. Our experiments convincingly show that Spearman's ρ produces consistent values in graphs of different sizes but similar structure, and it is able to reveal strong (positive or negative) dependencies in large graphs. In particular, we discover much stronger negative degree-degree dependencies in Web graphs than was previously thought. Rank correlations allow us to compare the assortativity of networks of different sizes, which is impossible with the assortativity coefficient due to its genuine dependence on the network size. We conclude that rank correlations provide a suitable and informative method for uncovering network mixing patterns.

  16. 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.

  17. 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.

  18. Greenhouse gas emissions from shallow uncovered coal seams

    Institute of Scientific and Technical Information of China (English)

    Saghafi Abouna

    2014-01-01

    This study discusses a method of quantifying emissions from surface coal mining that has been trialled in Australia. The method is based on direct measurement of surface emissions from uncovered coal seams in mine pits, concurrent measurement of residual gas content of blasted coal in mine pits, and measurement of pre-mining gas content of the same seam from cores retrieved from exploration boreholes drilled away from active mining. The results from one of the mines studied are presented in this paper. In this mine, the pre-mining gas content of the target seam was measured using cores from an exploration borehole away from active mining. Gas content varied from 0.7 to 0.8 m3/t and gas composition varied from 16% to 21% CH4 (84-79% CO2). In-pit measurements included seam surface emissions and residual gas content of blasted and ripped coal. Residual gas content varied from 0.09 to 0.15 m3/t, less than twofold across the mine pit. Composition of the residual gas was in general 90%CO2 and 10%CH4, with slight var-iation between samples. Coal seam surface emissions varied from 1.03 to 7.50 mL of CO2-e per minute and per square meter of the coal seam surface, a sevenfold variation across the mine pit.

  19. 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.

  20. 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.

  1. Uncovering labially impacted teeth: apically positioned flap and closed-eruption techniques.

    Science.gov (United States)

    Vermette, M E; Kokich, V G; Kennedy, D B

    1995-01-01

    The purpose of this study was to examine the esthetic and periodontal differences between two methods of uncovering labially impacted maxillary anterior teeth: the apically positioned flap and closed-eruption techniques. The sample consisted of 30 patients who were recalled a minimum of three months after orthodontic treatment of a unilateral labially impacted maxillary anterior tooth. Eighteen of the patients had undergone an apically positioned flap (APF) procedure, and the remaining twelve had undergone the closed-eruption (CE) technique. In the CE group, clinical examination showed less width of attached gingiva on the distal surface and increased probing bone level on the facial surface of the uncovered teeth relative to their contralateral controls. Uncovered teeth in the APF group showed more apical gingival margins on the mesial and facial surfaces; greater crown length on the midfacial surface; increased probing attachment level on the facial surface; increased width of attached gingiva on the facial surface; increased probing bone level on mesial, facial, and distal surfaces; and gingival scarring. Radiographic examination showed shorter roots on the uncovered teeth in both groups. Photographic examination revealed vertical relapse of the uncovered teeth in the APF group. We conclude that labially impacted maxillary anterior teeth uncovered with an apically positioned flap technique have more unesthetic sequalae than those uncovered with a closed-eruption technique.

  2. Characterization of a gene from chromosome 1B encoding the large subunit of ADPglucose pyrophosphorylase from wheat: evolutionary divergence and differential expression of Agp2 genes between leaves and developing endosperm.

    Science.gov (United States)

    Thorneycroft, David; Hosein, Felicia; Thangavelu, Madan; Clark, Joanna; Vizir, Igor; Burrell, Michael M; Ainsworth, Charles

    2003-07-01

    A full-length genomic clone containing the gene encoding the large subunit of the ADPglucose pyrophosphorylase (Agp2), was isolated from a genomic library prepared from etiolated shoots of hexaploid wheat (Triticum aestivum L., cv, Chinese Spring). The coding region of this gene is identical to one of the cDNA clones previously isolated from a developing wheat grain cDNA library and is therefore an actively transcribed gene. The sequence represented by the cDNA spans 4.8 kb of the genomic clone and contains 15 introns. 2852 bp of DNA flanking the transcription start site of the gene was cloned upstream of the GUS (beta-glucuronidase) reporter gene. This Agp2::GUS construct and promoter deletions were used to study the pattern of reporter gene expression in both transgenic tobacco and wheat plants. Histochemical analysis of GUS expression in transgenic tobacco demonstrated that the reporter gene was expressed in guard cells of leaves and throughout the seed. In transgenic wheat, reporter gene expression was confined to the endosperm and aleurone with no expression in leaves. The cloned Agp2 gene was located to chromosome 1B by gene-specific PCR with nullisomic-tetrasomic lines. Northern analysis demonstrated that the Agp2 genes are differentially expressed in leaves and developing endosperm; while all three classes of Agp2 genes are transcribed in developing wheat grain endosperm, only one is transcribed in leaves. The differences between the Agp2 genes are discussed in relation to the evolution of hexaploid wheat.

  3. Uncovering cognitive processes: Different techniques that can contribute to cognitive load research and instruction

    NARCIS (Netherlands)

    Van Gog, Tamara; Kester, Liesbeth; Nievelstein, Fleurie; Giesbers, Bas; Fred, Paas

    2009-01-01

    Van Gog, T., Kester, L., Nievelstein, F., Giesbers, B., & Paas, F. (2009). Uncovering cognitive processes: Different techniques that can contribute to cognitive load research and instruction. Computers in Human Behavior, 25, 325-331.

  4. 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

  5. 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…

  6. Uncovering the Best Skill Multimap by Constraining the Error Probabilities of the Gain-Loss Model

    Science.gov (United States)

    Anselmi, Pasquale; Robusto, Egidio; Stefanutti, Luca

    2012-01-01

    The Gain-Loss model is a probabilistic skill multimap model for assessing learning processes. In practical applications, more than one skill multimap could be plausible, while none corresponds to the true one. The article investigates whether constraining the error probabilities is a way of uncovering the best skill assignment among a number of…

  7. 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...

  8. 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…

  9. 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

  10. 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

  11. 76 FR 4290 - Uncovered Innerspring Units From the People's Republic of China: Final Results of First...

    Science.gov (United States)

    2011-01-25

    ... synthetic material or woven material and then glued together in a linear fashion. Uncovered innersprings are... innerspring. Pocketed and non-pocketed innerspring units are included in this definition. Non-pocketed innersprings are typically joined together with helical wire and border rods. Non-pocketed innersprings...

  12. 77 FR 21961 - Uncovered Innerspring Units From the People's Republic of China: Final Results and Final...

    Science.gov (United States)

    2012-04-12

    ... synthetic material or woven material and then glued together in a linear fashion. Uncovered innersprings are... innerspring. Pocketed and non-pocketed innerspring units are included in this definition. Non-pocketed innersprings are typically joined together with helical wire and border rods. Non-pocketed innersprings...

  13. 40 CFR 141.714 - Requirements for uncovered finished water storage facilities.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 22 2010-07-01 2010-07-01 false Requirements for uncovered finished water storage facilities. 141.714 Section 141.714 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS...

  14. 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…

  15. EXCHANGE RATES AND VOLATILITY IN CENTRAL AND EASTERN EUROPE: A TEST FOR UNCOVERED INTEREST PARITY

    Directory of Open Access Journals (Sweden)

    DUMITRESCU Dan-Gabriel

    2009-05-01

    Full Text Available At times of heightened global capital market volatility, high-yielding currencies tend to depreciate, while low-yielding currencies tend to serve as a€śsafe heavena€ť. We present the results of a test for Uncovered Interest Parity for selected European cu

  16. 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…

  17. 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…

  18. 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...

  19. Aeromonas surface glucan attached through the O-antigen ligase represents a new way to obtain UDP-glucose.

    Directory of Open Access Journals (Sweden)

    Susana Merino

    Full Text Available We previously reported that A. hydrophila GalU mutants were still able to produce UDP-glucose introduced as a glucose residue in their lipopolysaccharide core. In this study, we found the unique origin of this UDP-glucose from a branched α-glucan surface polysaccharide. This glucan, surface attached through the O-antigen ligase (WaaL, is common to the mesophilic Aeromonas strains tested. The Aeromonas glucan is produced by the action of the glycogen synthase (GlgA and the UDP-Glc pyrophosphorylase (GlgC, the latter wrongly indicated as an ADP-Glc pyrophosphorylase in the Aeromonas genomes available. The Aeromonas glycogen synthase is able to react with UDP or ADP-glucose, which is not the case of E. coli glycogen synthase only reacting with ADP-glucose. The Aeromonas surface glucan has a role enhancing biofilm formation. Finally, for the first time to our knowledge, a clear preference on behalf of bacterial survival and pathogenesis is observed when choosing to produce one or other surface saccharide molecules to produce (lipopolysaccharide core or glucan.

  20. Aeromonas surface glucan attached through the O-antigen ligase represents a new way to obtain UDP-glucose.

    Science.gov (United States)

    Merino, Susana; Bouamama, Lamiaa; Knirel, Yuriy A; Senchenkova, Sofya N; Regué, Miguel; Tomás, Juan M

    2012-01-01

    We previously reported that A. hydrophila GalU mutants were still able to produce UDP-glucose introduced as a glucose residue in their lipopolysaccharide core. In this study, we found the unique origin of this UDP-glucose from a branched α-glucan surface polysaccharide. This glucan, surface attached through the O-antigen ligase (WaaL), is common to the mesophilic Aeromonas strains tested. The Aeromonas glucan is produced by the action of the glycogen synthase (GlgA) and the UDP-Glc pyrophosphorylase (GlgC), the latter wrongly indicated as an ADP-Glc pyrophosphorylase in the Aeromonas genomes available. The Aeromonas glycogen synthase is able to react with UDP or ADP-glucose, which is not the case of E. coli glycogen synthase only reacting with ADP-glucose. The Aeromonas surface glucan has a role enhancing biofilm formation. Finally, for the first time to our knowledge, a clear preference on behalf of bacterial survival and pathogenesis is observed when choosing to produce one or other surface saccharide molecules to produce (lipopolysaccharide core or glucan).

  1. Monofluorophosphate Blocks Internal Polysaccharide Synthesis in Streptococcus mutans

    Science.gov (United States)

    Naleway, Conrad; Iglesias, Alberto A.; Ballicora, Miguel A.

    2017-01-01

    Streptococcus mutans is the leading cause of dental caries worldwide by accumulating a glycogen-like internal polysaccharide (IPS) that contributes to cariogenicity when sugars are in excess. Sodium monofluorophosphate (MFP) is an active anticariogenic compound in toothpastes. Herein, we show that MFP inhibits (with an I0.5 of 1.5 mM) the S. mutans ADP-glucose pyrophosphorylase (EC 2.7.7.27), which catalyzes the key step in IPS biosynthesis. Enzyme inhibition by MFP is similar to orthophosphate (Pi), except that the effect caused by MFP is not reverted by fructose-1,6-bisP, as occurs with Pi. Inhibition was correlated with a decrease in acidogenesis and IPS accumulation in S. mutans cells cultured with 2 mM sodium MFP. These effects were not mimicked by sodium fluoride. Considering that glycogen synthesis occurs by different pathways in mammals and bacteria, ADP-glucose pyrophosphorylase could be visualized as a molecular target for controlling S. mutans virulence. Our results strongly suggest that MFP is a suitable compound to affect such a target, inducing an anticariogenic effect primarily by inhibiting a key step in IPS synthesis. PMID:28125652

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

    OpenAIRE

    Salha M. Alzahrani; Naomie Salim; Vasile Palade

    2015-01-01

    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 su...

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

    OpenAIRE

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

  4. 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.

  5. The invisible Web uncovering information sources search engines can't see

    CERN Document Server

    Sherman, Chris

    2001-01-01

    Enormous expanses of the Internet are unreachable with standard web search engines. This book provides the key to finding these hidden resources by identifying how to uncover and use invisible web resources. Mapping the invisible Web, when and how to use it, assessing the validity of the information, and the future of Web searching are topics covered in detail. Only 16 percent of Net-based information can be located using a general search engine. The other 84 percent is what is referred to as the invisible Web-made up of information stored in databases. Unlike pages on the visible Web, informa

  6. Structural insight to mutation effects uncover a common allosteric site in class C GPCRs

    DEFF Research Database (Denmark)

    Harpsøe, Kasper; Boesgaard, Michael W; Munk, Christian;

    2017-01-01

    . Combining pharmacological site-directed mutagenesis data with the recent class C GPCR experimental structures will provide a foundation for rational design of new therapeutics. RESULTS: We uncover one common site for both positive and negative modulators with different amino acid layouts that can......MOTIVATION: Class C G protein-coupled receptors (GPCRs) regulate important physiological functions and allosteric modulators binding to the transmembrane domain constitute an attractive and, due to a lack of structural insight, a virtually unexplored potential for therapeutics and the food industry...

  7. 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...

  8. 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.

  9. 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.

  10. Uncovering signal transduction networks from high-throughput data by integer linear programming.

    Science.gov (United States)

    Zhao, Xing-Ming; Wang, Rui-Sheng; Chen, Luonan; Aihara, Kazuyuki

    2008-05-01

    Signal transduction is an important process that transmits signals from the outside of a cell to the inside to mediate sophisticated biological responses. Effective computational models to unravel such a process by taking advantage of high-throughput genomic and proteomic data are needed to understand the essential mechanisms underlying the signaling pathways. In this article, we propose a novel method for uncovering signal transduction networks (STNs) by integrating protein interaction with gene expression data. Specifically, we formulate STN identification problem as an integer linear programming (ILP) model, which can be actually solved by a relaxed linear programming algorithm and is flexible for handling various prior information without any restriction on the network structures. The numerical results on yeast MAPK signaling pathways demonstrate that the proposed ILP model is able to uncover STNs or pathways in an efficient and accurate manner. In particular, the prediction results are found to be in high agreement with current biological knowledge and available information in literature. In addition, the proposed model is simple to be interpreted and easy to be implemented even for a large-scale system.

  11. Representations of God uncovered in a spirituality group of borderline inpatients.

    Science.gov (United States)

    Goodman, Geoff; Manierre, Amy

    2008-01-01

    We present aspects of a psychoanalytically-oriented, exploratory spirituality group for nine female psychiatric inpatients diagnosed with borderline personality disorder. Through drawings and group process, the patients uncovered and elaborated on their representations of God. Two patterns of representations were identified: (1) representations of a punitive, judgmental, rigid God that seemed directly to reflect and correspond with parental representations and (2) representations of a depersonified, inanimate, abstract God entailing aspects of idealization that seemed to compensate for parental representations. Interestingly, the second pattern was associated with comorbid narcissistic features in the patients. Those patients who presented punitive God representations were able to begin the process of re-creating these representations toward more benign or benevolent images in the context of this group, while those participants who presented depersonified God representations seemed unable to do so.

  12. 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

  13. 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....... Therefore, we performed a genome-wide association study (GWAS) of circulating leptin levels from 32,161 individuals and followed up loci reaching Pleptin 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...

  14. 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.

  15. 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.

  16. 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...

  17. 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

  18. 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…

  19. 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

  20. Uncovering Molecular Relaxation Processes with Nonlinear Spectroscopies in the Deep UV

    Science.gov (United States)

    West, Brantley Andrew

    Conical intersections mediate internal conversion dynamics that compete with even the fastest nuclear motions in molecular systems. Traditional kinetic models do not apply in this regime of commensurate electronic and nuclear motion because the surroundings do not maintain equilibrium throughout the relaxation process. This dissertation focuses on uncovering the physics associated with vibronic interactions at conical intersections. Of particular interest are coherent nuclear motions driven by steep excited state potential energy gradients. Technical advances have only recently made these dynamics accessible in many systems including DNA nucleobases and cyclic polyene molecules. Optical analogues of multidimensional NMR spectroscopies have recently yielded transformative insight in relaxation processes ranging from energy transfer in photosynthesis to bond making and breaking in liquids. Prior to the start of this research, such experiments had only been conducted at infrared and visible wavelengths. Applications in the ultraviolet were motivated by studies of numerous biological systems (e.g., DNA, proteins), but had been challenged by technical issues. The work presented in this dissertation combines pulse generation techniques developed in the optical physics community with spectroscopic techniques largely pioneered by physical chemists to implement two-dimensional ultraviolet spectroscopy (2DUV). This technique is applied at the shortest wavelengths and with the best signal-to-noise ratios reported to date. Sub-picosecond excited state deactivation processes provide photo stability to the DNA double helix. Vibrational energy transfer from the solute to surrounding solvent enables relaxation of the highly non-equilibrium ground state produced by fast internal conversion. In this dissertation, nonlinear spectroscopies carried out at cryogenic temperatures are used to uncover the particular nuclear modes in the solvent that primarily accept vibrational energy from

  1. Plant Phenotyping using Probabilistic Topic Models: Uncovering the Hyperspectral Language of Plants.

    Science.gov (United States)

    Wahabzada, Mirwaes; Mahlein, Anne-Katrin; Bauckhage, Christian; Steiner, Ulrike; Oerke, Erich-Christian; Kersting, Kristian

    2016-03-09

    Modern phenotyping and plant disease detection methods, based on optical sensors and information technology, provide promising approaches to plant research and precision farming. In particular, hyperspectral imaging have been found to reveal physiological and structural characteristics in plants and to allow for tracking physiological dynamics due to environmental effects. In this work, we present an approach to plant phenotyping that integrates non-invasive sensors, computer vision, as well as data mining techniques and allows for monitoring how plants respond to stress. To uncover latent hyperspectral characteristics of diseased plants reliably and in an easy-to-understand way, we "wordify" the hyperspectral images, i.e., we turn the images into a corpus of text documents. Then, we apply probabilistic topic models, a well-established natural language processing technique that identifies content and topics of documents. Based on recent regularized topic models, we demonstrate that one can track automatically the development of three foliar diseases of barley. We also present a visualization of the topics that provides plant scientists an intuitive tool for hyperspectral imaging. In short, our analysis and visualization of characteristic topics found during symptom development and disease progress reveal the hyperspectral language of plant diseases.

  2. 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.

  3. The work is never ending: uncovering teamwork sustainability using realistic evaluation.

    Science.gov (United States)

    Frykman, Mandus; von Thiele Schwarz, Ulrica; Muntlin Athlin, Åsa; Hasson, Henna; Mazzocato, Pamela

    2017-03-20

    Purpose The purpose of this paper is to uncover the mechanisms influencing the sustainability of behavior changes following the implementation of teamwork. Design/methodology/approach Realistic evaluation was combined with a framework (DCOM®) based on applied behavior analysis to study the sustainability of behavior changes two and a half years after the initial implementation of teamwork at an emergency department. The DCOM® framework was used to categorize the mechanisms of behavior change interventions (BCIs) into the four categories of direction, competence, opportunity, and motivation. Non-participant observation and interview data were used. Findings The teamwork behaviors were not sustained. A substantial fallback in managerial activities in combination with a complex context contributed to reduced direction, opportunity, and motivation. Reduced direction made staff members unclear about how and why they should work in teams. Deterioration of opportunity was evident from the lack of problem-solving resources resulting in accumulated barriers to teamwork. Motivation in terms of management support and feedback was reduced. Practical implications The implementation of complex organizational changes in complex healthcare contexts requires continuous adaption and managerial activities well beyond the initial implementation period. Originality/value By integrating the DCOM® framework with realistic evaluation, this study responds to the call for theoretically based research on behavioral mechanisms that can explain how BCIs interact with context and how this interaction influences sustainability.

  4. 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.

  5. Uncovering secrets behind low-resistance planing craft hull forms through optimization

    Science.gov (United States)

    Mohamad Ayob, Ahmad F.; Ray, Tapabrata; Smith, Warren F.

    2011-11-01

    There has always been significant interest within the naval architectural research community to identify ship hull forms with low resistance. While numerous design optimization frameworks have been proposed over the years to support the activity, very little attention has been paid towards the process of gaining an understanding of 'what makes a good ship design superior?'. Furthermore, there have been limited attempts to identify computationally cheap indicators that can be used to distinguish between good and poor designs. A recent technique named discovery of innovative design principles, which is aimed at understanding the relationship between the design variables, is incorporated in this work. In this article, optimal high-speed planing craft hull forms with minimum calm-water resistance are identified through the use of three state-of-the-art optimization algorithms. Collections of such designs are then used to uncover insights into the underlying relationships between the variables. The importance of such relationships is further analysed to identify computationally cheap performance indicators that can be used in lieu of detailed calm-water resistance calculations. Such indicators are useful at the concept and preliminary design stages, where one needs to sieve efficiently through a number of candidate designs to identify the better ones for further analysis.

  6. DNA barcoding uncovers cryptic diversity in 50% of deep-sea Antarctic polychaetes.

    Science.gov (United States)

    Brasier, Madeleine J; Wiklund, Helena; Neal, Lenka; Jeffreys, Rachel; Linse, Katrin; Ruhl, Henry; Glover, Adrian G

    2016-11-01

    The Antarctic marine environment is a diverse ecosystem currently experiencing some of the fastest rates of climatic change. The documentation and management of these changes requires accurate estimates of species diversity. Recently, there has been an increased recognition of the abundance and importance of cryptic species, i.e. those that are morphologically identical but genetically distinct. This article presents the largest genetic investigation into the prevalence of cryptic polychaete species within the deep Antarctic benthos to date. We uncover cryptic diversity in 50% of the 15 morphospecies targeted through the comparison of mitochondrial DNA sequences, as well as 10 previously overlooked morphospecies, increasing the total species richness in the sample by 233%. Our ability to describe universal rules for the detection of cryptic species within polychaetes, or normalization to expected number of species based on genetic data is prevented by taxon-specific differences in phylogenetic outputs and genetic variation between and within potential cryptic species. These data provide the foundation for biogeographic and functional analysis that will provide insight into the drivers of species diversity and its role in ecosystem function.

  7. 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.

  8. 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...

  9. Antisocial behaviour and psychopathy: uncovering the externalizing link in the P3 modulation.

    Science.gov (United States)

    Pasion, Rita; Fernandes, Carina; Pereira, Mariana R; Barbosa, Fernando

    2017-03-22

    In 2009, Gao and Raine's meta-analysis analysed P3 modulation over the antisocial spectrum. However, some questions remained open regarding the P3 modulation patterns across impulsive and violent manifestations of antisocial behaviour, phenotypic components of psychopathy, and P3 components. A systematic review of 36 studies was conducted (N=3514) to extend previous results and to address these unresolved questions. A clear link between decreased P3 amplitude and antisocial behaviour was found. In psychopathy, dimensional approaches become more informative than taxonomic models. Distinct etiological pathways of psychopathy were evidenced in cognitive tasks: impulsive-antisocial psychopathic traits mainly predicted blunted P3 amplitude, while interpersonal-affective psychopathic traits explained enhanced P3 amplitude. Supporting the low fear hypothesis, the interpersonal-affective traits were associated with reduced P3 amplitude in emotional-affective learning tasks. From the accumulated knowledge we propose a framework of P3 amplitude modulation that uncovers the externalizing link between psychopathy and antisocial behaviour. However, the main hypotheses are exploratory and call for more data before stablishing robust conclusions.

  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. 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.

  12. Uncovering stem-cell heterogeneity in the microniche with label-free microfluidics

    Science.gov (United States)

    Sohn, Lydia L.

    2013-03-01

    Better suited for large number of cells from bulk tissue, traditional cell-screening techniques, such as fluorescence-activated cell sorting (FACS) and magnetic-activated cell sorting (MACS), cannot easily screen stem or progenitor cells from minute populations found in their physiological niches. Furthermore, they rely upon irreversible antibody binding, potentially altering cell properties, including gene expression and regenerative capacity. We have developed a label-free, single-cell analysis microfluidic platform capable of quantifying cell-surface marker expression of functional organ stem cells directly isolated from their micro-anatomical niche. With this platform, we have screened single quiescent muscle stem (satellite) cells derived from single myofibers, and we have uncovered an important heterogeneity in the surface-marker expression of these cells. By sorting the screened cells with our microfluidic device, we have determined what this heterogeneity means in terms of muscle stem-cell functionality. For instance, we show that the levels of beta1-integrin can predict the differentiation capacity of quiescent satellite cells, and in contrast to recent literature, that some CXCR4 + cells are not myogenic. Our results provide the first direct demonstration of a microniche-specific variation in gene expression in stem cells of the same lineage. Overall, our label-free, single-cell analysis and cell-sorting platform could be extended to other systems involving rare-cell subsets. This work was funded by the W. M. Keck Foundation, NIH, and California Institute of Regenerative Medicine

  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 a new role for peroxidase enzymes as drivers of angiogenesis.

    Science.gov (United States)

    Panagopoulos, Vasilios; Zinonos, Irene; Leach, Damien A; Hay, Shelley J; Liapis, Vasilios; Zysk, Aneta; Ingman, Wendy V; DeNichilo, Mark O; Evdokiou, Andreas

    2015-11-01

    Peroxidases are heme-containing enzymes released by activated immune cells at sites of inflammation. To-date their functional role in human health has mainly been limited to providing a mechanism for oxidative defence against invading bacteria and other pathogenic microorganisms. Our laboratory has recently identified a new functional role for peroxidase enzymes in stimulating fibroblast migration and collagen biosynthesis, offering a new insight into the causative association between inflammation and the pro-fibrogenic events that mediate tissue repair and regeneration. Peroxidases are found at elevated levels within and near blood vessels however, their direct involvement in angiogenesis has never been reported. Here we report for the first time that myeloperoxidase (MPO) and eosinophil peroxidase (EPO) are readily internalised by human umbilical vein endothelial cells (HUVEC) where they promote cellular proliferation, migration, invasion, and stimulate angiogenesis both in vitro and in vivo. These pro-angiogenic effects were attenuated using the specific peroxidase inhibitor 4-ABAH, indicating the enzyme's catalytic activity is essential in mediating this response. Mechanistically, we provide evidence that MPO and EPO regulate endothelial FAK, Akt, p38 MAPK, ERK1/2 phosphorylation and stabilisation of HIF-2α, culminating in transcriptional regulation of key angiogenesis pathways. These findings uncover for the first time an important and previously unsuspected role for peroxidases as drivers of angiogenesis, and suggest that peroxidase inhibitors may have therapeutic potential for the treatment of angiogenesis related diseases driven by inflammation.

  15. 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.

  16. 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...

  17. 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.

  18. Methods uncovering usability issues in medication-related alerting functions: results from a systematic review.

    Science.gov (United States)

    Marcilly, Romaric; Vasseur, Francis; Ammenwerth, Elske; Beuscart-Zephir, Marie-Catherine

    2014-01-01

    This paper aims at listing the methods used to evaluate the usability of medication-related alerting functions and at knowing what type of usability issues those methods allow to detect. A sub-analysis of data from this systematic review has been performed. Methods applied in the included papers were collected. Then, included papers were sorted in four types of evaluation: "expert evaluation", "user- testing/simulation", "on site observation" and "impact studies". The types of usability issues (usability flaws, usage problems and negative outcomes) uncovered by those evaluations were analyzed. Results show that a large set of methods are used. The largest proportion of papers uses "on site observation" evaluation. This is the only evaluation type for which every kind of usability flaws, usage problems and outcomes are detected. It is somehow surprising that, in a usability systematic review, most of the papers included use a method that is not often presented as a usability method. Results are discussed about the opportunity to provide usability information collected after the implementation of the technology during their design process, i.e. before their implementation.

  19. 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.

  20. 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.

  1. 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

    2016-02-01

    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.

  2. CHANG-ES - VIII. Uncovering hidden AGN activity in radio polarization

    Science.gov (United States)

    Irwin, Judith A.; Schmidt, Philip; 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

    2017-01-01

    We report on C-band (5-7 GHz) observations of the galaxy, NGC 2992, from the Continuum Halos in Nearby Galaxies - an EVLA Survey (CHANG-ES) sample. This galaxy displays an embedded nuclear double-lobed radio morphology within its spiral disc, as revealed in linearly polarized emission but 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 active galactic nucleus (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 (ISM) and offer new opportunities to investigate the interactions between nuclear outflows and the ISM in nearby galaxies. We also compare the radio emission with a new CHANDRA X-ray image of this galaxy. A new CHANG-ES image of NGC 3079 is also briefly shown as another example as to how much more obvious radio lobes appear in linear polarization as opposed to total intensity.

  3. 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.

  4. Uncovering Multiple Populations with Washington Photometry: I. The Globular Cluster NGC 1851

    CERN Document Server

    Cummings, Jeffrey D; Villanova, S; Carraro, G

    2014-01-01

    The analysis of multiple populations (MPs) in globular clusters (GCs) has become a forefront area of research in astronomy. Multiple red giant branches (RGBs), subgiant branches (SGBs), and even main sequences (MSs) have now been observed photometrically in many GCs. UV photometry has been crucial in discovering and analyzing these MPs, but the Johnson U and the Stromgren and Sloan u filters that have generally been used are relatively inefficient and very sensitive to reddening and atmospheric extinction. In contrast, the Washington C filter is much broader and redder than these competing UV filters. Here we investigate the use of the Washington system to uncover MPs using only a 1-meter telescope. Our analysis of the well-studied GC NGC 1851 finds that the C filter is both very efficient and effective at detecting its previously discovered MPs in the RGB and SGB. Remarkably, we have also detected an intrinsically broad MS best characterized by two distinct but heavily overlapping populations that cannot be ...

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Uncovering multiple populations with washington photometry. I. The globular cluster NGC 1851

    Energy Technology Data Exchange (ETDEWEB)

    Cummings, Jeffrey D.; Geisler, D.; Villanova, S. [Departamento de Astronomía, Casilla 160-C, Universidad de Concepción (Chile); Carraro, G. [ESO, Alonso de Cordova 3107, Casilla 19001, Santiago de Chile (Chile)

    2014-08-01

    The analysis of multiple populations (MPs) in globular clusters (GCs) has become a forefront area of research in astronomy. Multiple red giant branches (RGBs), subgiant branches (SGBs), and even main sequences (MSs) have now been observed photometrically in many GCs, while broad abundance distributions of certain elements have been detected spectroscopically in most, if not all, GCs. UV photometry has been crucial in discovering and analyzing these MPs, but the Johnson U and the Stromgren and Sloan u filters that have generally been used are relatively inefficient and very sensitive to reddening and atmospheric extinction. In contrast, the Washington C filter is much broader and redder than these competing UV filters, making it far more efficient at detecting MPs and much less sensitive to reddening and extinction. Here, we investigate the use of the Washington system to uncover MPs using only a 1 m telescope. Our analysis of the well-studied GC NGC 1851 finds that the C filter is both very efficient and effective at detecting its previously discovered MPs in the RGB and SGB. 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. The MS distribution is in very good agreement with that seen on the RGB, with ∼30% of the stars belonging to the second population. There is also evidence for two sequences in the red horizontal branch, but this appears to be unrelated to the MPs in this cluster. Neither of these latter phenomena have been observed previously in this cluster. The redder MS stars are also more centrally concentrated than the blue MS. This is the first time MPs in an MS have been discovered from the ground, and using only a 1 m 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.

  10. Uncovering Multiple Populations with Washington Photometry. I. The Globular Cluster NGC 1851

    Science.gov (United States)

    Cummings, Jeffrey D.; Geisler, D.; Villanova, S.; Carraro, G.

    2014-08-01

    The analysis of multiple populations (MPs) in globular clusters (GCs) has become a forefront area of research in astronomy. Multiple red giant branches (RGBs), subgiant branches (SGBs), and even main sequences (MSs) have now been observed photometrically in many GCs, while broad abundance distributions of certain elements have been detected spectroscopically in most, if not all, GCs. UV photometry has been crucial in discovering and analyzing these MPs, but the Johnson U and the Stromgren and Sloan u filters that have generally been used are relatively inefficient and very sensitive to reddening and atmospheric extinction. In contrast, the Washington C filter is much broader and redder than these competing UV filters, making it far more efficient at detecting MPs and much less sensitive to reddening and extinction. Here, we investigate the use of the Washington system to uncover MPs using only a 1 m telescope. Our analysis of the well-studied GC NGC 1851 finds that the C filter is both very efficient and effective at detecting its previously discovered MPs in the RGB and SGB. 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. The MS distribution is in very good agreement with that seen on the RGB, with ~30% of the stars belonging to the second population. There is also evidence for two sequences in the red horizontal branch, but this appears to be unrelated to the MPs in this cluster. Neither of these latter phenomena have been observed previously in this cluster. The redder MS stars are also more centrally concentrated than the blue MS. This is the first time MPs in an MS have been discovered from the ground, and using only a 1 m 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. 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

  12. Capsular glucan and intracellular glycogen of Mycobacterium tuberculosis: biosynthesis and impact on the persistence in mice

    DEFF Research Database (Denmark)

    Sambou, Tounkang; Dinadayala, Premkumar; Stadthagen, Gustavo;

    2008-01-01

    Mycobacterium tuberculosis and other pathogenic mycobacterial species produce large amounts of a glycogen-like alpha-glucan that represents the major polysaccharide of their outermost capsular layer. To determine the role of the surface-exposed glucan in the physiology and virulence...... of these bacteria, orthologues of the glg genes involved in the biosynthesis of glycogen in Escherichia coli were identified in M. tuberculosis H37Rv and inactivated by allelic replacement. Biochemical analyses of the mutants and complemented strains indicated that the synthesis of glucan and glycogen involves...... the alpha-1,4-glucosyltransferases Rv3032 and GlgA (Rv1212c), the ADP-glucose pyrophosphorylase GlgC (Rv1213) and the branching enzyme GlgB (Rv1326c). Disruption of glgC reduced by half the glucan and glycogen contents of M. tuberculosis, whereas the inactivation of glgA and Rv3032 affected the production...

  13. Luxury uptake of phosphorus changes the accumulation of starch and lipid in Chlorella sp. under nitrogen depletion.

    Science.gov (United States)

    Zhu, Shunni; Wang, Yajie; Xu, Jin; Shang, Changhua; Wang, Zhongming; Xu, Jingliang; Yuan, Zhenhong

    2015-12-01

    The aim of this research was to study the effect of phosphorus supply on starch and lipid production under nitrogen starvation using Chlorella sp. as a model. High phosphate level had marginal effect on cell density but increased biomass growth. Massive phosphorus was assimilated quickly and mainly stored in the form of polyphosphate. The algal cells ceased phosphorus uptake when intracellular phosphorus reached a certain level. 5mM phosphate in the culture rendered a 16.7% decrease of starch synthesis and a 22.4% increase of lipid synthesis relative to low phosphate (0.17 mM). It is plausible that phosphate can regulate carbon partitioning between starch and lipid synthesis pathway by influencing ADP-glucose pyrophosphorylase activity. Moreover, high phosphate concentration enhanced the abundance of oleic acid, improving oil quality for biodiesel production. It is a promising cultivation strategy by integration of phosphorus removal from wastewater with biodiesel production for this alga.

  14. Increases of 3-phosphoglyceric acid in potato plants through antisense reduction of cytoplasmic phosphoglycerate mutase impairs photosynthesis and growth, but does not increase starch contents

    DEFF Research Database (Denmark)

    Westram, A.; Lloyd, J.R.; Roessner, U.;

    2002-01-01

    in leaves were reduced, and the tuber yield of the plants was lowered. Plants with 30% of the wild-type PGAM activity in leaves and 55% in tubers showed reduced amounts of starch in tubers also. Tuber-specific reduction of PGAM expression in transgenic potato plants had no effect on starch metabolism...... and tuber yield, although the 3-PGA level was increased. This indicates that 3-PGA concentrations in potato tubers are not important for regulating ADP-glucose pyrophosphorylase activity in the production of starch under some environmental conditions.......A full-length cDNA encoding cytosolic phosphoglycerate mutase (PGAM; E.C. 5.4.2.1) from potato (Solanum tuberosum L.) was isolated. RNA blots indicated that the accumulation of PGAM transcript was similar in all organs studied. Transgenic potato plants with either constitutive, or tuber...

  15. 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.

  16. 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

  17. Partially uncovered Cheatham platinum-covered stent to treat complex aortic coarctation associated with aortic wall aneurysm.

    Science.gov (United States)

    Butera, Gianfranco; Piazza, Luciane

    2015-04-01

    Percutaneous treatment of aortic coarctation is a widely used option. Covered stents have increased the profile of efficacy and safety of this procedure. Here we report on a 32-year-old woman with significant aortic recoarctation associated with aortic wall aneurysm and close proximity of both lesions to the origin of both the subclavian arteries. It was decided to manually and partially uncover the proximal part of the stent to have a hybrid stent that could act as a bare stent at the level of the origin of the subclavian arteries and as a covered stent at the level of the aneurysm.

  18. The Production and Utilization of GDP-glucose in the Biosynthesis of Trehalose 6-Phosphate by Streptomyces venezuelae*

    Science.gov (United States)

    Asención Diez, Matías D.; Miah, Farzana; Stevenson, Clare E. M.; Lawson, David M.; Iglesias, Alberto A.; Bornemann, Stephen

    2017-01-01

    Trehalose-6-phosphate synthase OtsA from streptomycetes is unusual in that it uses GDP-glucose as the donor substrate rather than the more commonly used UDP-glucose. We now confirm that OtsA from Streptomyces venezuelae has such a preference for GDP-glucose and can utilize ADP-glucose to some extent too. A crystal structure of the enzyme shows that it shares twin Rossmann-like domains with the UDP-glucose-specific OtsA from Escherichia coli. However, it is structurally more similar to Streptomyces hygroscopicus VldE, a GDP-valienol-dependent pseudoglycosyltransferase enzyme. Comparison of the donor binding sites reveals that the amino acids associated with the binding of diphosphoribose are almost all identical in these three enzymes. By contrast, the amino acids associated with binding guanine in VldE (Asn, Thr, and Val) are similar in S. venezuelae OtsA (Asp, Ser, and Phe, respectively) but not conserved in E. coli OtsA (His, Leu, and Asp, respectively), providing a rationale for the purine base specificity of S. venezuelae OtsA. To establish which donor is used in vivo, we generated an otsA null mutant in S. venezuelae. The mutant had a cell density-dependent growth phenotype and accumulated galactose 1-phosphate, glucose 1-phosphate, and GDP-glucose when grown on galactose. To determine how the GDP-glucose is generated, we characterized three candidate GDP-glucose pyrophosphorylases. SVEN_3027 is a UDP-glucose pyrophosphorylase, SVEN_3972 is an unusual ITP-mannose pyrophosphorylase, and SVEN_2781 is a pyrophosphorylase that is capable of generating GDP-glucose as well as GDP-mannose. We have therefore established how S. venezuelae can make and utilize GDP-glucose in the biosynthesis of trehalose 6-phosphate. PMID:27903647

  19. Contribution of the Nurses’ Health Studies to Uncovering Risk Factors for Type 2 Diabetes: Diet, Lifestyle, Biomarkers, and Genetics

    Science.gov (United States)

    Ley, Sylvia H.; Ardisson Korat, Andres V.; Sun, Qi; Tobias, Deirdre K.; Zhang, Cuilin; Qi, Lu; Willett, Walter C.; Manson, JoAnn E.

    2016-01-01

    Objectives. To review the contribution of the Nurses’ Health Study (NHS) and the NHS II to addressing hypotheses regarding risk factors for type 2 diabetes. Methods. We carried out a narrative review of 1976 to 2016 NHS and NHS II publications. Results. The NHS and NHS II have uncovered important roles in type 2 diabetes for individual nutrients, foods, dietary patterns, and physical activity independent of excess body weight. Up to 90% of type 2 diabetes cases are potentially preventable if individuals follow a healthy diet and lifestyle. The NHS investigations have also identified novel biomarkers for diabetes, including adipokines, inflammatory cytokines, nutrition metabolites, and environmental pollutants, offering new insights into the pathophysiology of the disease. Global collaborative efforts have uncovered many common genetic variants associated with type 2 diabetes and improved our understanding of gene–environment interactions. Continued efforts to identify epigenetic, metagenomic, and metabolomic risk factors for type 2 diabetes have the potential to reveal new pathways and improve prediction and prevention. Conclusions. Over the past several decades, the NHS and NHS II have made major contributions to public health recommendations and strategies designed to reduce the global burden of diabetes. PMID:27459454

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. Machine learning classification of cell-specific cardiac enhancers uncovers developmental subnetworks regulating progenitor cell division and cell fate specification.

    Science.gov (United States)

    Ahmad, Shaad M; Busser, Brian W; Huang, Di; Cozart, Elizabeth J; Michaud, Sébastien; Zhu, Xianmin; Jeffries, Neal; Aboukhalil, Anton; Bulyk, Martha L; Ovcharenko, Ivan; Michelson, Alan M

    2014-02-01

    The Drosophila heart is composed of two distinct cell types, the contractile cardial cells (CCs) and the surrounding non-muscle pericardial cells (PCs), development of which is regulated by a network of conserved signaling molecules and transcription factors (TFs). Here, we used machine learning with array-based chromatin immunoprecipitation (ChIP) data and TF sequence motifs to computationally classify cell type-specific cardiac enhancers. Extensive testing of predicted enhancers at single-cell resolution revealed the added value of ChIP data for modeling cell type-specific activities. Furthermore, clustering the top-scoring classifier sequence features identified novel cardiac and cell type-specific regulatory motifs. For example, we found that the Myb motif learned by the classifier is crucial for CC activity, and the Myb TF acts in concert with two forkhead domain TFs and Polo kinase to regulate cardiac progenitor cell divisions. In addition, differential motif enrichment and cis-trans genetic studies revealed that the Notch signaling pathway TF Suppressor of Hairless [Su(H)] discriminates PC from CC enhancer activities. Collectively, these studies elucidate molecular pathways used in the regulatory decisions for proliferation and differentiation of cardiac progenitor cells, implicate Su(H) in regulating cell fate decisions of these progenitors, and document the utility of enhancer modeling in uncovering developmental regulatory subnetworks.

  5. An uncovered XIII century icon: particular use of organic pigments and gilding techniques highlighted by analytical methods.

    Science.gov (United States)

    Daveri, Alessia; Doherty, Brenda; Moretti, Patrizia; Grazia, Chiara; Romani, Aldo; Fiorin, Enrico; Brunetti, Brunetto Giovanni; Vagnini, Manuela

    2015-01-25

    The restoration of a panel painting depicting a Madonna and Child listed as an unknown Tuscan artist of the nineteenth century, permitted the hidden original version, a XIII century Medieval icon to be uncovered. It is discovery provided the opportunity for an extensive in situ campaign of non-invasive analytical investigations by portable imaging and spectroscopic techniques (infrared, X-ray fluorescence and diffraction, UV-Vis absorption and emission), followed by aimed micro-destructive investigations (Raman and SEM-EDS). This approach permitted characterization of the original ground and paint layers by complementary techniques. Furthermore, this protocol allowed supplementary particularities of great interest to be highlighted. Namely, numerous original gilding techniques have been accentuated in diverse areas and include the use of surrogate gold (disulphur tin), orpiment as a further false gold and an area with an original silver rich layer. Moreover, pigments including azurite mixed with indigo have been non-invasively identified. Micro-invasive analyses also allowed the diagnosis of organic colorants, namely, an animal anthraquinone lake, kermes and an unusual vegetal chalcone pigment, possibly safflower. The identification of the latter is extremely rare as a painting pigment and has been identified using an innovative adaption to surface enhanced Raman techniques on a cross-section. The resulting data contributes new hypotheses to the historic and artistic knowledge of materials and techniques utilized in XIII century icon paintings and ultimately provides scientific technical support of the recent restoration.

  6. Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing.

    Directory of Open Access Journals (Sweden)

    Stéphane Delmas

    Full Text Available A key challenge in the production of second generation biofuels is the conversion of lignocellulosic substrates into fermentable sugars. Enzymes, particularly those from fungi, are a central part of this process, and many have been isolated and characterised. However, relatively little is known of how fungi respond to lignocellulose and produce the enzymes necessary for dis-assembly of plant biomass. We studied the physiological response of the fungus Aspergillus niger when exposed to wheat straw as a model lignocellulosic substrate. Using RNA sequencing we showed that, 24 hours after exposure to straw, gene expression of known and presumptive plant cell wall-degrading enzymes represents a huge investment for the cells (about 20% of the total mRNA. Our results also uncovered new esterases and surface interacting proteins that might form part of the fungal arsenal of enzymes for the degradation of plant biomass. Using transcription factor deletion mutants (xlnR and creA to study the response to both lignocellulosic substrates and low carbon source concentrations, we showed that a subset of genes coding for degradative enzymes is induced by starvation. Our data support a model whereby this subset of enzymes plays a scouting role under starvation conditions, testing for available complex polysaccharides and liberating inducing sugars, that triggers the subsequent induction of the majority of hydrolases. We also showed that antisense transcripts are abundant and that their expression can be regulated by growth conditions.

  7. POTENTIAL OF INDUCED METABOLIC BIOLUMINESCENCE IMAGING TO UNCOVER METABOLIC EFFECTS OF ANTI-ANGIOGENIC THERAPY IN TUMORS

    Directory of Open Access Journals (Sweden)

    Stefano eIndraccolo

    2016-02-01

    Full Text Available Tumor heterogeneity at the genetic level has been illustrated by a multitude of studies on the genomics of cancer, but whether tumors can be heterogeneous at the metabolic level is an issue which has been less systematically investigated so far. A burning related question is whether the metabolic features of tumors can change either following natural tumor progression (i.e. in primary tumors versus metastasis or therapeutic interventions. In this regard, recent findings by independent teams indicate that anti-angiogenic drugs cause metabolic perturbations in tumors as well as metabolic adaptations associated with increased malignancy. Induced metabolic bioluminescence imaging (imBI is an imaging technique which enables detection of key metabolites associated with glycolysis, including lactate, glucose, pyruvate and ATP in tumor sections. Signals captured by imBI can be used to visualize the topographic distribution of these metabolites and quantify their absolute amount. ImBI can be very useful for metabolic classification of tumors as well as to track metabolic changes in the glycolytic pathway associated with certain therapies. Imaging of the metabolic changes induced by anti-angiogenic drugs in tumors by imBI or other emerging technologies is a valuable tool to uncover molecular sensors engaged by metabolic stress and offers an opportunity to understand how metabolism-based approaches could improve cancer therapy.

  8. 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.

  9. 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.

  10. An uncovered XIII century icon: Particular use of organic pigments and gilding techniques highlighted by analytical methods

    Science.gov (United States)

    Daveri, Alessia; Doherty, Brenda; Moretti, Patrizia; Grazia, Chiara; Romani, Aldo; Fiorin, Enrico; Brunetti, Brunetto Giovanni; Vagnini, Manuela

    2015-01-01

    The restoration of a panel painting depicting a Madonna and Child listed as an unknown Tuscan artist of the nineteenth century, permitted the hidden original version, a XIII century Medieval icon to be uncovered. It is discovery provided the opportunity for an extensive in situ campaign of non-invasive analytical investigations by portable imaging and spectroscopic techniques (infrared, X-ray fluorescence and diffraction, UV-Vis absorption and emission), followed by aimed micro-destructive investigations (Raman and SEM-EDS). This approach permitted characterization of the original ground and paint layers by complementary techniques. Furthermore, this protocol allowed supplementary particularities of great interest to be highlighted. Namely, numerous original gilding techniques have been accentuated in diverse areas and include the use of surrogate gold (disulphur tin), orpiment as a further false gold and an area with an original silver rich layer. Moreover, pigments including azurite mixed with indigo have been non-invasively identified. Micro-invasive analyses also allowed the diagnosis of organic colorants, namely, an animal anthraquinone lake, kermes and an unusual vegetal chalcone pigment, possibly safflower. The identification of the latter is extremely rare as a painting pigment and has been identified using an innovative adaption to surface enhanced Raman techniques on a cross-section. The resulting data contributes new hypotheses to the historic and artistic knowledge of materials and techniques utilized in XIII century icon paintings and ultimately provides scientific technical support of the recent restoration.

  11. 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.

  12. Uncovering Pompeii: Examining Evidence.

    Science.gov (United States)

    Yell, Michael M.

    2001-01-01

    Presents a lesson plan on Pompeii (Italy) for middle school students that utilizes a teaching technique called interactive presentation. Describes the technique's five phases: (1) discrepant event inquiry; (2) discussion/presentation; (3) cooperative learning activity; (4) writing for understanding activity; and (5) whole-class discussion and…

  13. 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

  14. 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

  15. Uncovering Discovery Layer Services

    Science.gov (United States)

    Kennedy, Sean P.

    2014-01-01

    Today's electronic information landscape is growing exponentially with no signs of slowing. This poses a significant challenge for academic libraries. Librarians must continually learn and adapt to harness this explosion of resources. To fulfill their claim as the leaders in the information field they must be effective in providing access and…

  16. Uncovering the Hidden 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...

  17. Uncovering Prepositional Senses

    DEFF Research Database (Denmark)

    Lassen, Tine

    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...... of these data stem from a small pre-defined set of relations, and the ontological type information stems from the SIMPLE ontology. The resulting data set was used as input to a machine-learning algorithm, and the result was a set of rules that predict the semantic relation of a preposition based...... 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...

  18. 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...

  19. 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.

  20. 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...

  1. 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.

  2. 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

  3. 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.

  4. 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

    2015-06-05

    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.

  5. 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.

  6. Expression profiles uncover the relationship between erythropoietin and cell proliferation in rat hepatocytes after a partial hepatectomy.

    Science.gov (United States)

    Zhang, Jihong; Yang, Yajuan; He, Tingting; Liu, Yunqing; Zhou, Yun; Chen, Yongkang; Xu, Cunshuan

    2014-09-01

    Erythropoietin (EPO) has a beneficial effect on hepatic cell proliferation during liver regeneration. However, the underlying mechanism has not yet been elucidated. To uncover the proliferation response of EPO in rat liver regeneration after partial hepatectomy (PH) at the cellular level, hepatocytes (HCs) were isolated using Percoll density gradient centrifugation. The genes of the EPO-mediated signaling pathway and the target genes of the transcription factor (TF) in the pathway were identified in a pathway and TF database search. Their expression profiles were then detected using Rat Genome 230 2.0 Microarray. The results indicated that the EPO-mediated signaling pathway is involved in 19 paths and that 124 genes participate, of which 32 showed significant changes and could be identified as liver regeneration-related genes. In addition, 443 targets regulated by the TFs of the pathway and 60 genes associated with cell proliferation were contained in the array. Subsequently, the synergetic effect of these genes in liver regeneration was analyzed using the E(t) mathematical model based on their expression profiles. The results demonstrated that the E(t) values of paths 3, 8, 12 and 14-17 were significantly strengthened in the progressing phase of liver regeneration through the RAS/MEK/ERK or PI3K/AκT pathways. The synergetic effect of the target genes, in parallel with target-related cell proliferation, was also enhanced 12-72 h after PH, suggesting a potential positive effect of EPO on HC proliferation during rat liver regeneration. These data imply that the EPO receptor may allow EPO to promote HC proliferation through paths 3, 8, 12 and 14-17, mediating the RAS/MEK/ERK and PI3K/AκT pathways in rat liver regeneration after PH.

  7. Uncovering Ultrastructural Defences in Daphnia magna – An Interdisciplinary Approach to Assess the Predator-Induced Fortification of the Carapace

    Science.gov (United States)

    Rabus, Max; Söllradl, Thomas; Clausen-Schaumann, Hauke; Laforsch, Christian

    2013-01-01

    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 Daphniamagna (Crustacea: Branchiopoda: Cladocera) has been shown to develop a bulky morphotype as an effective inducible morphological defence against the predatory tadpole shrimp Triopscancriformis (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. PMID:23776711

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

    Science.gov (United States)

    Rabus, Max; Söllradl, Thomas; Clausen-Schaumann, Hauke; Laforsch, Christian

    2013-01-01

    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.

  9. 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

  10. 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

  11. 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

  12. 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.

  13. Comparative analysis of gene expression: uncovering expression conservation and divergence between Salmonella enterica serovar Typhimurium strains LT2 and 14028S.

    Science.gov (United States)

    Sonego, Paolo; Meysman, Pieter; Moretto, Marco; Viola, Roberto; Laukens, Kris; Cavalieri, Duccio; Engelen, Kristof

    2015-01-01

    Different strains of the same organism can share a large amount of their genetic material, the so called core pangenome. Nevertheless, these species can display different lifestyles and it is still not well known to what extent the core pangenome plays a role in the divergence of lifestyles between the two organisms. Here, we present a procedure for uncovering the conservation and divergence of gene expression by using large expression compendia. We will use data from two Salmonella enterica serovar Typhimurium strains as an example here, strain LT2 and strain 14028S, to assess if there are orthologous gene pairs with different expression domains related in both strains.

  14. Uncovering Barriers to Teaching Assistants (TAs Implementing Inquiry Teaching: Inconsistent Facilitation Techniques, Student Resistance, and Reluctance to Share Control over Learning with Students

    Directory of Open Access Journals (Sweden)

    Cara Gormally

    2016-05-01

    Full Text Available Inquiry-based teaching approaches are increasingly being adopted in biology laboratories. Yet teaching assistants (TAs, often novice teachers, teach the majority of laboratory courses in US research universities. This study analyzed the perspectives of TAs and their students and used classroom observations to uncover challenges faced by TAs during their first year of inquiry-based teaching. Our study revealed three insights about barriers to effective inquiry teaching practices: 1 TAs lack sufficient facilitation skills; 2 TAs struggle to share control over learning with students as they reconcile long-standing teaching beliefs with newly learned approaches, consequently undermining their fledgling ability to use inquiry approaches; and 3 student evaluations reinforce teacher-centered behaviors as TAs receive positive feedback conflicting with inquiry approaches. We make recommendations, including changing instructional feedback to focus on learner-centered teaching practices. We urge TA mentors to engage TAs in discussions to uncover teaching beliefs underlying teaching choices and support TAs through targeted feedback and practice.

  15. Uncovering Barriers to Teaching Assistants (TAs) Implementing Inquiry Teaching: Inconsistent Facilitation Techniques, Student Resistance, and Reluctance to Share Control over Learning with Students †

    Science.gov (United States)

    Gormally, Cara; Sullivan, Carol Subiño; Szeinbaum, Nadia

    2016-01-01

    Inquiry-based teaching approaches are increasingly being adopted in biology laboratories. Yet teaching assistants (TAs), often novice teachers, teach the majority of laboratory courses in US research universities. This study analyzed the perspectives of TAs and their students and used classroom observations to uncover challenges faced by TAs during their first year of inquiry-based teaching. Our study revealed three insights about barriers to effective inquiry teaching practices: 1) TAs lack sufficient facilitation skills; 2) TAs struggle to share control over learning with students as they reconcile long-standing teaching beliefs with newly learned approaches, consequently undermining their fledgling ability to use inquiry approaches; and 3) student evaluations reinforce teacher-centered behaviors as TAs receive positive feedback conflicting with inquiry approaches. We make recommendations, including changing instructional feedback to focus on learner-centered teaching practices. We urge TA mentors to engage TAs in discussions to uncover teaching beliefs underlying teaching choices and support TAs through targeted feedback and practice. PMID:27158302

  16. Combined Genetic and Genealogic Studies Uncover a Large BAP1 Cancer Syndrome Kindred Tracing Back Nine Generations to a Common Ancestor from the 1700s.

    Science.gov (United States)

    Carbone, Michele; Flores, Erin G; Emi, Mitsuru; Johnson, Todd A; Tsunoda, Tatsuhiko; Behner, Dusty; Hoffman, Harriet; Hesdorffer, Mary; Nasu, Masaki; Napolitano, Andrea; Powers, Amy; Minaai, Michael; Baumann, Francine; Bryant-Greenwood, Peter; Lauk, Olivia; Kirschner, Michaela B; Weder, Walter; Opitz, Isabelle; Pass, Harvey I; Gaudino, Giovanni; Pastorino, Sandra; Yang, Haining

    2015-12-01

    We recently discovered an inherited cancer syndrome caused by BRCA1-Associated Protein 1 (BAP1) germline mutations, with high incidence of mesothelioma, uveal melanoma and other cancers and very high penetrance by age 55. To identify families with the BAP1 cancer syndrome, we screened patients with family histories of multiple mesotheliomas and melanomas and/or multiple cancers. We identified four families that shared an identical BAP1 mutation: they lived across the US and did not appear to be related. By combining family histories, molecular genetics, and genealogical approaches, we uncovered a BAP1 cancer syndrome kindred of ~80,000 descendants with a core of 106 individuals, whose members descend from a couple born in Germany in the early 1700s who immigrated to North America. Their descendants spread throughout the country with mutation carriers affected by multiple malignancies. Our data show that, once a proband is identified, extended analyses of these kindreds, using genomic and genealogical studies to identify the most recent common ancestor, allow investigators to uncover additional branches of the family that may carry BAP1 mutations. Using this knowledge, we have identified new branches of this family carrying BAP1 mutations. We have also implemented early-detection strategies that help identify cancers at early-stage, when they can be cured (melanomas) or are more susceptible to therapy (MM and other malignancies).

  17. Uncovering Barriers to Teaching Assistants (TAs) Implementing Inquiry Teaching: Inconsistent Facilitation Techniques, Student Resistance, and Reluctance to Share Control over Learning with Students.

    Science.gov (United States)

    Gormally, Cara; Sullivan, Carol Subiño; Szeinbaum, Nadia

    2016-05-01

    Inquiry-based teaching approaches are increasingly being adopted in biology laboratories. Yet teaching assistants (TAs), often novice teachers, teach the majority of laboratory courses in US research universities. This study analyzed the perspectives of TAs and their students and used classroom observations to uncover challenges faced by TAs during their first year of inquiry-based teaching. Our study revealed three insights about barriers to effective inquiry teaching practices: 1) TAs lack sufficient facilitation skills; 2) TAs struggle to share control over learning with students as they reconcile long-standing teaching beliefs with newly learned approaches, consequently undermining their fledgling ability to use inquiry approaches; and 3) student evaluations reinforce teacher-centered behaviors as TAs receive positive feedback conflicting with inquiry approaches. We make recommendations, including changing instructional feedback to focus on learner-centered teaching practices. We urge TA mentors to engage TAs in discussions to uncover teaching beliefs underlying teaching choices and support TAs through targeted feedback and practice.

  18. 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.

  19. Study of the features of outburst caused by rock cross-cut coal uncovering and the law of gas dilatation energy release

    Institute of Scientific and Technical Information of China (English)

    Yu Baohai; Su Chengxiang; Wang Deming

    2015-01-01

    To study the law of gas dilatation energy release of rock cross-cut coal uncovering face, according to the analysis of the physical parameters distribution features of coal and rock mass in front of crosscut face, the equations of elastic potential of coal and gas dilatation energy theory were set up to process a contrast calculation of the sizes of two kinds of energy. The results show that gas dilatation energy is the uppermost energy source causing outburst occurrence. Furthermore, the mathematical model of spherical flow field gas dilatation energy release was established and MATLAB software was applied to make a numerical calculation analysis on the law of gas dilatation energy release. The results indicate that the gas dilatation energy is closely related to gas parameters and its energy index does reflect the possibility of coal seam outburst.

  20. 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

    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...... be calculated to conduct statistical procedures such as multiple regression and MANOVA. We demonstrate the utility of the method for analysing events in the political sphere using data collected from 282 voters immediately after the British General Election of 2010 on voter preferences regarding the relative......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...

  1. 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.

  2. 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

  3. Human β Cell Transcriptome Analysis Uncovers lncRNAs That Are Tissue-Specific, Dynamically Regulated, and Abnormally Expressed in Type 2 Diabetes

    Science.gov (United States)

    Morán, Ignasi; Akerman, İldem; van de Bunt, Martijn; Xie, Ruiyu; Benazra, Marion; Nammo, Takao; Arnes, Luis; Nakić, Nikolina; García-Hurtado, Javier; Rodríguez-Seguí, Santiago; Pasquali, Lorenzo; Sauty-Colace, Claire; Beucher, Anthony; Scharfmann, Raphael; van Arensbergen, Joris; Johnson, Paul R; Berry, Andrew; Lee, Clarence; Harkins, Timothy; Gmyr, Valery; Pattou, François; Kerr-Conte, Julie; Piemonti, Lorenzo; Berney, Thierry; Hanley, Neil A; Gloyn, Anna L; Sussel, Lori; Langman, Linda; Brayman, Kenneth L; Sander, Maike; McCarthy, Mark I.; Ravassard, Philippe; Ferrer, Jorge

    2012-01-01

    SUMMARY A significant portion of the genome is transcribed as long non-coding RNAs (lncRNAs), several of which are known to control gene expression. The repertoire and regulation of lncRNAs in disease-relevant tissues, however, has not been systematically explored. We report a comprehensive strand-specific transcriptome map of human pancreatic islets and β-cells, and uncover >1100 intergenic and antisense islet-cell lncRNA genes. We find islet lncRNAs that are dynamically regulated, and show that they are an integral component of the β-cell differentiation and maturation program. We sequenced the mouse islet transcriptome, and identify lncRNA orthologs that are regulated like their human counterparts. Depletion of HI-LNC25, a β-cell specific lncRNA, downregulated GLIS3 mRNA, thus exemplifying a gene regulatory function of islet lncRNAs. Finally, selected islet lncRNAs were dysregulated in type 2 diabetes or mapped to genetic loci underlying diabetes susceptibility. These findings reveal a new class of islet-cell genes relevant to β-cell programming and diabetes pathophysiology. PMID:23040067

  4. Transcriptomic profiling of Yersinia pseudotuberculosis reveals reprogramming of the Crp regulon by temperature and uncovers Crp as a master regulator of small RNAs.

    Directory of Open Access Journals (Sweden)

    Aaron M Nuss

    2015-03-01

    Full Text Available One hallmark of pathogenic yersiniae is their ability to rapidly adjust their life-style and pathogenesis upon host entry. In order to capture the range, magnitude and complexity of the underlying gene control mechanisms we used comparative RNA-seq-based transcriptomic profiling of the enteric pathogen Y. pseudotuberculosis under environmental and infection-relevant conditions. We identified 1151 individual transcription start sites, multiple riboswitch-like RNA elements, and a global set of antisense RNAs and previously unrecognized trans-acting RNAs. Taking advantage of these data, we revealed a temperature-induced and growth phase-dependent reprogramming of a large set of catabolic/energy production genes and uncovered the existence of a thermo-regulated 'acetate switch', which appear to prime the bacteria for growth in the digestive tract. To elucidate the regulatory architecture linking nutritional status to virulence we also refined the CRP regulon. We identified a massive remodelling of the CRP-controlled network in response to temperature and discovered CRP as a transcriptional master regulator of numerous conserved and newly identified non-coding RNAs which participate in this process. This finding highlights a novel level of complexity of the regulatory network in which the concerted action of transcriptional regulators and multiple non-coding RNAs under control of CRP adjusts the control of Yersinia fitness and virulence to the requirements of their environmental and virulent life-styles.

  5. Eye Tracking, Cortisol, and a Sleep vs. Wake Consolidation Delay: Combining Methods to Uncover an Interactive Effect of Sleep and Cortisol on Memory

    Science.gov (United States)

    Bennion, Kelly A.; Mickley Steinmetz, Katherine R.; Kensinger, Elizabeth A.; Payne, Jessica D.

    2014-01-01

    Although rises in cortisol can benefit memory consolidation, as can sleep soon after encoding, there is currently a paucity of literature as to how these two factors may interact to influence consolidation. Here we present a protocol to examine the interactive influence of cortisol and sleep on memory consolidation, by combining three methods: eye tracking, salivary cortisol analysis, and behavioral memory testing across sleep and wake delays. To assess resting cortisol levels, participants gave a saliva sample before viewing negative and neutral objects within scenes. To measure overt attention, participants’ eye gaze was tracked during encoding. To manipulate whether sleep occurred during the consolidation window, participants either encoded scenes in the evening, slept overnight, and took a recognition test the next morning, or encoded scenes in the morning and remained awake during a comparably long retention interval. Additional control groups were tested after a 20 min delay in the morning or evening, to control for time-of-day effects. Together, results showed that there is a direct relation between resting cortisol at encoding and subsequent memory, only following a period of sleep. Through eye tracking, it was further determined that for negative stimuli, this beneficial effect of cortisol on subsequent memory may be due to cortisol strengthening the relation between where participants look during encoding and what they are later able to remember. Overall, results obtained by a combination of these methods uncovered an interactive effect of sleep and cortisol on memory consolidation. PMID:24962611

  6. Whole genomic sequencing of RT98 mitochondria derived from Oryza rufipogon and northern blot analysis to uncover a cytoplasmic male sterility-associated gene.

    Science.gov (United States)

    Igarashi, Keisuke; Kazama, Tomohiko; Motomura, Keiji; Toriyama, Kinya

    2013-02-01

    Cytoplasmic male sterility (CMS) is a maternally inherited trait resulting in the failure to produce functional pollen and is often observed when an alien cytoplasm is transferred into a cultivated species. An RT98A CMS line and an RT98C fertility restorer line were obtained by successive backcrossing between Oryza rufipogon W1109 and Oryza sativa cultivar Taichung 65. To uncover the CMS-associated mitochondrial genes, we determined the complete sequence of the RT98-CMS mitochondrial genome using next-generation pyrosequencing, and searched new open reading frames (orfs) absent in a reported mitochondrial genome of O. sativa Nipponbare. Then, six candidates were selected for the CMS-associated genes based on the criteria in which they were chimeric in structure or encoded a peptide with transmembrane domains. One of the candidates, orf113, showed different transcript sizes between RT98A and RT98C on Northern blot analysis. The orf113 gene was shown to be co-transcribed with atp4 and cox3 encoding ATP synthase F0 subunit 4 and Cyt c oxidase subunit 3, respectively, and their transcripts were distinctly processed in the presence of a fertility restorer gene. Our results indicate that orf113 is a CMS-associated gene of RT98-CMS.

  7. 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.

  8. Eye tracking, cortisol, and a sleep vs. wake consolidation delay: combining methods to uncover an interactive effect of sleep and cortisol on memory.

    Science.gov (United States)

    Bennion, Kelly A; Mickley Steinmetz, Katherine R; Kensinger, Elizabeth A; Payne, Jessica D

    2014-06-18

    Although rises in cortisol can benefit memory consolidation, as can sleep soon after encoding, there is currently a paucity of literature as to how these two factors may interact to influence consolidation. Here we present a protocol to examine the interactive influence of cortisol and sleep on memory consolidation, by combining three methods: eye tracking, salivary cortisol analysis, and behavioral memory testing across sleep and wake delays. To assess resting cortisol levels, participants gave a saliva sample before viewing negative and neutral objects within scenes. To measure overt attention, participants' eye gaze was tracked during encoding. To manipulate whether sleep occurred during the consolidation window, participants either encoded scenes in the evening, slept overnight, and took a recognition test the next morning, or encoded scenes in the morning and remained awake during a comparably long retention interval. Additional control groups were tested after a 20 min delay in the morning or evening, to control for time-of-day effects. Together, results showed that there is a direct relation between resting cortisol at encoding and subsequent memory, only following a period of sleep. Through eye tracking, it was further determined that for negative stimuli, this beneficial effect of cortisol on subsequent memory may be due to cortisol strengthening the relation between where participants look during encoding and what they are later able to remember. Overall, results obtained by a combination of these methods uncovered an interactive effect of sleep and cortisol on memory consolidation.

  9. Multiple-locus variable number of tandem repeat analysis (MLVA of Irish verocytotoxigenic Escherichia coli O157 from feedlot cattle: uncovering strain dissemination routes

    Directory of Open Access Journals (Sweden)

    O'Mahony Micheál

    2008-01-01

    Full Text Available Abstract Background The identification of the routes of dissemination of Escherichia coli (E. coli O157 through a cohort of cattle is a critical step to control this pathogen at farm level. The aim of this study was to identify potential routes of dissemination of E. coli O157 using Multiple-Locus Variable number of tandem repeat Analysis (MLVA. Results Thirty-eight environmental and sixteen cattle faecal isolates, which were detected in four adjacent pens over a four-month period were sub-typed. MLVA could separate these isolates into broadly defined clusters consisting of twelve MLVA types. Strain diversity was observed within pens, individual cattle and the environment. Conclusion Application of MLVA is a broadly useful and convenient tool when applied to uncover the dissemination of E. coli O157 in the environment and in supporting improved on-farm management of this important pathogen. These data identified diverse strain types based on amplification of VNTR markers in each case.

  10. 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

    2016-01-01

    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. PMID:26793200

  11. 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.

  12. 彭燕郊《混沌初开》细读%Close Reading of “The Uncovering of Chaos” by Peng Yanjiao

    Institute of Scientific and Technical Information of China (English)

    邱景华

    2016-01-01

    彭燕郊的《混沌初开》,继承了新诗史上中断很久的鲁迅《野草》传统,并接通了西方现代诗源头的波德莱尔。开创了一种以自我反思为主的新诗学,把“太空时代想象力”和“原型意象想象力”融为一体,创造出一种长篇散文诗的新诗体。%Peng Yanjiao’s “The Uncovering of Chaos” has inherited the traditional traits in Lu Xun’s “Weeds” which was deserted in a certain period in the history of Chinese new poetry and turned on the source of the western modern poetry represented by Baudelaire. Peng Yanjiao has initiated a new poetics mainly based on self-reflection and created a new verse style in the form of long prose poem by integrating “space-age imagination” and “archetype image imagination”.

  13. 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.

  14. Coupling between pupil fluctuations and resting-state fMRI uncovers a slow build-up of antagonistic responses in the human cortex.

    Science.gov (United States)

    Yellin, Dov; Berkovich-Ohana, Aviva; Malach, Rafael

    2015-02-01

    Even in absence of overt tasks, the human cortex manifests rich patterns of spontaneous "resting state" BOLD-fMRI fluctuations. However, the link of these spontaneous fluctuations to behavior is presently unclear. Attempts to directly investigate this link invariably lead to disruptions of the resting state. Here we took advantage of the well-established association between pupil diameter and attentional gain to address this issue by examining the correlation between the resting state BOLD and pupil fluctuations. Our results uncover a spontaneously emerging spatiotemporal pupil-BOLD correlation whereby a slow buildup of activity in default mode areas preceded both pupil dilation and wide-spread BOLD suppression in sensorimotor cortex. Control experiments excluded a role for luminance fluctuations or fixation. Comparing the pupil-correlated patterns to activation maps during visual imagery revealed a substantial overlap. Our results indicate a link between behavior, as indexed by pupil diameter, and resting state BOLD fluctuations. These pupil dilations, assumed to be related to attentional gain, were associated with spontaneously emerging antagonism between fundamental cortical networks.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. The reduction of starch accumulation in transgenic sugarcane cell suspension culture lines.

    Science.gov (United States)

    Ferreira, Stephanus J; Kossmann, Jens; Lloyd, James R; Groenewald, Jan-Hendrik

    2008-11-01

    Starch only occurs in small amounts in sugarcane, but is, nevertheless an unwanted product because it reduces the amount of sucrose that can be crystallized from molasses. In an attempt to reduce the starch content of sugarcane, the activities of ADP-glucose pyrophosphorylase (AGPase) and beta-amylase were manipulated using transgenic approaches. Transformation vectors to reduce AGPase activity and to increase plastidial beta-amylase activity were constructed and used for the transformation of sugarcane calli. The results of the manipulations were analyzed in suspension cultures. AGPase activity was reduced down to between 14 and 54% of the wild-type control. This led to a reduction in starch concentration down to 38% of the levels of the wild-type control. beta-Amylase activity was increased in the transgenic lines by 1.5-2 times that of the wild-type control. This increase in activity led to a reduction in starch amounts by 90% compared to wild-type control cells. In both experiments, the changes in starch concentrations could be correlated with the change in enzyme activity. There were no significant effects on sucrose concentrations in either experiment, indicating that these approaches might be useful to engineer regenerated sugarcane for optimized sucrose production.

  1. 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.

  2. 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.

  3. 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

  4. The Metabolic Signature of Biomass Formation in Barley.

    Science.gov (United States)

    Ghaffari, Mohammad R; Shahinnia, Fahimeh; Usadel, Björn; Junker, Björn; Schreiber, Falk; Sreenivasulu, Nese; Hajirezaei, Mohammad R

    2016-09-01

    The network analysis of genome-wide transcriptome responses, metabolic signatures and enzymes' relationship to biomass formation has been studied in a diverse panel of 12 barley accessions during vegetative and reproductive stages. The primary metabolites and enzymes involved in central metabolism that determine the accumulation of shoot biomass at the vegetative stage of barley development are primarily being linked to sucrose accumulation and sucrose synthase activity. Interestingly, the metabolic and enzyme links which are strongly associated with biomass accumulation during reproductive stages are related to starch accumulation and tricarboxylic acid (TCA) cycle intermediates citrate, malate, trans-aconitate and isocitrate. Additional significant associations were also found for UDP glucose, ATP and the amino acids isoleucine, valine, glutamate and histidine during the reproductive stage. A network analysis resulted in a combined identification of metabolite and enzyme signatures indicative for grain weight accumulation that was correlated with the activity of ADP-glucose pyrophosphorylase (AGPase), a rate-limiting enzyme involved in starch biosynthesis, and with that of alanine amino transferase involved in the synthesis of storage proteins. We propose that the mechanism related to vegetative and reproductive biomass formation vs. seed biomass formation is being linked to distinct fluxes regulating sucrose, starch, sugars and amino acids as central resources. These distinct biomarkers can be used to engineer biomass production and grain weight in barley.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Divergent evolutionary pattern of starch biosynthetic pathway genes in grasses and dicots.

    Science.gov (United States)

    Li, Chun; Li, Qi-Gang; Dunwell, Jim M; Zhang, Yuan-Ming

    2012-10-01

    Starch is the most widespread and abundant storage carbohydrate in crops and its production is critical to both crop yield and quality. In regard to the starch content in the seeds of crop plants, there is a distinct difference between grasses (Poaceae) and dicots. However, few studies have described the evolutionary pattern of genes in the starch biosynthetic pathway in these two groups of plants. In this study, therefore, an attempt was made to compare evolutionary rate, gene duplication, and selective pattern of the key genes involved in this pathway between the two groups, using five grasses and five dicots as materials. The results showed 1) distinct differences in patterns of gene duplication and loss between grasses and dicots; duplication in grasses mainly occurred before the divergence of grasses, whereas duplication mostly occurred in individual species within the dicots; there is less gene loss in grasses than in dicots, 2) a considerably higher evolutionary rate in grasses than in dicots in most gene families analyzed, and 3) evidence of a different selective pattern between grasses and dicots; positive selection may have occurred asymmetrically in grasses in some gene families, for example, ADP-glucose pyrophosphorylase small subunit. Therefore, we deduced that gene duplication contributes to, and a higher evolutionary rate is associated with, the higher starch content in grasses. In addition, two novel aspects of the evolution of the starch biosynthetic pathway were observed.

  12. 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.

  13. 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.

  14. 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.

  15. Functional Analysis of a Wheat AGPase Plastidial Small Subunit with a Truncated Transit Peptide

    Directory of Open Access Journals (Sweden)

    Yang Yang

    2017-03-01

    Full Text Available ADP-glucose pyrophosphorylase (AGPase, the key enzyme in starch synthesis, consists of two small subunits and two large subunits with cytosolic and plastidial isoforms. In our previous study, a cDNA sequence encoding the plastidial small subunit (TaAGPS1b of AGPase in grains of bread wheat (Triticum aestivum L. was isolated and the protein subunit encoded by this gene was characterized as a truncated transit peptide (about 50% shorter than those of other plant AGPS1bs. In the present study, TaAGPS1b was fused with green fluorescent protein (GFP in rice protoplast cells, and confocal fluorescence microscopy observations revealed that like other AGPS1b containing the normal transit peptide, TaAGPS1b-GFP was localized in chloroplasts. TaAGPS1b was further overexpressed in a Chinese bread wheat cultivar, and the transgenic wheat lines exhibited a significant increase in endosperm AGPase activities, starch contents, and grain weights. These suggested that TaAGPS1b subunit was targeted into plastids by its truncated transit peptide and it could play an important role in starch synthesis in bread wheat grains.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  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.

    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.

  3. Uncovering Settler Grammars in Curriculum

    Science.gov (United States)

    Calderon, Dolores

    2014-01-01

    In this article, I focus on making settler colonialism explicit in education. I turn to social studies curriculum as a clear example of how settler colonialism is deeply embedded in educational knowledge production in the United States that is rooted in a dialectic of Indigenous presence and absence. I argue that the United States, and the…

  4. 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".

  5. 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

  6. Trametes versicolor carboxylate reductase uncovered

    OpenAIRE

    Winkler, Margit; Winkler, Christoph K.

    2016-01-01

    Abstract The first carboxylate reductase from Trametes versicolor was identified, cloned, and expressed in Escherichia coli. The enzyme reduces aromatic acids such as benzoic acid and derivatives, cinnamic acid, and 3-phenylpropanoic acid, but also aliphatic acids such as octanoic acid are reduced. Graphical abstract

  7. Disordered Collarettes and Uncovered Tables

    DEFF Research Database (Denmark)

    Nørgaard, Nina

    2007-01-01

    -making resource worth considering in analyses of literature. In particular the article aims to demonstrate how the linguistic theory of polyphony known as ScaPoLine would be a useful tool for those who wish to understand and describe the various voices that are coded by negatives and the way negative polarity is...

  8. DISCOVER: Dutch Iliac Stent trial: COVERed balloon-expandable versus uncovered balloon-expandable stents in the common iliac artery: study protocol for a randomized controlled trial

    Directory of Open Access Journals (Sweden)

    Bekken Joost A

    2012-11-01

    Full Text Available Abstract Background Iliac artery atherosclerotic disease may cause intermittent claudication and critical limb ischemia. It can lead to serious complications such as infection, amputation and even death. Revascularization relieves symptoms and prevents these complications. Historically, open surgical repair, in the form of endarterectomy or bypass, was used. Over the last decade, endovascular repair has become the first choice of treatment for iliac arterial occlusive disease. No definitive consensus has emerged about the best endovascular strategy and which type of stent, if any, to use. However, in more advanced disease, that is, long or multiple stenoses or occlusions, literature is most supportive of primary stenting with a balloon-expandable stent in the common iliac artery (Jongkind V et al., J Vasc Surg 52:1376-1383,2010. Recently, a PTFE-covered balloon-expandable stent (Advanta V12, Atrium Medical Inc., Hudson, NH, USA has been introduced for the iliac artery. Covering stents with PTFE has been shown to lead to less neo-intimal hyperplasia and this might lower restenosis rates (Dolmatch B et al. J Vasc Interv Radiol 18:527-534,2007, Marin ML et al. J Vasc Interv Radiol 7:651-656,1996, Virmani R et al. J Vasc Interv Radiol 10:445-456,1999. However, only one RCT, of mediocre quality has been published on this stent in the common iliac artery (Mwipatayi BP et al. J Vasc Surg 54:1561-1570,2011, Bekken JA et al. J Vasc Surg 55:1545-1546,2012. Our hypothesis is that covered balloon-expandable stents lead to better results when compared to uncovered balloon-expandable stents. Methods/Design This is a prospective, randomized, controlled, double-blind, multi-center trial. The study population consists of human volunteers aged over 18 years, with symptomatic advanced atherosclerotic disease of the common iliac artery, defined as stenoses longer than 3 cm and occlusions. A total of 174 patients will be included. The control group will undergo

  9. Analysis of secretome changes uncovers an autocrine/paracrine component in the modulation of cell proliferation and motility by c-Myc.

    Science.gov (United States)

    Pocsfalvi, Gabriella; Votta, Giuseppina; De Vincenzo, Anna; Fiume, Immacolata; Raj, Delfin Albert Amal; Marra, Giancarlo; Stoppelli, Maria Patrizia; Iaccarino, Ingram

    2011-12-02

    Proteins secreted by cancer cells are a major component of tumor microenvironment. However, little is known on the impact of single oncogenic lesions on the expression of secreted proteins at early stages of tumor development. Because c-Myc overexpression is among the most frequent alterations in cancer, here we investigated the effect of sustained c-Myc expression on the secretome of a nontransformed human epithelial cell line (hT-RPE). By using a quantitative proteomic approach, we have identified 125 proteins in conditioned media of hT-RPE/MycER cells upon c-Myc induction. Analysis of the 49 proteins significantly down-regulated by c-Myc revealed a marked enrichment of factors associated with growth inhibition and cellular senescence. Accordingly, media conditioned by hT-RPE cells expressing c-Myc show an increased ability to sustain hT-RPE cellular proliferation/viability. We also find a marked down-regulation of several structural and regulatory components of the extracellular matrix (ECM), which correlates with an increased chemotactic potency of the conditioned media toward fibroblasts, a major cellular component of tumor stroma. In accordance with these data, the expression of the majority of the genes encoding proteins down-regulated in hT-RPE was significantly reduced also in colorectal adenomatous polyps, early tumors in which c-Myc is invariably overexpressed. These findings help to elucidate the significance of c-Myc overexpression at early stages of tumor development and uncover a remarkable autocrine/paracrine component in the ability of c-Myc to stimulate proliferation, sustain tumor maintenance, and modulate cell migration.

  10. 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

  11. Combinatorial approach of LC-MS/MS and LC-TOF-MS for uncovering in vivo kinetics and biotransformation of ochratoxin A in rat.

    Science.gov (United States)

    Han, Zheng; Zhao, Zhiyong; Shi, Jianxin; Liao, Yucai; Zhao, Zhihui; Zhang, Dabing; Wu, Yongning; De Saeger, Sarah; Wu, Aibo

    2013-04-15

    A combinatorial platform of liquid chromatography-tandem mass spectrometry (LC-MS/MS) and liquid chromatography coupled with time of flight mass spectrometry (LC-TOF-MS) has been developed to investigate the in vivo kinetics and biotransformation of ochratoxin A (OTA) in rats. The stable isotope dilution LC-MS/MS method was first validated by determining the linearity (R(2)≥0.9990), sensitivity (lower limit of quantitation of 0.05 ng mL(-1)), accuracy (83.3-108.3), precision (RSD≤15.6%) and stability (≥75.0%), and was approved for the determination OTA in plasma, heart, liver, spleen, lung, kidney and brain with a run time of 7.0 min. Simultaneously, an LC-TOF-MS method could unambiguously identify the metabolites of OTA in a total run time of 14 min. The subsequent studies on kinetics and distribution after oral administration of 0.2 mg/kg b.w. OTA in rat indicated that OTA could reach a maximum value of 1932.4±124.9 ng mL(-1) within 5h due to its fast absorption, and then was slowly eliminated in plasma with a half-life time (t1/2) of 75.6±29.0 h. Results of tissue accumulation after a daily oral administration of 0.1 mg/kg b.w. OTA during 20 days showed that the highest concentration of OTA was observed in lung (95.9±13.7 ng g(-1)), followed by liver (76.0±9.7 ng g(-1)), heart (62.0±4.2 ng g(-1)) and kidney (55.7±4.7 ng g(-1)). Furthermore, three less toxic metabolites of OTA were clearly identified: Ochratoxin β (OTβ) and ochratoxin B (OTB) methyl ester were found in kidney and spleen, respectively, while phenylalanine was detected in heart and kidney. Thus, a possible metabolic pathway of OTA was proposed. The above achieved results justified that the application of combinatorial LC-MS/MS and LC-TOF-MS methods are valuable tools to uncover the kinetics and metabolism of OTA for the interpretation of toxicological findings in animals and extrapolation of the resulting data as reference to humans.

  12. Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Wookyung [Pusan National University, Department of Physics, Center for Proteome Biophysics (Korea, Republic of); Lee, Woonghee; Lee, Weontae [Yonsei University, Department of Biochemistry, Structural Biochemistry and Molecular Biophysics Laboratory (Korea, Republic of); Kim, Suhkmann [Pusan National University, Department of Chemistry, Biochemistry and Bio-NMR Laboratory (Korea, Republic of); Chang, Iksoo, E-mail: iksoochang@pusan.ac.kr [Pusan National University, Department of Physics, Center for Proteome Biophysics (Korea, Republic of)

    2011-12-15

    Unravelling the complex correlation between chemical shifts of {sup 13}C{sup {alpha}}, {sup 13}C{sup {beta}}, {sup 13}C Prime , {sup 1}H{sup {alpha}}, {sup 15}N, {sup 1}H{sup N} atoms in amino acids of proteins from NMR experiment and local structural environments of amino acids facilitates the assignment of secondary structures of proteins. This is an important impetus for both determining the three-dimensional structure and understanding the biological function of proteins. The previous empirical correlation scores which relate chemical shifts of {sup 13}C{sup {alpha}}, {sup 13}C{sup {beta}}, {sup 13}C Prime , {sup 1}H{sup {alpha}}, {sup 15}N, {sup 1}H{sup N} atoms to secondary structures resulted in progresses toward assigning secondary structures of proteins. However, the physical-mathematical framework for these was elusive partly due to both the limited and orthogonal exploration of higher-dimensional chemical shifts of hetero-nucleus and the lack of physical-mathematical understanding underlying those correlation scores. Here we present a simple multi-dimensional hetero-nuclear chemical shift score function (MDHN-CSSF) which captures systematically the salient feature of such complex correlations without any references to a random coil state of proteins. We uncover the symmetry-breaking vector and its reliability order not only for distinguishing different secondary structures of proteins but also for capturing the delicate sensitivity interplayed among chemical shifts of {sup 13}C{sup {alpha}}, {sup 13}C{sup {beta}}, {sup 13}C Prime , {sup 1}H{sup {alpha}}, {sup 15}N, {sup 1}H{sup N} atoms simultaneously, which then provides a straightforward framework toward assigning secondary structures of proteins. MDHN-CSSF could correctly assign secondary structures of training (validating) proteins with the favourable (comparable) Q3 scores in comparison with those from the previous correlation scores. MDHN-CSSF provides a simple and robust strategy for the

  13. Impact Of The Ban On Uncovered SCDS Trade On the Interdependencies Between The CDS Market And Other Sectors Of Financial Markets. The Case Of Safe And Developed Versus Risky And Developing European Markets

    Directory of Open Access Journals (Sweden)

    Kliber Agata

    2016-03-01

    Full Text Available The aim of the article is to verify the impact of the ban on uncovered sCDS trade in Europe on the interdependencies between the sCDS market and other sectors of financial markets. We analyse two European markets: the safe and developed Swedish market, and the risky and developing Hungarian one. The study covers the period from October 2008 to October 2013. We analyse changes in the interdependencies between the sCDS market and the bond market, as well as between the sCDS market and the stock exchange. We found out that in the case of the safe Swedish market, the strength of relationships of each sector of financial markets with the sCDS one was much weaker than in the case of Hungary, which may suggest that the Swedish market is less prone to crisis transmission arising from herd behaviour or speculative attacks. In the end we show that in the two economies, the influence of the sCDS market on the other sectors of financial market indeed diminished following introduction of the ban on uncovered sCDS trade.

  14. 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

  15. 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.

  16. 快速测压方法在吴家峁煤矿石门揭煤施工中的应用%Fast Measuring Pressure Method Applied to the Process of Cross-cut Uncovering Coal in Wujiamao Mine

    Institute of Scientific and Technical Information of China (English)

    田潭; 王雨寒; 杨中玉

    2014-01-01

    T he vast majority of mines in China are gas mine injuries ,one of the most serious incidents caused by coal mine gas accident .T he accurate determination of coal seam gas pressure on mine effec-tively and reasonably adopt gas prevention and control measures ,so as to better predict the risk to en-sure safety in production of coal mine gas outburst ,has the vital significance .T his paper introduces the rapid method of measuring coal uncovering application in Wujiamao Mine shaft ,through the rapid manometric method in short time to test the return air shaft opened the 4 before the coal gas pressure , provide favorable conditions for the safe and fast uncovering coal.%我国绝大多数矿井均是瓦斯矿井,瓦斯事故是煤矿生产中造成人员伤害最严重的事故之一。准确测定煤层瓦斯压力对矿井有效而合理地采取瓦斯防治措施,预测煤层瓦斯突出危险性从而更好保障煤矿井下安全生产,具有重要意义。本文详细介绍了快速测压方法在吴家峁煤矿井筒揭煤过程中的应用,通过快速测压方法在较短时间内测得中央回风立井揭开4煤前的瓦斯压力,为安全快速揭煤提供了有利条件。

  17. News Conference: The Big Bangor Day Meeting Lecture: Charterhouse plays host to a physics day Festival: Science on Stage festival 2013 arrives in Poland Event: Scottish Physics Teachers' Summer School Meeting: Researchers and educators meet at Lund University Conference: Exeter marks the spot Recognition: European Physical Society uncovers an historic site Education: Initial teacher education undergoes big changes Forthcoming events

    Science.gov (United States)

    2013-09-01

    Conference: The Big Bangor Day Meeting Lecture: Charterhouse plays host to a physics day Festival: Science on Stage festival 2013 arrives in Poland Event: Scottish Physics Teachers' Summer School Meeting: Researchers and educators meet at Lund University Conference: Exeter marks the spot Recognition: European Physical Society uncovers an historic site Education: Initial teacher education undergoes big changes Forthcoming events

  18. 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

  19. 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.

  20. 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.

  1. 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..

  2. Low-temperature effect on enzyme activities involved in sucrose-starch partitioning in salt-stressed and salt-acclimated cotyledons of quinoa (Chenopodium quinoa Willd.) seedlings.

    Science.gov (United States)

    Rosa, Mariana; Hilal, Mirna; González, Juan A; Prado, Fernando E

    2009-04-01

    The effect of low temperature on growth, sucrose-starch partitioning and related enzymes in salt-stressed and salt-acclimated cotyledons of quinoa (Chenopodium quinoa Willd.) was studied. The growth of cotyledons and growing axes in seedlings grown at 25/20 degrees C (light/dark) and shifted to 5/5 degrees C was lower than in those only growing at 25/20 degrees C (unstressed). However, there were no significant differences between low-temperature control and salt-treated seedlings. The higher activities of sucrose phosphate synthase (SPS, EC 2.4.1.14) and soluble acid invertase (acid INV, EC 3.2.1.25) were observed in salt-stressed cotyledons; however, the highest acid INV activity was observed in unstressed cotyledons. ADP-glucose pyrophosphorylase (ADP-GPPase, EC 2.7.7.27) was higher in unstressed cotyledons than in stressed ones. However, between 0 and 4days the highest value was observed in salt-stressed cotyledons. The lowest value of ADP-GPPase was observed in salt-acclimated cotyledons. Low temperature also affected sucrose synthase (SuSy, EC 2.4.1.13) activity in salt-treated cotyledons. Sucrose and glucose were higher in salt-stressed cotyledons, but fructose was essentially higher in low-temperature control. Starch was higher in low-temperature control; however, the highest content was observed at 0day in salt-acclimated cotyledons. Results demonstrated that low temperature induces different responses on sucrose-starch partitioning in salt-stressed and salt-acclimated cotyledons. Data also suggest that in salt-treated cotyledons source-sink relations (SSR) are changed in order to supply soluble sugars and proline for the osmotic adjustment. Relationships between starch formation and SuSy activity are also discussed.

  3. Metabolic engineering of sugarcane to accumulate energy-dense triacylglycerols in vegetative biomass.

    Science.gov (United States)

    Zale, Janice; Jung, Je Hyeong; Kim, Jae Yoon; Pathak, Bhuvan; Karan, Ratna; Liu, Hui; Chen, Xiuhua; Wu, Hao; Candreva, Jason; Zhai, Zhiyang; Shanklin, John; Altpeter, Fredy

    2016-02-01

    Elevating the lipid content in vegetative tissues has emerged as a new strategy for increasing energy density and biofuel yield of crops. Storage lipids in contrast to structural and signaling lipids are mainly composed of glycerol esters of fatty acids, also known as triacylglycerol (TAG). TAGs are one of the most energy-rich and abundant forms of reduced carbon available in nature. Therefore, altering the carbon-partitioning balance in favour of TAG in vegetative tissues of sugarcane, one of the highest yielding biomass crops, is expected to drastically increase energy yields. Here we report metabolic engineering to elevate TAG accumulation in vegetative tissues of sugarcane. Constitutive co-expression of WRINKLED1 (WRI1), diacylglycerol acyltransferase1-2 (DGAT1-2) and oleosin1 (OLE1) and simultaneous cosuppression of ADP-glucose pyrophosphorylase (AGPase) and a subunit of the peroxisomal ABC transporter1 (PXA1) in transgenic sugarcane elevated TAG accumulation in leaves or stems by 95- or 43-fold to 1.9% or 0.9% of dry weight (DW), respectively, while expression or suppression of one to three of the target genes increased TAG levels by 1.5- to 9.5-fold. Accumulation of TAG in vegetative progeny plants was consistent with the results from primary transgenics and contributed to a total fatty acid content of up to 4.7% or 1.7% of DW in mature leaves or stems, respectively. Lipid droplets were visible within mesophyll cells of transgenic leaves by confocal fluorescence microscopy. These results provide the basis for optimizations of TAG accumulation in sugarcane and other high yielding biomass grasses and will open new prospects for biofuel applications.

  4. 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

  5. Lauric Acid Production in a Glycogen-Less Strain of Synechococcus sp. PCC 7002.

    Science.gov (United States)

    Work, Victoria H; Melnicki, Matthew R; Hill, Eric A; Davies, Fiona K; Kucek, Leo A; Beliaev, Alexander S; Posewitz, Matthew C

    2015-01-01

    The cyanobacterium Synechococcus sp. Pasteur culture collection 7002 was genetically engineered to synthesize biofuel-compatible medium-chain fatty acids (FAs) 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 FA in CO2-supplemented batch cultures. When grown at steady state over a range of light intensities in a light-emitting diode turbidostat photobioreactor, the C12-secreting mutant exhibited a modest reduction in growth rate and increased O2 evolution relative to the wild-type (WT). 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 FA synthesis. Deletion of AGPase led to a 10-fold decrease in reducing carbohydrates and secretion of organic acids during nitrogen deprivation consistent with an energy spilling phenotype. When the carbohydrate-deficient background (ΔglgC) 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 ΔglgC strain saturated at a lower light intensity than the WT, but O2 evolution was not compromised and became increasingly decoupled from growth rate with rising irradiance. Photophysiological properties of the ΔglgC strain suggest energy dissipation from photosystem II and reconfiguration of electron flow at the level of the plastoquinone pool.

  6. 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.

  7. 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.

  8. 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.

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

    Science.gov (United States)

    Sehnke, P C; Chung, H J; Wu, K; Ferl, R J

    2001-01-16

    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 participate in environmentally responsive phosphorylation-related regulatory functions in plants, and as such are potentially involved in starch regulation. We report here that reduction of the epsilon subgroup of Arabidopsis 14-3-3 proteins by antisense technology resulted in a 2- to 4-fold increase in leaf starch accumulation. Dark-governed starch breakdown was unaffected in these "antisense plants," indicating an unaltered starch-degradation pathway and suggesting a role for 14-3-3 proteins in regulation of starch synthesis. Absorption spectra and gelatinization properties indicate that the starch from the antisense plants has an altered branched glucan composition. Biochemical characterization of protease-treated starch granules from both Arabidopsis leaves and maize endosperm showed that 14-3-3 proteins are internal intrinsic granule proteins. These data suggest a direct role for 14-3-3 proteins in starch accumulation. The starch synthase III family is a possible target for 14-3-3 protein regulation because, uniquely among plastid-localized starch metabolic enzymes, all members of the family contain the conserved 14-3-3 protein phosphoserine/threonine-binding consensus motif. This possibility is strengthened by immunocapture using antibodies to DU1, a maize starch synthase III family member, and direct interaction with biotinylated 14-3-3 protein, both of which demonstrated an association between 14-3-3 proteins and DU1 or DU1-like proteins.

  10. 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.

  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. Construction and Detection Effect of CFG Pile Cap Using Concrete Completely Wet Uncovering Process%CFG桩帽混凝土完全湿揭法的施工与检测效果

    Institute of Scientific and Technical Information of China (English)

    常聚友

    2011-01-01

    Through detecting CFG pile (pile cap) integrity using reflection method, it is shown that reflection curve of some piles is featured of sine wave attenuation, long period and no reflected signal from pile bottom,which are caused by pile shadow vertical crack, horizontal crack, separation between pile cap and pile body during construction through analysis and verification.In order to ensure CFG pile (pile cap ) integrity,concrete completely wet uncovering process shall be applied for CFG pile cap with good effect.%由反射波法检测CFG桩(桩帽)完整性,一些桩的反射波曲线为正弦波衰减、周期大、无桩底反射信号,经分析和验证,原因是施工桩时,造成了桩浅部垂向裂纹、水平断裂、桩帽与桩没有连结成一体.为确保CFG桩(桩帽)质量完整,采用CFG桩帽混凝土完全湿揭法施工,效果良好.

  13. 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…

  14. 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.

  15. 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.

  16. 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.

  17. Uncovering deformation processes from surface displacements

    Science.gov (United States)

    Stramondo, Salvatore

    2013-04-01

    The aim of this talk is to provide an overview about the most recent outcomes in Earth Sciences, describe the role of satellite remote sensing, together with GPS, ground measurement and further data, for geophysical parameter retrieval in well known case studies where the combined approach dealing with the use of two or more techniques/datasets have demonstrated their effectiveness. The Earth Sciences have today a wide availability of instruments and sensors able to provide scientists with an unprecedented capability to study the physical processes driving earthquakes, volcanic eruptions, landslides, and other dynamic Earth systems. Indeed measurements from satellites allow systematic observation of the Earth surface covering large areas, over a long time period and characterized by growing sample intervals. Interferometric Synthetic Aperture Radar (InSAR) technique has demonstrated its effectiveness to investigate processes responsible for crustal faulting stemming from the detection of surface deformation patterns. Indeed using satellite data along ascending and descending orbits, as well as different incident angles, it is possible in principle to retrieve the full 3D character of the ground motion. To such aim the use of GPS stations providing 3D displacement components is a reliable complementary instrument. Finally, offset tracking techniques and Multiple Aperture Interferometry (MAI) may provide a contribution to the analysis of horizontal and NS deformation vectors. The estimation of geophysical parameters using InSAR has been widely discussed in seismology and volcanology, and also applied to deformation associated with groundwater and other subsurface fluids. These applications often involve the solution of an inverse problem, which means the retrieval of optimal source parameters at depth for volcanoes and earthquakes, from the knowledge of surface deformation from InSAR. In recent years, InSAR measurements combined with traditional seismological and geophysical data, such as teleseismic waveforms, strong motion records and GPS, have also been used by geophysicists for improved rupture models. Many models use equations for a uniform elastic half space stemming from the Okada formulation, but improved data constraints and the use of increasingly sophisticated modeling and inverse methods allowed for the exploration of models with variation of elastic properties in layers or more complex representation of fault and lithosphere structure and rheology. In volcanic studies the role of GPS and InSAR lies in the measurement of pre-eruptive inflation, co-eruptive deflation and the post-eruptive response. The spatio-temporal evolution of volcanic processes, the "breathing" of a volcano, can be monitored with temporal series of InSAR interferograms using multitemporal InSAR techniques. The measured deformation can be used as constraints for the formulation of the inverse problem, to retrieve information concerning the depth, size, shape of the magma chamber (and pressure change) and magma supply dynamics. Deformation modeling commonly relies on simple point sources, dikes and sills; or more complex volume-change sources to produce the different surface deformation patterns caused by magma intrusion.

  18. 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.

  19. 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 ...

  20. Uncovering the Deal in Classroom Management

    Science.gov (United States)

    McDonald, Joseph P.; Hudder, Daniel

    2014-01-01

    A teacher educator and a former student, now a classroom teacher, have a 14-year conversation about the deep dynamics of classroom management, which is more complicated than it first appears. The teacher educator introduces the classroom teacher to The Deal, an idea that can guide early-career teachers as well as veteran teachers. The Deal is, in…

  1. Uncovering the mysteries of hantavirus infections.

    Science.gov (United States)

    Vaheri, Antti; Strandin, Tomas; Hepojoki, Jussi; Sironen, Tarja; Henttonen, Heikki; Mäkelä, Satu; Mustonen, Jukka

    2013-08-01

    Hantaviruses are negative-sense single-stranded RNA viruses that infect many species of rodents, shrews, moles and bats. Infection in these reservoir hosts is almost asymptomatic, but some rodent-borne hantaviruses also infect humans, causing either haemorrhagic fever with renal syndrome (HFRS) or hantavirus cardiopulmonary syndrome (HCPS). In this Review, we discuss the basic molecular properties and cell biology of hantaviruses and offer an overview of virus-induced pathology, in particular vascular leakage and immunopathology.

  2. 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

  3. Uncovering effective strategies for hearing loss prevention.

    Science.gov (United States)

    Morata, Thais C; Meinke, Deanna

    2016-04-01

    Occupational health agencies, researchers and policy makers have recognized the need for evidence on the effectiveness of interventions designed to reduce or prevent workplace injuries and illnesses. While many workplaces comply with legal or obligatory requirements and implement recommended interventions, few publications exist documenting the effectiveness of these actions. Additionally, some workplaces have discovered through their own processes, novel ways to reduce the risk of injury. Peer-reviewed information on the effectiveness of the many strategies and approaches currently in use could help correct weaknesses, or further encourage their adoption and expansion. The evaluation of intervention effectiveness would certainly contribute to improved worker health and safety. This need is particularly relevant regarding noise exposure in the workplace and hearing loss prevention interventions. In a 2006 review of the U.S. National Institute for Occupational Safety and Health (NIOSH) Hearing Loss Research Program, the independent National Academies of Sciences recommended that NIOSH place greater emphasis on identifying the effectiveness of hearing loss prevention measures on the basis of outcomes that are as closely related as possible to reducing noise exposure and work related hearing loss (http://www.nap.edu/openbook.php?record_id=11721). NIOSH used two different approaches to address that recommendation: the first one was to conduct research, including broad systematic reviews on the effectiveness of interventions to prevent occupational noise-induced hearing loss. The second was to create an award program, the Safe-In-Sound Excellence in Hearing Loss Prevention Award™, to identify and honor excellent real-world examples of noise control and other hearing loss prevention practices and innovations.

  4. 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.

  5. 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…

  6. 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.

  7. Uncovering spiral structure in flocculent galaxies

    CERN Document Server

    Thornley, M D

    1996-01-01

    We present K'(2.1 micron) observations of four nearby flocculent spirals, which clearly show low-level spiral structure and suggest that kiloparsec-scale spiral structure is more prevalent in flocculent spirals than previously supposed. In particular, the prototypical flocculent spiral NGC 5055 is shown to have regular, two-arm spiral structure to a radius of 4 kpc in the near infrared, with an arm-interarm contrast of 1.3. The spiral structure in all four galaxies is weaker than that in grand design galaxies. Taken in unbarred galaxies with no large, nearby companions, these data are consistent with the modal theory of spiral density waves, which maintains that density waves are intrinsic to the disk. As an alternative, mechanisms for driving spiral structure with non-axisymmetric perturbers are also discussed. These observations highlight the importance of near infrared imaging for exploring the range of physical environments in which large-scale dynamical processes, such as density waves, are important.

  8. 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).

  9. Uncovering the nutritional landscape of food.

    Directory of Open Access Journals (Sweden)

    Seunghyeon Kim

    Full Text Available Recent progresses in data-driven analysis methods, including network-based approaches, are revolutionizing many classical disciplines. These techniques can also be applied to food and nutrition, which must be studied to design healthy diets. Using nutritional information from over 1,000 raw foods, we systematically evaluated the nutrient composition of each food in regards to satisfying daily nutritional requirements. The nutrient balance of a food was quantified and termed nutritional fitness; this measure was based on the food's frequency of occurrence in nutritionally adequate food combinations. Nutritional fitness offers a way to prioritize recommendable foods within a global network of foods, in which foods are connected based on the similarities of their nutrient compositions. We identified a number of key nutrients, such as choline and α-linolenic acid, whose levels in foods can critically affect the nutritional fitness of the foods. Analogously, pairs of nutrients can have the same effect. In fact, two nutrients can synergistically affect the nutritional fitness, although the individual nutrients alone may not have an impact. This result, involving the tendency among nutrients to exhibit correlations in their abundances across foods, implies a hidden layer of complexity when exploring for foods whose balance of nutrients within pairs holistically helps meet nutritional requirements. Interestingly, foods with high nutritional fitness successfully maintain this nutrient balance. This effect expands our scope to a diverse repertoire of nutrient-nutrient correlations, which are integrated under a common network framework that yields unexpected yet coherent associations between nutrients. Our nutrient-profiling approach combined with a network-based analysis provides a more unbiased, global view of the relationships between foods and nutrients, and can be extended towards nutritional policies, food marketing, and personalized nutrition.

  10. η Carinae Baby Homunculus uncovered by ALMA

    Energy Technology Data Exchange (ETDEWEB)

    Abraham, Zulema; Beaklini, Pedro P. B. [Instituto de Astronomia, Geofísica e Ciências Atmosféricas, Universidade de São Paulo, R. do Matão 1226, Cidade Universitária, CEP 05508-900 São Paulo, SP (Brazil); Falceta-Gonçalves, Diego, E-mail: zulema.abraham@iag.usp.br [Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, R. Arlindo Bettio 1000, 03828-000 São Paulo, SP (Brazil)

    2014-08-20

    We report observations of η 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 H42α, He42α, H40α, He40α, H50β, H28α, He28α, H21α, and He21α were also detected, and their intensities reveal non-local thermodynamic equilibrium 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 η 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 high-temperature gas and requires a high-energy ionizing photon flux, which must be provided by the companion star. The mass-loss rate and wind velocity, necessary to explain the formation of the shell, are compatible with an luminous blue variable eruption. The position, velocity, and physical parameters of the shell coincide with those of the Weigelt blobs. The dynamics found for the expanding shell correspond to matter ejected by η Carinae in 1941 in an event similar to that which formed the Little Homunculus; for that reason, we called the new ejecta the 'Baby Homunculus'.

  11. 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...

  12. 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…

  13. Uncovering the Hidden Costs of Offshoring

    DEFF Research Database (Denmark)

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

    2013-01-01

    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......-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...

  14. 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.

  15. 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.

  16. Uncovering deformation processes from surface displacements

    Science.gov (United States)

    Stramondo, Salvatore; Trasatti, Elisa; Albano, Matteo; Moro, Marco; Chini, Marco; Bignami, Christian; Polcari, Marco; Saroli, Michele

    2016-12-01

    Today, satellite remote sensing has reached a key role in Earth Sciences. In particular, Synthetic Aperture Radar (SAR) sensors and SAR Interferometry (InSAR) techniques are widely used for the study of dynamic processes occurring inside our living planet. Over the past 3 decades, InSAR has been applied for mapping topography and deformation at the Earth's surface. These maps are widely used in tectonics, seismology, geomorphology, and volcanology, in order to investigate the kinematics and dynamics of crustal faulting, the causes of postseismic and interseismic displacements, the dynamics of gravity driven slope failures, and the deformation associated with subsurface movement of water, hydrocarbons or magmatic fluids.

  17. Uncovering Heroes: A Conversation with Jennifer Armstrong.

    Science.gov (United States)

    Kerper, Richard M.

    2000-01-01

    Offers an interview with Jennifer Armstrong, writer of historical novels and nonfiction for children. Discusses her beginnings as a reader and a writer, her creative process, her purposes in writing nonfiction, her concerns about accuracy, and the origins of her second nonfiction book, "Shipwreck at the Bottom of the World: The Extraordinary…

  18. Uncovering stellar atmospheres with gravitational microlensing telescopes

    CERN Document Server

    Dominik, M

    2003-01-01

    A strong differential magnification over the face of the source star passing the caustic created by a binary lens star allows to measure its radial intensity profile with an angular resolution of 20-60 nas from broad-band photometric observations for ~15 stars per year and to study its chemical composition from time-resolved high-resolution spectroscopy for ~2 stars per year.

  19. Uncovering the information core in recommender systems

    Science.gov (United States)

    Zeng, Wei; Zeng, An; Liu, Hao; Shang, Ming-Sheng; Zhou, Tao

    2014-08-01

    With the rapid growth of the Internet and overwhelming amount of information that people are confronted with, recommender systems have been developed to effectively support users' decision-making process in online systems. So far, much attention has been paid to designing new recommendation algorithms and improving existent ones. However, few works considered the different contributions from different users to the performance of a recommender system. Such studies can help us improve the recommendation efficiency by excluding irrelevant users. In this paper, we argue that in each online system there exists a group of core users who carry most of the information for recommendation. With them, the recommender systems can already generate satisfactory recommendation. Our core user extraction method enables the recommender systems to achieve 90% of the accuracy of the top-L recommendation by taking only 20% of the users into account. A detailed investigation reveals that these core users are not necessarily the large-degree users. Moreover, they tend to select high quality objects and their selections are well diversified.

  20. 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.

  1. $\\eta$ 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...

  2. Cobalamins uncovered by modern electronic structure calculations

    DEFF Research Database (Denmark)

    Kepp, Kasper Planeta; Ryde, Ulf

    2009-01-01

    This review describes how computational methods have contributed to the held of cobalamin chemistry since the start of the new millennium. Cobalamins are cobalt-dependent cofactors that are used for alkyl transfer and radical initiation by several classes of enzymes. Since the entry of modern...

  3. Uncovering the nucleus candidate for NGC 253

    CERN Document Server

    Günthardt, G I; Camperi, J A; Díaz, R J; Gomez, P L; Bosch, G; Schirmer, M

    2015-01-01

    NGC253 is the nearest spiral galaxy with a nuclear starburst which becomes the best candidate to study the relationship between starburst and AGN 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. The near infrared spectroscopy could be advantageous in order to shed light on the true nucleus identity. Using Flamingos-2 at Gemini South we have taken deep K-band spectra along the major axis and through the brightest infrared source. We present evidence showing that the brightest near infrared and mid infrared source in the central region, already known as radio source TH7 and so far considered just a stellar supercluster, in fact, presents various symptoms of a genuine galactic nucleus. Therefore, it should be considered a valid nucleus candidate. It is the most massive compact infrared object in the central region, located at 2.0" of the symmetry center of the galactic bar. Moreover, our data indicate that this object i...

  4. 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.

  5. 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.

  6. 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.

  7. Research on primary parameters of high pressure water jet during rock cross-cut coal uncovering%高压水射流割缝揭穿煤层关键参数研究

    Institute of Scientific and Technical Information of China (English)

    张建国

    2011-01-01

    According to the problems of gas drainage in rock cross-cut coal uncovering on high gassy coal seam with low gas permeability coal seam,a novel technology which uses high pressure water jet to slot coal seam is presented to raise the methane drainage radius and permeability.Based on the distribution of water jet velocity,the relationship of impact force of water jet and characters of coal is analyzed.Besides,the velocity of coal partial basing on the relationship of force of partial and dip of drilling is studied.Then,the effective diameters of slotting are calculated.Finally,the novel technology is applied to the Pingdingshan mine.The results show that quantities is decreased 38.2%,gas drainage rate is increased 2.86 times and the period of gas drainage is reduced 57.1% and the area of the gas drainage is widened 2.05 times compared to original technology.%针对高瓦斯低透气性煤层石门揭煤过程中瓦斯抽采难的现状,提出了高压水射流割缝提高煤层透气性方法。在理论分析射流轴向速度的分布规律基础上,得出射流冲击力与煤体力学性质耦合作用关系;通过分析煤体颗粒运动、受力状态,得出钻孔倾角、水量与煤体颗粒流速之间的关系;基于连续损伤力学分析出煤体产生损伤破坏的临界值,确定了高压水射流割缝煤体有效半径;并将该技术在平顶山某矿-380mS4石门进行现场试验,试验结果表明钻进工程量减少了38.2%,瓦斯预抽率提高了2.86倍,预抽时间缩短了57.1%,预抽面积增加了2.05倍。

  8. 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.

  9. Optimizing the distribution of resources between enzymes of carbon metabolism can dramatically increase photosynthetic rate: a numerical simulation using an evolutionary algorithm.

    Science.gov (United States)

    Zhu, Xin-Guang; de Sturler, Eric; Long, Stephen P

    2007-10-01

    -saturated rate of photosynthesis. An overinvestment in PCOP enzymes and underinvestment in Rubisco, sedoheptulose-1,7-bisphosphatase, and fructose-1,6-bisphosphate aldolase were indicated. Increase in sink capacity, such as increase in ADP-glucose pyrophosphorylase, was also indicated to lead to increased CO(2) uptake rate. These results suggest that manipulation of partitioning could greatly increase carbon gain without any increase in the total protein-nitrogen investment in the apparatus for photosynthetic carbon metabolism.

  10. 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

  11. Deep sequencing reveals the complex and coordinated transcriptional regulation of genes related to grain quality in rice cultivars

    Directory of Open Access Journals (Sweden)

    An Gynheung

    2011-04-01

    Full Text Available Abstract Background Milling yield and eating quality are two important grain quality traits in rice. To identify the genes involved in these two traits, we performed a deep transcriptional analysis of developing seeds using both massively parallel signature sequencing (MPSS and sequencing-by-synthesis (SBS. Five MPSS and five SBS libraries were constructed from 6-day-old developing seeds of Cypress (high milling yield, LaGrue (low milling yield, Ilpumbyeo (high eating quality, YR15965 (low eating quality, and Nipponbare (control. Results The transcriptomes revealed by MPSS and SBS had a high correlation co-efficient (0.81 to 0.90, and about 70% of the transcripts were commonly identified in both types of the libraries. SBS, however, identified 30% more transcripts than MPSS. Among the highly expressed genes in Cypress and Ilpumbyeo, over 100 conserved cis regulatory elements were identified. Numerous specifically expressed transcription factor (TF genes were identified in Cypress (282, LaGrue (312, Ilpumbyeo (363, YR15965 (260, and Nipponbare (357. Many key grain quality-related genes (i.e., genes involved in starch metabolism, aspartate amino acid metabolism, storage and allergenic protein synthesis, and seed maturation that were expressed at high levels underwent alternative splicing and produced antisense transcripts either in Cypress or Ilpumbyeo. Further, a time course RT-PCR analysis confirmed a higher expression level of genes involved in starch metabolism such as those encoding ADP glucose pyrophosphorylase (AGPase and granule bound starch synthase I (GBSS I in Cypress than that in LaGrue during early seed development. Conclusion This study represents the most comprehensive analysis of the developing seed transcriptome of rice available to date. Using two high throughput sequencing methods, we identified many differentially expressed genes that may affect milling yield or eating quality in rice. Many of the identified genes are involved

  12. Effects of alginate-derived oligosaccharides synergistic urea on the photosynthetic characteristics and accumulation of carbon metabolites in rice%海藻寡糖增效尿素对水稻光合特性及碳代谢产物积累的影响

    Institute of Scientific and Technical Information of China (English)

    张运红; 孙克刚; 杜君; 和爱玲; 张起义

    2016-01-01

    Pot experiments were used to study the effects of alginate-derived oligosaccharide ( ADO) synergistic urea on photo-synthetic characteristics, key enzymes activities and carbon metabolites accumulation of rice ( Oryza. Sativa L. ) . The results showed that net photosynthetic rate ( Pn ) , stomatal conductance ( Gs ) , intercellular CO2 concentration ( Ci ) and water use efficiency ( WUE) of rice under ADO synergistic urea treatment were increased, and stomatal limitation value ( Ls ) was de-creased, compared with ordinary urea. Chlorophyll content and ribulose-1, 5-bisphosphate-caboxylase ( Rubisco) activity were also significantly raised. At booting, full heading and maturing stages, sucrose phosphate synthase ( SPS) , sucrose syn-thase (SUS) and ADP-glucose pyrophosphorylase (ADPase) activity in leaves or grain of rice were significantly enhanced, thus contributing to the accumulation of sucrose and starch in grain. Aboveground and belowground biomass were also signifi-cantly increased at all the four growth stages. Rice yield of ADO synergistic urea treatment was significantly raised by 9. 32%compared with the control, and was higher than that of ordinary urea treatment by 3. 94%.%采用盆栽试验,研究了海藻寡糖增效尿素对水稻光合特性、碳代谢关键酶活性及相关产物积累的影响。结果表明,和普通尿素相比,海藻寡糖增效尿素处理的水稻净光合速率( Pn )、气孔导度( Gs )、胞间CO2浓度(Ci)和水分利用效率(WUE)有所增加,气孔限制值(Ls)有所降低,叶绿素含量和核酮糖-1,5-二磷酸羧化加氧酶(Rubisco)活性显著提高。拔节期、齐穗期和成熟期叶中和籽粒中蔗糖磷酸合成酶(SPS)、蔗糖合成酶( SUS)和腺苷二磷酸葡萄糖焦磷酸化酶( ADPase)活性显著增强,从而促进籽粒中蔗糖和淀粉积累;地上部和地下部生物量在4个生育期也均显著增加,籽粒产量显著提高,其中较对照增加9.32%,较普通尿素处理增加3.94

  13. Changes in gravity affect gene expression, protein modulation and metabolite pools of arabidopsis

    Science.gov (United States)

    Hampp, R.; Martzivanou, M.; Maier, R. M.; Magel, E.

    Callus cultures of Arabidopsis thaliana (cv. Columbia) in Petri dishes / suspension cultures were exposed to altered g-forces by centrifugation (1 to 10 g), klinorotation, and μ g (sounding rocket flights). Using semi-quantitative RT-PCR, transcripts of genes coding for metabolic key enzymes (ADP-glucose pyrophosphorylase, ADPG-PP; ß-amylase, fructose-1,6-bisphosphatase, FBPase; glyceraldehyde-P dehydrogenase, GAPDH; hydroxymethylglutaryl-CoA reductase, HMG; phenylalanine-ammonium-lyase, PAL; PEP carboxylase, PEPC) were used to monitor threshold conditions for g-number (all) and time of exposure (ß-amylase) which led to altered amounts of the gene product. Exposure to approx. 5 g and higher for 1h resulted in altered transcript levels: transcripts of ß-amylase, PAL, and PEPC were increased, those of ADPG-PP decreased, while those of FBPase, GAPDH, and HMG were not affected. This probably indicates a shift from starch synthesis to starch degradation and increased rates of anaplerosis (PEPC: supply of ketoacids for amino acid synthesis). In order to get more information about g-related effects on gene expression, we used a 1h-exposure to 7 g for a microarray analysis. Transcripts of more than 200 genes were significantly increased in amount (ratio 7g / 1g control; 21.6 and larger). They fall into several categories. Transcripts coding for enzymes of major pathways form the largest group (25%), followed by gene products involved in cellular organisation and cell wall formation / rearrangement (17%), signalling, phosphorylation/dephosphorylation (12%), proteolysis and transport (10% each), hormone synthesis plus related events (8%), defense (4%), stress-response (2%), and gravisensing (2%). Many of the alterations are part of a general stress response, but some changes related to the synthesis / rearrangement of cell wall components could be more hyper-g-specific. Using macroarrays with selected genes according to our hypergravity study (metabolism / signalling

  14. 花后水分胁迫对春小麦淀粉形成及相关酶活性的影响%Effects of water stress after anthesis on starch formation and the activity of associated enzyme in spring wheat

    Institute of Scientific and Technical Information of China (English)

    李亚婷; 康建宏; 吴宏亮; 李昱; 姚珊

    2016-01-01

    近年来,气候变化导致农田干旱与渍水频繁发生.研究花后水分胁迫对春小麦(Triticum aestivum)淀粉形成的影响,对栽培稳产优质的春小麦品种具有重要意义.本研究以宁夏平原主栽春小麦宁春4号和宁春47号为试材,采用盆栽种植,人工控制土壤含水量,设置重度干旱、轻度干旱、正常处理和过度灌溉4个试验梯度.结果表明,花后干旱显著(P<0.05)提高了宁春4号灌浆前期籽粒中直链淀粉含量,显著降低了两种春小麦灌浆中后期直链、支链淀粉含量,最终使收获期籽粒中总淀粉含量显著降低.与籽粒中淀粉形成相关的4种关键酶,AGPP、UGPP、SBE及 SSS活性在整个灌浆期均呈单峰曲线,两种春小麦灌浆中后期受花后水分胁迫显著降低了酶活性,两种春小麦的直链淀粉积累速率与 SSS活性活性均呈极显著正相关(P<0.01).%Recently,frequent drought and waterlogging due to climate change caused severe yield loss in spring wheat.The research about the effects of water stress after anthesis on starch formation had great importance for cultivation of spring wheat with stable production and high quality.In the present study,two spring wheat varieties Ningchun 4 and Ningchun 47 which were domain varieties in Ningxia province were selected as materi-al.Four different soil moisture treatments including heavy drought,light drought,normal and water logging were performed by manipulating the post-anthesis soil moisture in pots.The results showed that post-anthesis drought significantly increased (P<0.05)the grain starch content during the earlier filling stage and signifi-cantly reduced (P<0.05)the amylose and amylopectin content during the mid and late filing stage so that sig-nificantly reduced (P<0.05)the total starch content during the late filing stage.The activities of four key en-zymes associated with starch formation,AGPP (ADP-glucose pyrophosphorylase),UGPP (UDP-glucose pyrophosphorylase

  15. 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…

  16. 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...

  17. Uncovering Urban Temporal Patterns from Geo-Tagged Photography

    Science.gov (United States)

    Paldino, Silvia; Kondor, Dániel; Sobolevsky, Stanislav; González, Marta C.; Ratti, Carlo

    2016-01-01

    We live in a world where digital trails of different forms of human activities compose big urban data, allowing us to detect many aspects of how people experience the city in which they live or come to visit. In this study we propose to enhance urban planning by taking into a consideration individual preferences using information from an unconventional big data source: dataset of geo-tagged photographs that people take in cities which we then use as a measure of urban attractiveness. We discover and compare a temporal behavior of residents and visitors in ten most photographed cities in the world. Looking at the periodicity in urban attractiveness, the results show that the strongest periodic patterns for visitors are usually weekly or monthly. Moreover, by dividing cities into two groups based on which continent they belong to (i.e., North America or Europe), it can be concluded that unlike European cities, behavior of visitors in the US cities in general is similar to the behavior of their residents. Finally, we apply two indices, called “dilatation attractiveness index” and “dilatation index”, to our dataset which tell us the spatial and temporal attractiveness pulsations in the city. The proposed methodology is not only important for urban planning, but also does support various business and public stakeholder decision processes, concentrated for example around the question how to attract more visitors to the city or estimate the impact of special events organized there. PMID:27935979

  18. Uncovering the hidden demographic history of the USSR.

    Science.gov (United States)

    Blum, A

    1991-01-01

    After the results of the 1937 census were calculated and the figures were lower than expected, Stalin arrested the census takers, altered the figures, and cancelled it. But, he did not destroy the records; they have remained in the archives of the Central National Archives for 50 years. They are now finally open to inspection thanks to glasnost. The records that are being examined are confirming what some in the West had suspected all along. Stalin wanted the 1937 census to show 170 million people, but because of famine, the actual number was more like 162 million. Stalin wanted the census to show the world that socialism was better than capitalism in terms of growth. However the forced collectivization of farms and the forced relocations of people resulted in a famine in 1933 which wiped out about 2.5 times more people over and above normal death rates. In some regions this figure is 4.5 times what is normally was. The number of people lost during WWII is also being revised in light of these new records. It appears that 26 million people died as the result of hostilities between 1941-45. This is in addition to the number normally expected to die during the same time.

  19. Uncovering the Hidden Molecular Signatures of Breast Cancer

    Science.gov (United States)

    2013-05-01

    lines were generated using TNE lysis buffer (50 mM Tris at pH 8.0, 150 mM NaCl, 1% Nonidet P - 40 , 2 mMEDTA at pH 8.0, 1 mM phenylmethylsulfonyl fluoride, 1...Jeffrey! SS,! Thorsen! T,! Quist! H,! Matese! JC,! Brown! PO,! Botstein! D,! Eystein! Lønning! P ,! BørresenLDale! AL.! Gene! expression! patterns! of...Langerød! A,! Green! A,! Provenzano! E,!Wishart! G,! Pinder! S,!Watson! P ,!Markowetz! F,! Murphy!L,!Ellis!I,!Purushotham!A,!BørresenLDale!AL,!Brenton!JD

  20. Uncovering disease-disease relationships through the incomplete human interactome

    Science.gov (United States)

    Menche, Jörg; Sharma, Amitabh; Kitsak, Maksim; Ghiassian, Susan; Vidal, Marc; Loscalzo, Joseph; Barabási, Albert-László

    2015-01-01

    According to the disease module hypothesis the cellular components associated with a disease segregate in the same neighborhood of the human interactome, the map of biologically relevant molecular interactions. Yet, given the incompleteness of the interactome and the limited knowledge of disease-associated genes, it is not obvious if the available data has sufficient coverage to map out modules associated with each disease. Here we derive mathematical conditions for the identifiability of disease modules and show that the network-based location of each disease module determines its pathobiological relationship to other diseases. For example, diseases with overlapping network modules show significant co-expression patterns, symptom similarity, and comorbidity, while diseases residing in separated network neighborhoods are clinically distinct. These tools represent an interactome-based platform to predict molecular commonalities between clinically related diseases, even if they do not share disease genes. PMID:25700523

  1. 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.

  2. Uncovering RNA editing sites in long non-coding RNAs

    Directory of Open Access Journals (Sweden)

    Ernesto ePicardi

    2014-12-01

    Full Text Available RNA editing is an important co/post-transcriptional molecular process able to modify RNAs by nucleotide insertions/deletions or substitutions. In human, the most common RNA editing event involves the deamination of adenosine (A into inosine (I through the adenosine deaminase acting on RNA (ADAR proteins. Although A-to-I editing can occur in both coding and non coding RNAs, recent findings, based on RNA-seq experiments, have clearly demonstrated that a large fraction of RNA editing events alter non-coding RNAs sequences including untranslated regions of mRNAs (UTRs, introns, long non-coding RNAs (lncRNA and low molecular weight RNAs (tRNA, miRNAs and others. An accurate detection of A-to-I events occurring in non-coding RNAs is of utmost importance to clarify yet unknown functional roles of RNA editing in the context of gene expression regulation and maintenance of cell homeostasis. In the last few years, massive transcriptome sequencing has been employed to identify putative RNA editing changes at genome scale. Despite several efforts, the computational prediction of A-to-I sites in complete eukaryotic genomes is yet a challenging task. We have recently developed a software package, called REDItools, in order to simplify the detection of RNA editing events from deep sequencing data. In the present work, we show the potential of our tools in recovering A-to-I candidates from RNA-Seq experiments as well as guidelines to improve the RNA editing detection in non-coding RNAs, with specific attention to the lncRNAs.

  3. 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…

  4. 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.

  5. 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.

  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. Uncovering Architectural Challenges in a System of Systems

    Science.gov (United States)

    2013-01-16

    UAVs are re-directed N+4 FCQ tracks are developed from UAV inputs Architecting in a Complex World Twitter #SEIVirtualEvent © 2013 Carnegie... FCQ ) tracks directly to the two ships. A two-pronged attack on the fleet occurs: • five aircraft-launched missiles from the Southeast • three minutes...track the missiles. 1. The legacy Defensive Engagement Sys- tem (DES) cannot use external tracks to form a FCQ track. 2. Within X seconds 3

  8. Who really makes the bed? Uncovering technologic dissonance in nursing.

    Science.gov (United States)

    Purnell, M J

    1998-07-01

    Technologic dissonance in the practice arena is demonstrated in the use of nonnursing technologies that are present in but technically incongruent with a nursing environment. Technology in nursing is not necessarily nursing technology. The article traces the influences of technologic dissonance beyond the reductionist purview of the medical model to their source in design and engineering philosophies. The vision of technologic consonance in nursing may be realized in the influence and expression of the caring nurse in the design, engineering, ownership, and use of nursing technology.

  9. Systems Biology of Metabolic Networks: Uncovering Regulatory and stoichiometric Principles

    DEFF Research Database (Denmark)

    Patil, Kiran Raosaheb

    2007-01-01

    metoder til analyse af levende cellers stofskifte. Metoderne er baseret på anvendelsen af metabolske modeller til integration af både transkriptionsdata og metabolome-data. Således er det vist at cellers respons til ændringer i deres miljø eller deres genetiske baggrund, i stor udstrækning involverer...

  10. Uncovering the 'Spy' Network: Is Spyware Watching Your Library Computers?

    Science.gov (United States)

    Ferrer, Daniel Fidel; Mead, Mary

    2003-01-01

    Describes spyware, discusses how it gets on a computer. Explains how spyware can be useful for parents, employers, and libraries. Discusses how spyware is more often used for others' gain or for surveillance without notification, how it can go undetected, and how libraries can help keep computers and patrons protected from remote installation of…

  11. Budagovsky 9 rootstock: uncovering a novel resistance to fire blight

    Science.gov (United States)

    Budagovsky 9 (B.9) apple rootstock, displayed a high level of susceptibility (similar to M.9 rootstock) to fire blight bacteria (Erwinia amylovora) when leaves of non-grafted B.9 plants were inoculated. However, when older B.9 rootstock tissue was inoculated directly with E. amylovora, rootstock tis...

  12. 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...

  13. 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.

  14. Uncovering the forces between nucleosomes using DNA origami.

    Science.gov (United States)

    Funke, Jonas J; Ketterer, Philip; Lieleg, Corinna; Schunter, Sarah; Korber, Philipp; Dietz, Hendrik

    2016-11-01

    Revealing the energy landscape for nucleosome association may contribute to the understanding of higher-order chromatin structures and their impact on genome regulation. We accomplish this in a direct measurement by integrating two nucleosomes into a DNA origami-based force spectrometer, which enabled subnanometer-resolution measurements of nucleosome-nucleosome distance frequencies via single-particle electron microscopy imaging. From the data, we derived the Boltzmann-weighted distance-dependent energy landscape for nucleosome pair interactions. We find a shallow but long-range (~6 nm) attractive nucleosome pair potential with a minimum of -1.6 kcal/mol close to direct contact distances. The relative nucleosome orientation had little influence, but histone H4 acetylation or removal of histone tails drastically decreased the interaction strength. Because of the weak and shallow pair potential, higher-order nucleosome assemblies will be compliant and experience dynamic shape fluctuations in the absence of additional cofactors. Our results contribute to a more accurate description of chromatin and our force spectrometer provides a powerful tool for the direct and high-resolution study of molecular interactions using imaging techniques.

  15. 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.

  16. Structural Analysis Uncovers Lipid-Binding Properties of Notch Ligands

    Directory of Open Access Journals (Sweden)

    Chandramouli R. Chillakuri

    2013-11-01

    Full Text Available The Notch pathway is a core cell-cell signaling system in metazoan organisms with key roles in cell-fate determination, stem cell maintenance, immune system activation, and angiogenesis. Signals are initiated by extracellular interactions of the Notch receptor with Delta/Serrate/Lag-2 (DSL ligands, whose structure is highly conserved throughout evolution. To date, no structure or activity has been associated with the extreme N termini of the ligands, even though numerous mutations in this region of Jagged-1 ligand lead to human disease. Here, we demonstrate that the N terminus of human Jagged-1 is a C2 phospholipid recognition domain that binds phospholipid bilayers in a calcium-dependent fashion. Furthermore, we show that this activity is shared by a member of the other class of Notch ligands, human Delta-like-1, and the evolutionary distant Drosophila Serrate. Targeted mutagenesis of Jagged-1 C2 domain residues implicated in calcium-dependent phospholipid binding leaves Notch interactions intact but can reduce Notch activation. These results reveal an important and previously unsuspected role for phospholipid recognition in control of this key signaling system.

  17. Uncovering Notch pathway in the parasitic flatworm Schistosoma mansoni.

    Science.gov (United States)

    Magalhães, Lizandra G; Morais, Enyara R; Machado, Carla B; Gomes, Matheus S; Cabral, Fernanda J; Souza, Julia M; Soares, Cláudia S; Sá, Renata G; Castro-Borges, William; Rodrigues, Vanderlei

    2016-10-01

    Several signaling molecules that govern development in higher animals have been identified in the parasite Schistosoma mansoni, including the transforming growth factor β, protein tyrosine kinases, nuclear hormone receptors, among others. The Notch pathway is a highly conserved signaling mechanism which is involved in a wide variety of developmental processes including embryogenesis and oogenesis in worms and flies. Here we aimed to provide the molecular reconstitution of the Notch pathway in S. mansoni using the available transcriptome and genome databases. Our results also revealed the presence of the transcripts coded for SmNotch, SmSu(H), SmHes, and the gamma-secretase complex (SmNicastrin, SmAph-1, and SmPen-2), throughout all the life stages analyzed. Besides, it was observed that the viability and separation of adult worm pairs were not affected by treatment with N-[N(3,5)-difluorophenacetyl)-L-Alanyl]-S-phenylglycine t-butyl ester (DAPT), a Notch pathway inhibitor. Moreover, DAPT treatment decreased the production of phenotypically normal eggs and arrested their development in culture. Our results also showed a significant decrease in SmHes transcript levels in both adult worms and eggs treated with DAPT. These results provide, for the first time, functional validation of the Notch pathway in S. mansoni and suggest its involvement in parasite oogenesis and embryogenesis. Given the complexity of the Notch pathway, further experiments shall highlight the full repertoire of Notch-mediated cellular processes throughout the S. mansoni life cycle.

  18. Uncovering Adiponectin Replenishing Property of Sujiaonori Algal Biomaterial in Humans.

    Science.gov (United States)

    Ngatu, Nlandu Roger; Ikeda, Mitsunori; Watanabe, Hiroyuki; Tanaka, Mamoru; Inoue, Masataka; Kanbara, Sakiko; Nojima, Sayumi

    2017-02-08

    The replenishment of adiponectin-an adipocyte-derived hormone with salutary health effects-has recently been proposed as a new approach to treat hypertension, also ameliorate cardiovascular and metabolic risks. We conducted a prospective placebo-controlled, non-randomized and investigator-blinded dietary intervention study to evaluate the health effects of dietary intake of Sujiaonori (Ulva/Enteromorpha prolifera Müller) algal biomaterial (SBM), especially on adiponectin production, blood pressure (BP), and body mass index (BMI) in human subjects. Participants (N = 32) were divided into two equally sized groups (n = 16 for each group): SBM group (subjects supplemented with 3 g SBM powder twice a day during meal) and the control group (subjects who took 3 g of a supplement made of 70% corn starch powder and 30% spinach twice a day) for four weeks. Two health survey questionnaires (dietary and current health questionnaires) were completed anonymously, saliva sampling was done for adiponectin measurement by ELISA, and blood pressure (BP) and anthropometric parameters were measured at baseline and four weeks later. Student paired t-test was performed to compare baseline and post-intervention data on outcome variables between the two study groups. Results showed a 2.24-fold increase in adiponectin level in SBM group (2.81 and 6.26 ng/mL at baseline and at the end of study, respectively) (p 0.05). In SBM subjects, an improvement of BP profile was noted with a significant decrease in systolic BP (p < 0.01). A positive correlation was found between SBM supplementation and adiponectin level, whereas an inverse correlation was noted between SBM supplementation and blood pressure, and also BMI. These findings suggest that SBM-increased adiponectin level and improved BP in a sample of Japanese young adults, and has the potential to improve blood pressure in humans.

  19. 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.

  20. Uncovering and Validating Toughening Mechanisms in High Performance Composites

    Science.gov (United States)

    2015-09-17

    start [Patek, S.N., Korff, W.L. & Caldwell, R.L. Biomechanics : Deadly strike mechanism of a mantis shrimp - This shrimp packs a punch powerful enough to...channels running left to right (highlighted in yellow), with the mineralized fibers that make up each layer of the striated region extending from top to...with SEM micrographs is shown in (K). Scale bar in (K) is 2 µm. Pore channels run from the interior of the club outward, traversing the entire club

  1. 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.

  2. "海王星"揭秘%The "Neptune" Uncovering Story

    Institute of Scientific and Technical Information of China (English)

    王大锐; 王颂

    2001-01-01

    @@ 在我国40岁上下的人群中,大多都记得20世纪60年代初至中期,我人民解放军痛歼进入我国领空的美制国民党军各种侦察机的辉煌战果,其中就有3架被我地面高炮部队、空军和海军航空兵击落的P2V电子侦察机.

  3. 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.

  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. 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...

  6. 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.

  7. 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…

  8. 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

  9. [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.

  10. Hiring Practices Initiative: Uncovering an Untapped Employment Pool

    Science.gov (United States)

    Mulvihill, Patrick; Repetto, Jeanne B.; Andrews, Drew; Gritz, Sheila

    2008-01-01

    Through current hiring practices, many school districts may be missing an untapped pool of potential employees--individuals with disabilities. In this article, the authors describe the Hiring Practice Initiative (HPI) and its implementation in 17 Florida school districts. The Hiring Practice Initiative Project goals are to: (a) increase the…

  11. 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…

  12. Transition Initiatives as Light Intentional Communities: Uncovering Liminality and Friction

    Directory of Open Access Journals (Sweden)

    Elisabeth van de Grift

    2017-03-01

    Full Text Available The Transition Network is a global grassroots network that supports community-led resilience in the face of global change. This paper reports on an ethnographic study of one of its longest-running projects, Transition Town Lewes (TTL in the United Kingdom. The aim of the study is to analyse TTL as a community. More specifically, we ask two questions: (1 what type of community is TTL? and (2 what are the challenges TTL faces as a community? With this, we contribute to the existing literature on local sustainability initiatives and in particular on Transition initiatives, by providing an in-depth understanding of the challenges and social dynamics at play in a day-to-day setting. We conducted three months of intensive ethnographic fieldwork using participant observation, interviews, and a focus group. Our analysis shows that TTL is a community that, on the one hand, is motivated by explicit intentions and goals, but that, on the other hand, leaves openness and flexibility regarding the level and specifics of participants’ engagement. We introduce the novel concept of ‘light intentional community’ to describe this type of community. We first investigate intentionality in TTL, finding that differences exist between individual participant motivations and stated TTL objectives. We go on to describe the ‘light’ aspect of TTL—the differences in levels of engagement between community participants. Our analysis shows that TTL and its participants face two main challenges. First, TTL participants experience ‘multi-dimensional liminality’: they operate in a liminal space between mainstream society and TTL practices, and additionally experience a continuous sense of transitioning toward a moving goal. Second, TTL as a community faces internal and external frictions. These challenges are interrelated and stem from the structure and dynamics of TTL as a light intentional community. We conclude by reflecting on our analysis of the nature and challenges of ‘light intentional communities’, identifying what opportunities this concept brings for overcoming the challenges of grassroots globalization initiatives amidst mainstream society.

  13. 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 ...

  14. 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.

  15. Uncovering the dynamics of interaction in development cooperation

    DEFF Research Database (Denmark)

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

    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...... adopting more analytically and conceptually diverse approaches to study the interaction between heterogeneous development actors and homogenising forces in the field of development cooperation, recognising the complexity and (dis)continuities of stability and change in this arena....

  16. Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Lamour, Kurt H [ORNL; McDonald, W Hayes [ORNL; Savidor, Alon [ORNL

    2006-01-01

    Genome sequences of the soybean pathogen, Phytophthora sojae, and the sudden oak death pathogen, Phytophthora ramorum, suggest a photosynthetic past and reveal recent massive expansion and diversification of potential pathogenicity gene families. Abstract: Draft genome sequences of the soybean pathogen, Phytophthora sojae, and the sudden oak death pathogen, Phytophthora ramorum, have been determined. O mycetes 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 support 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 o mycete avirulence genes.

  17. Uncovering gender discrimination cues in a realistic setting.

    Science.gov (United States)

    Dupuis-Roy, Nicolas; Fortin, Isabelle; Fiset, Daniel; Gosselin, Frédéric

    2009-02-10

    Which face cues do we use for gender discrimination? Few studies have tried to answer this question and the few that have tried typically used only a small set of grayscale stimuli, often distorted and presented a large number of times. Here, we reassessed the importance of facial cues for gender discrimination in a more realistic setting. We applied Bubbles-a technique that minimizes bias toward specific facial features and does not necessitate the distortion of stimuli-to a set of 300 color photographs of Caucasian faces, each presented only once to 30 participants. Results show that the region of the eyes and the eyebrows-probably in the light-dark channel-is the most important facial cue for accurate gender discrimination; and that the mouth region is driving fast correct responses (but not fast incorrect responses)-the gender discrimination information in the mouth region is concentrated in the red-green color channel. Together, these results suggest that, when color is informative in the mouth region, humans use it and respond rapidly; and, when it's not informative, they have to rely on the more robust but more sluggish luminance information in the eye-eyebrow region.

  18. 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.

  19. Uncovering the sources of DNA found on the Turin Shroud.

    Science.gov (United States)

    Barcaccia, Gianni; Galla, Giulio; Achilli, Alessandro; Olivieri, Anna; Torroni, Antonio

    2015-10-05

    The Turin Shroud is traditionally considered to be the burial cloth in which the body of Jesus Christ was wrapped after his death approximately 2000 years ago. Here, we report the main findings from the analysis of genomic DNA extracted from dust particles vacuumed from parts of the body image and the lateral edge used for radiocarbon dating. Several plant taxa native to the Mediterranean area were identified as well as species with a primary center of origin in Asia, the Middle East or the Americas but introduced in a historical interval later than the Medieval period. Regarding human mitogenome lineages, our analyses detected sequences from multiple subjects of different ethnic origins, which clustered into a number of Western Eurasian haplogroups, including some known to be typical of Western Europe, the Near East, the Arabian Peninsula and the Indian sub-continent. Such diversity does not exclude a Medieval origin in Europe but it would be also compatible with the historic path followed by the Turin Shroud during its presumed journey from the Near East. Furthermore, the results raise the possibility of an Indian manufacture of the linen cloth.

  20. Uncovering hierarchical data structure in single molecule transport

    Science.gov (United States)

    Wu, Ben H.; Ivie, Jeffrey A.; Johnson, Tyler K.; Monti, Oliver L. A.

    2017-03-01

    Interpretation of single molecule transport data is complicated by the fact that all such data are inherently highly stochastic in nature. Features are often broad, seemingly unstructured and distributed over more than an order of magnitude. However, the distribution contains information necessary for capturing the full variety of processes relevant in nanoscale transport, and a better understanding of its hierarchical structure is needed to gain deeper insight into the physics and chemistry of single molecule electronics. Here, we describe a novel data analysis approach based on hierarchical clustering to aid in the interpretation of single molecule conductance-displacement histograms. The primary purpose of statistically partitioning transport data is to provide avenues for unbiased hypothesis generation in single molecule break junction experiments by revealing otherwise potentially hidden aspects in the conductance data. Our approach is generalizable to the analysis of a wide variety of other single molecule experiments in molecular electronics, as well as in single molecule fluorescence spectroscopy, force microscopy, and ion-channel conductance measurements.

  1. 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

  2. In the Minds of OSCE Examiners: Uncovering Hidden Assumptions

    Science.gov (United States)

    Chahine, Saad; Holmes, Bruce; Kowalewski, Zbigniew

    2016-01-01

    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…

  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 zoonoses awareness in an emerging disease 'hotspot'.

    Science.gov (United States)

    Paige, Sarah B; Malavé, Carly; Mbabazi, Edith; Mayer, Jonathan; Goldberg, Tony L

    2015-03-01

    Emerging infectious diseases from animals pose significant and increasing threats to human health; places of risk are simultaneously viewed as conservation and emerging disease 'hotspots'. The One World/One Health paradigm is an 'assemblage' discipline. Extensive research from the natural and social sciences, as well as public health have contributed to designing surveillance and response policy within the One World/One Health framework. However, little research has been undertaken that considers the lives of those who experience risk in hotspots on a daily basis. As a result, policymakers and practitioners are unable to fully comprehend the social and ecological processes that catalyze cross-species pathogen exchange. This study examined local populations' comprehension of zoonotic disease. From October 2008-May 2009 we collected data from people living on the periphery of Kibale National Park, in western Uganda. We administered a survey to 72 individuals and conducted semi-structured, in-depth interviews with 14 individuals. Results from the survey showed respondents had statistically significant awareness that transmission of diseases from animals was possible compared to those who did not think such transmission was possible (x(2) = 30.68, df = 1, p zoonoses and provided biomedically accurate examples of possible infections and corresponding animal sources (e.g., worm infection from pigs and Ebola from primates). Qualitative data also revealed expectations about the role of the State in managing the prevention of zoonoses from wildlife. As a result of this research, we recommend meaningful discourse with people living at the frontlines of animal contact in emerging disease and conservation hotspots in order to develop informed and relevant zoonoses prevention practices that take into account local knowledge and perceptions.

  5. Uncovering the meaning of 'being safe' in practice.

    Science.gov (United States)

    Smythe, Elizabeth

    2003-04-01

    This paper moves away from the prevalent discourse of competence to consider the meaning of the experience of 'being safe' within the context of childbirth. It offers findings from a doctoral study, informed by the philosophies of Heidegger and Gadamer. Following ethical approval, the data was collected in New Zealand by tape-recorded interviews of 5 midwives, 4 obstetricians, 1 general practitioner and 10 women. The method was informed by van Manen. The findings reveal that in seeking the meaning of being safe one needs to be aware that the unsafety may already be present in the situation. Practitioners may be able to do little to rectify the unsafeness. There is, however, a spirit of safe practice, explicated in this paper, that is likely to make practice as safe as it can possibly be. Wise practitioners are ever mindful that a situation may be or become unsafe, and are always aware of their own limitations.

  6. 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.

  7. 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

  8. Uncovering the basis for nonideal behavior of biological molecules.

    Science.gov (United States)

    Rösgen, Jörg; Pettitt, Bernard Montgomery; Bolen, David Wayne

    2004-11-16

    The molecular origin of the nonideal behavior for concentrated binary solutions of biochemical compounds is examined. The difference between activities expressed in the molar and molal conventions can be large. Considering the range from dilute to concentrated, we show that molar activity coefficients can be represented by simple but rigorous equations involving between one and three parameters only. We derive a universal relationship interconverting the scales of molarity and molality without requiring the density of the solution. The equations are developed from first principles using a statistical thermodynamic theory of molar activity coefficients. It is shown how to express activity coefficients in different concentration scales, and the advantages and disadvantages of using certain scales are discussed and compared with the experimental data. Several classes of biochemically relevant compounds, many of which are naturally occurring osmolytes, are discussed: six saccharides (glucose, xylose, maltose, mannose, raffinose, and sucrose), four polyols (glycerol, mannitol, erythritol, and sorbitol), five amino acids (glycine, alanine, sarcosine, glycine betaine, and proline), and urea. Of the 16 solutes, 10 could be described in terms of a single parameter that is due to pure first-order effects (packing, hydration, or space limitation). The remaining six exhibit significant second-order effects (solute-solute interactions) and require two additional parameters, one typically identified with the volume occupied per solute molecule in the pure solute (crystal or liquid) and the other with a self-association constant. The activity coefficients of the osmolytes roughly display the rank order found with respect to their ability to stabilize proteins. These findings are discussed in terms of the physical principles that give rise to the activity coefficients.

  9. Uncovering Mental Representations with Markov Chain Monte Carlo

    Science.gov (United States)

    Sanborn, Adam N.; Griffiths, Thomas L.; Shiffrin, Richard M.

    2010-01-01

    A key challenge for cognitive psychology is the investigation of mental representations, such as object categories, subjective probabilities, choice utilities, and memory traces. In many cases, these representations can be expressed as a non-negative function defined over a set of objects. We present a behavioral method for estimating these…

  10. Uncovering Discrete Non-Linear Dependence with Information Theory

    Directory of Open Access Journals (Sweden)

    Anton Golub

    2015-04-01

    Full Text Available In this paper, we model discrete time series as discrete Markov processes of arbitrary order and derive the approximate distribution of the Kullback-Leibler divergence between a known transition probability matrix and its sample estimate. We introduce two new information-theoretic measurements: information memory loss and information codependence structure. The former measures the memory content within a Markov process and determines its optimal order. The latter assesses the codependence among Markov processes. Both measurements are evaluated on toy examples and applied on high frequency foreign exchange data, focusing on 2008 financial crisis and 2010/2011 Euro crisis.

  11. Uncovering sensory axonal dysfunction in asymptomatic type 2 diabetic neuropathy.

    Science.gov (United States)

    Sung, Jia-Ying; Tani, Jowy; Chang, Tsui-San; Lin, Cindy Shin-Yi

    2017-01-01

    This study investigated sensory and motor nerve excitability properties to elucidate the development of diabetic neuropathy. A total of 109 type 2 diabetes patients were recruited, and 106 were analyzed. According to neuropathy severity, patients were categorized into G0, G1, and G2+3 groups using the total neuropathy score-reduced (TNSr). Patients in the G0 group were asymptomatic and had a TNSr score of 0. Sensory and motor nerve excitability data from diabetic patients were compared with data from 33 healthy controls. Clinical assessment, nerve conduction studies, and sensory and motor nerve excitability testing data were analyzed to determine axonal dysfunction in diabetic neuropathy. In the G0 group, sensory excitability testing revealed increased stimulus for the 50% sensory nerve action potential (Pmotor excitability only had significantly increased stimulus for the 50% compound motor nerve action potential (Pdevelopment of axonal dysfunction in sensory axons occurred prior to and in a different fashion from motor axons. Additionally, sensory nerve excitability tests can detect axonal dysfunction even in asymptomatic patients. These insights further our understanding of diabetic neuropathy and enable the early detection of sensory axonal abnormalities, which may provide a basis for neuroprotective therapeutic approaches.

  12. Concealment and Uncovering in Moral Philosophy and Moral Practice.

    Science.gov (United States)

    Packer, Martin J.

    1985-01-01

    Draws parallels between MacIntyre's account, in "After Virtue," of contemporary moral theory and practice and the conduct of young adults in conflicts developed over the breaking of an agreement to cooperate. Implications of the similarities and differences are discussed. (Author/RH)

  13. 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. ...

  14. 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

  15. Uncovering the end uses of the rare earth elements

    Energy Technology Data Exchange (ETDEWEB)

    Du, Xiaoyue, E-mail: xiaoyue.du@empa.ch [Swiss Federal Laboratories for Materials Science and Technology (EMPA), Lerchenfeldstrasse 5, 9014 St. Gallen (Switzerland); Yale University, 195 Prospect Street, New Haven CT 06511 (United States); Graedel, T.E. [Yale University, 195 Prospect Street, New Haven CT 06511 (United States)

    2013-09-01

    The rare earth elements (REE) are a group of fifteen elements with unique properties that make them indispensable for a wide variety of emerging and conventional established technologies. However, quantitative knowledge of REE remains sparse, despite the current heightened interest in future availability of the resources. Mining is heavily concentrated in China, whose monopoly position and potential restriction of exports render primary supply vulnerable to short term disruption. We have drawn upon the published literature and unpublished materials in different languages to derive the first quantitative annual domestic production by end use of individual rare earth elements from 1995 to 2007. The information is illustrated in Sankey diagrams for the years 1995 and 2007. Other years are available in the supporting information. Comparing 1995 and 2007, the production of the rare earth elements in China, Japan, and the US changed dramatically in quantities and structure. The information can provide a solid foundation for industries, academic institutions and governments to make decisions and develop strategies. - Highlights: • We have derived the first quantitative end use information of the rare earths (REE). • The results are for individual REE from 1995 to 2007. • The end uses of REE in China, Japan, and the US changed dramatically in quantities and structure. • This information can provide solid foundation for decision and strategy making.

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

    Science.gov (United States)

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

    2016-02-02

    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.

  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.

  18. 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.

  19. 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…

  20. Uncovering the footprint of former ice streams off Antarctica

    Science.gov (United States)

    COHIMAR/SEDANO Scientific Party

    Antarctic ice sheets and ice caps have been expanding and contracting following global climatic cycles. The last time the Antarctic ice cover peaked, at least in Western Antarctica, was ca. 21 ky ago during the Last Glacial Maximum (LGM). The strong warming (nearly 2.8°C) over the past 50 years, and the yearly recent collapse of limited portions (hundreds to a few thousands of square miles per event) of ice shelves around the Antarctic Peninsula have brought to the headlines the debate about the potential collapse of the West Antarctic Ice Sheet (WAIS) in the near future under the influence of global warming.Such a catastrophe would substantially contribute to global sea level rise (a resulting 5 m increase is expected); alter water mass conditions, circulation, and productivity around Antarctica and in the world ocean; and modify the Earth's climate.The economic,social, and ecological impacts of these changes would depend greatly on the rate at which they might take place [Bindschadler, 1998” . A detailed knowledge of the past extent of ice sheets and the timing of their advances and retreats thus becomes essential to quantify the rates of change and to properly assess the future stability of the WAIS and nearby ice caps. The stability of ice sheets is largely dependent on ice drainage, which mostly occurs via ice streaming along glacial troughs. Ice streams are thus a key element to solve the puzzle linking ice sheet stability, sea level rise, and climate change at a global scale.

  1. 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.

  2. UNCOVERING THEIR STORIES: THE RUBBLE OF MEMORY AND BOMBING WAR

    OpenAIRE

    Rasch, William; Universidad de Indiana

    2006-01-01

    In this brilliant essay, WILLIAM RASCH traces current ideas about global war to their first installment in the post-war climate of occupied Germany. RASCH takes issue, in particular, with the current transformation in the nature of war —so called zero casualties war or war at a distance—, hailed as the most important transformation in the field of international relations and international law in the 21st century, and rediscovers its articulation with the carpet bombing (bombenkrieg) of World ...

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

    DEFF Research Database (Denmark)

    Krystallis Krontalis, Athanasios

    2013-01-01

    ; and second within product attributes, switching among family brands for smaller brands. Social implications – These findings have profound implications for the development of anti-smoking policy in terms of the exact functioning of product differentiation as part of the tobacco industry’s strategy. Public......Purpose – The purpose of this paper is to examine the importance of tobacco differentiation attributes (i.e. nicotine and tar content, length, flavor and thickness) in market performance and loyalty levels of brands. Design/methodology/approach – The study adopts a stochastic approach to measure...... brand loyalty at the attribute level using the Dirichlet model as a benchmark tool. Data based on the Juster Probability Scale were collected from a sample of n ¼ 155 young smokers in Iceland. Findings – Product differentiation strategies operate differently. Light nicotine and tar content encourages...

  4. 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.

  5. Planetary Nebula Candidates Uncovered with the HASH Research Platform

    CERN Document Server

    Fragkou, Vasiliki; Frew, David; Parker, Quentin

    2016-01-01

    A detailed examination of new high quality radio catalogues (e.g. Cornish) in combination with available mid-infrared (MIR) satellite imagery (e.g. Glimpse) has allowed us to find 70 new planetary nebula (PN) candidates based on existing knowledge of their typical colors and fluxes. To further examine the nature of these sources, multiple diagnostic tools have been applied to these candidates based on published data and on available imagery in the HASH (Hong Kong/ AAO/ Strasbourg H{\\alpha} planetary nebula) research platform. Some candidates have previously-missed optical counterparts allowing for spectroscopic follow-up. Indeed, the single object spectroscopically observed so far has turned out to be a bona fide PN.

  6. Uncovering Adiponectin Replenishing Property of Sujiaonori Algal Biomaterial in Humans

    Science.gov (United States)

    Ngatu, Nlandu Roger; Ikeda, Mitsunori; Watanabe, Hiroyuki; Tanaka, Mamoru; Inoue, Masataka; Kanbara, Sakiko; Nojima, Sayumi

    2017-01-01

    The replenishment of adiponectin—an adipocyte-derived hormone with salutary health effects—has recently been proposed as a new approach to treat hypertension, also ameliorate cardiovascular and metabolic risks. We conducted a prospective placebo-controlled, non-randomized and investigator-blinded dietary intervention study to evaluate the health effects of dietary intake of Sujiaonori (Ulva/Enteromorpha prolifera Müller) algal biomaterial (SBM), especially on adiponectin production, blood pressure (BP), and body mass index (BMI) in human subjects. Participants (N = 32) were divided into two equally sized groups (n = 16 for each group): SBM group (subjects supplemented with 3 g SBM powder twice a day during meal) and the control group (subjects who took 3 g of a supplement made of 70% corn starch powder and 30% spinach twice a day) for four weeks. Two health survey questionnaires (dietary and current health questionnaires) were completed anonymously, saliva sampling was done for adiponectin measurement by ELISA, and blood pressure (BP) and anthropometric parameters were measured at baseline and four weeks later. Student paired t-test was performed to compare baseline and post-intervention data on outcome variables between the two study groups. Results showed a 2.24-fold increase in adiponectin level in SBM group (2.81 and 6.26 ng/mL at baseline and at the end of study, respectively) (p 0.05). In SBM subjects, an improvement of BP profile was noted with a significant decrease in systolic BP (p < 0.01). A positive correlation was found between SBM supplementation and adiponectin level, whereas an inverse correlation was noted between SBM supplementation and blood pressure, and also BMI. These findings suggest that SBM-increased adiponectin level and improved BP in a sample of Japanese young adults, and has the potential to improve blood pressure in humans. PMID:28208744

  7. 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.

  8. 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.

  9. 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.

  10. Uncovering Web search strategies in South African higher education

    Directory of Open Access Journals (Sweden)

    Surika Civilcharran

    2016-04-01

    Full Text Available Background: In spite of the enormous amount of information available on the Web and the fact that search engines are continuously evolving to enhance the search experience, students are nevertheless faced with the difficulty of effectively retrieving information. It is, therefore, imperative for the interaction between students and search tools to be understood and search strategies to be identified, in order to promote successful information retrieval.Objectives: This study identifies the Web search strategies used by postgraduate students and forms part of a wider study into information retrieval strategies used by postgraduate students at the University of KwaZulu-Natal (UKZN, Pietermaritzburg campus, South Africa. Method: Largely underpinned by Thatcher’s cognitive search strategies, the mixed-methods approach was utilised for this study, in which questionnaires were employed in Phase 1 and structured interviews in Phase 2. This article reports and reflects on the findings of Phase 2, which focus on identifying the Web search strategies employed by postgraduate students. The Phase 1 results were reported in Civilcharran, Hughes and Maharaj (2015.Results: Findings reveal the Web search strategies used for academic information retrieval. In spite of easy access to the invisible Web and the advent of meta-search engines, the use of Web search engines still remains the preferred search tool. The UKZN online library databases and especially the UKZN online library, Online Public Access Catalogue system, are being underutilised.Conclusion: Being ranked in the top three percent of the world’s universities, UKZN is investing in search tools that are not being used to their full potential. This evidence suggests an urgent need for students to be trained in Web searching and to have a greater exposure to a variety of search tools. This article is intended to further contribute to the design of undergraduate training programmes in order to deal with the information retrieval frustrations of novice users.

  11. Uncovering sensory axonal dysfunction in asymptomatic type 2 diabetic neuropathy

    Science.gov (United States)

    Sung, Jia-Ying; Tani, Jowy; Chang, Tsui-San; Lin, Cindy Shin-Yi

    2017-01-01

    This study investigated sensory and motor nerve excitability properties to elucidate the development of diabetic neuropathy. A total of 109 type 2 diabetes patients were recruited, and 106 were analyzed. According to neuropathy severity, patients were categorized into G0, G1, and G2+3 groups using the total neuropathy score-reduced (TNSr). Patients in the G0 group were asymptomatic and had a TNSr score of 0. Sensory and motor nerve excitability data from diabetic patients were compared with data from 33 healthy controls. Clinical assessment, nerve conduction studies, and sensory and motor nerve excitability testing data were analyzed to determine axonal dysfunction in diabetic neuropathy. In the G0 group, sensory excitability testing revealed increased stimulus for the 50% sensory nerve action potential (P<0.05), shortened strength-duration time constant (P<0.01), increased superexcitability (P<0.01), decreased subexcitability (P<0.05), decreased accommodation to depolarizing current (P<0.01), and a trend of decreased accommodation to hyperpolarizing current in threshold electrotonus. All the changes progressed into G1 (TNSr 1–8) and G2+3 (TNSr 9–24) groups. In contrast, motor excitability only had significantly increased stimulus for the 50% compound motor nerve action potential (P<0.01) in the G0 group. This study revealed that the development of axonal dysfunction in sensory axons occurred prior to and in a different fashion from motor axons. Additionally, sensory nerve excitability tests can detect axonal dysfunction even in asymptomatic patients. These insights further our understanding of diabetic neuropathy and enable the early detection of sensory axonal abnormalities, which may provide a basis for neuroprotective therapeutic approaches. PMID:28182728

  12. 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.

  13. 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.

  14. Uncovering Molecular Bases Underlying Bone Morphogenetic Protein Receptor Inhibitor Selectivity.

    Directory of Open Access Journals (Sweden)

    Abdelaziz Alsamarah

    Full Text Available Abnormal alteration of bone morphogenetic protein (BMP signaling is implicated in many types of diseases including cancer and heterotopic ossifications. Hence, small molecules targeting BMP type I receptors (BMPRI to interrupt BMP signaling are believed to be an effective approach to treat these diseases. However, lack of understanding of the molecular determinants responsible for the binding selectivity of current BMP inhibitors has been a big hindrance to the development of BMP inhibitors for clinical use. To address this issue, we carried out in silico experiments to test whether computational methods can reproduce and explain the high selectivity of a small molecule BMP inhibitor DMH1 on BMPRI kinase ALK2 vs. the closely related TGF-β type I receptor kinase ALK5 and vascular endothelial growth factor receptor type 2 (VEGFR2 tyrosine kinase. We found that, while the rigid docking method used here gave nearly identical binding affinity scores among the three kinases; free energy perturbation coupled with Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD simulations reproduced the absolute binding free energies in excellent agreement with experimental data. Furthermore, the binding poses identified by FEP/H-REMD led to a quantitative analysis of physical/chemical determinants governing DMH1 selectivity. The current work illustrates that small changes in the binding site residue type (e.g. pre-hinge region in ALK2 vs. ALK5 or side chain orientation (e.g. Tyr219 in caALK2 vs. wtALK2, as well as a subtle structural modification on the ligand (e.g. DMH1 vs. LDN193189 will cause distinct binding profiles and selectivity among BMP inhibitors. Therefore, the current computational approach represents a new way of investigating BMP inhibitors. Our results provide critical information for designing exclusively selective BMP inhibitors for the development of effective pharmacotherapy for diseases caused by aberrant BMP signaling.

  15. 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...

  16. Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus.

    Science.gov (United States)

    Andersen, Kristian G; Shapiro, B Jesse; Matranga, Christian B; Sealfon, Rachel; Lin, Aaron E; Moses, Lina M; Folarin, Onikepe A; Goba, Augustine; Odia, Ikponmwonsa; Ehiane, Philomena E; Momoh, Mambu; England, Eleina M; Winnicki, Sarah; Branco, Luis M; Gire, Stephen K; Phelan, Eric; Tariyal, Ridhi; Tewhey, Ryan; Omoniwa, Omowunmi; Fullah, Mohammed; Fonnie, Richard; Fonnie, Mbalu; Kanneh, Lansana; Jalloh, Simbirie; Gbakie, Michael; Saffa, Sidiki; Karbo, Kandeh; Gladden, Adrianne D; Qu, James; Stremlau, Matthew; Nekoui, Mahan; Finucane, Hilary K; Tabrizi, Shervin; Vitti, Joseph J; Birren, Bruce; Fitzgerald, Michael; McCowan, Caryn; Ireland, Andrea; Berlin, Aaron M; Bochicchio, James; Tazon-Vega, Barbara; Lennon, Niall J; Ryan, Elizabeth M; Bjornson, Zach; Milner, Danny A; Lukens, Amanda K; Broodie, Nisha; Rowland, Megan; Heinrich, Megan; Akdag, Marjan; Schieffelin, John S; Levy, Danielle; Akpan, Henry; Bausch, Daniel G; Rubins, Kathleen; McCormick, Joseph B; Lander, Eric S; Günther, Stephan; Hensley, Lisa; Okogbenin, Sylvanus; Schaffner, Stephen F; Okokhere, Peter O; Khan, S Humarr; Grant, Donald S; Akpede, George O; Asogun, Danny A; Gnirke, Andreas; Levin, Joshua Z; Happi, Christian T; Garry, Robert F; Sabeti, Pardis C

    2015-08-13

    The 2013-2015 West African epidemic of Ebola virus disease (EVD) reminds us of how little is known about biosafety level 4 viruses. Like Ebola virus, Lassa virus (LASV) can cause hemorrhagic fever with high case fatality rates. We generated a genomic catalog of almost 200 LASV sequences from clinical and rodent reservoir samples. We show that whereas the 2013-2015 EVD epidemic is fueled by human-to-human transmissions, LASV infections mainly result from reservoir-to-human infections. We elucidated the spread of LASV across West Africa and show that this migration was accompanied by changes in LASV genome abundance, fatality rates, codon adaptation, and translational efficiency. By investigating intrahost evolution, we found that mutations accumulate in epitopes of viral surface proteins, suggesting selection for immune escape. This catalog will serve as a foundation for the development of vaccines and diagnostics. VIDEO ABSTRACT.

  17. Uncovering the forces between nucleosomes using DNA origami

    Science.gov (United States)

    Funke, Jonas J.; Ketterer, Philip; Lieleg, Corinna; Schunter, Sarah; Korber, Philipp; Dietz, Hendrik

    2016-01-01

    Revealing the energy landscape for nucleosome association may contribute to the understanding of higher-order chromatin structures and their impact on genome regulation. We accomplish this in a direct measurement by integrating two nucleosomes into a DNA origami–based force spectrometer, which enabled subnanometer-resolution measurements of nucleosome-nucleosome distance frequencies via single-particle electron microscopy imaging. From the data, we derived the Boltzmann-weighted distance-dependent energy landscape for nucleosome pair interactions. We find a shallow but long-range (~6 nm) attractive nucleosome pair potential with a minimum of −1.6 kcal/mol close to direct contact distances. The relative nucleosome orientation had little influence, but histone H4 acetylation or removal of histone tails drastically decreased the interaction strength. Because of the weak and shallow pair potential, higher-order nucleosome assemblies will be compliant and experience dynamic shape fluctuations in the absence of additional cofactors. Our results contribute to a more accurate description of chromatin and our force spectrometer provides a powerful tool for the direct and high-resolution study of molecular interactions using imaging techniques. PMID:28138524

  18. 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...

  19. 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).

  20. Finding the Balance: Uncovering Resilience in the Veterinary Literature.

    Science.gov (United States)

    Cake, Martin A; McArthur, Michelle M; Matthew, Susan M; Mansfield, Caroline F

    2017-01-01

    Resilience is an issue of emerging importance in veterinary education and research, as in other professional contexts. The aim of this study was to perform an appraisal of how resilience is portrayed in the contemporary (1995-present) research and education literature around veterinary mental health, and to attempt a provisional synthesis informing a conception of resilience in the veterinary context. Qualitative analysis of the literature (59 sources included) revealed a dominant emphasis on mental health problems, particularly stress, which outweighs and potentially obscures complementary approaches to well-being and resilience. We found the construct of resilience underdeveloped in the veterinary literature and in need of further research, but provide a preliminary synthesis of key themes emerging from the current literature (emotional competence, motivation, personal resources, social support, organizational culture, life balance, and well-being strategies). We advocate for greater balance between complementary perspectives in veterinary mental health education and research, and propose that an increasing focus on resilience (here endorsed as a dynamic and multi-dimensional process involving personal and contextual resources, strategies, and outcomes) will help to address this balance.

  1. 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.

  2. Tfh cell differentiation: missing Stat3 uncovers interferons' interference.

    Science.gov (United States)

    Edelmann, Stephanie L; Heissmeyer, Vigo

    2014-03-20

    Viral infection induces a number of cytokines that shape T cell responses. In this issue of Immunity, Ray et al. (2014) describe how CD4(+) T cells decide on T follicular helper (Tfh) or T helper 1 (Th1) cell skewed gene expression during acute viral infection.

  3. Uncovering representations of sleep-associated hippocampal ensemble spike activity

    Science.gov (United States)

    Chen, Zhe; Grosmark, Andres D.; Penagos, Hector; Wilson, Matthew A.

    2016-08-01

    Pyramidal neurons in the rodent hippocampus exhibit spatial tuning during spatial navigation, and they are reactivated in specific temporal order during sharp-wave ripples observed in quiet wakefulness or slow wave sleep. However, analyzing representations of sleep-associated hippocampal ensemble spike activity remains a great challenge. In contrast to wake, during sleep there is a complete absence of animal behavior, and the ensemble spike activity is sparse (low occurrence) and fragmental in time. To examine important issues encountered in sleep data analysis, we constructed synthetic sleep-like hippocampal spike data (short epochs, sparse and sporadic firing, compressed timescale) for detailed investigations. Based upon two Bayesian population-decoding methods (one receptive field-based, and the other not), we systematically investigated their representation power and detection reliability. Notably, the receptive-field-free decoding method was found to be well-tuned for hippocampal ensemble spike data in slow wave sleep (SWS), even in the absence of prior behavioral measure or ground truth. Our results showed that in addition to the sample length, bin size, and firing rate, number of active hippocampal pyramidal neurons are critical for reliable representation of the space as well as for detection of spatiotemporal reactivated patterns in SWS or quiet wakefulness.

  4. 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.

  5. 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.

  6. Uncovering deep mysteries: the underwater life of an amphibious louse.

    Science.gov (United States)

    Leonardi, Maria Soledad; Aznar, F Javier; Crespo, Enrique A; Lazzari, Claudio R

    2014-12-01

    Despite the incredible success of insects in colonizing almost every habitat, they remain virtually absent in one major environment--the open sea. A variety of hypotheses have been raised to explain why just a few insect species are present in the ocean, but none of them appears to be fully explanatory. Lice belonging to the family Echinophthiriidae are ectoparasites on different species of pinnipeds and river otters, i.e. they have amphibious hosts, who regularly perform long excursions into the open sea reaching depths of hundreds of meters (thousands of feets). Consequently, lice must be able to support not only changes in their surrounding media, but also extreme variations in hydrostatic pressure as well as breathing in a low oxygen atmosphere. In order to shed some light on the way lice can survive during the diving excursions of their hosts, we have performed a series of experiments to test the survival capability of different instars of Antarctophthirus microchir (Phthiraptera: Anoplura) from South American sea lions Otaria flavescens, when submerged into seawater. These experiments were aimed at analyzing: (a) immersion tolerance along the louse life; (b) lice's ability to obtain oxygen from seawater; (c) physiological responses and mechanisms involved in survival underwater. Our experiments showed that the forms present in non-diving pups--i.e. eggs and first-instar nymphs--were unable to tolerate immersion in water, while following instars and adults, all usually found in diving hosts, supported it very well. Furthermore, as long as the level of oxygen dissolved in water was higher, the lice survival capability underwater increased, and the recovery period after returning to air declined. These results are discussed in relation to host ecology, host exploitation and lice functional morphology.

  7. 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.

  8. 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.

  9. Human Rights Disclosure Litigation: Uncovering Invisible Medical Records

    Directory of Open Access Journals (Sweden)

    Ena Chadha

    2010-02-01

    Full Text Available This article examines disclosure process and disclosure jurisprudence in human rights litigation. Based on a study of a decade of human rights disclosure rulings from across the country, this article finds that there have been increasing numbers of disclosure demands in human rights litigation and a substantial number of cases in which the disclosure pertained to personal documents and medical records of human rights claimants. While disclosure applications were adjudicated according to a relevance-confidentiality framework used ostensibly to balance privacy and procedural fairness, in reality significant personal information was disclosed based on assumptions of relevancy and under the guise of neutral labels. A closer examination of the different types of materials sought for disclosure in three employment human rights cases reveals that the medical core of certain records are rendered invisible and thereby open for access when tribunals neglect to look behind document categories and titles. The article concludes that there is heightened vulnerability on the part of persons with disabilities as targets of disclosure demands for their confidential medical information. Cet article examine le processus de divulgation et la jurisprudence sur la divulgation dans le domaine de litiges en rapport avec les droits de la personne. Basé sur une étude d’une dizaine d’années de décisions partout au pays au sujet de la divulgation dans le domaine des droits de la personne, cet article conclut que le nombre de demandes de divulgation dans le domaine de litiges en rapport avec les droits de la personne augmente et que dans un nombre considérable de cas, la divulgation avait rapport à des documents personnels et des dossiers médicaux des réclamants de droits de la personne. Quoique on ait statué au sujet de requêtes de divulgation selon un cadre de pertinence/confidentialité utilisé de toute apparence pour maintenir un équilibre entre le respect de la vie privée et l’équité de la procédure, en réalité des renseignements personnels significatifs ont été divulgués basé sur des suppositions de pertinence et sous l’apparence d’étiquettes neutres. En regardant de plus près les diverses sortes de matériaux dont la divulgation a été demandée dans trois cas de droits de la personne dans le domaine de l’emploi, on trouve que la partie centrale médicale de certains documents ont été rendus invisibles les ouvrant ainsi à l’accès lorsque les tribunaux négligent de regarder au-delà des catégories de documents et des titres. L’auteur conclut que les personnes ayant des déficiences sont plus vulnérables en tant que cibles de demandes de divulgation de leurs renseignements médicaux confidentiels.

  10. 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.

  11. Genome-Wide Enzyme Annotation with Precision Control: Catalytic Families (CatFam) Databases

    Science.gov (United States)

    2008-01-01

    2.4.1.21 ( starch synthase using ADP-glucose) predicted for proteins SSG1_HORVU and SSG1_MANES are sub- sumed by EC 2.4.1.242 ( starch synthase using...glucan glucanohydrolase [Cyclodextrin glucanotransferase] SSG1_HORVUf 2.4.1.21 2.4.1.242 Starch synthase that uses either UDP- or ADP- glucose [ Starch ...exonuclease [DNA-directed DNA polymerase] MGTA_THENE 3.2.1.1 2.4.1.25 14 4-a-glucanotransferase [a- amylase ] GUX6_HUMIN 3.2.1.4 3.2.1.91 12 Exoglucanase

  12. EVALUACIÓN DE LA EXPRESIÓN DE GENES IMPLICADOS EN LA BIOSÍNTESIS DE ALMIDÓN EN DIFERENTES VARIEDADES DE YUCA

    Directory of Open Access Journals (Sweden)

    Simón Pedro Cortés Sierra

    2014-10-01

    Full Text Available Las raíces almacenadoras de yuca representan una fuente importante de almidón. La ruta metabólica del almidón ha sido reconstruida recientemente en yuca gracias a la liberación de la secuencia completa de su genoma. En este estudio se evaluó la expresión de los genes que codifican para las enzimas Pululanasa, Isoamilasa, α-amilasa, Enzima Desproporcionante, ADP-glucosa pirofoforilasa, Almidón sintasa unida al gránulo, Enzima ramificante del almidón y Sintasa soluble del almidón, en las raíces almacenadoras de plantas de 5 y 11 meses de edad, en un grupo de cinco variedades de yuca. Se evidenciaron diferencias importantes en la expresión de estos genes entre las variedades evaluadas y entre los dos tiempos. Las variedades CM523-7 y SM1219-2 presentaron uno de los niveles más altos de expresión para los genes ADP-glucosa pirofoforilasa y Almidón sintasa unida al gránulo mientras que el gen para α-amilasa fue el más bajo en estas dos variedades. Aunque  la variedad TMS60444 presentó niveles de expresión similares en genes implicados en la síntesis de almidón, fue la que presentó el mayor nivel de expresión de la α-amilasa. Estos datos se pueden correlacionar con el relativo bajo contenido de materia seca en esta variedad. Los datos de expresión génica presentados en este trabajo permitirán complementar información sobre actividad enzimática con miras a identificar los elementos más importantes en la acumulación diferencial de almidón entre variedades de yuca.ABSTRACTCassava storage roots represent an important starch source. Recently, the starch metabolic pathway in cassava has been reconstructed thanks to the full release of its genome. In this study gene expression was evaluated for genes coding Pullulanase, Isoamylase, α-amylase, Deproportionating enzyme, ADP-glucose pyrophosphorylase, Granule bound starch synthase, Starch branching enzyme and Soluble starch synthase, in cassava storage roots 5 and 11 months

  13. Effects of alginate-derived oligosaccharides synergistic urea on the photosynthetic characteristics and accumulation of carbon metabolites in rice%海藻寡糖增效尿素对水稻光合特性及碳代谢产物积累的影响

    Institute of Scientific and Technical Information of China (English)

    张运红; 孙克刚; 杜君; 和爱玲; 张起义

    2016-01-01

    采用盆栽试验,研究了海藻寡糖增效尿素对水稻光合特性、碳代谢关键酶活性及相关产物积累的影响。结果表明,和普通尿素相比,海藻寡糖增效尿素处理的水稻净光合速率( Pn )、气孔导度( Gs )、胞间CO2浓度(Ci)和水分利用效率(WUE)有所增加,气孔限制值(Ls)有所降低,叶绿素含量和核酮糖-1,5-二磷酸羧化加氧酶(Rubisco)活性显著提高。拔节期、齐穗期和成熟期叶中和籽粒中蔗糖磷酸合成酶(SPS)、蔗糖合成酶( SUS)和腺苷二磷酸葡萄糖焦磷酸化酶( ADPase)活性显著增强,从而促进籽粒中蔗糖和淀粉积累;地上部和地下部生物量在4个生育期也均显著增加,籽粒产量显著提高,其中较对照增加9.32%,较普通尿素处理增加3.94%。%Pot experiments were used to study the effects of alginate-derived oligosaccharide ( ADO) synergistic urea on photo-synthetic characteristics, key enzymes activities and carbon metabolites accumulation of rice ( Oryza. Sativa L. ) . The results showed that net photosynthetic rate ( Pn ) , stomatal conductance ( Gs ) , intercellular CO2 concentration ( Ci ) and water use efficiency ( WUE) of rice under ADO synergistic urea treatment were increased, and stomatal limitation value ( Ls ) was de-creased, compared with ordinary urea. Chlorophyll content and ribulose-1, 5-bisphosphate-caboxylase ( Rubisco) activity were also significantly raised. At booting, full heading and maturing stages, sucrose phosphate synthase ( SPS) , sucrose syn-thase (SUS) and ADP-glucose pyrophosphorylase (ADPase) activity in leaves or grain of rice were significantly enhanced, thus contributing to the accumulation of sucrose and starch in grain. Aboveground and belowground biomass were also signifi-cantly increased at all the four growth stages. Rice yield of ADO synergistic urea treatment was significantly raised by 9. 32%compared with the control, and was higher than that of

  14. Primer Dependent and Independent Forms of Soluble Starch Synthetase from Developing Barley Endosperms

    DEFF Research Database (Denmark)

    Kreis, M.

    1980-01-01

    The activity of soluble starch synthetase (ADP-glucose: agr-1,4-glucan agr-4-glucosyltransferase) in the non-purified extract from 16 day-old Bomi barley endosperms (Hordeum vulgare L.) was low and the reaction was non-linear when plotted against protein concentration. Starch synthetase was purif...

  15. Comparison of ixekizumab with etanercept or placebo in moderate-to-severe psoriasis (UNCOVER-2 and UNCOVER-3): results from two phase 3 randomised trials

    NARCIS (Netherlands)

    Griffiths, C.E.; Reich, K.; Lebwohl, M.; Kerkhof, P. van de; Paul, C.; Menter, A.; Cameron, G.S.; Erickson, J.; Zhang, L.; Secrest, R.J.; Ball, S.; Braun, D.K.; Osuntokun, O.O.; Heffernan, M.P.; Nickoloff, B.J.; Papp, K.

    2015-01-01

    BACKGROUND: Ixekizumab is a humanised monoclonal antibody against the proinflammatory cytokine interleukin 17A. We report two studies of ixekizumab compared with placebo or etanercept to assess the safety and efficacy of specifically targeting interleukin 17A in patients with widespread moderate-to-

  16. Read clouds uncover variation in complex regions of the human genome.

    Science.gov (United States)

    Bishara, Alex; Liu, Yuling; Weng, Ziming; Kashef-Haghighi, Dorna; Newburger, Daniel E; West, Robert; Sidow, Arend; Batzoglou, Serafim

    2015-10-01

    Although an increasing amount of human genetic variation is being identified and recorded, determining variants within repeated sequences of the human genome remains a challenge. Most population and genome-wide association studies have therefore been unable to consider variation in these regions. Core to the problem is the lack of a sequencing technology that produces reads with sufficient length and accuracy to enable unique mapping. Here, we present a novel methodology of using read clouds, obtained by accurate short-read sequencing of DNA derived from long fragment libraries, to confidently align short reads within repeat regions and enable accurate variant discovery. Our novel algorithm, Random Field Aligner (RFA), captures the relationships among the short reads governed by the long read process via a Markov Random Field. We utilized a modified version of the Illumina TruSeq synthetic long-read protocol, which yielded shallow-sequenced read clouds. We test RFA through extensive simulations and apply it to discover variants on the NA12878 human sample, for which shallow TruSeq read cloud sequencing data are available, and on an invasive breast carcinoma genome that we sequenced using the same method. We demonstrate that RFA facilitates accurate recovery of variation in 155 Mb of the human genome, including 94% of 67 Mb of segmental duplication sequence and 96% of 11 Mb of transcribed sequence, that are currently hidden from short-read technologies.

  17. Fish genomes : a powerful tool to uncover new functional elements in vertebrates

    NARCIS (Netherlands)

    Stupka, Elia

    2011-01-01

    This thesis spans several years of work dedicated to understanding fish genomes. In the first chapter it describes the genome of the first fish for which the entire genome was sequenced through a large-scale international project, Fugu rubripes. the pufferfish. In particular, it highlights how this

  18. Uncovering dispersion properties in semiconductor waveguides to study photon-pair generation

    CERN Document Server

    Laiho, K; Schlager, A; Suchomel, H; Höfling, S; Kamp, M; Schneider, C; Weihs, G

    2016-01-01

    We investigate the dispersion properties of ridge Bragg-reflection waveguides to deduce their phasematching characteristics. These are crucial for exploiting them as sources of parametric down-conversion (PDC). In order to estimate the phasematching bandwidth we first determine the group refractive indices of the interacting modes via Fabry-Perot experiments in two distant wavelength regions. Second, by measuring the spectra of the emitted PDC photons we gain access to their group index dispersion. Our results offer a simple approach for determining the PDC process parameters in the spectral domain and provide an important feedback for designing such sources, especially in the broadband case.

  19. Uncovering curvilinear relationships between conscientiousness and job performance: how theoretically appropriate measurement makes an empirical difference.

    Science.gov (United States)

    Carter, Nathan T; Dalal, Dev K; Boyce, Anthony S; O'Connell, Matthew S; Kung, Mei-Chuan; Delgado, Kristin M

    2014-07-01

    The personality trait of conscientiousness has seen considerable attention from applied psychologists due to its efficacy for predicting job performance across performance dimensions and occupations. However, recent theoretical and empirical developments have questioned the assumption that more conscientiousness always results in better job performance, suggesting a curvilinear link between the 2. Despite these developments, the results of studies directly testing the idea have been mixed. Here, we propose this link has been obscured by another pervasive assumption known as the dominance model of measurement: that higher scores on traditional personality measures always indicate higher levels of conscientiousness. Recent research suggests dominance models show inferior fit to personality test scores as compared to ideal point models that allow for curvilinear relationships between traits and scores. Using data from 2 different samples of job incumbents, we show the rank-order changes that result from using an ideal point model expose a curvilinear link between conscientiousness and job performance 100% of the time, whereas results using dominance models show mixed results, similar to the current state of the literature. Finally, with an independent cross-validation sample, we show that selection based on predicted performance using ideal point scores results in more favorable objective hiring outcomes. Implications for practice and future research are discussed.

  20. Uncovering the Affective Core of Conscientiousness: The Role of Self-Conscious Emotions

    OpenAIRE

    Fayard, Jennifer V.; Roberts, Brent W.; Robins, Richard W.; Watson, David

    2012-01-01

    We conducted 3 studies to test the idea that guilt is a key affective component of Conscientiousness and that it can account for the relation between Conscientiousness and negative affect. Study 1 used meta-analysis to show that Conscientiousness was associated with specific emotions and overall negative affect but was most strongly associated with guilt. Conscientiousness was negatively related to guilt experience but positively related to guilt proneness. Also, guilt experience mediated the...

  1. Uncovering the affective core of conscientiousness: the role of self-conscious emotions.

    Science.gov (United States)

    Fayard, Jennifer V; Roberts, Brent W; Robins, Richard W; Watson, David

    2012-02-01

    We conducted 3 studies to test the idea that guilt is a key affective component of Conscientiousness and that it can account for the relation between Conscientiousness and negative affect. Study 1 used meta-analysis to show that Conscientiousness was associated with specific emotions and overall negative affect but was most strongly associated with guilt. Conscientiousness was negatively related to guilt experience but positively related to guilt proneness. Also, guilt experience mediated the relation between Conscientiousness and negative affect. Study 2 (N = 142) examined the relation between facets of Conscientiousness and guilt. We replicated results from Study 1 and showed that the relation between Conscientiousness and guilt was not due to overlap with Extraversion and Neuroticism. Study 3 (n = 176) examined the interplay between Conscientiousness and guilt on grades in a short-term longitudinal study. These studies showed that Conscientiousness is primarily related to guilt and highlighted the importance of examining the emotional substrate of Conscientiousness.

  2. Isothermal titration calorimetry uncovers substrate promiscuity of bicupin oxalate oxidase from Ceriporiopsis subvermispora

    Directory of Open Access Journals (Sweden)

    Hassan Rana

    2016-03-01

    Full Text Available Isothermal titration calorimetry (ITC may be used to determine the kinetic parameters of enzyme-catalyzed reactions when neither products nor reactants are spectrophotometrically visible and when the reaction products are unknown. We report here the use of the multiple injection method of ITC to characterize the catalytic properties of oxalate oxidase (OxOx from Ceriporiopsis subvermispora (CsOxOx, a manganese dependent enzyme that catalyzes the oxygen-dependent oxidation of oxalate to carbon dioxide in a reaction coupled with the formation of hydrogen peroxide. CsOxOx is the first bicupin enzyme identified that catalyzes this reaction. The multiple injection ITC method of measuring OxOx activity involves continuous, real-time detection of the amount of heat generated (dQ during catalysis, which is equal to the number of moles of product produced times the enthalpy of the reaction (ΔHapp. Steady-state kinetic constants using oxalate as the substrate determined by multiple injection ITC are comparable to those obtained by a continuous spectrophotometric assay in which H2O2 production is coupled to the horseradish peroxidase-catalyzed oxidation of 2,2′-azinobis-(3-ethylbenzthiazoline-6-sulfonic acid and by membrane inlet mass spectrometry. Additionally, we used multiple injection ITC to identify mesoxalate as a substrate for the CsOxOx-catalyzed reaction, with a kinetic parameters comparable to that of oxalate, and to identify a number of small molecule carboxylic acid compounds that also serve as substrates for the enzyme.

  3. Using Caenorhabditis elegans to Uncover Conserved Functions of Omega-3 and Omega-6 Fatty Acids.

    Science.gov (United States)

    Watts, Jennifer L

    2016-02-02

    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.

  4. Using Caenorhabditis elegans to Uncover Conserved Functions of Omega-3 and Omega-6 Fatty Acids

    OpenAIRE

    Watts, Jennifer L.

    2016-01-01

    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 a...

  5. Single cell analysis of Vibrio harveyi uncovers functional heterogeneity in response to quorum sensing signals

    Directory of Open Access Journals (Sweden)

    Anetzberger Claudia

    2012-09-01

    Full Text Available Abstract Background Vibrio harveyi and closely related species are important pathogens in aquaculture. A complex quorum sensing cascade involving three autoinducers controls bioluminescence and several genes encoding virulence factors. Single cell analysis of a V. harveyi population has already indicated intercellular heterogeneity in the production of bioluminescence. This study was undertaken to analyze the expression of various autoinducer-dependent genes in individual cells. Results Here we used reporter strains bearing promoter::gfp fusions to monitor the induction/repression of three autoinducer-regulated genes in wild type conjugates at the single cell level. Two genes involved in pathogenesis - vhp and vscP, which code for an exoprotease and a component of the type III secretion system, respectively, and luxC (the first gene in the lux operon were chosen for analysis. The lux operon and the exoprotease gene are induced, while vscP is repressed at high cell density. As controls luxS and recA, whose expression is not dependent on autoinducers, were examined. The responses of the promoter::gfp fusions in individual cells from the same culture ranged from no to high induction. Importantly, simultaneous analysis of two autoinducer induced phenotypes, bioluminescence (light detection and exoproteolytic activity (fluorescence of a promoter::gfp fusion, in single cells provided evidence for functional heterogeneity within a V. harveyi population. Conclusions Autoinducers are not only an indicator for cell density, but play a pivotal role in the coordination of physiological activities within the population.

  6. Uncovering the Hidden Histories: Black and Asian People in the Two World Wars

    Science.gov (United States)

    Gaze, Rupert

    2005-01-01

    The stories we tell in history are often stories about ourselves. This can lead to tremendous distortion. Rupert Gaze was shocked when a young black student told him that there was no point in his studying the Second World War because it had nothing to do with him or his family. While Gaze has worked for the Imperial War Museum (IWM) North, it has…

  7. 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.

  8. Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

    OpenAIRE

    Kohler, Annegret; Balestrini, Raffaella; Coutinho, Pedro; Jaillon, Olivier; Percudani, Riccardo; Porcel, Bettina; Rubini, Andrea; Amicucci, Antonella; Amselem, Joelle; Anthouard, Véronique; Arcioni, Sergio; Artiguenave, François; Aury, Jean-Marc; Ballario, Paola; Bolchi, Angelo

    2010-01-01

    The Périgord black truffle (Tuber melanosporum Vittad.) and the Piedmont white truffle dominate today’s truffle market. The hypogeous fruiting body of T. melanosporum is a gastronomic delicacy produced by an ectomycorrhizal symbiont endemic to calcareous soils in southern Europe. The worldwide demand for this truffle has fuelled intense efforts at cultivation. Identification of processes that condition and trigger fruit body and symbiosis formation, ultimately leading to efficient crop produc...

  9. Uncovering the Molecular Mechanism of Actions between Pharmaceuticals and Proteins on the AD Network.

    Directory of Open Access Journals (Sweden)

    Shujuan Cao

    Full Text Available This study begins with constructing the mini metabolic networks (MMNs of beta amyloid (Aβ and acetylcholine (ACh which stimulate the Alzheimer's Disease (AD. Then we generate the AD network by incorporating MMNs of Aβ and ACh, and other MMNs of stimuli of AD. The panel of proteins contains 49 enzymes/receptors on the AD network which have the 3D-structure in PDB. The panel of drugs is formed by 5 AD drugs and 5 AD nutraceutical drugs, and 20 non-AD drugs. All of these complexes formed by these 30 drugs and 49 proteins are transformed into dyadic arrays. Utilizing the prior knowledge learned from the drug panel, we propose a statistical classification (dry-lab. According to the wet-lab for the complex of amiloride and insulin degrading enzyme, and the complex of amiloride and neutral endopeptidase, we are confident that this dry-lab is reliable. As the consequences of the dry-lab, we discover many interesting implications. Especially, we show that possible causes of Tacrine, donepezil, galantamine and huperzine A cannot improve the level of ACh which is against to their original design purpose but they still prevent AD to be worse as Aβ deposition appeared. On the other hand, we recommend Miglitol and Atenolol as the safe and potent drugs to improve the level of ACh before Aβ deposition appearing. Moreover, some nutrients such as NADH and Vitamin E should be controlled because they may harm health if being used in wrong way and wrong time. Anyway, the insights shown in this study are valuable to be developed further.

  10. Uncovering the deformation mechanisms of origami metamaterials by introducing generic degree-four vertices.

    Science.gov (United States)

    Fang, Hongbin; Li, Suyi; Ji, Huimin; Wang, K W

    2016-10-01

    Origami-based design holds promise for developing new mechanical metamaterials whose overall kinematic and mechanical properties can be programmed using purely geometric criteria. In this article, we demonstrate that the deformation of a generic degree-four vertex (4-vertex) origami cell is a combination of contracting, shearing, bending, and facet-binding. The last three deformation mechanisms are missing in the current rigid-origami metamaterial investigations, which focus mainly on conventional Miura-ori patterns. We show that these mechanisms provide the 4-vertex origami sheets and blocks with new deformation patterns as well as extraordinary kinematical and mechanical properties, including self-locking, tridirectional negative Poisson's ratios, flipping of stiffness profiles, and emerging shearing stiffness. This study reveals that the 4-vertex cells offer a better platform and greater design space for developing origami-based mechanical metamaterials than the conventional Miura-ori cell.

  11. Uncovering changes in spider orb-web topology owing to aerodynamic effects.

    Science.gov (United States)

    Zaera, Ramón; Soler, Alejandro; Teus, Jaime

    2014-09-06

    An orb-weaving spider's likelihood of survival is influenced by its ability to retain prey with minimum damage to its web and at the lowest manufacturing cost. This set of requirements has forced the spider silk to evolve towards extreme strength and ductility to a degree that is rare among materials. Previous studies reveal that the performance of the web upon impact may not be based on the mechanical properties of silk alone, aerodynamic drag could play a role in the dissipation of the prey's energy. Here, we present a thorough analysis of the effect of the aerodynamic drag on wind load and prey impact. The hypothesis considered by previous authors for the evaluation of the drag force per unit length of thread has been revisited according to well-established principles of fluid mechanics, highlighting the functional dependence on thread diameter that was formerly ignored. Theoretical analysis and finite-element simulations permitted us to identify air drag as a relevant factor in reducing deterioration of the orb web, and to reveal how the spider can take greater-and not negligible-advantage of drag dissipation. The study shows the beneficial air drag effects of building smaller and less dense webs under wind load, and larger and denser webs under prey impact loads. In essence, it points out why the aerodynamics need to be considered as an additional driving force in the evolution of silk threads and orb webs.

  12. 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

  13. The SALUT Project: Study of Advanced Laser Techniques for the Uncovering of Polychromed Works of Art

    Science.gov (United States)

    van der Snickt, G.; De Boeck, A.; Keutgens, K.; Anthierens, D.

    In order to find out whether the existing laser systems can be employed to remove superimposed layers of paint on secco wall paintings in a selective way, laser tests were carried out on three types of prepared samples simulating three stratigraphies that are frequently encountered in practice. OM, EPMA, colorimetry, μRaman, and FT-IR were used to evaluate the results. It was found that Q-switched Nd:YAG lasers emitting at 1,064nm could be employed to remove unwanted layers of oil paint and limewash, but the treatment of large areas requires implementation of a computer-controlled X-Y-Z station in order to control the parameters. However, the applicability of this technique will remain limited as ablation at the established optimum parameters implied a discoloration of the pigments cinnabar, yellow ochre, and burnt sienna. Moreover, it was observed that no ablation took place when the limewash thickness exceeds 25 μm. Unwanted layers of acrylic could be removed in an efficient way with an excimer laser emitting at 193 nm.

  14. Uncovering a context-specific connectional fingerprint of human dorsal premotor cortex

    DEFF Research Database (Denmark)

    Moisa, Marius; Siebner, Hartwig R; Pohmann, Rolf

    2012-01-01

    Primate electrophysiological and lesion studies indicate a prominent role of the left dorsal premotor cortex (PMd) in action selection based on learned sensorimotor associations. Here we applied transcranial magnetic stimulation (TMS) to human left PMd at low or high intensity while right-handed ...

  15. Whole report uncovers correctly identified but incorrectly placed target information under visual crowding.

    Science.gov (United States)

    Zhang, Jun-Yun; Zhang, Gong-Liang; Liu, Lei; Yu, Cong

    2012-07-10

    Multiletter identification studies often find correctly identified letters being reported in wrong positions. However, how position uncertainty impacts crowding in peripheral vision is not fully understood. The observation of a flanker being reported as the central target cannot be taken as unequivocal evidence for position misperception because the observers could be biased to report a more identifiable flanker when failing to identify the central target. In addition, it has never been reported whether a correctly identified central target can be perceived at a flanker position under crowding. Empirical investigation into this possibility holds the key to demonstrating letter-level position uncertainty in crowding, because the position errors of the least identifiable central target cannot be attributed to response bias. We asked normally-sighted observers to report either the central target of a trigram (partial report) or all three characters (whole report). The results showed that, for radially arranged trigrams, the rate of reporting the central target regardless of the reported position in the whole report was significantly higher than the partial report rate, and the extra target reports mostly ended up in flanker positions. Error analysis indicated that target-flanker position swapping and misalignment (lateral shift of the target and one flanker) underlay this target misplacement. Our results thus establish target misplacement as a source of crowding errors and ascertain the role of letter-level position uncertainty in crowding.

  16. New National Telescope at La Silla - TRAPPIST to Scout the Sky and Uncover Exoplanets and Comets

    Science.gov (United States)

    2010-06-01

    A new robotic telescope has had first light at ESO's La Silla Observatory, in Chile. TRAPPIST (TRAnsiting Planets and PlanetesImals Small Telescope) is devoted to the study of planetary systems through two approaches: the detection and characterisation of planets located outside the Solar System (exoplanets) and the study of comets orbiting around the Sun. The 60-cm telescope is operated from a control room in Liège, Belgium, 12 000 km away. "The two themes of the TRAPPIST project are important parts of an emerging interdisciplinary field of research - astrobiology - that aims at studying the origin and distribution of life in the Universe," explains Michaël Gillon, who is in charge of the exoplanet studies. "Terrestrial planets similar to our Earth are obvious targets for the search for life outside the Solar System, while comets are suspected to have played an important role in the appearance and development of life on our planet," adds his colleague Emmanuël Jehin, who leads the cometary part of the project. TRAPPIST will detect and characterise exoplanets by making high precision measurements of "brightness dips" that might possibly be caused by exoplanet transits. During such a transit, the observed brightness of the star decreases slightly because the planet blocks a part of the starlight. The larger the planet, the more of the light is blocked and the more the brightness of the star will decrease [1]. "ESO's La Silla Observatory on the outskirts of the Atacama Desert is certainly one of the best astronomical sites in the world," says Gillon. "And because it is already home to two superb exoplanet hunters, we couldn't have found a better place to install our robotic telescope." The astronomers behind the TRAPPIST initiative will work very closely with the teams using HARPS on the 3.6-metre telescope and CORALIE attached to the Swiss 1.2-metre Leonhard Euler Telescope, both at La Silla. TRAPPIST is a collaboration between the University of Liège and the Geneva Observatory, Switzerland. The telescope is installed in the building that housed the old Swiss T70 telescope. Thanks to this collaboration, the whole project is on a fast track: it took only two years between taking the decision to build and first light. TRAPPIST will also be used for the study of southern comets. To this aim, the telescope is equipped with special large, high quality cometary filters, allowing astronomers to study regularly and in detail the ejection of several types of molecules by comets during their journey around the Sun. "With dozens of comets observed each year, this will provide us with a unique dataset, bringing important information about their nature," says Jehin. TRAPPIST is a lightweight 0.6-metre robotic telescope, fully automated and moving precisely across the sky at a high speed. The observing programme is prepared in advance and the telescope can perform a full night of observations unattended. A meteorological station monitors the weather continuously and decides to close the dome if necessary. Notes [1] A planetary transit occurs when a celestial body passes in front of its host star and blocks some of the star's light. This type of eclipse causes changes in the apparent brightness of the star and enables the planet's diameter to be measured. Combined with radial velocity measurements, it is also possible to deduce the mass and, hence, the density of the planet. More information TRAPPIST (TRAnsiting Planets and PlanetesImals Small Telescope) is a project led by the Department of Astrophysics, Geophysics and Oceanography (AGO) of the University of Liège (Belgium), in close collaboration with the Observatory of Geneva (Switzerland). TRAPPIST is mostly funded by the Belgian Fund for Scientific Research (FNRS) with the participation of the Swiss National Science Foundation (SNF). The team is composed of Emmanuël Jehin, Michaël Gillon, Pierre Magain, Virginie Chantry, Jean Manfroid, and Damien Hutsemékers (University of Liège, Belgium) and Didier Queloz and Stéphane Udry (Observatory of Geneva, Switzerland). The name TRAPPIST was given to the telescope to underline the Belgian origin of the project. Trappist beers are famous all around the world and most of them are Belgian. Moreover, the team members really appreciate them!

  17. Uncovering noisy social signals: Using optimization methods from experimental physics to study social phenomena

    Science.gov (United States)

    2017-01-01

    Due to the ubiquitous presence of treatment heterogeneity, measurement error, and contextual confounders, numerous social phenomena are hard to study. Precise control of treatment variables and possible confounders is often key to the success of studies in the social sciences, yet often proves out of the realm of control of the experimenter. To amend this situation we propose a novel approach coined “lock-in feedback” which is based on a method that is routinely used in high-precision physics experiments to extract small signals out of a noisy environment. Here, we adapt the method to noisy social signals in multiple dimensions and evaluate it by studying an inherently noisy topic: the perception of (subjective) beauty. We show that the lock-in feedback approach allows one to select optimal treatment levels despite the presence of considerable noise. Furthermore, through the introduction of an external contextual shock we demonstrate that we can find relationships between noisy variables that were hitherto unknown. We therefore argue that lock-in methods may provide a valuable addition to the social scientist’s experimental toolbox and we explicitly discuss a number of future applications. PMID:28306728

  18. 16 CFR 1610.34 - Only uncovered or exposed parts of wearing apparel to be tested.

    Science.gov (United States)

    2010-01-01

    ... FLAMMABLE FABRICS ACT REGULATIONS STANDARD FOR THE FLAMMABILITY OF CLOTHING TEXTILES Rules and Regulations... 1610—Standard for the Flammability of Clothing Textiles or part 1611. However, if the...

  19. 77 FR 30501 - Uncovered Innerspring Units From the People's Republic of China: Initiation of Anticircumvention...

    Science.gov (United States)

    2012-05-23

    ... encasement around the innerspring. Pocketed and non-pocketed innerspring units are included in this definition. Non-pocketed innersprings are typically joined together with helical wire and border rods. Non...'' or ``sock'' of a nonwoven synthetic material or woven material and then glued together in a...

  20. Uncovering the genetic history of the present-day greenlandic population

    DEFF Research Database (Denmark)

    Moltke, Ida; Fumagalli, Matteo; Korneliussen, Thorfinn Sand

    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...

  1. Uncovering spider silk nanocrystalline variations that facilitate wind-induced mechanical property changes.

    Science.gov (United States)

    Blamires, Sean J; Wu, Chao-Chia; Wu, Chung-Lin; Sheu, Hwo-Shuenn; Tso, I-Min

    2013-10-14

    Spider major ampullate (MA) silk varies in mechanical properties when spun in different environments. Amino acid compositional changes induced by variations in MaSp1 and MaSp2 expression, and various biochemical and physiological glandular processes induce silk property variability. Quantifying the contributions of these mechanisms on silk variability may facilitate the development of silk biomimetics. Wind is a medium that induces variations in MA silk mechanics. We exposed the spider Cyclosa mulmeinensis to wind and measured the amino acid composition, tensile mechanics, and crystalline structure of its MA silk using HPLC, tensile tests, and X-ray diffraction. We found the mechanical properties of MA silks from spiders exposed to wind to differ from unexposed spiders. The amino acid compositions did not differ, but X-ray diffraction found a lower crystal density and greater β-sheet alignment relative to the fiber axis in the silks of spiders exposed to wind. We found no evidence that the mechanical property variations were a product of profound changes to the alignment of the protein within the amorphous region. We conclude that variations in the density and alignment of the crystalline β-sheets, probably accompanied by some alignment change in the amorphous region as a result of "stretching" during spinning of the silk, probably explains the mechanical property variations that we found across treatment subgroups. As C. mulmeinensis MA silk increases both in strength and elasticity when the spiders are exposed to wind, bioengineers may consider it as a model for the development of high-performance silk biomimetics.

  2. Flux Analysis Uncovers Key Role of Functional Redundancy in Formaldehyde Metabolism

    OpenAIRE

    Christopher J Marx; Van Dien, Stephen J.; Mary E Lidstrom

    2005-01-01

    Genome-scale analysis of predicted metabolic pathways has revealed the common occurrence of apparent redundancy for specific functional units, or metabolic modules. In many cases, mutation analysis does not resolve function, and instead, direct experimental analysis of metabolic flux under changing conditions is necessary. In order to use genome sequences to build models of cellular function, it is important to define function for such apparently redundant systems. Here we describe direct flu...

  3. The thrill of the chase: uncovering illegal sport hunting in Brazil through YouTube™ posts

    Directory of Open Access Journals (Sweden)

    Hani R. El Bizri

    2015-09-01

    Full Text Available The impacts of unregulated sport hunting can severely affect populations of target game species. Because hunting in Brazil is limited by law, obtaining data on illegal sport hunting in this country is challenging. We used an unusual online resource, YouTube™, to detect the occurrence of sport hunting in Brazil, measure the impacts of the activity on the main Brazilian game species and biomes, evaluate the opinions of hunters and internet users on sport hunting, and discuss the need for policy interventions in wildlife conservation in this country. We found 383 videos related to Brazilian sport hunting on YouTube™, accounting for more than 15 million views. Most videos were produced in the Cerrado (Brazilian savannah and approximately 70% of them depicted events of pursuit and killing of wild animals, especially lowland pacas (Cuniculus paca and armadillos (Family Dasypodidae. Videos were posted primarily in July and December, coinciding with the two main Brazilian vacation periods. Furthermore, the shotguns identified on videos show that sport hunters expend large sums of money to undertake their hunts. These results indicate that Brazilian sport hunters are possibly wealthier urban residents who travel to rural areas to hunt, contrasting with previous hunting studies in the country. Most viewers declared themselves in favor of sport hunting in comments (n = 2893 and ratings (n = 36,570 of the videos. Discussions generated by comments suggest that Brazilian sport hunters employ several informal management strategies to maintain game species stocks for future hunting and intensely question the restrictions of Brazilian environmental policies. Our results demonstrate that solutions are needed for the regulation of sport hunting in Brazil. Government actions, whether to increase surveillance or legalize hunting programs, should take into account the opinions of sport hunters and their perceptions on hunting dynamics to support effective policy decisions on wildlife conservation in Brazil.

  4. Key courses of academic curriculum uncovered by data mining of students' grades

    CERN Document Server

    Gajewski, Łukasz; Hołyst, Janusz

    2016-01-01

    Learning is a complex cognitive process that depends not only on an individual capability of knowledge absorption but it can be also influenced by various group interactions and by the structure of an academic curriculum. We have applied methods of statistical analyses and data mining (Principal Component Analysis and Maximal Spanning Tree) for anonymized students' scores at Faculty of Physics, Warsaw University of Technology. A slight negative linear correlation exists between mean and variance of course grades, i.e. courses with higher mean scores tend to possess a lower scores variance. There are courses playing a central role, e.g. their scores are highly correlated to other scores and they are in the centre of corresponding Maximal Spanning Trees. Other courses contribute significantly to students' score variance as well to the first principal component and they are responsible for differentiation of students' scores. Correlations of the first principal component to courses' mean scores and scores varian...

  5. Understanding the Manga Hype: Uncovering the Multimodality of Comic-Book Literacies

    Science.gov (United States)

    Schwartz, Adam; Rubinstein-Avila, Eliane

    2006-01-01

    The authors introduce manga to educators, inspired by the comics' explosive entry into U.S. popular culture. The word "manga" refers specifically to printed, Japanese-style comics found in graphic-novel format--not to be confused with "anime" (animated Japanese cartoons, including moving images on television, movies, video…

  6. The taxonomy statistic uncovers novel clinical patterns in a population of ischemic stroke patients.

    Directory of Open Access Journals (Sweden)

    Andrzej Tukiendorf

    Full Text Available In this paper, we describe a simple taxonomic approach for clinical data mining elaborated by Marczewski and Steinhaus (M-S, whose performance equals the advanced statistical methodology known as the expectation-maximization (E-M algorithm. We tested these two methods on a cohort of ischemic stroke patients. The comparison of both methods revealed strong agreement. Direct agreement between M-S and E-M classifications reached 83%, while Cohen's coefficient of agreement was κ = 0.766(P < 0.0001. The statistical analysis conducted and the outcomes obtained in this paper revealed novel clinical patterns in ischemic stroke patients. The aim of the study was to evaluate the clinical usefulness of Marczewski-Steinhaus' taxonomic approach as a tool for the detection of novel patterns of data in ischemic stroke patients and the prediction of disease outcome. In terms of the identification of fairly frequent types of stroke patients using their age, National Institutes of Health Stroke Scale (NIHSS, and diabetes mellitus (DM status, when dealing with rough characteristics of patients, four particular types of patients are recognized, which cannot be identified by means of routine clinical methods. Following the obtained taxonomical outcomes, the strong correlation between the health status at moment of admission to emergency department (ED and the subsequent recovery of patients is established. Moreover, popularization and simplification of the ideas of advanced mathematicians may provide an unconventional explorative platform for clinical problems.

  7. Uncovering molecular structural mechanisms of signaling mediated by the prion protein

    Energy Technology Data Exchange (ETDEWEB)

    Romano, Sebastian A.; Linden, Rafael [Universidade Federal do Rio de Janeiro (IBCCF/UFRl), RJ (Brazil). Inst. de Biofisica Carlos Chagas Filho; Cordeiro, Yraima; Rocha e Lima, Luis M.T. da [Universidade Federal do Rio de Janeiro (FF/UFRl), RJ (Brazil). Fac. de Farmacia; Lopes, Marilene H. [Instituto Ludwig de Pesquisa de Cancer, Sao Paulo, SP (Brazil); Silva, Jerson L.; Foguel, Debora [Universidade Federal do Rio de Janeiro (IBqM/UFRl), RJ (Brazil). Inst. de Bioquimica Medica

    2009-07-01

    The glycosyl phosphatidylinositol (GPI) - anchored prion protein (PrP{sup c}), usually associated with neurodegenerative diseases, modulates various cellular responses and may scaffold multiprotein cell surface signaling complexes. Engagement of PrP{sup c} with the secretable cochaperone hop/STI 1 induces neurotrophic transmembrane signals through unknown molecular mechanisms. We addressed whether interaction of Pr P{sup c} and hop STI 1 entails structural rearrangements relevant for signaling. Circular dichroism and fluorescence spectroscopy showed that PrP{sup c}:hop/STI 1 interaction triggers loss of PrP helical structures, involving at least a perturbation of the Pr P{sup c}{sub 143-153} beta-helix. Novel SAXS models revealed a significant C-terminal compaction of hop/STI 1 when bound to PrP{sup c}. 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 P{sup c}{sub 143-153} beta-helix may engage the transmembrane signaling protein laminin receptor precursor and neural cell adhesion molecule, both of which bind that domain of Pr P{sup c}, 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 P{sup c}:hop/STI 1 interaction, consistent with the hypothesis that Pr P{sup c} scaffolds multiprotein signaling complexes at the cell surface. (author)

  8. An antioxidant nanozyme that uncovers the cytoprotective potential of vanadia nanowires

    Science.gov (United States)

    Vernekar, Amit A.; Sinha, Devanjan; Srivastava, Shubhi; Paramasivam, Prasath U.; D'Silva, Patrick; Mugesh, Govindasamy

    2014-11-01

    Nanomaterials with enzyme-like properties has attracted significant interest, although limited information is available on their biological activities in cells. Here we show that V2O5 nanowires (Vn) functionally mimic the antioxidant enzyme glutathione peroxidase by using cellular glutathione. Although bulk V2O5 is known to be toxic to the cells, the property is altered when converted into a nanomaterial form. The Vn nanozymes readily internalize into mammalian cells of multiple origin (kidney, neuronal, prostate, cervical) and exhibit robust enzyme-like activity by scavenging the reactive oxygen species when challenged against intrinsic and extrinsic oxidative stress. The Vn nanozymes fully restore the redox balance without perturbing the cellular antioxidant defense, thus providing an important cytoprotection for biomolecules against harmful oxidative damage. Based on our findings, we envision that biocompatible Vn nanowires can provide future therapeutic potential to prevent ageing, cardiac disorders and several neurological conditions, including Parkinson’s and Alzheimer’s disease.

  9. Uncovering the Role of BMP Signaling in Melanocyte Development and Melanoma Tumorigenesis

    Science.gov (United States)

    2014-07-01

    generated using TALEN -mediated mutagenesis3, transfections into human primed melanocytes and melanoma cells performed, and lines stably expressing GDF6...Cermak, E.J. Doyle, et al., Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nuc. Acids Res. 39

  10. Tissue-Specific Gain of RTK Signalling Uncovers Selective Cell Vulnerability during Embryogenesis.

    Directory of Open Access Journals (Sweden)

    Yannan Fan

    Full Text Available The successive events that cells experience throughout development shape their intrinsic capacity to respond and integrate RTK inputs. Cellular responses to RTKs rely on different mechanisms of regulation that establish proper levels of RTK activation, define duration of RTK action, and exert quantitative/qualitative signalling outcomes. The extent to which cells are competent to deal with fluctuations in RTK signalling is incompletely understood. Here, we employ a genetic system to enhance RTK signalling in a tissue-specific manner. The chosen RTK is the hepatocyte growth factor (HGF receptor Met, an appropriate model due to its pleiotropic requirement in distinct developmental events. Ubiquitously enhanced Met in Cre/loxP-based Rosa26(stopMet knock-in context (Del-R26(Met reveals that most tissues are capable of buffering enhanced Met-RTK signalling thus avoiding perturbation of developmental programs. Nevertheless, this ubiquitous increase of Met does compromise selected programs such as myoblast migration. Using cell-type specific Cre drivers, we genetically showed that altered myoblast migration results from ectopic Met expression in limb mesenchyme rather than in migrating myoblasts themselves. qRT-PCR analyses show that ectopic Met in limbs causes molecular changes such as downregulation in the expression levels of Notum and Syndecan4, two known regulators of morphogen gradients. Molecular and functional studies revealed that ectopic Met expression in limb mesenchyme does not alter HGF expression patterns and levels, but impairs HGF bioavailability. Together, our findings show that myoblasts, in which Met is endogenously expressed, are capable of buffering increased RTK levels, and identify mesenchymal cells as a cell type vulnerable to ectopic Met-RTK signalling. These results illustrate that embryonic cells are sensitive to alterations in the spatial distribution of RTK action, yet resilient to fluctuations in signalling levels of an RTK when occurring in its endogenous domain of activity.

  11. RNA-Seq of Aradopsis pollen uncovers novel transcription and alternative splicing

    Science.gov (United States)

    Pollen grains of Arabidopsis (Arabidopsis thaliana) contain two haploid sperm cells enclosed in a haploid vegetative cell. Upon germination, the vegetative cell extrudes a pollen tube that carries the sperm to an ovule for fertilization. Knowing the identity, relative abundance, and splicing pattern...

  12. Transition metal ion FRET uncovers K+ regulation of a neurotransmitter/sodium symporter

    Science.gov (United States)

    Billesbølle, Christian B.; Mortensen, Jonas S.; Sohail, Azmat; Schmidt, Solveig G.; Shi, Lei; Sitte, Harald H.; Gether, Ulrik; Loland, Claus J.

    2016-01-01

    Neurotransmitter/sodium symporters (NSSs) are responsible for Na+-dependent reuptake of neurotransmitters and represent key targets for antidepressants and psychostimulants. LeuT, a prokaryotic NSS protein, constitutes a primary structural model for these transporters. Here we show that K+ inhibits Na+-dependent binding of substrate to LeuT, promotes an outward-closed/inward-facing conformation of the transporter and increases uptake. To assess K+-induced conformational dynamics we measured fluorescence resonance energy transfer (FRET) between fluorescein site-specifically attached to inserted cysteines and Ni2+ bound to engineered di-histidine motifs (transition metal ion FRET). The measurements supported K+-induced closure of the transporter to the outside, which was counteracted by Na+ and substrate. Promoting an outward-open conformation of LeuT by mutation abolished the K+-effect. The K+-effect depended on an intact Na1 site and mutating the Na2 site potentiated K+ binding by facilitating transition to the inward-facing state. The data reveal an unrecognized ability of K+ to regulate the LeuT transport cycle. PMID:27678200

  13. Transition metal ion FRET uncovers K(+) regulation of a neurotransmitter/sodium symporter.

    Science.gov (United States)

    Billesbølle, Christian B; Mortensen, Jonas S; Sohail, Azmat; Schmidt, Solveig G; Shi, Lei; Sitte, Harald H; Gether, Ulrik; Loland, Claus J

    2016-09-28

    Neurotransmitter/sodium symporters (NSSs) are responsible for Na(+)-dependent reuptake of neurotransmitters and represent key targets for antidepressants and psychostimulants. LeuT, a prokaryotic NSS protein, constitutes a primary structural model for these transporters. Here we show that K(+) inhibits Na(+)-dependent binding of substrate to LeuT, promotes an outward-closed/inward-facing conformation of the transporter and increases uptake. To assess K(+)-induced conformational dynamics we measured fluorescence resonance energy transfer (FRET) between fluorescein site-specifically attached to inserted cysteines and Ni(2+) bound to engineered di-histidine motifs (transition metal ion FRET). The measurements supported K(+)-induced closure of the transporter to the outside, which was counteracted by Na(+) and substrate. Promoting an outward-open conformation of LeuT by mutation abolished the K(+)-effect. The K(+)-effect depended on an intact Na1 site and mutating the Na2 site potentiated K(+) binding by facilitating transition to the inward-facing state. The data reveal an unrecognized ability of K(+) to regulate the LeuT transport cycle.

  14. Scraping through the ice: uncovering the role of TRPM8 in cold transduction.

    Science.gov (United States)

    McCoy, Daniel D; Knowlton, Wendy M; McKemy, David D

    2011-06-01

    The proper detection of environmental temperatures is essential for the optimal growth and survival of organisms of all shapes and phyla, yet only recently have the molecular mechanisms for temperature sensing been elucidated. The discovery of temperature-sensitive ion channels of the transient receptor potential (TRP) superfamily has been pivotal in explaining how temperatures are sensed in vivo, and here we will focus on the lone member of this cohort, TRPM8, which has been unequivocally shown to be cold sensitive. TRPM8 is expressed in somatosensory neurons that innervate peripheral tissues such as the skin and oral cavity, and recent genetic evidence has shown it to be the principal transducer of cool and cold stimuli. It is remarkable that this one channel, unlike other thermosensitive TRP channels, is associated with both innocuous and noxious temperature transduction, as well as cold hypersensitivity during injury and, paradoxically, cold-mediated analgesia. With ongoing research, the field is getting closer to answering a number of fundamental questions regarding this channel, including the cellular mechanisms of TRPM8 modulation, the molecular context of TRPM8 expression, as well as the full extent of the role of TRPM8 in cold signaling in vivo. These findings will further our understanding of basic thermotransduction and sensory coding, and may have important implications for treatments for acute and chronic pain.

  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.

  16. NIH mice study uncovers pathway critical for UV-induced melanoma

    Science.gov (United States)

    Scientists have made an unanticipated discovery in mice that interferon-gamma, a type of protein primarily used by the immune system for intercellular communication, acts as a promoter for the deadly form of skin cancer known as melanoma.

  17. Understanding the Manga Hype: Uncovering the Multimodality of Comic-Book Literacies

    Science.gov (United States)

    Schwartz, Adam; Rubinstein-Avila, Eliane

    2006-01-01

    The authors introduce manga to educators, inspired by the comics' explosive entry into U.S. popular culture. The word "manga" refers specifically to printed, Japanese-style comics found in graphic-novel format--not to be confused with "anime" (animated Japanese cartoons, including moving images on television, movies, video games). There are two…

  18. Uncovering the relation of a di-photon scalar resonance to the Higgs boson

    CERN Document Server

    Carmona, Adrian; Papaefstathiou, Andreas

    2016-01-01

    We consider the associated production of a scalar resonance, decaying to a pair of photons, with the standard model Higgs boson. We demonstrate via a realistic phenomenological analysis that couplings of such a resonance to the Higgs boson can be constrained in a meaningful way in future runs of the LHC, providing insights on its origin and its relation to the electroweak symmetry breaking sector. Moreover, the final state can provide a direct way to determine whether the new resonance is produced predominantly in gluon fusion or quark-anti-quark annihilation. The analysis focusses on a resonance with a mass of 750 GeV, coming from a scalar field with vanishing vacuum expectation value. It can however be straightforwardly generalised to other scenarios.

  19. Microsatellite markers uncover cryptic species of Odontotermes (Termitoidae: Termitidae) from Peninsular Malaysia.

    Science.gov (United States)

    Cheng, S; Lee, C T; Wan, M N; Tan, S G

    2013-04-15

    Termites from the genus Odontotermes are known to contain numerous species complexes that are difficult to tell apart morphologically or with mitochondrial DNA sequences. We developed markers for one such cryptic species complex, that is, Odontotermes srinakarinensis sp. nov. from Maxwell Hill Forest Reserve (Perak, Malaysia), and characterised them using a sample of 41 termite workers from three voucher samples from the same area. We then genotyped 150 termite individuals from 23 voucher samples/colonies of this species complex from several sites in Peninsular Malaysia. We analysed their population by constructing dendograms from the proportion of shared-alleles between individuals and genetic distances between colonies; additionally, we examined the Bayesian clustering pattern of their genotype data. All methods of analysis indicated that there were two distinct clusters within our data set. After the morphologies of specimens from each cluster were reexamined, we were able to separate the two species morphologically and found that a single diagnostic character found on the mandibles of its soldiers could be used to separate the two species quite accurately. The additional species in the clade was identified as Odontotermes denticulatus after it was matched to type specimens at the NHM London and Cambridge Museum of Zoology.

  20. Genetic selection designed to stabilize proteins uncovers a chaperone called Spy.

    Science.gov (United States)

    Quan, Shu; Koldewey, Philipp; Tapley, Tim; Kirsch, Nadine; Ruane, Karen M; Pfizenmaier, Jennifer; Shi, Rong; Hofmann, Stephan; Foit, Linda; Ren, Guoping; Jakob, Ursula; Xu, Zhaohui; Cygler, Miroslaw; Bardwell, James C A

    2011-03-01

    To optimize the in vivo folding of proteins, we linked protein stability to antibiotic resistance, thereby forcing bacteria to effectively fold and stabilize proteins. When we challenged Escherichia coli to stabilize a very unstable periplasmic protein, it massively overproduced a periplasmic protein called Spy, which increases the steady-state levels of a set of unstable protein mutants up to 700-fold. In vitro studies demonstrate that the Spy protein is an effective ATP-independent chaperone that suppresses protein aggregation and aids protein refolding. Our strategy opens up new routes for chaperone discovery and the custom tailoring of the in vivo folding environment. Spy forms thin, apparently flexible cradle-shaped dimers. The structure of Spy is unlike that of any previously solved chaperone, making it the prototypical member of a new class of small chaperones that facilitate protein refolding in the absence of energy cofactors.

  1. Uncovering biologically significant lipid isomers with liquid chromatography, ion mobility spectrometry and mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Kyle, Jennifer E.; Zhang, Xing; Weitz, Karl K.; Monroe, Matthew E.; Ibrahim, Yehia M.; Moore, Ronald J.; Cha, Jeeyeon; Sun, Xiaofei; Lovelace, Erica S.; Wagoner, Jessica; Polyak, Steve; Metz, Thomas O.; Dey, Sudhansu K.; Smith, Richard D.; Burnum-Johnson, Kristin E.; Baker, Erin Shammel

    2016-01-01

    Understanding how biological molecules are generated, metabolized and eliminated in living systems is important for interpreting processes such as immune response and disease pathology. While genomic and proteomic studies have provided vast amounts of information over the last several decades, interest in lipidomics has also grown due to improved analytical technologies revealing altered lipid metabolism in type 2 diabetes, cancer, and lipid storage disease. Liquid chromatography and mass spectrometry (LC-MS) measurements are currently the dominant approach for characterizing the lipidome by providing detailed information on the spatial and temporal composition of lipids. However, interpreting lipids’ biological roles is challenging due to the existence of numerous structural and stereoisomers (i.e. distinct acyl chain and double-bond positions), which are unresolvable using present LC-MS approaches. Here we show that combining structurally-based ion mobility spectrometry (IMS) with LC-MS measurements distinguishes lipid isomers and allows insight into biological and disease processes.

  2. Transcriptome atlas of eight liver cell types uncovers effects of histidine catabolites on rat liver regeneration

    Indian Academy of Sciences (India)

    C. F. Chang; J. Y. Fan; F. C. Zhang; J. Ma; C. S. Xu

    2010-12-01

    Eight liver cell types were isolated using the methods of Percoll density gradient centrifugation and immunomagnetic beads to explore effects of histidine catabolites on rat liver regeneration. Rat Genome 230 2.0 Array was used to detect the expression profiles of genes associated with metabolism of histidine and its catabolites for the above-mentioned eight liver cell types, and bioinformatic and systems biology approaches were employed to analyse the relationship between above genes and rat liver regeneration. The results showed that the urocanic acid (UA) was degraded from histidine in Kupffer cells, acts on Kupffer cells itself and dendritic cells to generate immune suppression by autocrine and paracrine modes. Hepatocytes, biliary epithelia cells, oval cells and dendritic cells can convert histidine to histamine, which can promote sinusoidal endothelial cells proliferation by GsM pathway, and promote the proliferation of hepatocytes and biliary epithelia cells by GqM pathway.

  3. 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.

  4. Transcriptional profiling uncovers a network of cholesterol-responsive atherosclerosis target genes.

    Directory of Open Access Journals (Sweden)

    Josefin Skogsberg

    2008-03-01

    Full Text Available Despite the well-documented effects of plasma lipid lowering regimes halting atherosclerosis lesion development and reducing morbidity and mortality of coronary artery disease and stroke, the transcriptional response in the atherosclerotic lesion mediating these beneficial effects has not yet been carefully investigated. We performed transcriptional profiling at 10-week intervals in atherosclerosis-prone mice with human-like hypercholesterolemia and a genetic switch to lower plasma lipoproteins (Ldlr(-/-Apo(100/100Mttp(flox/flox Mx1-Cre. Atherosclerotic lesions progressed slowly at first, then expanded rapidly, and plateaued after advanced lesions formed. Analysis of lesion expression profiles indicated that accumulation of lipid-poor macrophages reached a point that led to the rapid expansion phase with accelerated foam-cell formation and inflammation, an interpretation supported by lesion histology. Genetic lowering of plasma cholesterol (e.g., lipoproteins at this point all together prevented the formation of advanced plaques and parallel transcriptional profiling of the atherosclerotic arterial wall identified 37 cholesterol-responsive genes mediating this effect. Validation by siRNA-inhibition in macrophages incubated with acetylated-LDL revealed a network of eight cholesterol-responsive atherosclerosis genes regulating cholesterol-ester accumulation. Taken together, we have identified a network of atherosclerosis genes that in response to plasma cholesterol-lowering prevents the formation of advanced plaques. This network should be of interest for the development of novel atherosclerosis therapies.

  5. Uncovering the planets and stellar activity of CoRoT-7 using only radial velocities

    CERN Document Server

    Faria, J P; Brewer, B J; Figueira, P; Oshagh, M; Santerne, A; Santos, N C

    2016-01-01

    Stellar activity can induce signals in the radial velocities of stars, complicating the detection of orbiting low-mass planets. We present a method to determine the number of planetary signals present in radial-velocity datasets of active stars, using only radial-velocity observations. Instead of considering separate fits with different number of planets, we use a birth-death Markov chain Monte Carlo algorithm to infer the posterior distribution for the number of planets in a single run. In a natural way, the marginal distributions for the orbital parameters of all planets are also inferred. This method is applied to HARPS data of CoRoT-7. We confidently recover both CoRoT-7b and CoRoT-7c although the data show evidence for additional signals.

  6. Uncovering star formation feedback and magnetism in galaxies with radio continuum surveys

    Science.gov (United States)

    Tabatabaei, F. S.

    2017-03-01

    Recent studies show the importance of the star formation feedback in changing the energetic and structure of galaxies. Dissecting the physics of the feedback is hence crucial to understand the evolution of galaxies. Full polarization radio continuum surveys can be ideally performed to trace not only star formation but also the energetic components of the interstellar medium (ISM), the magnetic fields and cosmic ray electrons. Using the SKA precursors, we investigate the effect of the massive star formation on the ISM energy balance in nearby galaxies. Our multi-scale and multi-frequency surveys show that cosmic rays are injected in star forming regions and lose energy propagating away from their birth place. Due to the star formation feedback, cosmic ray electron population becomes younger and more energetic. Star formation also amplifies the turbulent magnetic field inserting a high pressure which is important in energy balance in the ISM and structure formation in the host galaxy.

  7. Uncovering star formation feedback and magnetism in galaxies with radio continuum surveys

    CERN Document Server

    Tabatabaei, Fatemeh S

    2016-01-01

    Recent studies show the importance of the star formation feedback in changing the energetic and structure of galaxies. Dissecting the physics of the feedback is hence crucial to understand the evolution of galaxies. Full polarization radio continuum surveys can be ideally performed to trace not only star formation but also the energetic components of the interstellar medium (ISM), the magnetic fields and cosmic ray electrons. Using the SKA precursors, we investigate the effect of the massive star formation on the ISM energy balance in nearby galaxies. Our multi-scale and multi-frequency surveys show that cosmic rays are injected in star forming regions and lose energy propagating away from their birth place. Due to the star formation feedback, cosmic ray electron population becomes younger and more energetic. Star formation also amplifies the turbulent magnetic field inserting a high pressure which is important in energy balance in the ISM and structure formation in the host galaxy.

  8. 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

    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...... vector machines. Features were dereplicated by tandem mass spectrometry (MS/MS) networking to identify molecular families of the same biosynthetic origin, and the associated pathways were probed using comparative genomics. Most of the discriminating features were related to antibacterial compounds...

  9. Uncovering early response of gene regulatory networks in ES cells by systematic induction of transcription factors

    Science.gov (United States)

    Nishiyama, Akira; Xin, Li; Sharov, Alexei A.; Thomas, Marshall; Mowrer, Gregory; Meyers, Emily; Piao, Yulan; Mehta, Samir; Yee, Sarah; Nakatake, Yuhki; Stagg, Carole; Sharova, Lioudmila; Correa-Cerro, Lina S.; Bassey, Uwem; Hoang, Hien; Kim, Eugene; Tapnio, Richard; Qian, Yong; Dudekula, Dawood; Zalzman, Michal; Li, Manxiang; Falco, Geppino; Yang, Hsih-Te; Lee, Sung-Lim; Monti, Manuela; Stanghellini, Ilaria; Islam, Md. Nurul; Nagaraja, Ramaiah; Goldberg, Ilya; Wang, Weidong; Longo, Dan L.; Schlessinger, David; Ko, Minoru S. H.

    2009-01-01

    SUMMARY To examine transcription factor (TF) network(s), we created mouse ES cell lines, in each of which one of 50 TFs tagged with a FLAG moiety is inserted into a ubiquitously controllable tetracycline-repressible locus. Of the 50 TFs, Cdx2 provoked the most extensive transcriptome perturbation in ES cells, followed by Esx1, Sox9, Tcf3, Klf4, and Gata3. ChIP-Seq revealed that CDX2 binds to promoters of up-regulated target genes. By contrast, genes down-regulated by CDX2 did not show CDX2 binding, but were enriched with binding sites for POU5F1, SOX2, and NANOG. Genes with binding sites for these core TFs were also down-regulated by the induction of at least 15 other TFs, suggesting a common initial step for ES cell differentiation mediated by interference with the binding of core TFs to their target genes. These ES cell lines provide a fundamental resource to study biological networks in ES cells and mice. PMID:19796622

  10. Uncovering the deformation mechanisms of origami metamaterials by introducing generic degree-four vertices

    Science.gov (United States)

    Fang, Hongbin; Li, Suyi; Ji, Huimin; Wang, K. W.

    2016-10-01

    Origami-based design holds promise for developing new mechanical metamaterials whose overall kinematic and mechanical properties can be programmed using purely geometric criteria. In this article, we demonstrate that the deformation of a generic degree-four vertex (4-vertex) origami cell is a combination of contracting, shearing, bending, and facet-binding. The last three deformation mechanisms are missing in the current rigid-origami metamaterial investigations, which focus mainly on conventional Miura-ori patterns. We show that these mechanisms provide the 4-vertex origami sheets and blocks with new deformation patterns as well as extraordinary kinematical and mechanical properties, including self-locking, tridirectional negative Poisson's ratios, flipping of stiffness profiles, and emerging shearing stiffness. This study reveals that the 4-vertex cells offer a better platform and greater design space for developing origami-based mechanical metamaterials than the conventional Miura-ori cell.

  11. Uncovering the genetic basis of attenuation in Marek’s disease virus

    Science.gov (United States)

    While in vitro serial passage of Marek’s disease virus (MDV) is a proven method to attenuate MDV strains, the underlying genetic changes responsible for attenuation remains unknown. To identify candidate genes and mutations, a virulent MDV generated from an Md5-containing BAC clone was serially pass...

  12. Induced Pluripotent Stem Cell Models of Progranulin-Deficient Frontotemporal Dementia Uncover Specific Reversible Neuronal Defects

    Directory of Open Access Journals (Sweden)

    Sandra Almeida

    2012-10-01

    Full Text Available The pathogenic mechanisms of frontotemporal dementia (FTD remain poorly understood. Here we generated multiple induced pluripotent stem cell lines from a control subject, a patient with sporadic FTD, and an FTD patient with a novel heterozygous GRN mutation (progranulin [PGRN] S116X. In neurons and microglia differentiated from PGRN S116X induced pluripotent stem cells, the levels of intracellular and secreted PGRN were reduced, establishing patient-specific cellular models of PGRN haploinsufficiency. Through a systematic screen of inducers of cellular stress, we found that PGRN S116X neurons, but not sporadic FTD neurons, exhibited increased sensitivity to staurosporine and other kinase inhibitors. Moreover, the serine/threonine kinase S6K2, a component of the phosphatidylinositol 3-kinase and mitogen-activated protein kinase pathways, was specifically downregulated in PGRN S116X neurons. Both increased sensitivity to kinase inhibitors and reduced S6K2 were rescued by PGRN expression. Our findings identify cell-autonomous, reversible defects in patient neurons with PGRN deficiency, and provide a compelling model for studying PGRN-dependent pathogenic mechanisms and testing potential therapies.

  13. Silencing the Majority of Cerebellar Granule Cells Uncovers Their Essential Role in Motor Learning and Consolidation

    Directory of Open Access Journals (Sweden)

    Elisa Galliano

    2013-04-01

    Full Text Available Cerebellar granule cells (GCs account for more than half of all neurons in the CNS of vertebrates. Theoretical work has suggested that the abundance of GCs is advantageous for sparse coding during memory formation. Here, we minimized the output of the majority of GCs by selectively eliminating their CaV2.1 (P/Q-type Ca2+ channels, which mediate the bulk of their neurotransmitter release. This resulted in reduced GC output to Purkinje cells (PCs and stellate cells (SCs as well as in impaired long-term plasticity at GC-PC synapses. As a consequence modulation amplitude and regularity of simple spike (SS output were affected. Surprisingly, the overall motor performance was intact, whereas demanding motor learning and memory consolidation tasks were compromised. Our findings indicate that a minority of functionally intact GCs is sufficient for the maintenance of basic motor performance, whereas acquisition and stabilization of sophisticated memories require higher numbers of normal GCs controlling PC firing.

  14. Comparative Perspective of Human Behavior Patterns to Uncover Ownership Bias among Mobile Phone Users

    Directory of Open Access Journals (Sweden)

    Ayumi Arai

    2016-06-01

    Full Text Available With the rapid spread of mobile devices, call detail records (CDRs from mobile phones provide more opportunities to incorporate dynamic aspects of human mobility in addressing societal issues. However, it has been increasingly observed that CDR data are not always representative of the population under study because it only includes device users alone. To understand the discrepancy between the population captured by CDRs and the general population, we profile principal populations of CDRs by analyzing routines based on time spent at key locations and compare these data with those of the general population. We employ a topic model to estimate typical routines of mobile phone users using CDRs as topics. The routines are extracted from field survey data and compared between those of the general population and mobile phone users. We found that there are two main population groups of mobile phone users in Dhaka: males engaged in an income-generating activity at a specific location other than home and females performing household tasks and spending most of their time at home. We determine that CDRs tend to omit students, who form a significant component of the Dhaka population.

  15. Meiotic double-strand breaks uncover and protect against mitotic errors in the C. elegans germline.

    Science.gov (United States)

    Stevens, Deanna; Oegema, Karen; Desai, Arshad

    2013-12-01

    In sexually reproducing multicellular organisms, genetic information is propagated via the germline, the specialized tissue that generates haploid gametes. The C. elegans germline generates gametes in an assembly line-like process-mitotic divisions under the control of the stem cell niche produce nuclei that, upon leaving the niche, enter into meiosis and progress through meiotic prophase [1]. Here, we characterize the effects of perturbing cell division in the mitotic region of the C. elegans germline. We show that mitotic errors result in a spindle checkpoint-dependent cell-cycle delay, but defective nuclei are eventually formed and enter meiosis. These defective nuclei are eliminated by programmed cell death during meiotic prophase. The cell death-based removal of defective nuclei does not require the spindle checkpoint but instead depends on the DNA damage checkpoint. Removal of nuclei resulting from errors in mitosis also requires Spo11, the enzyme that creates double-strand breaks to initiate meiotic recombination. Consistent with this, double-strand breaks are increased in number and persist longer in germlines with mitotic defects. These findings reveal that the process of initiating meiotic recombination inherently selects against nuclei with abnormal chromosomal content generated by mitotic errors, thereby ensuring the genomic integrity of gametes.

  16. 76 FR 76126 - Uncovered Innerspring Units from the People's Republic of China: Preliminary Results and...

    Science.gov (United States)

    2011-12-06

    ... (``HTSUS''). The HTSUS subheadings are provided for convenience and customs purposes only; the written... accordance with 19 CFR 351.212(b)(1), we will calculate importer- (or customer-) specific assessment rates..., we will calculate importer- (or customer-) specific ad valorem rates by aggregating the...

  17. ‘Arcobacter porcinus’ sp. nov., a novel Arcobacter species uncovered by Arcobacter thereius

    Directory of Open Access Journals (Sweden)

    M.J. Figueras

    2017-01-01

    Full Text Available Arcobacter thereius is a species associated with human disease. A group of A. thereius pork strains (represented by strain LMG 24487 clustered separately from the type strain (LMG 24486T in the 16S rRNA and multilocus phylogenetic trees. In silico DNA-DNA hybridization and average nucleotide identity results between their genomes (93.3 and 51.1% confirmed ‘Arcobacter porcinus’ (LMG 24487T as a new species.

  18. Beliefs of Chilean University English Teachers: Uncovering Their Role in the Teaching and Learning Process

    Directory of Open Access Journals (Sweden)

    Díaz Larenas Claudio

    2013-10-01

    Full Text Available Beliefs continue to be an important source to get to know teachers’ thinking processes and pedagogical decisions. Research in teachers’ beliefs has traditionally come from English-speaking contexts; however, a great deal of scientific work has been written lately in Brazil, Mexico, Colombia, and Argentina. This study elicits 30 Chilean university teachers’ beliefs about their own role in the teaching and learning of English in university environments. Through a qualitative research design, the data collected from interviews and journals were analyzed, triangulated, and categorized based on semantic content analysis. Results of the study indicate that university teachers reveal challenging and complex views about what it is like to teach English as a foreign language in a university context in Chile. The article concludes with a call to reflect on the importance of beliefs unravelling in teacher education programmes.Las creencias continúan siendo una fuente de importancia para conocer los procesos de pensamiento y los estilos pedagógicos de los docentes. Los estudios sobre las creencias docentes provienen en su mayoría de contextos angloparlantes; sin embargo, en los últimos años se ha escrito una gran cantidad de trabajos científicos en Brasil, México, Colombia y Argentina. Este estudio recoge las creencias de treinta docentes universitarios chilenos sobre su papel en la enseñanza y aprendizaje del inglés en ambientes universitarios. A partir de un diseño de investigación cualitativo, los datos recolectados por medio de entrevistas y diarios personales fueron analizados, triangulados y categorizados según el análisis de contenido semántico. Los resultados indicaron que los docentes de educación superior tienen visiones desafiantes y complejas sobre lo que significa enseñar inglés como lengua extranjera en un contexto universitario en Chile. El artículo concluye con una invitación a reflexionar sobre la importancia de transparentar las creencias en los programas de formación inicial docente.

  19. Uncovering a solvent-controlled preferential growth of buckminsterfullerene (C60) nanowires

    DEFF Research Database (Denmark)

    Geng, Junfeng; Solov'yov, Ilia; Zhou, Wuzong

    2009-01-01

    The fullerene (C_60) nanowires, which possess a highly unusual morphology featured by a prismlike central core and three nanobelt-like wings joined along the growth direction to give an overall Y-shaped cross section, were studied. The experimental observation coupled with theoretical calculation...

  20. Sri Lankan National Melioidosis Surveillance Program Uncovers a Nationwide Distribution of Invasive Melioidosis.

    Science.gov (United States)

    Corea, Enoka M; Merritt, Adam J; Ler, Yi-Horng; Thevanesam, Vasanthi; Inglis, Timothy J J

    2016-02-01

    The epidemiologic status of melioidosis in Sri Lanka was unclear from the few previous case reports. We established laboratory support for a case definition and started a nationwide case-finding study. Suspected Burkholderia pseudomallei isolates were collated, identified by polymerase chain reaction assay, referred for Matrix Assisted Laser Desorption Ionization-Time of Flight analysis and multilocus sequence typing (MLST), and named according to the international MLST database. Between 2006 and early 2014, there were 32 patients with culture-confirmed melioidosis with an increasing annual total and a falling fatality rate. Patients were predominantly from rural communities, diabetic, and male. The major clinical presentations were sepsis, pneumonia, soft tissue and joint infections, and other focal infection. Burkholderia pseudomallei isolates came from all parts of Sri Lanka except the Sabaragamuwa Province, the south central hill country, and parts of northern Sri Lanka. Bacterial isolates belonged to 18 multilocus sequence types, one of which (ST 1137) was associated with septicemia and a single-organ focus (Fisher's exact, P = 0.004). Melioidosis is an established endemic infection throughout Sri Lanka, and is caused by multiple genotypes of B. pseudomallei, which form a distinct geographic group based upon related sequence types (BURST) cluster at the junction of the southeast Asian and Australasian clades.

  1. Uncovering neutrinos from cosmic ray factories: the Multi Point Source method

    CERN Document Server

    Sestayo, Yolanda

    2013-01-01

    We present a novel method for the search of high energy extraterrestrial neutrinos in extended regions. The method is based on the study of the spatial correlations between the events recorded by neutrino telescopes. Extended regions radiating neutrinos may exist in the Galaxy due to the hierarchical clustering of massive stars, the progenitors of all the Galactic accelerators known so far. The neutrino emission associated to such extended regions might be faint and complex due to both the escape of cosmic rays and the intricate distribution of gas in the environment of the accelerators. We have simulated extended neutrino emission over an area of 10deg x 10deg, where the intensity fluctuations across the region are modelled as a Gaussian random field with a given correlation structure. We tested our proposed method over realizations of this intensity field plus a uniform random field representative of the spatial distribution of the atmospheric neutrino background. Our results indicate that the method propos...

  2. Analysis of the Legionella longbeachae genome and transcriptome uncovers unique strategies to cause Legionnaires' disease.

    Directory of Open Access Journals (Sweden)

    Christel Cazalet

    2010-02-01

    Full Text Available Legionella pneumophila and L. longbeachae are two species of a large genus of bacteria that are ubiquitous in nature. L. pneumophila is mainly found in natural and artificial water circuits while L. longbeachae is mainly present in soil. Under the appropriate conditions both species are human pathogens, capable of causing a severe form of pneumonia termed Legionnaires' disease. Here we report the sequencing and analysis of four L. longbeachae genomes, one complete genome sequence of L. longbeachae strain NSW150 serogroup (Sg 1, and three draft genome sequences another belonging to Sg1 and two to Sg2. The genome organization and gene content of the four L. longbeachae genomes are highly conserved, indicating strong pressure for niche adaptation. Analysis and comparison of L. longbeachae strain NSW150 with L. pneumophila revealed common but also unexpected features specific to this pathogen. The interaction with host cells shows distinct features from L. pneumophila, as L. longbeachae possesses a unique repertoire of putative Dot/Icm type IV secretion system substrates, eukaryotic-like and eukaryotic domain proteins, and encodes additional secretion systems. However, analysis of the ability of a dotA mutant of L. longbeachae NSW150 to replicate in the Acanthamoeba castellanii and in a mouse lung infection model showed that the Dot/Icm type IV secretion system is also essential for the virulence of L. longbeachae. In contrast to L. pneumophila, L. longbeachae does not encode flagella, thereby providing a possible explanation for differences in mouse susceptibility to infection between the two pathogens. Furthermore, transcriptome analysis revealed that L. longbeachae has a less pronounced biphasic life cycle as compared to L. pneumophila, and genome analysis and electron microscopy suggested that L. longbeachae is encapsulated. These species-specific differences may account for the different environmental niches and disease epidemiology of these two Legionella species.

  3. Uncovering the role of cathode buffer layer in organic solar cells

    Science.gov (United States)

    Qi, Boyuan; Zhang, Zhi-Guo; Wang, Jizheng

    2015-01-01

    Organic solar cells (OSCs) as the third generation photovoltaic devices have drawn intense research, for their ability to be easily deposited by low-cost solution coating technologies. However the cathode in conventional OSCs, Ca, can be only deposited by thermal evaporation and is highly unstable in ambient. Therefore various solution processible cathode buffer layers (CBLs) are synthesized as substitute of Ca and show excellent effect in optimizing performance of OSCs. Yet, there is still no universal consensus on the mechanism that how CBL works, which is evidently a critical scientific issue that should be addressed. In this article detailed studies are targeted on the interfacial physics at the interface between active layer and cathode (with and without treatment of a polar CBL) by using ultraviolet photoelectron spectroscopy, capacitance-voltage measurement, and impedance spectroscopy. The experimental data demonstrate that CBL mainly takes effect in three ways: suppressing surface states at the surface of active layer, protecting the active layer from being damaged by thermally evaporated cathode, and changing the energy level alignment by forming dipole moments with active layer and/or cathode. Our findings here provide a comprehensive picture of interfacial physics in devices with and without CBL.

  4. Metabolite profiling uncovers plasmid-induced cobalt limitation under methylotrophic growth conditions.

    Directory of Open Access Journals (Sweden)

    Patrick Kiefer

    Full Text Available BACKGROUND: The introduction and maintenance of plasmids in cells is often associated with a reduction of growth rate. The reason for this growth reduction is unclear in many cases. METHODOLOGY/PRINCIPAL FINDINGS: We observed a surprisingly large reduction in growth rate of about 50% of Methylobacterium extorquens AM1 during methylotrophic growth in the presence of a plasmid, pCM80 expressing the tetA gene, relative to the wild-type. A less pronounced growth delay during growth under non-methylotrophic growth conditions was observed; this suggested an inhibition of one-carbon metabolism rather than a general growth inhibition or metabolic burden. Metabolome analyses revealed an increase in pool sizes of ethylmalonyl-CoA and methylmalonyl-CoA of more than 6- and 35-fold, respectively, relative to wild type, suggesting a strongly reduced conversion of these central intermediates, which are essential for glyoxylate regeneration in this model methylotroph. Similar results were found for M. extorquens AM1 pCM160 which confers kanamycin resistance. These intermediates of the ethylmalonyl-CoA pathway have in common their conversion by coenzyme B(12-dependent mutases, which have cobalt as a central ligand. The one-carbon metabolism-related growth delay was restored by providing higher cobalt concentrations, by heterologous expression of isocitrate lyase as an alternative path for glyoxylate regeneration, or by identification and overproduction of proteins involved in cobalt import. CONCLUSIONS/SIGNIFICANCE: This study demonstrates that the introduction of the plasmids leads to an apparent inhibition of the cobalt-dependent enzymes of the ethylmalonyl-CoA pathway. Possible explanations are presented and point to a limited cobalt concentration in the cell as a consequence of the antibiotic stress.

  5. Gene expression analysis uncovers novel hedgehog interacting protein (HHIP) effects in human bronchial epithelial cells.

    Science.gov (United States)

    Zhou, Xiaobo; Qiu, Weiliang; Sathirapongsasuti, J Fah; Cho, Michael H; Mancini, John D; Lao, Taotao; Thibault, Derek M; Litonjua, Augusto A; Bakke, Per S; Gulsvik, Amund; Lomas, David A; Beaty, Terri H; Hersh, Craig P; Anderson, Christopher; Geigenmuller, Ute; Raby, Benjamin A; Rennard, Stephen I; Perrella, Mark A; Choi, Augustine M K; Quackenbush, John; Silverman, Edwin K

    2013-05-01

    Hedgehog interacting protein (HHIP) was implicated in chronic obstructive pulmonary disease (COPD) by genome-wide association studies (GWAS). However, it remains unclear how HHIP contributes to COPD pathogenesis. To identify genes regulated by HHIP, we performed gene expression microarray analysis in a human bronchial epithelial cell line (Beas-2B) stably infected with HHIP shRNAs. HHIP silencing led to differential expression of 296 genes; enrichment for variants nominally associated with COPD was found. Eighteen of the differentially expressed genes were validated by real-time PCR in Beas-2B cells. Seven of 11 validated genes tested in human COPD and control lung tissues demonstrated significant gene expression differences. Functional annotation indicated enrichment for extracellular matrix and cell growth genes. Network modeling demonstrated that the extracellular matrix and cell proliferation genes influenced by HHIP tended to be interconnected. Thus, we identified potential HHIP targets in human bronchial epithelial cells that may contribute to COPD pathogenesis.

  6. The SEA of the Future: Uncovering the Productivity Promise of Rural Education. Volume 4

    Science.gov (United States)

    Gross, Betheny, Ed.; Jochim, Ashley, Ed.

    2015-01-01

    "The SEA of the Future" is an education publication series examining how state education agencies can shift from a compliance to a performance-oriented organization through strategic planning and performance management tools to meet growing demands to support education reform while improving productivity. This is the fourth volume in the…

  7. Conched out: Total reconstructed fisheries catches for the Turks and Caicos Islands uncover unsustainable resource usage

    Directory of Open Access Journals (Sweden)

    Aylin eUlman

    2016-05-01

    Full Text Available The Turks and Caicos Islands’ total marine fisheries catches were estimated for 1950-2012 using a catch reconstruction approach, estimating all removals, including reported catch destined for export, and unreported domestic artisanal and subsistence catches. Total reconstructed catch for the period is approximately 2.8 times that reported by Turks and Caicos to the FAO, and 86% higher than the export-adjusted national reported baseline. The pattern of total catches (strong decline to 1970, followed by gradual increase differs distinctly from that shown by data reported to FAO. Reported landings show a steady increase from less than 1,000 t∙year-1 in the 1950s to around 6,000 t∙year-1 in the 2000s. In contrast, the total reconstructed catches suggest declines in total catches from around 20,000 t in 1950 to a low of about 5,000 t in 1970, before gradual increases to about 12 500 t·year-1 in the late 2000s. Major discrepancies between reported and reconstructed data are under-reported artisanal catches in the early decades (accounting for 86% of total catches, and the absence of subsistence catches (14% of total catches in reported data. Queen conch (Strombus gigas and Caribbean spiny lobster (Panulirus argus dominate reconstructed catches. No discards were estimated as fishing has been highly selective, carried out by hand collection (conch, trap or hook (lobster, or hook and line (finfish. New data published here from local seafood consumption surveys demonstrates that the total local consumption of conch equates to almost the entire total allowable catch, before exported amounts are even factored. Policy-makers in the Turks and Caicos need to act if the sustainability of the fisheries stock and fishing industry is to be ensured.

  8. Metastatic breast carcinoma uncovered in an otherwise unremarkable “random colon biopsy”

    Directory of Open Access Journals (Sweden)

    Mike Black

    2016-06-01

    Full Text Available Breast cancer is one of the most devastating cancers afflicting women, being a main cause of cancer related death. Approximately 50% of these patients have developed regional or distant metastases at the time of diagnosis; hence, an early diagnosis and surgery with indicated neoadjuvant therapy are crucial in eradicating this disease and improving patient survival. A significant percentage of patients, even after initial satisfactory tumor removal, still face the threat of metastatic diseases which could plague a wide spectrum of body sites such as bones, lungs, central nervous system, liver and gastrointestinal tract (mostly upper gastrointestinal locations. Colonic and anorectal involvement by metastatic breast cancer has been less frequently reported in disseminated diseases. Typically, metastatic disease presents as a mass, enteric stenosis, or obstruction. Rare cases, however, may not form an endoscopically or radiologically recognizable lesion, and thus could be overlooked. Here we report a unique case of random colon biopsies in a patient presenting with epigastric pain, whose stomach biopsy showed Helicobacter pylori-associated chronic active gastritis. No colonoscopic lesion was present; however, microscopic examination of the “random biopsy” revealed scattered single and small clusters of tumor cells involving the lamina propria of the colonic mucosa, morphologically and immunophenotypically consistent with metastatic disease from breast carcinoma. The clinical presentation and histopathology of the case were reviewed and compared with limited cases reported in the literature. We conclude that high levels of suspicion and alertness are essential to identify occult microscopic gastrointestinal metastatic breast cancer in the absence of a grossly appreciable lesion.

  9. Uncovering the Near-IR Dwarf Galaxy Population of the Coma Cluster with Spitzer IRAC

    CERN Document Server

    Jenkins, L P; Mobasher, B; Alexander, D M; Bauer, F E

    2007-01-01

    We present the first results of a Spitzer IRAC (Infrared Array Camera) wide-field survey of two regions of the Coma cluster, in which we detect a large population of dwarf galaxies. The observations cover two fields of different galaxy densities; the first is a 0.733 deg^2 region in the core of the cluster (Coma 1), the second a 0.555 deg^2 off-center region located ~57 arcmin (1.7 Mpc) south-west from the center (Coma 3). The observations, although short 70-90 second exposures, are very sensitive; we detect ~29200 sources at 3.6 micron over the total ~1.3 deg^2 survey area. After identifying and excluding foreground stars, we construct 3.6 micron galaxy luminosity functions (LFs) for each field using selection functions based on spectroscopic redshifts to account for background objects. At the bright end, the LFs are well modeled by a traditional Schechter function; [M^star (3.6 micron), alpha_1] = [-25.17, -1.18] and [-24.69, -1.30] for Coma 1 and Coma 3 respectively. However, at the faint end M(3.6 micron)...

  10. Uncovering Reading Habits of University Students in Uganda: Does ICT Matter?

    Science.gov (United States)

    Mlay, Samali V.; Sabi, Humphrey M.; Tsuma, Clive K.; Langmia, Kehbuma

    2015-01-01

    This paper investigates how Information and Communication Technology (ICT) can improve reading habits among university students. We also investigated the influence of home culture, school culture and disposable income on reading habit. Our main objective was to assess the effect of ICT on the reading habit of particularly university students in…

  11. Gene expression ontogeny of spermatogenesis in the marmoset uncovers primate characteristics during testicular development.

    Science.gov (United States)

    Lin, Zachary Yu-Ching; Hirano, Takamasa; Shibata, Shinsuke; Seki, Naomi M; Kitajima, Ryunosuke; Sedohara, Ayako; Siomi, Mikiko C; Sasaki, Erika; Siomi, Haruhiko; Imamura, Masanori; Okano, Hideyuki

    2015-04-01

    Mammalian spermatogenesis has been investigated extensively in rodents and a strictly controlled developmental process has been defined at cellular and molecular levels. In comparison, primate spermatogenesis has been far less well characterized. However, important differences between primate and rodent spermatogenesis are emerging so it is not always accurate to extrapolate findings in rodents to primate systems. Here, we performed an extensive immunofluorescence study of spermatogenesis in neonatal, juvenile, and adult testes in the common marmoset (Callithrix jacchus) to determine primate-specific patterns of gene expression that underpin primate germ cell development. Initially we characterized adult spermatogonia into two main classes; mitotically active C-KIT(+)Ki67(+) cells and mitotically quiescent SALL4(+)PLZF(+)LIN28(+)DPPA4(+) cells. We then explored the expression of a set of markers, including PIWIL1/MARWI, VASA, DAZL, CLGN, RanBPM, SYCP1 and HAPRIN, during germ cell differentiation from early spermatocytes through round and elongating spermatids, and a clear program of gene expression changes was determined as development proceeded. We then examined the juvenile marmoset testis. Markers of gonocytes demonstrated two populations; one that migrates to the basal membrane where they form the SALL4(+) or C-KIT(+) spermatogonia, and another that remains in the lumen of the seminiferous tubule. This later population, historically identified as pre-spermatogonia, expressed meiotic and apoptotic markers and were eliminated because they appear to have failed to correctly migrate. Our findings provide the first platform of gene expression dynamics in adult and developing germ cells of the common marmoset. Although we have characterized a limited number of genes, these results will facilitate primate spermatogenesis research and understanding of human reproduction.

  12. Model Wheat Genotypes as Tools to Uncover Effective Defense Mechanisms Against the Hemibiotrophic Fungus Bipolaris sorokiniana.

    Science.gov (United States)

    Ibeagha, Aloysius Ebelechukwu; Hückelhoven, Ralph; Schäfer, Patrick; Singh, Devendra Pal; Kogel, Karl-Heinz

    2005-05-01

    ABSTRACT We investigated the interaction of several differentially resistant wheatwith the hemibiotrophic phytopathogenic fungus Bipolaris sorokiniana (teleomorph Cochliobolus sativus). Wheat genotypes Yangmai, M 3 (W7976), Shanghai 4, and Chirya 7 showed higher levels of resistancewith cv. Sonalika, used as a susceptible control. In amicroscopic inspection, we found that fungal penetration intoepidermal layer failed mostly through a cell wall-associated defense. In cases where the fungus successfully overcame epidermal, its spread within the mesophyll tissue (necrotrophic phase) wasin the more resistant genotypes. Epidermal cell wall-associated, spreading as well as the extent of electrolyte leakage of infected, correlated well with field resistance. We propose that cellular hostsuch as formation of cell wall appositions as well as the degreeearly mesophyll spreading of fungal hyphae are indicative of thepotential of the respective host genotype and, therefore, could befor the characterization of new spot blotch resistance traits in cereals.

  13. Using Think-Aloud Protocols to Uncover Misconceptions and Improve Developmental Math Instruction: An Exploratory Study

    Directory of Open Access Journals (Sweden)

    Charles Secolsky

    2016-01-01

    Full Text Available Deficiencies in education continue to escalate around the world. The focus on outcomes assessment has narrowed instructional research and curriculum evaluation to standardized testing in certain subject areas. A prototype for a quantitative literacy assessment instrument was developed with the goal of diagnosing student misconceptions of basic mathematics content and changing instructional practices to undo the misconceptions by applying cognitive psychological theory. Two hundred thirty-eight basic math high school students and 209 remedial community college students in New Jersey and New York were administered the instrument, which had been based on coded data from think-aloud protocols. The instrument asked students to answer 20 basic mathematics items and, in addition, to evaluate four possible solution strategies. For each item, frequencies of selected solution strategies and the association between strategy selection and performance on the 20-question math test are presented as a means for improving instruction. Follow-up research is proposed for determining whether undoing the student misconceptions first before teaching material on a new unit of instruction may yield more positive student outcomes.

  14. Fear memory uncovered: Prediction error as the key to memory plasticity

    NARCIS (Netherlands)

    Sevenster, D.

    2014-01-01

    Anxiety disorders rank among the most prevalent and chronic forms of psychopathology. While commonly used therapeutic techniques such as exposure therapy are effective in reducing fear, many patients suffer from relapse of fear. This can be explained by the observation that during therapy a new memo

  15. Genetic architecture of vitamin B12 and folate levels uncovered applying deeply sequenced large datasets

    DEFF Research Database (Denmark)

    Grarup, Niels; Sulem, Patrick; Sandholt, Camilla H;

    2013-01-01

    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 B12 (B12) and folate. Up to 22.9 million sequence variants were analyzed in combined...... in serum B12 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....

  16. Assembling a game development scene? Uncovering Finland’s largest demo party

    Directory of Open Access Journals (Sweden)

    Heikki Tyni

    2014-03-01

    Full Text Available The study takes look at Assembly, a large-scale LAN and demo party founded in 1992 and organized annually in Helsinki, Finland. Assembly is used as a case study to explore the relationship between computer hobbyism – including gaming, demoscene and other related activities – and professional game development. Drawing from expert interviews, a visitor query and news coverage we ask what kind of functions Assembly has played for the scene in general, and on the formation and fostering of the Finnish game industry in particular. The conceptual contribution of the paper is constructed around the interrelated concepts of scene, technicity and gaming capital.

  17. NIH study uncovers new mechanism of action for class of chemotherapy drugs

    Science.gov (United States)

    NIH researchers have discovered a significant new mechanism of action for a class of chemotherapy drugs known as poly (ADP-ribose) polymerase inhibitors, or PARP inhibitors. They have also identified differences in the toxic capabilities of three drugs in

  18. 76 FR 47151 - Uncovered Innerspring Units From the People's Republic of China: Preliminary Intent To Rescind...

    Science.gov (United States)

    2011-08-04

    ... comments and surrogate value data from Quan Li and Yongnuo, as well as from Petitioner.\\3\\ \\3\\ The... sizes corresponding to the sizes of adult mattresses (e.g., twin, twin long, full, full long, queen... regulations. Public Comment and FOP Data In accordance with section 351.301(c)(3)(ii) of the...

  19. Shadowing: Who Benefits and How? Uncovering a Booming EFL Teaching Technique for Listening Comprehension

    Science.gov (United States)

    Hamada, Yo

    2016-01-01

    This study examines common claims associated with shadowing. Studies in Japan conclude that shadowing is effective for improving learners' listening skills. Two common claims are that shadowing is effective for lower-proficiency learners and that it enhances learners' phoneme perception, thus improving listening comprehension skills. The former…

  20. A first step toward uncovering the truth about weight tuning in deformable image registration

    Science.gov (United States)

    Pirpinia, Kleopatra; Bosman, Peter A. N.; Sonke, Jan-Jakob; van Herk, Marcel; Alderliesten, Tanja

    2016-03-01

    Deformable image registration is currently predominantly solved by optimizing a weighted linear combination of objectives. Successfully tuning the weights associated with these objectives is not trivial, leading to trial-and-error approaches. Such an approach assumes an intuitive interplay between weights, optimization objectives, and target registration errors. However, it is not known whether this always holds for existing registration methods. To investigate the interplay between weights, optimization objectives, and registration errors, we employ multi-objective optimization. Here, objectives of interest are optimized simultaneously, causing a set of multiple optimal solutions to exist, called the optimal Pareto front. Our medical application is in breast cancer and includes the challenging prone-supine registration problem. In total, we studied the interplay in three different ways. First, we ran many random linear combinations of objectives using the well-known registration software elastix. Second, since the optimization algorithms used in registration are typically of a local-search nature, final solutions may not always form a Pareto front. We therefore employed a multi-objective evolutionary algorithm that finds weights that correspond to registration outcomes that do form a Pareto front. Third, we examined how the interplay differs if a true multi-objective (i.e., weight-free) image registration method is used. Results indicate that a trial-and-error weight-adaptation approach can be successful for the easy prone to prone breast image registration case, due to the absence of many local optima. With increasing problem difficulty the use of more advanced approaches can be of value in finding and selecting the optimal registration outcomes.