Powdery mildew fungal effector candidates share N-terminal Y/F/WxC-motif

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Emmersen Jeppe

2010-05-01

Full Text Available Abstract Background Powdery mildew and rust fungi are widespread, serious pathogens that depend on developing haustoria in the living plant cells. Haustoria are separated from the host cytoplasm by a plant cell-derived extrahaustorial membrane. They secrete effector proteins, some of which are subsequently transferred across this membrane to the plant cell to suppress defense. Results In a cDNA library from barley epidermis containing powdery mildew haustoria, two-thirds of the sequenced ESTs were fungal and represented ~3,000 genes. Many of the most highly expressed genes encoded small proteins with N-terminal signal peptides. While these proteins are novel and poorly related, they do share a three-amino acid motif, which we named "Y/F/WxC", in the N-terminal of the mature proteins. The first amino acid of this motif is aromatic: tyrosine, phenylalanine or tryptophan, and the last is always cysteine. In total, we identified 107 such proteins, for which the ESTs represent 19% of the fungal clones in our library, suggesting fundamental roles in haustoria function. While overall sequence similarity between the powdery mildew Y/F/WxC-proteins is low, they do have a highly similar exon-intron structure, suggesting they have a common origin. Interestingly, searches of public fungal genome and EST databases revealed that haustoria-producing rust fungi also encode large numbers of novel, short proteins with signal peptides and the Y/F/WxC-motif. No significant numbers of such proteins were identified from genome and EST sequences from either fungi which do not produce haustoria or from haustoria-producing Oomycetes. Conclusion In total, we identified 107, 178 and 57 such Y/F/WxC-proteins from the barley powdery mildew, the wheat stem rust and the wheat leaf rust fungi, respectively. All together, our findings suggest the Y/F/WxC-proteins to be a new class of effectors from haustoria-producing pathogenic fungi.

Role of phonon scattering by elastic strain field in thermoelectric Sr1−xYxTiO3−δ

KAUST Repository

Bhattacharya, S.

2014-06-12

Perovskite-type SrTiO3-δ ceramics are multifunctional materials with significant potential as n-type thermoelectric (TE) materials. The electronic and thermal transport properties of spark plasma sintered polycrystalline Sr1-xYxTiO3-δ (x=0.05, 0.075, 0.1) ceramics are systematically investigated from (15-800) K. The Sr0.9Y0.1TiO3-δ simultaneously exhibits a large Seebeck coefficient, α>-80μV/K and moderately high electrical resistivity, ρ∼0.8mΩ-cm at a carrier concentration of ∼1021cm-3 at 300K resulting in a high TE power factor defined herein as (α2σT)∼0.84W/m-K at 760K. Despite the similar atomic masses of Sr (87.6g/mol) and Y (88.9g/mol), the lattice thermal conductivity (κL) of Sr1-xY xTiO3-δ is significantly reduced with increased Y-doping, owing to the smaller ionic radii of Y3+ (∼1.23Å, coordination number 12) compared to Sr2+ (∼1.44Å, coordination number 12) ions. In order to understand the thermal conductivity reduction mechanism, the κL in the Sr1-xY xTiO3-δ series are phenomenologically modeled with a modified Callaway\\'s equation from 30-600K. Phonon scattering by elastic strain field due to ionic radii mismatch is found to be the prominent scattering mechanism in reducing κL of these materials. In addition, the effect of Y-doping on the elastic moduli of Sr1-xY xTiO3-δ (x=0, 0.1) is investigated using resonant ultrasound spectroscopy, which exhibits an anomaly in x=0.1 in the temperature range 300-600K. As a result, the phonon mean free path is found to be further reduced in the Sr0.9Y0.1TiO3-δ compared to that of SrTiO3-δ, resulting in a considerably low thermal conductivity κ∼2.7W/m-K at 760K. Finally, we report a thermoelectric figure of merit (ZT)∼0.3 at 760K in the Sr0.9Y 0.1TiO3-δ, the highest ZT value reported in the Y-doped SrTiO3 ceramics thus far. © 2014 AIP Publishing LLC.

Role of phonon scattering by elastic strain field in thermoelectric Sr1−xYxTiO3−δ

KAUST Repository

Bhattacharya, S.; Mehdizadeh Dehkordi, A.; Tennakoon, S.; Adebisi, R.; Gladden, J. R.; Darroudi, T.; Alshareef, Husam N.; Tritt, T. M.

2014-01-01

Perovskite-type SrTiO3-δ ceramics are multifunctional materials with significant potential as n-type thermoelectric (TE) materials. The electronic and thermal transport properties of spark plasma sintered polycrystalline Sr1-xYxTiO3-δ (x=0.05, 0.075, 0.1) ceramics are systematically investigated from (15-800) K. The Sr0.9Y0.1TiO3-δ simultaneously exhibits a large Seebeck coefficient, α>-80μV/K and moderately high electrical resistivity, ρ∼0.8mΩ-cm at a carrier concentration of ∼1021cm-3 at 300K resulting in a high TE power factor defined herein as (α2σT)∼0.84W/m-K at 760K. Despite the similar atomic masses of Sr (87.6g/mol) and Y (88.9g/mol), the lattice thermal conductivity (κL) of Sr1-xY xTiO3-δ is significantly reduced with increased Y-doping, owing to the smaller ionic radii of Y3+ (∼1.23Å, coordination number 12) compared to Sr2+ (∼1.44Å, coordination number 12) ions. In order to understand the thermal conductivity reduction mechanism, the κL in the Sr1-xY xTiO3-δ series are phenomenologically modeled with a modified Callaway's equation from 30-600K. Phonon scattering by elastic strain field due to ionic radii mismatch is found to be the prominent scattering mechanism in reducing κL of these materials. In addition, the effect of Y-doping on the elastic moduli of Sr1-xY xTiO3-δ (x=0, 0.1) is investigated using resonant ultrasound spectroscopy, which exhibits an anomaly in x=0.1 in the temperature range 300-600K. As a result, the phonon mean free path is found to be further reduced in the Sr0.9Y0.1TiO3-δ compared to that of SrTiO3-δ, resulting in a considerably low thermal conductivity κ∼2.7W/m-K at 760K. Finally, we report a thermoelectric figure of merit (ZT)∼0.3 at 760K in the Sr0.9Y 0.1TiO3-δ, the highest ZT value reported in the Y-doped SrTiO3 ceramics thus far. © 2014 AIP Publishing LLC.

Producción de acido láctico por Lactobacillus plantarum L10 en cultivos batch y continuo

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Waldir Estela

2013-04-01

Full Text Available Se ha ensayado a escala de laboratorio la cepa Lactobacillus plantarum L10, para la producción de ácido láctico en cultivos batch y continuo; además se ha optimizado la composición del medio y las condiciones de cultivo para este propósito. Los mejores parámetros de producción de ácido láctico encontrados en cultivo batch fueron los siguientes: YP/S 86,1%; PP 5,4 g/L/h; unido a YX/S 13,2%; PX 1,2 g/L/h y μ = 0,2 h-1, el cultivo se ha llevado a cabo en un medio conteniendo glucosa 70 g/L; extracto de levadura 12,1 g/L; KH2PO4 1,2 g/L; (NH42HPO4 1,2 g/L; citrato de amonio 3,0 g/L; MgSO4. 7H2O 0,3 g/L y MnSO4. 4H2O 0,03 g/L. Así mismo los mejores parámetros de producción de ácido láctico encontrados en cultivo continuo fueron los siguientes: YP/S 96%; P´P 6,0 g/L/h; unido a YX/S 19 %; P´X 1,2 g/L/h; y tasa de dilución (D 0,46 h-1.

High-pressure synthesis and crystal structure of α-Y{sub 2}B{sub 4}O{sub 9}

Energy Technology Data Exchange (ETDEWEB)

Schmitt, Martin K.; Huppertz, Hubert [Innsbruck Univ. (Austria). Inst. fuer Allgemeine, Anorganische und Theoretische Chemie

2017-07-01

α-Y{sub 2}B{sub 4}O{sub 9} was synthesized in a high-pressure/high-temperature experiment at 12.3 GPa/1020 C. The crystal structure has been determined via single-crystal X-ray diffraction. α-Y{sub 2}B{sub 4}O{sub 9} is isotypic to the lanthanide borates α-Ln{sub 2}B{sub 4}O{sub 9} (Ln = Sm-Ho) and crystallizes in the monoclinic space group C2/c (no. 15) with the following lattice parameters: a = 25.084(2), b = 4.3913(2), c = 24.726(2) Aa, and β = 99.97(1) . The compound was further characterized via X-ray powder diffraction as well as IR and Raman spectroscopy.

Lithium-deficient Li YMn2O4 spinels (0.9 ≤ Y < 1): Lithium content, synthesis temperature, thermal behaviour and electrochemical properties

International Nuclear Information System (INIS)

Pascual, Laura; Perez-Revenga, M. Luz; Rojas, Rosa M.; Rojo, Jose M.; Amarilla, J. Manuel

2006-01-01

Lithium-deficient Li Y Mn 2 O 4 spinels (LD-Li Y Mn 2 O 4 ) with nominal composition (0.9 ≤ Y 2 O 3 and LiNO 3 at temperatures ranging from 700 deg. C to 850 deg. C. X-ray diffraction data show that LD-Li Y Mn 2 O 4 spinels are obtained as single phases in the range Y = 0.975-1 at 700 deg. C and 750 deg. C. Morphological characterization by transmission electron microscopy shows that the particle size of LD-Li Y Mn 2 O 4 spinels increases on decreasing the Li-content. The influence of the Li-content and the synthesis temperature on the thermal and electrochemical behaviours has been systematically studied. Thermal analysis studies indicate that the temperature of the first thermal effect in the differential thermal analysis (DTA)/thermogravimetric (TG) curves, T C1 , linearly increases on decreasing the Li-content. The electrochemical properties of LD-Li Y Mn 2 O 4 spinels, determined by galvanostatic cycling, notably change with the synthesis conditions. So, the first discharge capacity, Q disch. , at C rate increases on rising the Li-content and the synthesis temperature. The sample Li 0.975 Mn 2 O 4 synthesized at 700 deg. C has a Q disch. = 123 mAh g -1 and a capacity retention of 99.77% per cycle. This LD-Li Y Mn 2 O 4 sample had the best electrochemical characteristics of the series

SAW propagation characteristics of TeO3/3C-SiC/LiNbO3 layered structure

Science.gov (United States)

Soni, Namrata D.

2018-04-01

Surface acoustic wave (SAW) devices based on Lithium Niobate (LiNbO3) single crystal are advantageous because of its high SAW phase velocity, electromechanical coupling coefficient and cost effectiveness. In the present work a new multi-layered TeO3/3C-SiC/128° Y-X LiNbO3 SAW device has been proposed. SAW propagation properties such as phase velocity, coupling coefficient and temperature coefficient of delay (TCD) of the TeO3/SiC/128° Y-X LiNbO3 multi layered structure is examined using theoretical calculations. It is found that the integration of 0.09λ thick 3C-SiC over layer on 128° Y-X LiNbO3 increases its electromechanical coupling coefficient from 5.3% to 9.77% and SAW velocity from 3800 ms‑1 to 4394 ms‑1. The SiC/128° Y-X LiNbO3 bilayer SAW structure exhibits a high positive TCD value. A temperature stable layered SAW device could be obtained with introduction of 0.007λ TeO3 over layer on SiC/128° Y-X LiNbO3 bilayer structure without sacrificing the efficiency of the device. The proposed TeO3/3C-SiC/128° Y-X LiNbO3 multi-layered SAW structure is found to be cost effective, efficient, temperature stable and suitable for high frequency application in harsh environment.

Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2

DEFF Research Database (Denmark)

Miller, Martin Lee; Hanke, S.; Hinsby, A. M.

2008-01-01

set of 481 unique phosphotyrosine (Tyr(P)) peptides by sequence similarity to known ligands of the Src homology 2 (SH2) and the phosphotyrosine binding (PTB) domains. From 20 clusters we extracted 16 known and four new interaction motifs. Using quantitative mass spectrometry we pulled down Tyr......(P)-specific binding partners for peptides corresponding to the extracted motifs. We confirmed numerous previously known interaction motifs and found 15 new interactions mediated by phosphosites not previously known to bind SH2 or PTB. Remarkably, a novel hydrophobic N-terminal motif ((L/V/I)(L/V/I)pY) was identified...

An intact PDZ motif is essential for correct P2Y12 purinoceptor traffic in human platelets.

Science.gov (United States)

Nisar, Shaista; Daly, Martina E; Federici, Augusto B; Artoni, Andrea; Mumford, Andrew D; Watson, Stephen P; Mundell, Stuart J

2011-11-17

The platelet P2Y(12) purinoceptor (P2Y(12)R), which plays a crucial role in hemostasis, undergoes internalization and subsequent recycling to maintain receptor responsiveness, processes that are essential for normal platelet function. Here, we observe that P2Y(12)R function is compromised after deletion or mutation of the 4 amino acids at the extreme C-terminus of this receptor (ETPM), a putative postsynaptic density 95/disc large/zonula occludens-1 (PDZ)-binding motif. In cell line models, removal of this sequence or mutation of one of its core residues (P341A), attenuates receptor internalization and receptor recycling back to the membrane, thereby blocking receptor resensitization. The physiologic significance of these findings in the regulation of platelet function is shown by identification of a patient with a heterozygous mutation in the PDZ binding sequence of their P2Y(12)R (P341A) that is associated with reduced expression of the P2Y(12)R on the cell surface. Importantly, platelets from this subject showed significantly compromised P2Y(12)R recycling, emphasizing the importance of the extreme C-terminus of this receptor to ensure correct receptor traffic.

Overexpression, purification, crystallization and preliminary X-ray analysis of CheY4 from Vibrio cholerae O395

International Nuclear Information System (INIS)

Biswas, Maitree; Khamrui, Susmita; Sen, Udayaditya; Dasgupta, Jhimli

2011-01-01

The chemotaxis response regulator CheY4 from V. cholerae has been cloned, overexpressed, purified and crystallized in monoclinic and hexagonal space groups; the crystals diffracted to 1.67 and 1.9 Å resolution, respectively. Chemotaxis and motility greatly influence the infectivity of Vibrio cholerae, although the role of chemotaxis genes in V. cholerae pathogenesis is poorly understood. In contrast to the single copy of CheY found in Escherichia coli and Salmonella typhimurium, four CheYs (CheY1–CheY4) are present in V. cholerae. While insertional disruption of the cheY4 gene results in decreased motility, insertional duplication of this gene increases motility and causes enhanced expression of the two major virulence genes. Additionally, cheY3/cheY4 influences the activation of the transcription factor NF-κB, which triggers the generation of acute inflammatory responses. V. cholerae CheY4 was cloned, overexpressed and purified by Ni–NTA affinity chromatography followed by gel filtration. Crystals of CheY4 grown in space group C2 diffracted to 1.67 Å resolution, with unit-cell parameters a = 94.4, b = 31.9, c = 32.6 Å, β = 96.5°, whereas crystals grown in space group P3 2 21 diffracted to 1.9 Å resolution, with unit-cell parameters a = b = 56.104, c = 72.283 Å, γ = 120°

Identification of four families of yCCR4- and Mg2+-dependent endonuclease-related proteins in higher eukaryotes, and characterization of orthologs of yCCR4 with a conserved leucine-rich repeat essential for hCAF1/hPOP2 binding

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Corbo Laura

2001-11-01

Full Text Available Abstract Background The yeast yCCR4 factor belongs to the CCR4-NOT transcriptional regulatory complex, in which it interacts, through its leucine-rich repeat (LRR motif with yPOP2. Recently, yCCR4 was shown to be a component of the major cytoplasmic mRNA deadenylase complex, and to contain a fold related to the Mg2+-dependent endonuclease core. Results Here, we report the identification of nineteen yCCR4-related proteins in eukaryotes (including yeast, plants and animals, which all contain the yCCR4 endonuclease-like fold, with highly conserved CCR4-specific residues. Phylogenetic and genomic analyses show that they form four distinct families, one of which contains the yCCR4 orthologs. The orthologs in animals possess a leucine-rich repeat domain. We show, using two-hybrid and far-Western assays, that the human member binds to the human yPOP2 homologs, i.e. hCAF1 and hPOP2, in a LRR-dependent manner. Conclusions We have identified the mammalian orthologs of yCCR4 and have shown that the human member binds to the human yPOP2 homologs, thus strongly suggesting conservation of the CCR4-NOT complex from yeast to human. All members of the four identified yCCR4-related protein families show stricking conservation of the endonuclease-like catalytic motifs of the yCCR4 C-terminal domain and therefore constitute a new family of potential deadenylases in mammals.

The KYxxL motif in Rad17 protein is essential for the interaction with the 9–1–1 complex

Energy Technology Data Exchange (ETDEWEB)

Fukumoto, Yasunori, E-mail: fukumoto@faculty.chiba-u.jp [Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675 (Japan); Ikeuchi, Masayoshi; Nakayama, Yuji [Department of Biochemistry & Molecular Biology, Kyoto Pharmaceutical University, Kyoto 607-8414 (Japan); Yamaguchi, Naoto, E-mail: nyama@faculty.chiba-u.jp [Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675 (Japan)

2016-09-02

ATR-dependent DNA damage checkpoint is the major DNA damage checkpoint against UV irradiation and DNA replication stress. The Rad17–RFC and Rad9–Rad1–Hus1 (9–1–1) complexes interact with each other to contribute to ATR signaling, however, the precise regulatory mechanism of the interaction has not been established. Here, we identified a conserved sequence motif, KYxxL, in the AAA+ domain of Rad17 protein, and demonstrated that this motif is essential for the interaction with the 9–1–1 complex. We also show that UV-induced Rad17 phosphorylation is increased in the Rad17 KYxxL mutants. These data indicate that the interaction with the 9–1–1 complex is not required for Rad17 protein to be an efficient substrate for the UV-induced phosphorylation. Our data also raise the possibility that the 9–1–1 complex plays a negative regulatory role in the Rad17 phosphorylation. We also show that the nucleotide-binding activity of Rad17 is required for its nuclear localization. - Highlights: • We have identified a conserved KYxxL motif in Rad17 protein. • The KYxxL motif is crucial for the interaction with the 9–1–1 complex. • The KYxxL motif is dispensable or inhibitory for UV-induced Rad17 phosphorylation. • Nucleotide binding of Rad17 is required for its nuclear localization.

Growth, thermal and laser properties of Yb:YxLu1−xVO4 mixed crystal

International Nuclear Information System (INIS)

Zhong, Degao; Teng, Bing; Kong, Weijin; Li, Jianhong; Zhang, Shiming; Li, Yuyi; Cao, Lifeng; Yang, Liting; He, Linxiang; Huang, Wanxia

2015-01-01

New mixed crystal of Yb: Y 0.78 Lu 0.22 VO 4 with Yb ion concentration of 0.3 at% was grown by Czochralski method. Transmission synchrotron X-ray topography implies that this mixed crystal follows a rotational growth pattern. Crystal structure of this crystal was determined by X-ray diffraction. It showed that this crystal possesses a tetragonal zircon structure (ZrSiO 4 , space group I41/amd), as YVO 4 and LuVO 4 do. Thermal properties of this crystal were characterized by measuring its specific heat, thermal expansion coefficients and thermal conductivities. The specific heat was determined to be 0.500 J g −1 K −1 at 293 K. The average linear thermal expansion coefficients were calculated to be α 11 = 1.73 × 10 −6 K −1 and α 33 = 9.43 × 10 −6 K −1 , over the temperature range of 300–777 K. The thermal conductivities were calculated to be κ 11 = 5.47 W m −1 K −1 and κ 33 = 6.64 W m −1 K −1 at 303 K. Continuous-wave (cw) laser test on Yb: Y 0.78 Lu 0.22 VO 4 was conducted at room temperature in the wavelength range of 1035.7–1048.3 nm, and a 13.5% optical-to-optical efficiency was achieved. The good thermal properties of Yb:Y 0.78 Lu 0.22 VO 4 mixed crystal and its attractive cw laser performance make it very suitable for practical applications. - Highlights: • New Yb:Y 0.78 Lu 0.22 VO 4 mixed laser crystals were grown. • The thermal expansion, thermal diffusivity and specific heat were measured. • Cw laser operation was realized at room temperature in the range of 1035.7–1048.3 nm

Study of formation of deep trapping mechanism by UV, beta and gamma irradiated Eu(3+) activated SrY2O4 and Y4Al2O9 phosphors.

Science.gov (United States)

Dubey, Vikas; Kaur, Jagjeet; Parganiha, Yogita; Suryanarayana, N S; Murthy, K V R

2016-04-01

This paper reports the thermoluminescence properties of Eu(3+) doped different host matrix phosphors (SrY2O4 and Y4Al2O9). The phosphor is prepared by high temperature solid state reaction method. The method is suitable for large scale production and fixed concentration of boric acid using as a flux. The prepared samples were characterized by X-ray diffraction technique and the crystallite size calculated by Scherer's formula. The prepared phosphor characterized by Scanning Electron Microscopic (SEM), Fourier Transform Infrared (FTIR), Energy Dispersive X-ray analysis (EDX), thermoluminescence (TL) and Transmission Electron Microscopic (TEM) techniques. The prepared phosphors for different concentration of Eu(3+) ions were examined by TL glow curve for UV, beta and gamma irradiation. The UV 254nm source used for UV irradiation, Sr(90) source was used for beta irradiation and Co(60) source used for gamma irradiation. SrY2O4:Eu(3+)and Y4Al2O9:Eu(3+) phosphors which shows both higher temperature peaks and lower temperature peaks for UV, beta and gamma irradiation. Here UV irradiated sample shows the formation of shallow trap (surface trapping) and the gamma irradiated sample shows the formation of deep trapping. The estimation of trap formation was evaluated by knowledge of trapping parameters. The trapping parameters such as activation energy, order of kinetics and frequency factor were calculated by peak shape method. Here most of the peak shows second order of kinetics. The effect of gamma, beta and UV exposure on TL studies was also examined and it shows linear response with dose which indicate that the samples may be useful for TL dosimetry. Formation of deep trapping mechanism by UV, beta and gamma irradiated Eu(3+) activated SrY2O4 and Y4Al2O9 phosphors is discussed in this paper. Copyright © 2015 Elsevier Ltd. All rights reserved.

Influence of Y doping concentration on the properties of nanostructured MxZn1-xO (M=Y) thin film deposited by nebulizer spray pyrolysis technique

Science.gov (United States)

Mariappan, R.; Ponnuswamy, V.; Chandra Bose, A.; Suresh, R.; Ragavendar, M.

2014-09-01

Yttrium doped Zinc Oxide (YxZn1-xO) thin films deposited at a substrate temperature 400 °C. The effect of substrate temperature on the structural, surface morphology, compositional, optical and electrical properties of YxZn1-xO thin films was studied. X-ray diffraction studies show that all films are polycrystalline in nature with hexagonal crystal structure having highly textured (002) plane parallel to the surface of the substrate. The structural parameters, such as lattice constants (a and c), crystallite size (D), dislocation density (δ), microstrain (σ) and texture coefficient were calculated for different yttrium doping concentrations (x). High resolution scanning electron microscopy measurements reveal that the surface morphology of the films change from platelet like grains to hexagonal structure with grain size increase due to the yttrium doping. Energy dispersive spectroscopy confirms the presence of Y, Zn and O elements in the films prepared. Optical studies showed that all samples have a strong optical transmittance higher than 70% in the visible range. A slight shift of the absorption edge towards the large wavelengths was observed as the Y doping concentration increased. This result shows that the band gap is slightly decreased from 3.10 to 2.05 eV with increase of the yttrium doping concentrations (up to 7.5%) and then slightly increased. Room temperature PL measurements were done and the band-to-band emission energies of films were determined and reported. The complex impedance of the 10%Y doped ZnO film shows two distinguished semicircles and the diameter of the arcs got decreased in diameter as the temperature increases from 70 to 175 °C.

Crystal structures and electronic properties of UTixNb3-xO10 (x=0,1/3,1) and of the intercalation compound Li0.9UTiNb2O10

International Nuclear Information System (INIS)

Dickens, P.G.; Flynn, G.J.; Patat, S.; Stuttart, G.P.

1997-01-01

Complete crystal structures of the related phases UTi x Nb 3-x O 10 (x=0,1/3,1) and of the intercalation compound Li 0.9 UTiNb 2 O 10 have been determined by Rietveld analysis of room-temperature powder neutron diffraction data. The new structural data combined with magnetic susceptibility measurements made in the range 5 y 1 U V 1+y-x U VI x-y Ti IV x Nb V 3-x O 10 (y≤ x ≤1) with U V (f 1 ) being the only paramagnetic species present. (Author)

Mitochondrial and Y chromosome haplotype motifs as diagnostic markers of Jewish ancestry: a reconsideration.

Directory of Open Access Journals (Sweden)

Sergio eTofanelli

2014-11-01

Full Text Available Several authors have proposed haplotype motifs based on site variants at the mitochondrial genome (mtDNA and the non-recombining portion of the Y chromosome (NRY to trace the genealogies of Jewish people. Here, we analyzed their main approaches and test the feasibility of adopting motifs as ancestry markers through construction of a large database of mtDNA and NRY haplotypes from public genetic genealogical repositories. We verified the reliability of Jewish ancestry prediction based on the Cohen and Levite Modal Haplotypes in their classical 6 STR marker format or in the extended 12 STR format, as well as four founder mtDNA lineages (HVS-I segments accounting for about 40% of the current population of Ashkenazi Jews. For this purpose we compared haplotype composition in individuals of self-reported Jewish ancestry with the rest of European, African or Middle Eastern samples, to test for non-random association of ethno-geographic groups and haplotypes. Overall, NRY and mtDNA based motifs, previously reported to differentiate between groups, were found to be more represented in Jewish compared to non-Jewish groups. However, this seems to stem from common ancestors of Jewish lineages being rather recent respect to ancestors of non-Jewish lineages with the same haplotype signatures. Moreover, the polyphyly of haplotypes which contain the proposed motifs and the misuse of constant mutation rates heavily affected previous attempts to correctly dating the origin of common ancestries. Accordingly, our results stress the limitations of using the above haplotype motifs as reliable Jewish ancestry predictors and show its inadequacy for forensic or genealogical purposes.

Multi-layered control of Galectin-8 mediated autophagy during adenovirus cell entry through a conserved PPxY motif in the viral capsid.

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Charlotte Montespan

2017-02-01

Full Text Available Cells employ active measures to restrict infection by pathogens, even prior to responses from the innate and humoral immune defenses. In this context selective autophagy is activated upon pathogen induced membrane rupture to sequester and deliver membrane fragments and their pathogen contents for lysosomal degradation. Adenoviruses, which breach the endosome upon entry, escape this fate by penetrating into the cytosol prior to autophagosome sequestration of the ruptured endosome. We show that virus induced membrane damage is recognized through Galectin-8 and sequesters the autophagy receptors NDP52 and p62. We further show that a conserved PPxY motif in the viral membrane lytic protein VI is critical for efficient viral evasion of autophagic sequestration after endosomal lysis. Comparing the wildtype with a PPxY-mutant virus we show that depletion of Galectin-8 or suppression of autophagy in ATG5-/- MEFs rescues infectivity of the PPxY-mutant virus while depletion of the autophagy receptors NDP52, p62 has only minor effects. Furthermore we show that wildtype viruses exploit the autophagic machinery for efficient nuclear genome delivery and control autophagosome formation via the cellular ubiquitin ligase Nedd4.2 resulting in reduced antigenic presentation. Our data thus demonstrate that a short PPxY-peptide motif in the adenoviral capsid permits multi-layered viral control of autophagic processes during entry.

4-(3-Bromopropyloxy-1-hydroxy-9,10-anthraquinone

Directory of Open Access Journals (Sweden)

Natsumi Ohira

2016-05-01

Full Text Available In the molecule of the title compound, C17H13BrO4, the anthraquinone ring system is slightly bent, with a dihedral angle of 169.99 (7° between the planes of the two benzene rings. The side chain (O—C—C—C—Br has a gauche–gauche conformation, as indicated by the O—C—C—C and C—C—C—Br torsion angles of −66.9 (2 and −65.8 (2°, respectively. In addition, there is an intramolecular O—H...O hydrogen bond enclosing an S(6 ring motif. The hydrogen-bond donor is bifurcated; in the crystal, a pair of O—H...O hydrogen bonds connects two molecules, forming an inversion dimer with an R22(12 ring motif.

The investigation of topological phase of Gd1-xYxAuPb (x = 0, 0.25, 0.5, 0.75, 1) alloys under hydrostatic pressure

Science.gov (United States)

Saeidi, Parviz; Nourbakhsh, Zahra

2018-04-01

Topological phase of Gd1-xYxAuPb (x = 0, 0.25, 0.5, 0.75, 1) alloys have been studied utilizing density function theory by WIEN2k code. The generalized gradient approximation (GGA), generalized gradient approximation plus Hubbard parameter (GGA + U), Modified Becke and Johnson (MBJ) and GGA Engel-vosko in the presence of spin orbit coupling have been used to investigate the topological band structure of Gd1-xYxAuPb alloys at zero pressure. The topological phase and band order of these alloys within GGA and GGA + U approaches under hydrostatic pressure are also investigated. We find that under hydrostatic pressure in some percentages of Gd1-xYxAuPb (x = 0, 0.25, 0.5, 0.75, 1) alloys in both GGA and GGA + U approaches, the trivial topological phase is converted into nontrivial topological phase. In addition, the band inversion strength versus lattice constant of these alloys is studied. Moreover, the schematic plan is represented in order to show the trivial and nontrivial topological phase of Gd1-xYxAuPb (x = 0, 0.25, 0.5, 0.75, 1) alloys in both GGA and GGA + U approaches.

Rtt107/Esc4 binds silent chromatin and DNA repair proteins using different BRCT motifs

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Jockusch Rebecca A

2006-11-01

Full Text Available Abstract Background By screening a plasmid library for proteins that could cause silencing when targeted to the HMR locus in Saccharomyces cerevisiae, we previously reported the identification of Rtt107/Esc4 based on its ability to establish silent chromatin. In this study we aimed to determine the mechanism of Rtt107/Esc4 targeted silencing and also learn more about its biological functions. Results Targeted silencing by Rtt107/Esc4 was dependent on the SIR genes, which encode obligatory structural and enzymatic components of yeast silent chromatin. Based on its sequence, Rtt107/Esc4 was predicted to contain six BRCT motifs. This motif, originally identified in the human breast tumor suppressor gene BRCA1, is a protein interaction domain. The targeted silencing activity of Rtt107/Esc4 resided within the C-terminal two BRCT motifs, and this region of the protein bound to Sir3 in two-hybrid tests. Deletion of RTT107/ESC4 caused sensitivity to the DNA damaging agent MMS as well as to hydroxyurea. A two-hybrid screen showed that the N-terminal BRCT motifs of Rtt107/Esc4 bound to Slx4, a protein previously shown to be involved in DNA repair and required for viability in a strain lacking the DNA helicase Sgs1. Like SLX genes, RTT107ESC4 interacted genetically with SGS1; esc4Δ sgs1Δ mutants were viable, but exhibited a slow-growth phenotype and also a synergistic DNA repair defect. Conclusion Rtt107/Esc4 binds to the silencing protein Sir3 and the DNA repair protein Slx4 via different BRCT motifs, thus providing a bridge linking silent chromatin to DNA repair enzymes.

Site Occupancies, Luminescence, and Thermometric Properties of LiY9(SiO4)6O2:Ce3+ Phosphors.

Science.gov (United States)

Zhou, Weijie; Pan, Fengjuan; Zhou, Lei; Hou, Dejian; Huang, Yan; Tao, Ye; Liang, Hongbin

2016-10-04

In this work, we report the tunable emission properties of Ce 3+ in an apatite-type LiY 9 (SiO 4 ) 6 O 2 compound via adjusting the doping concentration or temperature. The occupancies of Ce 3+ ions at two different sites (Wyckoff 6h and 4f sites) in LiY 9 (SiO 4 ) 6 O 2 have been determined by Rietveld refinements. Two kinds of Ce 3+ f-d transitions have been studied in detail and then assigned to certain sites. The effects of temperature and doping concentration on Ce 3+ luminescence properties have been systematically investigated. It is found that the Ce 3+ ions prefer occupying Wyckoff 6h sites and the energy transfer between Ce 3+ at two sites becomes more efficient with an increase in doping concentration. In addition, the charge-transfer vibronic exciton (CTVE) induced by the existence of free oxygen ion plays an important role in the thermal quenching of Ce 3+ at 6h sites. Because of the tunable emissions from cyan to blue with increasing temperature, the phosphors LiY 9 (SiO 4 ) 6 O 2 :Ce 3+ are endowed with possible thermometric applications.

Crystallization and preliminary X-ray diffraction analysis of motif N from Saccharomyces cerevisiae Dbf4

International Nuclear Information System (INIS)

Matthews, Lindsay A.; Duong, Andrew; Prasad, Ajai A.; Duncker, Bernard P.; Guarné, Alba

2009-01-01

To understand the role of the Cdc7–Dbf4 complex in checkpoint responses, a fragment of Saccharomyces cerevisiae Dbf4 encompassing motif N was isolated, overproduced and crystallized. The Cdc7–Dbf4 complex plays an instrumental role in the initiation of DNA replication and is a target of replication-checkpoint responses in Saccharomyces cerevisiae. Cdc7 is a conserved serine/threonine kinase whose activity depends on association with its regulatory subunit, Dbf4. A conserved sequence near the N-terminus of Dbf4 (motif N) is necessary for the interaction of Cdc7–Dbf4 with the checkpoint kinase Rad53. To understand the role of the Cdc7–Dbf4 complex in checkpoint responses, a fragment of Saccharomyces cerevisiae Dbf4 encompassing motif N was isolated, overproduced and crystallized. A complete native data set was collected at 100 K from crystals that diffracted X-rays to 2.75 Å resolution and structure determination is currently under way

Effects of carbon sources, oxygenation and ethanol on the production of inulinase by Kluyveromyces marxianus YX01

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JIAOQI GAO

2012-01-01

Full Text Available Inulinase is one of the most important factors in consolidated bioprocessing, which combines enzyme production, inulin saccharification, and ethanol fermentation into a single process. In our study, inulinase production and cell growth of Kluyveromyces marxianus YX01 under different conditions were studied. Carbon source was shown to be significant on the production of inulinase, because the activity of inulinase was higher using inulin as a carbon source compared with glucose or fructose. The concentration of the carbon source had a repressive effect on the activity of inulinase. When the concentration was increased to 60 g/L, inulinase activity was only 50% compared with carbon source concentration of 20 g/L. Enzyme activity was also strongly influenced by aeration rate. It has been shown that the activity of inulinase and cell growth under anaerobic conditions were maintained at low levels, but aeration at 1.0 vvm (air volume/broth volume minute led to higher activity. Inulinase activity per unit biomass was not significantly different under different aeration rates. Ethanol had a repressive effect on the cell growth. Cells ceased growing when the level of ethanol was greater than 9% (v/v, but ethanol did not affect the activity of secreted inulinase and the enzyme was stable at ethanol concentration up to 15%.

Improved i-motif thermal stability by insertion of anthraquinone monomers

DEFF Research Database (Denmark)

Gouda, Alaa S; Amine, Mahasen S.; Pedersen, Erik Bjerregaard

2017-01-01

In order to gain insight into how to improve thermal stability of i-motifs when used in the context of biomedical and nanotechnological applications, novel anthraquinone-modified i-motifs were synthesized by insertion of 1,8-, 1,4-, 1,5- and 2,6-disubstituted anthraquinone monomers into the TAA...... loops of a 22mer cytosine-rich human telomeric DNA sequence. The influence of the four anthraquinone linkers on the i-motif thermal stability was investigated at 295 nm and pH 5.5. Anthraquinone monomers modulate the i-motif stability in a position-depending manner and the modulation also depends...... unlocked nucleic acid monomers or twisted intercalating nucleic acid. The 2,6-disubstituted anthraquinone linker replacing T10 enabled a significant increase of i-motif thermal melting by 8.2 °C. A substantial increase of 5.0 °C in i-motif thermal melting was recorded when both A6 and T16 were modified...

Influence of tritium aging on kinetics feature of LaNi4.9Al0.1

International Nuclear Information System (INIS)

Xiong Yifu; Luo Deli; Li Rong

2001-01-01

Kinetics parameters were measured at different aging time on LaNi 4.9 Al 0.1 alloy. The influence of tritium aging on kinetics feature of LaNi 4.9 Al 0.1 alloy was assessed. The results show that tritium aging does not change deuterating-dedeuterating reaction order. Reaction rate decrease with aging time. Activation energy (E) increases with aging time

A novel greenish yellow-orange red Ba3Y4O9:Bi(3+),Eu(3+) phosphor with efficient energy transfer for UV-LEDs.

Science.gov (United States)

Li, Kai; Lian, Hongzhou; Shang, Mengmeng; Lin, Jun

2015-12-21

A series of novel color-tunable Ba3Y4O9:Bi(3+),Eu(3+) phosphors were prepared for the first time via the high-temperature solid-state reaction route. The effect of Bi(3+) concentration on the emission intensity of Ba3Y4O9:Bi(3+) was investigated. The emission spectra of the Ba3Y4O9:Bi(3+),Eu(3+) phosphors present both a greenish yellow band of Bi(3+) emission centered at 523 nm, and many characteristic emission lines of Eu(3+), derived from the allowed (3)P1-(1)S0 transition of the Bi(3+) ion and the (5)D0-(7)FJ transition of the Eu(3+) ion, respectively. The energy transfer phenomenon from Bi(3+) to Eu(3+) ions is observed under UV excitation in Bi(3+), Eu(3+) co-doped Ba3Y4O9 phosphors, and their transfer mechanism is demonstrated to be a resonant type via dipole-quadrupole interaction. The critical distance between Bi(3+) and Eu(3+) for the energy transfer effect was calculated via the concentration quenching and spectral overlap methods. Results show that color tuning from greenish yellow to orange red can be realized by adjusting the mole ratio of Bi(3+) and Eu(3+) concentrations based on the principle of energy transfer. Moreover, temperature-dependent PL properties, CIE chromaticity coordinates and quantum yields of Ba3Y4O9:Bi(3+),Eu(3+) phosphors were also supplied. It is illustrated that the as-prepared Ba3Y4O9:Bi(3+),Eu(3+) phosphors can be potential candidates for color-tunable phosphors applied in UV-pumped LEDs.

Structural and electrical characterisation of SrCe1-xYxOxi

DEFF Research Database (Denmark)

Phillips, R.J.; Bonanos, N.; Poulsen, F.W.

1999-01-01

The acceptor-doped perovskite proton conductor SrCe1-xYxOxi (x = 0.025 to 0.20, xi = 3 - x/2) has been prepared and characterised using X-ray diffraction and AC impedance spectroscopy, and the effect of the yttrium dopant concentration on structure and electrical properties has been investigated. X......-ray diffraction studies show a decrease in lattice volume with increasing yttrium content. Electrical conductivity studies have been made as a function of oxygen partial pressure, and at a partial pressure of water vapour of 0.007 atm. The total conductivity has been separated into different components by fitting...

Synthesis and electrochemical properties of xLiMn0.9Fe0.1PO4·yLi3V2(PO4)3/C composite cathode materials for lithium–ion batteries

International Nuclear Information System (INIS)

Wu, Ling; Lu, JiaJia; Wei, Gui; Wang, Pengfei; Ding, Hao; Zheng, Junwei; Li, Xiaowei; Zhong, Shengkui

2014-01-01

Highlights: • xLiMn 0.9 Fe 0.1 PO4·yLi 3 V 2 (PO 4 ) 3 /C composites are prepared by a solid-state method. • The addition of Li 3 V 2 (PO 4 ) 3 can improve the properties of LiMn 0.9 Fe 0.1 PO 4 . • Mutual doping occurrs between the LiMn 0.9 Fe 0.1 PO 4 and Li 3 V 2 (PO 4 ) 3 phases. • 5LiMn 0.9 Fe 0.1 PO 4 ·Li 3 V 2 (PO 4 ) 3 /C shows the best electrochemical properties. - Abstract: The xLiMn 0.9 Fe 0.1 PO 4 ·yLi 3 V 2 (PO 4 ) 3 /C (x:y=1:0, 9:1 5:1, 3:1, 1:1 and 0:1) cathode materials are synthesized by a ball–milling and post–calcination method. XRD results reveal that the xLiMn 0.9 Fe 0.1 PO 4 ·yLi 3 V 2 (PO 4 ) 3 /C (x,y≠0) composites are composed of LiMn 0.9 Fe 0.1 PO 4 and Li 3 V 2 (PO 4 ) 3 phases, and no impurities are detected. In LiMn 0.9 Fe 0.1 PO 4 –Li 3 V 2 (PO 4 ) 3 system, most of the manganese, iron and vanadium elements in the raw materials tend to form the two major phases, and only small amounts of V, Mn and Fe as dopants enter into the lattice of LiMn 0.9 Fe 0.1 PO 4 and Li 3 V 2 (PO 4 ) 3 . Electrochemical tests show that the xLiMn 0.9 Fe 0.1 PO 4 ·yLi 3 V 2 (PO 4 ) 3 /C (x,y≠0) composites exhibit much better performance than the single LiMn 0.9 Fe 0.1 PO 4 /C. Among the samples, 5LiMn 0.9 Fe 0.1 PO 4 ·Li 3 V 2 (PO 4 ) 3 /C shows the best electrochemical performance. The sample delivers the specific capacities of 158.1, 140.7 and 100.2 mAh g −1 at 0.05, 1 and 4 C rates in the potential range of 2.5–4.5 V, and exhibits very long and flat discharge plateau around 4.0 V up to 1 C rate. The sample also shows good cycling performance at various C–rates

A PDZ-Like Motif in the Biliary Transporter ABCB4 Interacts with the Scaffold Protein EBP50 and Regulates ABCB4 Cell Surface Expression.

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Quitterie Venot

Full Text Available ABCB4/MDR3, a member of the ABC superfamily, is an ATP-dependent phosphatidylcholine translocator expressed at the canalicular membrane of hepatocytes. Defects in the ABCB4 gene are associated with rare biliary diseases. It is essential to understand the mechanisms of its canalicular membrane expression in particular for the development of new therapies. The stability of several ABC transporters is regulated through their binding to PDZ (PSD95/DglA/ZO-1 domain-containing proteins. ABCB4 protein ends by the sequence glutamine-asparagine-leucine (QNL, which shows some similarity to PDZ-binding motifs. The aim of our study was to assess the potential role of the QNL motif on the surface expression of ABCB4 and to determine if PDZ domain-containing proteins are involved. We found that truncation of the QNL motif decreased the stability of ABCB4 in HepG2-transfected cells. The deleted mutant ABCB4-ΔQNL also displayed accelerated endocytosis. EBP50, a PDZ protein highly expressed in the liver, strongly colocalized and coimmunoprecipitated with ABCB4, and this interaction required the QNL motif. Down-regulation of EBP50 by siRNA or by expression of an EBP50 dominant-negative mutant caused a significant decrease in the level of ABCB4 protein expression, and in the amount of ABCB4 localized at the canalicular membrane. Interaction of ABCB4 with EBP50 through its PDZ-like motif plays a critical role in the regulation of ABCB4 expression and stability at the canalicular plasma membrane.

Helper component proteinase of the genus Potyvirus is an interaction partner of translation initiation factors eIF(iso)4E and eIF4E and contains a 4E binding motif.

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Ala-Poikela, Marjo; Goytia, Elisa; Haikonen, Tuuli; Rajamäki, Minna-Liisa; Valkonen, Jari P T

2011-07-01

The multifunctional helper component proteinase (HCpro) of potyviruses (genus Potyvirus; Potyviridae) shows self-interaction and interacts with other potyviral and host plant proteins. Host proteins that are pivotal to potyvirus infection include the eukaryotic translation initiation factor eIF4E and the isoform eIF(iso)4E, which interact with viral genome-linked protein (VPg). Here we show that HCpro of Potato virus A (PVA) interacts with both eIF4E and eIF(iso)4E, with interactions with eIF(iso)4E being stronger, as judged by the data of a yeast two-hybrid system assay. A bimolecular fluorescence complementation assay on leaves of Nicotiana benthamiana showed that HCpro from three potyviruses (PVA, Potato virus Y, and Tobacco etch virus) interacted with the eIF(iso)4E and eIF4E of tobacco (Nicotiana tabacum); interactions with eIF(iso)4E and eIF4E of potato (Solanum tuberosum) were weaker. In PVA-infected cells, interactions between HCpro and tobacco eIF(iso)4E were confined to round structures that colocalized with 6K2-induced vesicles. Point mutations introduced to a 4E binding motif identified in the C-terminal region of HCpro debilitated interactions of HCpro with translation initiation factors and were detrimental to the virulence of PVA in plants. The 4E binding motif conserved in HCpro of potyviruses and HCpro-initiation factor interactions suggest new roles for HCpro and/or translation factors in the potyvirus infection cycle.

CompariMotif: quick and easy comparisons of sequence motifs.

Science.gov (United States)

Edwards, Richard J; Davey, Norman E; Shields, Denis C

2008-05-15

CompariMotif is a novel tool for making motif-motif comparisons, identifying and describing similarities between regular expression motifs. CompariMotif can identify a number of different relationships between motifs, including exact matches, variants of degenerate motifs and complex overlapping motifs. Motif relationships are scored using shared information content, allowing the best matches to be easily identified in large comparisons. Many input and search options are available, enabling a list of motifs to be compared to itself (to identify recurring motifs) or to datasets of known motifs. CompariMotif can be run online at http://bioware.ucd.ie/ and is freely available for academic use as a set of open source Python modules under a GNU General Public License from http://bioinformatics.ucd.ie/shields/software/comparimotif/

Enhanced SUMOylation of proteins containing a SUMO-interacting motif by SUMO-Ubc9 fusion

International Nuclear Information System (INIS)

Kim, Eui Tae; Kim, Kyeong Kyu; Matunis, Mike J.; Ahn, Jin-Hyun

2009-01-01

Identifying new targets for SUMO and understanding the function of protein SUMOylation are largely limited by low level of SUMOylation. It was found recently that Ubc9, the SUMO E2 conjugating enzyme, is covalently modified by SUMO at a lysine 14 in the N-terminal alpha helix, and that SUMO-modified Ubc9 has enhanced conjugation activity for certain target proteins containing a SUMO-interacting motif (SIM). Here, we show that, compared to intact Ubc9, the SUMO-Ubc9 fusion protein has higher conjugating activity for SIM-containing targets such as Sp100 and human cytomegalovirus IE2. Assays using an IE2 SIM mutant revealed the requirement of SIM for the enhanced IE2 SUMOylation by SUMO-Ubc9. In pull-down assays with cell extracts, the SUMO-Ubc9 fusion protein bound to more diverse cellular proteins and interacted with some SIM-containing proteins with higher affinities than Ubc9. Therefore, the devised SUMO-Ubc9 fusion will be useful for identifying SIM-containing SUMO targets and producing SUMO-modified proteins.

The development of a wireless Love wave biosensor on 41° YX LiNbO3

International Nuclear Information System (INIS)

Oh, Hae-Kwan; Wang, Wen; Lee, Keekeun; Min, Churlki; Yang, Sangsik

2009-01-01

This paper presents a novel wireless Love-wave-based biosensor using a polymethyl methacrylate (PMMA) waveguide and protein A receptor layers on a 41° YX LiNbO 3 piezoelectric substrate for immunoglobulin G (IgG) detection. A 440 MHz reflective delay line composed of single-phase unidirectional transducers (SPUDTs) and three shorted grating reflectors was fabricated as the sensor element. A theoretical modeling was performed to describe the wave propagation of Love wave devices on a 41° YX LiNbO 3 piezoelectric substrate with large piezoelectricity. The fabricated devices were wirelessly characterized by using the network analyzer as the reader unit. The resultant reflection peaks showed large signal/noise ratio, sharp peaks, and few spurious signals. The binding of the IgG to the protein A receptor layer induced large phase shifts of the reflection peaks due to the mass loading effect. Good linearity, reproducibility, and high sensitivity were observed in the IgG concentration range 1–65 nM. Unique advantages such as high sensitivity and a simple wireless measurement method over other currently available biosensors are also presented

Mutations of the central tyrosines of putative cholesterol recognition amino acid consensus (CRAC) sequences modify folding, activity, and sterol-sensing of the human ABCG2 multidrug transporter.

Science.gov (United States)

Gál, Zita; Hegedüs, Csilla; Szakács, Gergely; Váradi, András; Sarkadi, Balázs; Özvegy-Laczka, Csilla

2015-02-01

Human ABCG2 is a plasma membrane glycoprotein causing multidrug resistance in cancer. Membrane cholesterol and bile acids are efficient regulators of ABCG2 function, while the molecular nature of the sterol-sensing sites has not been elucidated. The cholesterol recognition amino acid consensus (CRAC, L/V-(X)(1-5)-Y-(X)(1-5)-R/K) sequence is one of the conserved motifs involved in cholesterol binding in several proteins. We have identified five potential CRAC motifs in the transmembrane domain of the human ABCG2 protein. In order to define their roles in sterol-sensing, the central tyrosines of these CRACs (Y413, 459, 469, 570 and 645) were mutated to S or F and the mutants were expressed both in insect and mammalian cells. We found that mutation in Y459 prevented protein expression; the Y469S and Y645S mutants lost their activity; while the Y570S, Y469F, and Y645F mutants retained function as well as cholesterol and bile acid sensitivity. We found that in the case of the Y413S mutant, drug transport was efficient, while modulation of the ATPase activity by cholesterol and bile acids was significantly altered. We suggest that the Y413 residue within a putative CRAC motif has a role in sterol-sensing and the ATPase/drug transport coupling in the ABCG2 multidrug transporter. Copyright © 2014. Published by Elsevier B.V.

[Personal motif in art].

Science.gov (United States)

Gerevich, József

2015-01-01

One of the basic questions of the art psychology is whether a personal motif is to be found behind works of art and if so, how openly or indirectly it appears in the work itself. Analysis of examples and documents from the fine arts and literature allow us to conclude that the personal motif that can be identified by the viewer through symbols, at times easily at others with more difficulty, gives an emotional plus to the artistic product. The personal motif may be found in traumatic experiences, in communication to the model or with other emotionally important persons (mourning, disappointment, revenge, hatred, rivalry, revolt etc.), in self-searching, or self-analysis. The emotions are expressed in artistic activity either directly or indirectly. The intention nourished by the artist's identity (Kunstwollen) may stand in the way of spontaneous self-expression, channelling it into hidden paths. Under the influence of certain circumstances, the artist may arouse in the viewer, consciously or unconsciously, an illusionary, misleading image of himself. An examination of the personal motif is one of the important research areas of art therapy.

Reducing renal uptake of 9Y- and 177Lu-labeled alpha-melanocyte stimulating hormone peptide analogues

International Nuclear Information System (INIS)

Miao Yubin; Fisher, Darrell R.; Quinn, Thomas P.

2006-01-01

Objective: The purpose of this study was to improve the tumor-to-kidney uptake ratios of 9 Y- and 177 Lu-[1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid-Re-Cys 3,4,1 , D-Phe 7 , Arg 11 ]α-melanocyte stimulating hormone 3-13 {DOTA-Re(Arg 11 )CCMSH} through coupling a negatively charged glutamic acid (Glu) to the peptide sequence. Methods: A new peptide of DOTA-Re(Glu 2 , Arg 11 )CCMSH was designed, synthesized and labeled with 9 Y and 177 Lu. Pharmacokinetics of 9 Y- and 177 Lu-DOTA-Re(Glu 2 , Arg 11 )CCMSH was determined in B16/F1 murine melanoma-bearing C57 mice. Results: 9 Y- and 177 Lu-DOTA-Re(Glu 2 , Arg 11 )CCMSH exhibited significantly (P 9 Y- and 177 Lu-DOTA-Re(Arg 11 )CCMSH at 30 min and at 2, 4 and 24 h after dose administration. The renal uptake values of 9 Y- and 177 Lu-DOTA-Re(Glu 2 , Arg 11 )CCMSH were 28.16% and 28.81% of those of 9 Y- and 177 Lu-DOTA-Re(Arg 11 )CCMSH, respectively, at 4 h postinjection. 9 Y- and 177 Lu-DOTA-Re(Glu 2 , Arg 11 )CCMSH displayed higher tumor-to-kidney uptake ratios than 9 Y- and 177 Lu-DOTA-Re(Arg 11 )CCMSH at 30 min and at 2, 4 and 24 h after dose administration. The tumor-to-kidney uptake ratio of 9 Y- and 177 Lu-DOTA-Re(Glu 2 , Arg 11 )CCMSH was 2.28 and 1.69 times of 9 Y- and 177 Lu-DOTA-Re(Arg 11 )CCMSH, respectively, at 4 h postinjection. The 9 Y- and 177 Lu-DOTA-Re(Glu 2 , Arg 11 )CCMSH activity accumulation was low in normal organs except for kidney. Conclusions: Coupling a negatively charged amino acid (Glu) to the CCMSH peptide sequence dramatically reduced the renal uptake values and increased the tumor-to-kidney uptake ratios of 9 Y- and 177 Lu-DOTA-Re(Glu 2 , Arg 11 )CCMSH, facilitating their potential applications as radiopharmaceuticals for targeted radionuclide therapy of melanoma

Genome Analysis of Conserved Dehydrin Motifs in Vascular Plants

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Ahmad A. Malik

2017-05-01

Full Text Available Dehydrins, a large family of abiotic stress proteins, are defined by the presence of a mostly conserved motif known as the K-segment, and may also contain two other conserved motifs known as the Y-segment and S-segment. Using the dehydrin literature, we developed a sequence motif definition of the K-segment, which we used to create a large dataset of dehydrin sequences by searching the Pfam00257 dehydrin dataset and the Phytozome 10 sequences of vascular plants. A comprehensive analysis of these sequences reveals that lysine residues are highly conserved in the K-segment, while the amino acid type is often conserved at other positions. Despite the Y-segment name, the central tyrosine is somewhat conserved, but can be substituted with two other small aromatic amino acids (phenylalanine or histidine. The S-segment contains a series of serine residues, but in some proteins is also preceded by a conserved LHR sequence. In many dehydrins containing all three of these motifs the S-segment is linked to the K-segment by a GXGGRRKK motif (where X can be any amino acid, suggesting a functional linkage between these two motifs. An analysis of the sequences shows that the dehydrin architecture and several biochemical properties (isoelectric point, molecular mass, and hydrophobicity score are dependent on each other, and that some dehydrin architectures are overexpressed during certain abiotic stress, suggesting that they may be optimized for a specific abiotic stress while others are involved in all forms of dehydration stress (drought, cold, and salinity.

Preparation of human Melanocortin-4 receptor agonist libraries: linear peptides X-Y-DPhe7-Arg8-Trp(or 2-Nal)9-Z-NH2.

Science.gov (United States)

Cheung, Adrian Wai-Hing; Qi, Lida; Gore, Vijay; Chu, Xin-Jie; Bartkovitz, David; Kurylko, Grazyna; Swistok, Joseph; Danho, Waleed; Chen, Li; Yagaloff, Keith

2005-12-15

Two libraries of hMC4R agonists, X-Y-DPhe(7)-Arg(8)-2-Nal(9)-Z-NH(2) and X-Y-DPhe(7)-Arg(8)-Trp(9)-Z-NH(2), totaling 185 peptides were prepared using Irori radiofrequency tagging technology and Argonaut Quest 210 Synthesizer, where X stands for N-caps, Y for His(6) surrogates and Z for Gly(10) surrogates. As a result of this study, His-modified pentapeptides with Trp were found to be more hMC4R potent than the corresponding 2-Nal analogs, novel N-caps and Gly surrogates were identified and 19 new peptides which are potent hMC4R agonists (EC(50) 1-15nM) and selective against hMC1R were discovered.

Role of 4 f electrons in crystallographic and magnetic complexity

Science.gov (United States)

Pathak, Arjun K.; Paudyal, Durga; Mudryk, Yaroslav; Pecharsky, Vitalij K.

2017-08-01

The functionality of many magnetic materials critically depends on first manipulating and then taking advantage of highly nonlinear changes of properties that occur during phase transformations. Unique to lanthanides, property-defining 4 f electrons are highly localized and, as commonly accepted, play little to no role in chemical bonding. Yet here we demonstrate that the competition between 4 f -electron energy landscapes of Dy (4 f9 ) and Er (4 f11 ) is the key element of the puzzle required to explain complex interplay of magnetic and structural features observed in E r1 -xD yxC o2 , and likely many other mixed lanthanide systems. Unlike the parent binaries—DyC o2 and ErC o2 —E r1 -xD yxC o2 exhibits two successive magnetostructural transitions: a first order at TC, followed by a second order in the ferrimagnetically ordered state. Supported by first-principles calculations, our results offer new opportunities for targeted design of magnetic materials with multiple functionalities, and also provide a critical insight into the role of 4 f electrons in controlling the magnetism and structure of lanthanide intermetallics.

Transition metal-centered trigonal prisms as building units in RE{sub 14}T{sub 3}In{sub 3} (RE = Y, Ho, Er, Tm, Lu; T = Pd, Ir, Pt) and Y{sub 4}IrIn

Energy Technology Data Exchange (ETDEWEB)

Zaremba, R.; Rodewald, U.C.; Poettgen, R. [Inst. fuer Anorganische und Analytische Chemie, Univ. Muenster (Germany)

2007-12-15

The indides RE{sub 14}T{sub 3}In{sub 3} (RE = Y, Ho, Er, Tm, Lu; T = Pd, Ir, Pt) and Y{sub 4}IrIn were synthesized from the elements by are-melting and subsequent annealing for crystal growth. Their structures were characterized on the basis of X-ray powder and single crystal data: Lu{sub 14}Co{sub 3}In{sub 3}-type, space group P4{sub 2}/nmc, a = 970.2(1), c = 2340.7(5) pm for Y{sub 13.95}Pd{sub 3}In{sub 3.05}, a = 959.7(1), c = 2309.0(5) pm for Ho{sub 14}Pd{sub 2.95}In{sub 3}, a = 955.5(1), c = 2305.1(5) pm for Er{sub 14}Pd{sub 3}In{sub 3}, a = 950.9(1), c = 2291.6(5) pm for Tm{sub 13.90}Pd{sub 3}In{sub 3.10}, a = 944.4(1), c = 2275.5(5) pm for Lu{sub 13.93}Pd{sub 3}In{sub 3.07}, a = 962.9(1), c = 2343.0(5) pm for Y{sub 13.86}Ir{sub 2.97}In{sub 3.02}, a = 967.6(1), c = 2347.8(5) pm for Y{sub 13.92}Pt{sub 3.05}In{sub 2.91}, and Gd{sub 4}RhIn-type, space group F anti 43m, a = 1368.6(2) pm for Y{sub 4}IrIn. The main structural motifs are transition metal-centered trigonal prisms of the rare Earth elements which are condensed to two-dimensional networks in the RE{sub 14}T{sub 3}In{sub 3} indides and to a three-dimensional one in Y{sub 4}IrIn. The indium atoms in both structure types show segregation in the metal-rich matrix, i.e. In{sub 2} dumbbells in the RE{sub 14}T{sub 3}In{sub 3} indides (309 pm In2-In2 in Y{sub 13.86}Ir{sub 2.97}In{sub 3.02}) and In{sub 4} tetrahedra (322 pm In-In) in Y{sub 4}IrIn. The crystal chemical peculiarities of both structure types are discussed. (orig.)

A Novel Protein Interaction between Nucleotide Binding Domain of Hsp70 and p53 Motif

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Asita Elengoe

2015-01-01

Full Text Available Currently, protein interaction of Homo sapiens nucleotide binding domain (NBD of heat shock 70 kDa protein (PDB: 1HJO with p53 motif remains to be elucidated. The NBD-p53 motif complex enhances the p53 stabilization, thereby increasing the tumor suppression activity in cancer treatment. Therefore, we identified the interaction between NBD and p53 using STRING version 9.1 program. Then, we modeled the three-dimensional structure of p53 motif through homology modeling and determined the binding affinity and stability of NBD-p53 motif complex structure via molecular docking and dynamics (MD simulation. Human DNA binding domain of p53 motif (SCMGGMNR retrieved from UniProt (UniProtKB: P04637 was docked with the NBD protein, using the Autodock version 4.2 program. The binding energy and intermolecular energy for the NBD-p53 motif complex were −0.44 Kcal/mol and −9.90 Kcal/mol, respectively. Moreover, RMSD, RMSF, hydrogen bonds, salt bridge, and secondary structure analyses revealed that the NBD protein had a strong bond with p53 motif and the protein-ligand complex was stable. Thus, the current data would be highly encouraging for designing Hsp70 structure based drug in cancer therapy.

MSDmotif: exploring protein sites and motifs

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Henrick Kim

2008-07-01

Full Text Available Abstract Background Protein structures have conserved features – motifs, which have a sufficient influence on the protein function. These motifs can be found in sequence as well as in 3D space. Understanding of these fragments is essential for 3D structure prediction, modelling and drug-design. The Protein Data Bank (PDB is the source of this information however present search tools have limited 3D options to integrate protein sequence with its 3D structure. Results We describe here a web application for querying the PDB for ligands, binding sites, small 3D structural and sequence motifs and the underlying database. Novel algorithms for chemical fragments, 3D motifs, ϕ/ψ sequences, super-secondary structure motifs and for small 3D structural motif associations searches are incorporated. The interface provides functionality for visualization, search criteria creation, sequence and 3D multiple alignment options. MSDmotif is an integrated system where a results page is also a search form. A set of motif statistics is available for analysis. This set includes molecule and motif binding statistics, distribution of motif sequences, occurrence of an amino-acid within a motif, correlation of amino-acids side-chain charges within a motif and Ramachandran plots for each residue. The binding statistics are presented in association with properties that include a ligand fragment library. Access is also provided through the distributed Annotation System (DAS protocol. An additional entry point facilitates XML requests with XML responses. Conclusion MSDmotif is unique by combining chemical, sequence and 3D data in a single search engine with a range of search and visualisation options. It provides multiple views of data found in the PDB archive for exploring protein structures.

Stem/Progenitor Cell Proteoglycans Decorated with 7-D-4, 4-C-3 and 3-B-3(-) Chondroitin Sulphate Motifs Are Morphogenetic Markers Of Tissue Development.

Science.gov (United States)

Hayes, Anthony J; Smith, Susan M; Caterson, Bruce; Melrose, James

2018-06-11

This study reviewed the occurrence of chondroitin sulphate (CS) motifs 4-C-3, 7-D-4 and 3-B-3(-) which are expressed by progenitor cells in tissues undergoing morphogenesis. These motifs have a transient early expression pattern during tissue development and also appear in mature tissues during pathological remodeling and attempted repair processes by activated adult stem cells. The CS motifs are information and recognition modules, which may regulate cellular behavior and delineate stem cell niches in developmental tissues. One of the difficulties in determining the precise role of stem cells in tissue development and repair processes is their short engraftment period and the lack of specific markers, which differentiate the activated stem cell lineages from the resident cells. The CS sulphation motifs 7-D-4, 4-C-3 and 3-B-3 (-) decorate cell surface proteoglycans on activated stem/progenitor cells and appear to identify these cells in transitional areas of tissue development and in tissue repair and may be applicable to determining a more precise role for stem cells in tissue morphogenesis. This article is protected by copyright. All rights reserved. © 2018 AlphaMed Press.

MotifNet: a web-server for network motif analysis.

Science.gov (United States)

Smoly, Ilan Y; Lerman, Eugene; Ziv-Ukelson, Michal; Yeger-Lotem, Esti

2017-06-15

Network motifs are small topological patterns that recur in a network significantly more often than expected by chance. Their identification emerged as a powerful approach for uncovering the design principles underlying complex networks. However, available tools for network motif analysis typically require download and execution of computationally intensive software on a local computer. We present MotifNet, the first open-access web-server for network motif analysis. MotifNet allows researchers to analyze integrated networks, where nodes and edges may be labeled, and to search for motifs of up to eight nodes. The output motifs are presented graphically and the user can interactively filter them by their significance, number of instances, node and edge labels, and node identities, and view their instances. MotifNet also allows the user to distinguish between motifs that are centered on specific nodes and motifs that recur in distinct parts of the network. MotifNet is freely available at http://netbio.bgu.ac.il/motifnet . The website was implemented using ReactJs and supports all major browsers. The server interface was implemented in Python with data stored on a MySQL database. estiyl@bgu.ac.il or michaluz@cs.bgu.ac.il. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Semaphorin4D Drives CD8+ T-Cell Lesional Trafficking in Oral Lichen Planus via CXCL9/CXCL10 Upregulations in Oral Keratinocytes.

Science.gov (United States)

Ke, Yao; Dang, Erle; Shen, Shengxian; Zhang, Tongmei; Qiao, Hongjiang; Chang, Yuqian; Liu, Qing; Wang, Gang

2017-11-01

Chemokine-mediated CD8 + T-cell recruitment is an essential but not well-established event for the persistence of oral lichen planus (OLP). Semaphorin 4D (Sema4D)/CD100 is implicated in immune dysfunction, chemokine modulation, and cell migration, which are critical aspects for OLP progression, but its implication in OLP pathogenesis has not been determined. In this study, we sought to explicate the effect of Sema4D on human oral keratinocytes and its capacity to drive CD8 + T-cell lesional trafficking via chemokine modulation. We found that upregulations of sSema4D in OLP tissues and blood were positively correlated with disease severity and activity. In vitro observation revealed that Sema4D induced C-X-C motif chemokine ligand 9/C-X-C motif chemokine ligand 10 production by binding to plexin-B1 via protein kinase B-NF-κB cascade in human oral keratinocytes, which elicited OLP CD8 + T-cell migration. We also confirmed using clinical samples that elevated C-X-C motif chemokine ligand 9/C-X-C motif chemokine ligand 10 levels were positively correlated with sSema4D levels in OLP lesions and serum. Notably, we determined matrix metalloproteinase-9 as a new proteolytic enzyme for the cleavage of sSema4D from the T-cell surface, which may contribute to the high levels of sSema4D in OLP lesions and serum. Our findings conclusively revealed an amplification feedback loop involving T cells, chemokines, and Sema4D-dependent signal that promotes OLP progression. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Kopi dan Kakao dalam Kreasi Motif Batik Khas Jember

Directory of Open Access Journals (Sweden)

Irfa'ina Rohana Salma

2015-06-01

Full Text Available ABSTRAK Batik Jember selama ini identik dengan motif daun tembakau. Visualisasi daun tembakau dalam motif Batik Jember cukup lemah, yaitu kurang berkarakter karena motif yang muncul adalah seperti gambar daun pada umumnya. Oleh karena itu perlu diciptakan desain motif batik khas Jember yang sumber inspirasinya digali dari kekayaan alam lainnya dari Jember yang mempunyai bentuk spesifik dan karakteristik sehingga identitas motif bisa didapatkan dengan lebih kuat. Hasil alam khas Jember tersebut adalah kopi dan kakao. Tujuan penciptaan seni ini adalah untuk menghasilkan motif batik  baru yang mempunyai ciri khas Jember. Metode yang digunakan yaitu pengumpulan data, pengamatan mendalam terhadap objek penciptaan, pengkajian sumber inspirasi, pembuatan desain motif, dan perwujudan menjadi batik. Dari penciptaan seni ini berhasil dikreasikan 6 (enam motif batik yaitu: (1 Motif Uwoh Kopi; (2 Motif Godong Kopi;  (3 Motif Ceplok Kakao; (4 Motif Kakao Raja; (5 Motif Kakao Biru; dan (6 Motif Wiji Mukti. Berdasarkan hasil penilaian “Selera Estetika” diketahui bahwa motif yang paling banyak disukai adalah Motif Uwoh Kopi dan Motif Kakao Raja. Kata kunci: Motif Woh Kopi, Motif Godong Kopi, Motif Ceplok Kakao, Motif Kakao Raja, Motif Kakao Biru, Motif Wiji Mukti ABSTRACTBatik Jember is synonymous with tobacco leaf motif. Tobacco leaf shape is quite weak in the visual appearance characterized as that motif emerges like a picture of leaves in general. Therefore, it is necessary to create a distinctive design motif extracted from other natural resources of Jember that have specific shapes and characteristics that can be obtained as the stronger motif identity. The typical natural resources from Jember are coffee and cocoa. The purpose of the creation of this art is to produce the unique, creative and innovative batik and have specific characteristics of Jember. The method used are data collection, observation of the object, reviewing inspiration sources

Switching between solid solution and two-phase regimes in the Li1-xFe1-yMnyPO4 cathode materials during lithium (de)insertion: combined PITT, in situ XRPD and electron diffraction tomography study

International Nuclear Information System (INIS)

Drozhzhin, Oleg A.; Sumanov, Vasiliy D.; Karakulina, Olesia M.; Abakumov, Artem M.; Hadermann, Joke; Baranov, Andrey N.; Stevenson, Keith J.; Antipov, Evgeny V.

2016-01-01

The electrochemical properties and phase transformations during (de)insertion of Li + in LiFePO 4 , LiFe 0.9 Mn 0.1 PO 4 and LiFe 0.5 Mn 0.5 PO 4 are studied by means of galvanostatic cycling, potential intermittent titration technique (PITT) and in situ X-ray powder diffraction. Different modes of switching between the solid solution and two-phase regimes are revealed which are influenced by the Mn content in Li 1-x Fe 1-y Mn y PO 4 . Additionally, an increase in electrochemical capacity with the Mn content is observed at high rates of galvanostatic cycling (10C, 20C), which is in good agreement with the numerically estimated contribution of the solid solution mechanism determined from PITT data. The observed asymmetric behavior of the phase transformations in Li 1-x Fe 0.5 Mn 0.5 PO 4 during charge and discharge is discussed. For the first time, the crystal structures of electrochemically deintercalated Li 1-x Fe 0.5 Mn 0.5 PO 4 with different Li content – LiFe 0.5 Mn 0.5 PO 4 , Li 0.5 Fe 0.5 Mn 0.5 PO 4 and Li 0.1 Fe 0.5 Mn 0.5 PO 4 – are refined, including the occupancy factors of the Li position. This refinement is done using electron diffraction tomography data. The crystallographic analyses of Li 1-x Fe 0.5 Mn 0.5 PO 4 reveal that at x = 0.5 and 0.9 the structure retains the Pnma symmetry and the main motif of the pristine x = 0 structure without noticeable short range order effects.

Luminescence properties of Sr{sub 3-x-3y/2}M{sub x}Ce{sub y}AlO{sub 4}F (M=Ca, Ba, 0{<=}x{<=}0.9, 0.001{<=}y{<=}0.05) phosphors

Energy Technology Data Exchange (ETDEWEB)

Choi, Hye-Min [Department of Engineering in Energy and Applied Chemistry, Silla University, Busan 617-736 (Korea, Republic of); Park, Sangmoon, E-mail: spark@silla.ac.kr [Department of Engineering in Energy and Applied Chemistry, Silla University, Busan 617-736 (Korea, Republic of)

2012-09-15

Luminescent materials composed of Sr{sub 3-x-3y/2}M{sub x}Ce{sub y}AlO{sub 4}F (M=Ca, Ba, 0{<=}x{<=}0.9, 0.001{<=}y{<=}0.05) were prepared by the solid-state reaction method. X-ray diffraction (XRD) patterns of the obtained oxyfluorides are exhibited for indexing peak positions. Dynamic excitation and emission spectra of the Ce{sup 3+}-activated oxyfluoride phosphors are clearly monitored. The critical emission quenching as a function of Ce{sup 3+} contents in Sr{sub 2.5-3y/2}M{sub 0.5}Ce{sub y}AlO{sub 4}F phosphors is revealed at quite low concentrations of the activator. CIE coordinates of blue and green Sr{sub 2.5-3y/2}M{sub 0.5}Ce{sub y}AlO{sub 4}F phosphors are clearly measured. The relative quantum efficiency of Sr{sub 2.4985}Ca{sub 0.5}Ce{sub 0.005}AlO{sub 4}F based on the integrated emission is determined. The Sr{sub 3-x-3y/2}M{sub x}Ce{sub y}AlO{sub 4}F phosphors excited near 410 nm light could be prominent phosphors in applications of NUV-LED. - Highlights: Black-Right-Pointing-Pointer Blue and green emitting oxyfluoride phosphors are excitated near 410 nm Black-Right-Pointing-Pointer Ce{sup 3+}-activated oxyfluoride phosphors are quite effective to prepare white light for near-UV LED applications. Black-Right-Pointing-Pointer Gradual substitution of Ce{sup 3+} content in the oxyfluoride hosts changes CIE values.

BayesMotif: de novo protein sorting motif discovery from impure datasets.

Science.gov (United States)

Hu, Jianjun; Zhang, Fan

2010-01-18

Protein sorting is the process that newly synthesized proteins are transported to their target locations within or outside of the cell. This process is precisely regulated by protein sorting signals in different forms. A major category of sorting signals are amino acid sub-sequences usually located at the N-terminals or C-terminals of protein sequences. Genome-wide experimental identification of protein sorting signals is extremely time-consuming and costly. Effective computational algorithms for de novo discovery of protein sorting signals is needed to improve the understanding of protein sorting mechanisms. We formulated the protein sorting motif discovery problem as a classification problem and proposed a Bayesian classifier based algorithm (BayesMotif) for de novo identification of a common type of protein sorting motifs in which a highly conserved anchor is present along with a less conserved motif regions. A false positive removal procedure is developed to iteratively remove sequences that are unlikely to contain true motifs so that the algorithm can identify motifs from impure input sequences. Experiments on both implanted motif datasets and real-world datasets showed that the enhanced BayesMotif algorithm can identify anchored sorting motifs from pure or impure protein sequence dataset. It also shows that the false positive removal procedure can help to identify true motifs even when there is only 20% of the input sequences containing true motif instances. We proposed BayesMotif, a novel Bayesian classification based algorithm for de novo discovery of a special category of anchored protein sorting motifs from impure datasets. Compared to conventional motif discovery algorithms such as MEME, our algorithm can find less-conserved motifs with short highly conserved anchors. Our algorithm also has the advantage of easy incorporation of additional meta-sequence features such as hydrophobicity or charge of the motifs which may help to overcome the limitations of

Cofactor interactions in the activation of tissue non-specific alkaline ...

African Journals Online (AJOL)

JTEkanem

stabilization of protein structure and regulation of enzymatic ... structure of ALP at low and high concentrations respectively4,5. ..... Zhang, Y.X., Zhu, Y., Xi, H.W., Liu, Y.L. and Zhou, H.M. ... Garen, A. and Levinthal, C. (1960) A fine structure ...

Nuclear magnetic resonance study of hydrogen mobility in LaY2Ni9Hx and CeY2Ni9Hx

International Nuclear Information System (INIS)

Soloninin, A.V.; Buzlukov, A.L.; Skripov, A.V.; Latroche, M.; Paul-Boncour, V.

2009-01-01

In order to investigate the mobility of hydrogen in the ternary compounds LaY 2 Ni 9 and CeY 2 Ni 9 , we have measured the proton nuclear magnetic resonance (NMR) spectra and the proton spin-lattice relaxation rates R 1 for LaY 2 Ni 9 H x (x=0.78 and 10.3) and CeY 2 Ni 9 H x (x=0.79 and 7.2). The measurements have been performed at the resonance frequencies of 14, 23.8 and 90 MHz over the temperature range of 11-404 K. For LaY 2 Ni 9 H x , the behavior of R 1 is consistent with the presence of a considerable contribution due to motionally modulated dipole-dipole interaction between nuclear spins. This contribution can be satisfactorily described in terms of the Bloembergen-Purcell-Pound model with a Gaussian distribution of activation energies for hydrogen diffusion; the value of the average activation energy resulting from such a description for LaY 2 Ni 9 H 10.3 is approximately 0.36 eV. For CeY 2 Ni 9 H x compounds, the measured proton spin-lattice relaxation rates are dominated by the contribution due to the interaction between proton spins and paramagnetic centers over the entire temperature range studied. Only qualitative information on H mobility in these compounds has been obtained from the narrowing of NMR spectra. Possible paths of H diffusion in LaY 2 Ni 9 H x and CeY 2 Ni 9 H x are discussed in terms of the distances between the interstitial sites occupied by hydrogen. - Graphical abstract: The temperature dependences of the proton spin-lattice relaxation rates R 1 measured at 14, 23.8 and 90 MHz for LaY 2 Ni 9 H 10.3 . The frequency-dependent increase in R 1 at T>250 K indicates the onset of the motional contribution to the relaxation rates

RNA recognition motif (RRM)-containing proteins in Bombyx mori

African Journals Online (AJOL)

STORAGESEVER

2009-03-20

Mar 20, 2009 ... Recognition Motif (RRM), sometimes referred to as. RNP1, is one of the first identified domains for RNA interaction. RRM is very common ..... Apart from the RRM motif, eIF3-S9 has a Trp-Asp. (WD) repeat domain, Poly (A) ...

Amorphization reaction in thin films of elemental Cu and Y

Science.gov (United States)

Johnson, R. W.; Ahn, C. C.; Ratner, E. R.

1989-10-01

Compositionally modulated thin films of Cu and Y were prepared in an ultrahigh-vacuum dc ion-beam deposition chamber. The amorphization reaction was monitored by in situ x-ray-diffraction measurements. Growth of amorphous Cu1-xYx is observed at room temperature with the initial formation of a Cu-rich amorphous phase. Further annealing in the presence of unreacted Y leads to Y enrichment of the amorphous phase. Growth of crystalline CuY is observed for T=469 K. Transmission-electron-microscopy measurements provide real-space imaging of the amorphous interlayer and growth morphology. Models are developed, incorporating metastable interfacial and bulk free-energy diagrams, for the early stage of the amorphization reaction.

Efficient sequential and parallel algorithms for finding edit distance based motifs.

Science.gov (United States)

Pal, Soumitra; Xiao, Peng; Rajasekaran, Sanguthevar

2016-08-18

Motif search is an important step in extracting meaningful patterns from biological data. The general problem of motif search is intractable and there is a pressing need to develop efficient, exact and approximation algorithms to solve this problem. In this paper, we present several novel, exact, sequential and parallel algorithms for solving the (l,d) Edit-distance-based Motif Search (EMS) problem: given two integers l,d and n biological strings, find all strings of length l that appear in each input string with atmost d errors of types substitution, insertion and deletion. One popular technique to solve the problem is to explore for each input string the set of all possible l-mers that belong to the d-neighborhood of any substring of the input string and output those which are common for all input strings. We introduce a novel and provably efficient neighborhood exploration technique. We show that it is enough to consider the candidates in neighborhood which are at a distance exactly d. We compactly represent these candidate motifs using wildcard characters and efficiently explore them with very few repetitions. Our sequential algorithm uses a trie based data structure to efficiently store and sort the candidate motifs. Our parallel algorithm in a multi-core shared memory setting uses arrays for storing and a novel modification of radix-sort for sorting the candidate motifs. The algorithms for EMS are customarily evaluated on several challenging instances such as (8,1), (12,2), (16,3), (20,4), and so on. The best previously known algorithm, EMS1, is sequential and in estimated 3 days solves up to instance (16,3). Our sequential algorithms are more than 20 times faster on (16,3). On other hard instances such as (9,2), (11,3), (13,4), our algorithms are much faster. Our parallel algorithm has more than 600 % scaling performance while using 16 threads. Our algorithms have pushed up the state-of-the-art of EMS solvers and we believe that the techniques introduced in

Magnetic properties of Ruddlesden-Popper phases Sr3 -xYx(Fe1.25Ni0.75) O7 -δ : A combined experimental and theoretical investigation

Science.gov (United States)

Keshavarz, Samara; Kontos, Sofia; Wardecki, Dariusz; Kvashnin, Yaroslav O.; Pereiro, Manuel; Panda, Swarup K.; Sanyal, Biplab; Eriksson, Olle; Grins, Jekabs; Svensson, Gunnar; Gunnarsson, Klas; Svedlindh, Peter

2018-04-01

We present a comprehensive study of the magnetic properties of Sr3 -xYx(Fe1.25Ni0.75) O7 -δ (0 ≤x ≤0.75 ). Experimentally, the magnetic properties are investigated using superconducting quantum interference device (SQUID) magnetometry and neutron powder diffraction (NPD). This is complemented by a theoretical study based on density functional theory as well as the Heisenberg exchange parameters. Experimental results show an increase in the Néel temperature (TN) with an increase of Y concentrations and O occupancy. The NPD data reveal that all samples are antiferromagnetically ordered at low temperatures, which has been confirmed by our theoretical simulations for the selected samples. Our first-principles calculations suggest that the three-dimensional magnetic order is stabilized due to finite interlayer exchange couplings. The latter give rise to finite interlayer spin-spin correlations, which disappear above TN.

Triadic motifs in the dependence networks of virtual societies

Science.gov (United States)

Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing

2014-06-01

In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs.

Triadic motifs in the dependence networks of virtual societies.

Science.gov (United States)

Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing

2014-06-10

In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs.

Alkali-resistant low-temperature atomic-layer-deposited oxides for optical fiber sensor overlays

Science.gov (United States)

Kosiel, K.; Dominik, M.; Ściślewska, I.; Kalisz, M.; Guziewicz, M.; Gołaszewska, K.; Niedziółka-Jonsson, J.; Bock, W. J.; Śmietana, M.

2018-04-01

This paper presents an investigation of properties of selected metallic oxides deposited at a low temperature (100 °C) by atomic layer deposition (ALD) technique, relating to their applicability as thin overlays for optical fiber sensors resistant in alkaline environments. Hafnium oxide (Hf x O y with y/x approx. 2.70), tantalum oxide (Ta x O y with y/x approx. 2.75) and zirconium oxide (Zr x O y with y/x approx. 2.07), which deposition was based, respectively, on tetrakis(ethylmethyl)hafnium, tantalum pentachloride and tetrakis(ethylmethyl)zirconium with deionized water, were tested as thin layers on planar Si (100) and glass substrates. Growth per cycle (GPC) in the ALD processes was 0.133-0.150 nm/cycle. Run-to-run GPC reproducibility of the ALD processes was best for Hf x O y (0.145 ± 0.001 nm/cycle) and the poorest for Ta x O y (0.133 ± 0.003 nm/cycle). Refractive indices n of the layers were 2.00-2.10 (at the wavelength λ = 632 nm), with negligible k value (at λ for 240-930 nm). The oxides examined by x-ray diffractometry proved to be amorphous, with only small addition of crystalline phases for the Zr x O y . The surfaces of the oxides had grainy but smooth topographies with root-mean square roughness ˜0.5 nm (at 10 × 10 μm2 area) according to atomic force microscopy. Ellipsometric measurements, by contrast, suggest rougher surfaces for the Zr x O y layers. The surfaces were also slightly rougher on the glass-based samples than on the Si-based ones. Nanohardness and Young modules were 4.90-8.64 GPa and 83.7-104.4 GPa, respectively. The tests of scratch resistance revealed better tribological properties for the Hf x O y and the Ta x O y than for the Zr x O y . The surfaces were hydrophilic, with wetting angles of 52.5°-62.9°. The planar oxides on Si, being resistive even to concentrated alkali (pH 14), proved to be significantly more alkali-resistive than Al2O3. The Ta x O y overlay was deposited on long-period grating sensor induced in optical

UKIRAN KERAWANG ACEH GAYO SEBAGAI INSPIRASI PENCIPTAAN MOTIF BATIK KHAS GAYO

Directory of Open Access Journals (Sweden)

Irfa ina Rohana Salma

2016-12-01

Full Text Available ABSTRAK Industri batik mulai berkembang di Gayo, tetapi belum memiliki motif batik khas daerah. Oleh karena itu perlu diciptakan motif batik khas Gayo, dengan mengambil inspirasi dari ukiran yang terdapat pada rumah tradisional yang biasa disebut ukiran kerawang Gayo. Tujuan penciptaan seni ini adalah untuk menciptakan motif batik yang memiliki ciri khas Gayo. Metode yang digunakan yaitu eksplorasi ide, perancangan, dan perwujudan menjadi motif batik. Dalam kegiatan ini telah diciptakan enam motif batik khas Gayo yaitu: (1 Motif Ceplok Gayo; (2 Motif Gayo Tegak; (3 Motif Gayo Lurus; (4 Motif Parang Gayo; (5 Motif Gayo Lembut; dan (6 Motif Geometris Gayo. Hasil uji kesukaan terhadap motif kepada lima puluh responden menunjukkan bahwa Motif Ceplok Gayo paling banyak dipilih oleh responden yaitu sebesar 19%, sedangkan Motif Parang Gayo 18%, Motif Gayo Lembut 17%, Motif Geometris Gayo 17%, Motif Gayo Lurus 15% dan Motif Gayo Tegak 14%. Rata-rata motif yang dihasilkan mendapatkan apresiasi yang baik dari responden, sehingga semua motif layak diproduksi sebagai batik khas Gayo.Kata kunci: batik Gayo, Motif Ceplok Gayo, Motif Parang Gayo.ABSTRACTBatik industry began to develop in Gayo, but have not had a typical batik motif itself. Therefore, it is necessary to create batik motifs of Gayo, by taking inspiration from the carvings found in traditional houses commonly called kerawang Gayo. The purpose of this art is to create motifs those have a Gayo characteristic. The method used are the idea exploration, design, and motifs embodiment. In this activity has created six Gayo batik motifs, namely: (1 Motif Ceplok Gayo; (2 Motif Gayo Tegak; (3 Motif GayoLurus; (4 Motif Parang Gayo; (5 Motif Gayo Lembut; dan (6 Motif Geometris Gayo. The test results fondness of the motives to fifty respondents indicated that the Motif Ceplok Gayo most preferred by respondents ie 19%, while Motif Parang Gayo 18%, Motif Gayo Lembut 17%, Motif Geometris Gayo 17%, Motif Gayo

MotifMark: Finding regulatory motifs in DNA sequences.

Science.gov (United States)

Hassanzadeh, Hamid Reza; Kolhe, Pushkar; Isbell, Charles L; Wang, May D

2017-07-01

The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding sites and the specificity of target proteins in binding to these regions are two important steps in understanding the mechanisms of these biological activities. A number of high-throughput technologies have recently emerged that try to quantify the affinity between proteins and DNA motifs. Despite their success, these technologies have their own limitations and fall short in precise characterization of motifs, and as a result, require further downstream analysis to extract useful and interpretable information from a haystack of noisy and inaccurate data. Here we propose MotifMark, a new algorithm based on graph theory and machine learning, that can find binding sites on candidate probes and rank their specificity in regard to the underlying transcription factor. We developed a pipeline to analyze experimental data derived from compact universal protein binding microarrays and benchmarked it against two of the most accurate motif search methods. Our results indicate that MotifMark can be a viable alternative technique for prediction of motif from protein binding microarrays and possibly other related high-throughput techniques.

High-temperature electrical properties of the Bi2.1Sr1.9(Ca1-xYx)Cu2Oy solid solution

International Nuclear Information System (INIS)

Hong, Byungsun; Mason, T.O.

1993-01-01

By a combination of conventional physical property measurements and high temperature electrical property studies, the solid solution limit, transport parameters, and potential defect regimes of the Bi 2.1 Sr 1.9 (Ca 1 - x Y x )Cu 2 O y solid solution were established. A continuous solid solution extends to x = 0.7 or 0.8. The electrical properties indicate that the product of the hole density-of-states and mobility for semiconducting compositions is approximately an order of magnitude smaller than for the other p-type superconducting cuprates. A pronounced drop in hole concentration accompanies the tetragonal-to-orthorhombic transition at x = 0.5, where after superconductivity disappears. The electrical properties also indicate that a composition x ≥ 0.7 is the appropriate ''reference'' compound for the solid solution series. Upon doping this yttrium-rich insulating composition with calcium, holes are introduced. With increased calcium content (decreased yttrium content) the system exhibits several defect regimes reminiscent of the behavior in the La 2 - x AE x CuO 4 (AE = Sr or Ba) system. Oxygen defects (interstitial and vacancies) are believed to play an important role in the defect structure

Differential operators associated with Gegenbauer polynomials - 3. The regular case

International Nuclear Information System (INIS)

Onyango-Otieno, V.P.

1989-07-01

We study the regular case of the Gegenbauer differential equation - ((1-x 2 ) v+1/2 y 1 (x)) 1 +v 2 (1-x 2 ) v-1/2 y(x) = λ(1-x 2 ) v-1/2 y(x), (x is an element of (-1,1),-1/2 w 2 (-1,1) and H p,q 2 (-1,1). (author). 13 refs

Improvement of photoluminescence properties and thermal stability of Y2.9Ce0.1Al5−xSixO12 phosphors with Si3N4 addition

International Nuclear Information System (INIS)

Zhang, Fangfang; Song, Kaixin; Jiang, Jun; Wu, Song; Zheng, Peng; Huang, Qingming; Xu, Junming; Qin, Huibin

2014-01-01

Highlights: • Y 2.9 Ce 0.1 Al 5−x Si x O 12 phosphors were prepared by solid-state reaction in reduced air ambience. • Si 4+ could be incorporated into the host lattice of Y 3 Al 5 O 12 through partial occupation of the Al 3+ sites. • Si 3 N 4 addition can improve photoluminescence efficiency and thermal stability of Y 3 Al 5 O 12 :Ce. - Abstract: A series of Si 3 N 4 doping Y 2.9 Ce 0.1 Al 5−x Si x O 12−3x/2 N 4x/3 phosphors were prepared by solid-state reaction in 95%N 2 –5%H 2 reduced air ambience. The XRD characteristics plus Rietveld refinement results shows that the as-sintered powders are unique crystal phase with the same crystal structure of Y 3 Al 5 O 12 (PDF No. 79-1891). The N element was not detected by the analysis of X-ray photoelectron spectroscopy (XPS) and energy dispersive X-ray spectrum (EDS). The photoluminescence spectra (PL and PLE) tests show that the exciting and emitting intensity of PLE and PL gradually increase due to the increase of Si 3 N 4 concentration. Meanwhile, the phosphorescence decay times are prolonged from 45 ns (x = 0) to 78 ns (x = 0.3), under the monitor of 530 nm wavelength. The thermoluminescence tests (TL) confirm the thermal stability of as-phosphors with Si 3 N 4 addition is much better than that of the pristine Y 2.9 Ce 0.1 Al 5 O 12 phosphors

Víctimas del conflicto armado colombiano en granada, Antioquia, a la luz de un análisis semántico de Mateo 5, 4 y 5, 9

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Vivian Yaneidy Puentes Roncancio

2017-01-01

Full Text Available Con la finalidad de hacer una aproximación hermenéutica a la realidad de las víctimas del conflicto armado en Colombia, se ha realizado un análisis semántico de las bienaventuranzas de Mt 5, 3-10, específicamente los vv. 4 y 9. En un primer momento, se estudia el contexto literario del texto y se propone una estructura del mismo; posteriormente, se le efectúa una revisión semántica profundizando en los campos de los lexemas de los vv. 4 y 9. Por último, se propone presentar a las víctimas de Granada (Antioquia-Colombia como bienaventuradas por ser “capaces de tristeza”, es decir, capaces de ser solidarios, y por ende, contribuir a la construcción de la paz.

Exposure to persistent organic pollutants and sperm sex chromosome ratio in men from the Faroe Islands

DEFF Research Database (Denmark)

Kvist, L; Giwercman, A; Weihe, P

2014-01-01

People in the Arctic as well as fishermen on the polluted Swedish east coast are highly exposed to persistent organic pollutants (POPs). These compounds have been shown to affect the sperm Y:X chromosome ratio. In present study, the aim was to investigate whether polychlorinated biphenyl (PCB......,p'-DDE and ΣPCB correlated significantly (r=0.927, pboth Inuit and Swedish fishermen (0.512 for both......). In conclusion, Faroese men presented with lower Y:X ratio than Greenland Inuit and Swedish fishermen. Although no direct health effects are expected due to the lower Faroese Y:X ratio, it could be indicative of adverse effects on the reproductive system....

On the structure of rare earth periodates of LnIO5x4H2O (Ln=Pr-Lu, Y)

International Nuclear Information System (INIS)

Shamraj, N.B.; Varfolomeev, M.B.; Saf'yanov, Yu.N.; Kuz'min, Eh.A.; Ilyukhin, V.V.; AN SSSR, Moscow. Inst. Kristallografii)

1977-01-01

The crystal structure of three representatives of an isotypic series of monoclinic periodates of rare earth elements in the series from Pr to Lu and Y was deciphered. The monoclinic cell for all LnIO 5 x4H 2 O contains Z=4 formula units. The architectural motif consists in layers of octahedra of IO 4 (OH) 2 and polyhedra of LnO 5 (H 2 O 3 ) parallel to the (100) plane. Adhesion between the layers is achieved through H-bonds

The regulatory G4 motif of the Kirsten ras (KRAS) gene is sensitive to guanine oxidation

DEFF Research Database (Denmark)

Cogoi, Susanna; Ferino, Annalisa; Miglietta, Giulia

2018-01-01

KRAS is one of the most mutated genes in human cancer. It is controlled by a G4 motif located upstream of the transcription start site. In this paper, we demonstrate that 8-oxoguanine (8-oxoG), being more abundant in G4 than in non-G4 regions, is a new player in the regulation of this oncogene. W...

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African Journals Online (AJOL)

Items 401 - 450 of 1178 ... Y-X Zhou, J Chen, J-P Li, Y-L Wang, X-D Jin ... Vol 4, No 3 (2007), Comparative Chemical And Analgesic Properties Of Essential Oils ... Pilar Carranza-Rosales, Omar Heredia-Rodríguez, Gerardo Lozano-Garza, Angel ...

Y-Chromosome Markers for the Red Fox.

Science.gov (United States)

Rando, Halie M; Stutchman, Jeremy T; Bastounes, Estelle R; Johnson, Jennifer L; Driscoll, Carlos A; Barr, Christina S; Trut, Lyudmila N; Sacks, Benjamin N; Kukekova, Anna V

2017-09-01

The de novo assembly of the red fox (Vulpes vulpes) genome has facilitated the development of genomic tools for the species. Efforts to identify the population history of red foxes in North America have previously been limited by a lack of information about the red fox Y-chromosome sequence. However, a megabase of red fox Y-chromosome sequence was recently identified over 2 scaffolds in the reference genome. Here, these scaffolds were scanned for repeated motifs, revealing 194 likely microsatellites. Twenty-three of these loci were selected for primer development and, after testing, produced a panel of 11 novel markers that were analyzed alongside 2 markers previously developed for the red fox from dog Y-chromosome sequence. The markers were genotyped in 76 male red foxes from 4 populations: 7 foxes from Newfoundland (eastern Canada), 12 from Maryland (eastern United States), and 9 from the island of Great Britain, as well as 48 foxes of known North American origin maintained on an experimental farm in Novosibirsk, Russia. The full marker panel revealed 22 haplotypes among these red foxes, whereas the 2 previously known markers alone would have identified only 10 haplotypes. The haplotypes from the 4 populations clustered primarily by continent, but unidirectional gene flow from Great Britain and farm populations may influence haplotype diversity in the Maryland population. The development of new markers has increased the resolution at which red fox Y-chromosome diversity can be analyzed and provides insight into the contribution of males to red fox population diversity and patterns of phylogeography. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

IMPACT OF MANNOSE-BINDING PROTEIN GENE POLYMORPHISMS IN OMANI SICKLE CELL DISEASE PATIENTS

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Mathew Zachariah

2016-02-01

Full Text Available Objectives: Our objective was to study mannose binding protein (MBP polymorphisms in exonic and promoter region and correlate associated infections and vasoocculsive (VOC episodes, since MBP plays an important role in innate immunity by activating the complement system. Methods: We studied the genetic polymorphisms in the Exon 1 (alleles A/O and promoter region (alleles Y/X; H/L, P/Q of the MBL2 gene, in sickle cell disease (SCD patients as increased incidence of infections is seen in these patients. A PCR-based, targeted genomic DNA sequencing of MBL2 was used to study 68 SCD Omani patients and 44 controls (voluntary blood donors. Results: The observed frequencies of MBL2 promoter polymorphism (-221, Y/X were 44.4% and 20.5% for the heterozygous genotype Y/X and 3.2% and 2.2% for the homozygous (X/X respectively between SCD patients and controls. MBL2 Exon1 gene mutations were 29.4% and 50% for the heterozygous genotype A/O and 5.9% and 6.8% respectively for the homozygous (O/O genotype between SCD patients and controls. The distribution of variant MBL2 polymorphisms did not show any correlation in SCD patients with or without vasoocculsive crisis (VOC attacks (p=0.162; OR-0.486; CI=0.177 -1.33, however, it was correlated with infections (p=0.0162; OR-3.55; CI 1.25-10.04. Conclusions: Although the frequency of the genotypes and haplotypes of MBL2 in SCD patients did not differ from controls, overall in the SCD patient cohort the increased representation of variant alleles was significantly correlated with infections (p<0.05. However, these variant MBL2 polymorphisms did not seem to play a significant role in the VOC episodes in this SCD cohort. Keywords: Mannose-binding lectin, polymorphism, promoter, Sickle cell disease, MBL2, MBP

UCHUVA MÍNIMAMENTE PROCESADA IMPREGNADA AL VACÍO CON CALCIO Y VITAMINAS B9, D Y E

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FABIOLA PEÑA

Full Text Available Se evaluó la respuesta a la impregnación a vacío (IV de la uchuva ecotipo Colombia con diferentes líquidos, para formular una emulsión fortificante con calcio y vitaminas B9, D y E. La fracción volumétrica de impregnación y porosidad efectiva de la uchuva identifican una buena porosidad disponible al proceso. De acuerdo al índice R, la emulsión de impregnación es estable durante 35 días a 4°C. El proceso de IV no afectósignificativamente las uchuvas en cuanto a sus propiedades físico-químicas y niveles de vitamina C. Se obtuvieron uchuvas impregnadas que aportan, en una porción de 200g, niveles del 69, 82, 40, 50 y 15% de los valores diarios de referencia para las vitaminas C, B9, D, y E y el calcio, respectivamente. Micrografías tomadas por microscopia electrónica de barrido, evidenciaron la incorporación de las partículas oleosas en los poros del pedúnculo de la uchuva.

External temperature and pressure effects on thermodynamic properties and mechanical stability of yttrium chalcogenides YX (X=S, Se and Te)

Energy Technology Data Exchange (ETDEWEB)

Seddik, T. [Laboratoire de Physique Quantique et de Modélisation Mathématique, Université de Mascara, 29000 Mascara (Algeria); Khenata, R., E-mail: khenata_rabah@yahoo.fr [Laboratoire de Physique Quantique et de Modélisation Mathématique, Université de Mascara, 29000 Mascara (Algeria); Bouhemadou, A.; Guechi, N. [Laboratory for Developing New Materials and their Characterization, Department of Physics, Faculty of Science, University of Setif, 19000 Setif (Algeria); Sayede, A. [Université Lille Nord de France, F-59000 Lille (France); Université-Artois, UCCS, F-62300 Lens (France); CNRS, UMR 8181, F-59650 Villeneuve d’Ascq (France); Varshney, D. [Materials Science Laboratory, School of Physics, Vigyan Bhavan, Devi Ahilya University, Khandwa Road Campus, Indore 452001, Madhya Pradesh (India); Al-Douri, Y. [Institute of Nono Electronic Engineering, University Malaysia Perlis, 01000 Kangar, Perlis (Malaysia); Reshak, A.H. [Institute of Complex Systems, FFPW, CENAKVA, University of South Bohemia in CB, Nove Hrady 37333 (Czech Republic); Center of Excellence Geopolymer and Green Technology, School of Material Engineering, University Malaysia Perlis, 01007 Kangar, Perlis (Malaysia); Bin-Omran, S. [Department of Physics and Astronomy, Faculty of Science, King Saud University, PO Box 2455, Riyadh 11451 (Saudi Arabia)

2013-11-01

The full potential linearized augmented plane wave method within the framework of density functional theory is employed to investigate the structural, thermodynamic and elastic properties of the yttrium chalcogenides (YX: X=S, Se, and Te) in their low-pressure phase (Fm3{sup ¯}m) and high-pressure phase (Pm3{sup ¯}m). The exchange-correlation potential is treated with the generalized gradient approximation of Perdew–Burke–Ernzerhof (GGA-PBE). Temperature dependence of the volume and both adiabatic and isothermal bulk moduli is predicted for a temperature range from 0to1200K for the both phases of the herein considered materials. Furthermore, we have analyzed the thermodynamic properties such as the heat capacities, C{sub V} and C{sub P}, thermal expansion, α, and Debye temperature, Θ{sub D,} under variable pressure and temperature. We have calculated the isothermal elastic constants C{sub ij}{sup T} of the YX monochalcogenides in both NaCl-B1 and CsCl-B2 phases at zero pressure and a temperature range 0−1200K. The results show that rare earth yttrium monochalcogenides are mechanically stable at high temperature. The elastic anisotropy of all studied materials in the two phases has been studied using three different methods.

The human Ago2 MC region does not contain an eIF4E-like mRNA cap binding motif

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Grishin Nick V

2009-01-01

Full Text Available Abstract Background Argonaute (Ago proteins interact with small regulatory RNAs to mediate gene regulatory pathways. A recent report by Kiriakidou et al. 1 describes an MC sequence region identified in Ago2 that displays similarity to the cap-binding motif in translation initiation factor 4E (eIF4E. In a cap-bound eIF4E structure, two important aromatic residues of the motif stack on either side of a 7-methylguanosine 5'-triphosphate (m7Gppp base. The corresponding Ago2 aromatic residues (F450 and F505 were hypothesized to perform the same cap-binding function. However, the detected similarity between the MC sequence and the eIF4E cap-binding motif was questionable. Results A number of sequence-based and structure-based bioinformatics methods reveal the reported similarity between the Ago2 MC sequence region and the eIF4E cap-binding motif to be spurious. Alternatively, the MC sequence region is confidently assigned to the N-terminus of the Ago piwi module, within the mid domain of experimentally determined prokaryotic Ago structures. Confident mapping of the Ago2 MC sequence region to the piwi mid domain results in a homology-based structure model that positions the identified aromatic residues over 20 Å apart, with one of the aromatic side chains (F450 contributing instead to the hydrophobic core of the domain. Conclusion Correct functional prediction based on weak sequence similarity requires substantial evolutionary and structural support. The evolutionary context of the Ago mid domain suggested by multiple sequence alignment is limited to a conserved hydrophobicity profile required for the fold and a motif following the MC region that binds guide RNA. Mapping of the MC sequence to the mid domain structure reveals Ago2 aromatics that are incompatible with eIF4E-like mRNA cap-binding, yet display some limited local structure similarities that cause the chance sequence match to eIF4E. Reviewers This article was reviewed by Arcady Mushegian

Ternary silicides ScIr{sub 4}Si{sub 2} and RERh{sub 4}Si{sub 2} (RE = Sc, Y, Tb-Lu) and quaternary derivatives RERh{sub 4}Si{sub 2-x}Sn{sub x} (RE = Y, Nd, Sm, Gd-Lu) - structure, chemical bonding, and solid state NMR spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Vosswinkel, Daniel; Benndorf, Christopher; Poettgen, Rainer [Muenster Univ. (Germany). Inst. fuer Anorganische und Analytische Chemie; Eckert, Hellmut [Muenster Univ. (Germany). Inst. fuer Physikalische Chemie; Sao Paulo Univ., Sao Carlos (Brazil). Inst. of Physics; Matar, Samir F. [Bordeaux Univ., CNRS, ICMCB, UPR 9048, Pessac (France)

2016-11-01

The silicides ScIr{sub 4}Si{sub 2} and RERh{sub 4}Si{sub 2} (RE = Sc, Y, Tb-Lu) and silicide stannides RERh{sub 4}Si{sub 2-x}Sn{sub x}(RE = Y, Nd, Sm, Gd-Lu) were synthesized from the elements by arc-melting and subsequent annealing. The new compounds crystallize with the orthorhombic YRh{sub 4}Ge{sub 2} type structure, space group Pnma. They were characterized by X-ray powder patterns and several structures were refined from single crystal X-ray diffractometer data. The main structural motifs of this series of silicides are tricapped trigonal prisms formed by the transition metal and rare earth atoms. One of the two crystallographically independent silicon sites allows for formation of solid solutions with tin, exemplarily studied for ErRh{sub 4}Si{sub 2-x}Sn{sub x}. Electronic structure calculations reveal strong covalent Rh-Si bonding as the main stability factor. Multinuclear ({sup 29}Si, {sup 45}Sc, and {sup 89}Y) magic-angle spinning (MAS) NMR spectra of the structure representatives with diamagnetic rare-earth elements (Sc, Y, Lu) are found to be consistent with the crystallographic data and specifically confirm the selective substitution of Sn in the Si2 sites in the quaternary compounds YRh{sub 4}SiSn and LuRh{sub 4}SiSn.

Site-selective laser spectroscopy of Sm{sup 3+} ions in Y{sub 4}Al{sub 2}O{sub 9}

Energy Technology Data Exchange (ETDEWEB)

Kaczkan, M., E-mail: m.kaczkan@elka.pw.edu.pl [Institute of Microelectronics and Optoelectronics, Koszykowa 75, Warsaw 00-662 (Poland); Boruc, Z. [Institute of Microelectronics and Optoelectronics, Koszykowa 75, Warsaw 00-662 (Poland); Turczyński, S.; Pawlak, D. [Institute of Electronic Materials Technology, Wolczynska 133, Warsaw 01-919 (Poland); Malinowski, M. [Institute of Microelectronics and Optoelectronics, Koszykowa 75, Warsaw 00-662 (Poland)

2016-02-15

Sm{sup 3+} doped Y{sub 4}Al{sub 2}O{sub 9} (YAM) crystals were prepared by the micro-pulling down method. Optical-absorption and laser-selective-excitation techniques along with luminescence decays have been used to reveal that Sm{sup 3+} ions in YAM normally occupy four sites, which were characterized and discussed. The comprehensive sets of Stark energy levels of the four Sm{sup 3+} centers in YAM were established. The intensity ratio of forced electric dipole ({sup 4}G{sub 5/2} → {sup 6}H{sub 9/2}) and magnetic dipole ({sup 4}G{sub 5/2} → {sup 6}H{sub 5/2}) transitions has been used to estimate the degree of asymmetry of Sm{sup 3+} sites. The lifetime of Sm{sup 3+} ions and the cross-relaxation rates were experimentally determined as a function of concentration for two distinct crystallographic Sm{sup 3+} centers. The dependencies of the nearest surroundings on the relaxation of the {sup 4}G{sub 5/2} excited state was discussed.

Ratio dependence of the visible light photocatalytic efficiency for Zn{sub 2}Ti{sub 0.9}Cr{sub y}Fe{sub [0.1-y]}O{sub 4}: Cr/Fe (0.02 < y < 0.08) photocatalyst synthesized by using a solid state reaction method

Energy Technology Data Exchange (ETDEWEB)

Borse, P. H. [International Advanced Research Center for Powder Metallurgy and New Materials, Hyderabad (India); Cho, C. R. [Pusan National University, Miryang (Korea, Republic of); Lim, K. T. [Pukyong National University, Busan (Korea, Republic of); Lee, Y. J.; Bae, J. S.; Jeong, E. D.; Kim, H. G. [Korea Basic Science Institute, Busan (Korea, Republic of)

2011-07-15

We synthesized four different photocatalyst systems of Zn{sub 2}TiO{sub 4}, Zn{sub 2}Ti{sub 1-x}Fe{sub x}O{sub 4}, Zn{sub 2}Ti{sub 1-x}Cr{sub x}O{sub 4} (0 {<=} x < 0.8) and Zn{sub 2}Ti{sub 0.9}Cr{sub y}Fe{sub [0.1]-y}O{sub 4} (0.02 < y < 0.08) by using a solid state reaction method. For the first time, the UV-active photocatalyst Zn{sub 2}TiO{sub 4} was converted to a visible light active material by controlled doping/co-doping with Cr and Fe metal-ions at Ti substitutional sites, and investigated the structural, optical and photocatalytic water decomposition properties of that materials. The co-doping induces strong absorption bands (at {lambda} {approx} 480 nm and {lambda} {approx} 620 nm) within the Zn{sub 2}TiO{sub 4} band gap. The optimum system of Zn{sub 2}Ti{sub 0.9}Cr{sub 0.05}Fe{sub 0.05}O{sub 4} yielded maximum H{sub 2} generation. In contrast to the visible light inactivity of Fe- and Cr-doped Zn{sub 2}TiO{sub 4}, the H{sub 2} production from co-doped samples under visible light irradiation increased till the optimum 'y' value. Consequently, here exists an optimal co-dopant concentration for efficient photocatalytic hydrogen production under visible light ({lambda} {>=} 420 nm).

Titanium Dioxide-Based 64∘ YX LiNbO3 Surface Acoustic Wave Hydrogen Gas Sensors

Directory of Open Access Journals (Sweden)

A. Z. Sadek

2008-01-01

Full Text Available Amorphous titanium dioxide (TiO2 and gold (Au doped TiO2-based surface acoustic wave (SAW sensors have been investigated as hydrogen gas detectors. The nanocrystal-doped TiO2 films were synthesized through a sol-gel route, mixing a Ti-butoxide-based solution with diluted colloidal gold nanoparticles. The films were deposited via spin coating onto 64∘ YX LiNbO3 SAW transducers in a helium atmosphere. The SAW gas sensors were operated at various temperatures between 150 and 310∘C. It was found that gold doping on TiO2 increased the device sensitivity and reduced the optimum operating temperature.

Structural modelling and phylogenetic analyses of PgeIF4A2 (Eukaryotic translation initiation factor) from Pennisetum glaucum reveal signature motifs with a role in stress tolerance and development.

Science.gov (United States)

Agarwal, Aakrati; Mudgil, Yashwanti; Pandey, Saurabh; Fartyal, Dhirendra; Reddy, Malireddy K

2016-01-01

Eukaryotic translation initiation factor 4A (eIF4A) is an indispensable component of the translation machinery and also play a role in developmental processes and stress alleviation in plants and animals. Different eIF4A isoforms are present in the cytosol of the cell, namely, eIF4A1, eIF4A2, and eIF4A3 and their expression is tightly regulated in cap-dependent translation. We revealed the structural model of PgeIF4A2 protein using the crystal structure of Homo sapiens eIF4A3 (PDB ID: 2J0S) as template by Modeller 9.12. The resultant PgeIF4A2 model structure was refined by PROCHECK, ProSA, Verify3D and RMSD that showed the model structure is reliable with 77 % amino acid sequence identity with template. Investigation revealed two conserved signatures for ATP-dependent RNA Helicase DEAD-box conserved site (VLDEADEML) and RNA helicase DEAD-box type, Q-motif in sheet-turn-helix and α-helical region respectively. All these conserved motifs are responsible for response during developmental stages and stress tolerance in plants.

Effects of Yttrium and Iron co-doping on the high temperature thermoelectric properties of Ca{sub 3}Co{sub 4}O{sub 9+δ}

Energy Technology Data Exchange (ETDEWEB)

Wu, NingYu, E-mail: niwu@dtu.dk; Van Nong, Ngo; Pryds, Nini; Linderoth, Søren

2015-07-25

Highlights: • The Fe and Fe/Y doping at the Co- and Ca-sites of Ca{sub 3}Co{sub 4}O{sub 9+δ} were investigated. • The rising ρ by Y doping can be mitigated by the coupled Fe doping. • The increased Seebeck coefficient by Y doping can be maintained in co-doped system. • The co-doped system leads to an improvement of the thermoelectric performance. • The co-doped system may preserve the merits from each component doping. - Abstract: A series of Y and Fe co-doped Ca{sub 3−x}Y{sub x}Co{sub 4−y}Fe{sub y}O{sub 9+δ} (0 ⩽ x ⩽ 0.3, 0 ⩽ y ⩽ 0.1) samples synthesized by auto-combustion reaction and followed by a spark plasma sintering (SPS) processing with the effects of Fe and Y doping on the high temperature (RT to 800 °C) thermoelectric properties were systematically investigated. For the Fe-doped system (x = 0, y ⩽ 0.1), the electrical resistivity (ρ) decreased over the whole measured temperature range, while the Seebeck coefficient (S) remained almost the same. For the co-doped system, at any fixed Fe doping content, both ρ and S tended to increase with increasing Y dopants, however, the effect is more substantial on ρ than on S, particularly in the low temperature regime. In contrast to ρ and S, the in-plane thermal conductivity (κ) is only slightly influenced by Y and Fe substitutions. Among all the investigated samples, the co-doped sample with x = 0.1 and y = 0.03 showed a decrease of ρ, enhanced power factor over the measured temperature range, and improved ZT at 800 °C as compared to un-doped Ca{sub 3}Co{sub 4}O{sub 9+δ}.

Orchestration of Structural, Stereoelectronic, and Hydrogen-Bonding Effects in Stabilizing Triplexes from Engineered Chimeric Collagen Peptides (Pro(X)-Pro(Y)-Gly)6 Incorporating 4(R/S)-Aminoproline.

Science.gov (United States)

Umashankara, Muddegowda; Sonar, Mahesh V; Bansode, Nitin D; Ganesh, Krishna N

2015-09-04

Collagens are an important family of structural proteins found in the extracellular matrix with triple helix as the characteristic structural motif. The collagen triplex is made of three left-handed polyproline II (PPII) helices with each PPII strand consisting of repetitive units of the tripeptide motif X-Y-Gly, where the amino acids X and Y are most commonly proline (Pro) and 4R-hydroxyproline (Hyp), respectively. A C4-endo pucker at X-site and C4-exo pucker at Y-site have been proposed to be the key for formation of triplex, and the nature of pucker is dependent on both the electronegativity and stereochemistry of the substituent. The present manuscript describes a new class of collagen analogues-chimeric cationic collagens-wherein both X- and Y-sites in collagen triad are simultaneously substituted by a combination of 4(R/S)-(OH/NH2/NH3(+)/NHCHO)-prolyl units and triplex stabilities measured at different pHs and in EG:H2O. Based on the results a model has been proposed with the premise that any factors which specifically favor the ring puckers of C4-endo at X-site and C4-exo at Y-site stabilize the PPII conformation and hence the derived triplexes. The pH-dependent triplex stability uniquely observed with ionizable 4-amino substituent on proline enables one to define the critical combination of factors C4-(exo/endo), intraresidue H-bonding, stereoelectronic (R/S) and n → π* interactions in dictating the triplex strength. The ionizable NH2 substituent at C4 in R/S configuration is thus a versatile probe for delineating the triplex stabilizing factors and the results have potential for designing of collagen analogues with customized properties for material and biological applications.

Dynamic motifs in socio-economic networks

Science.gov (United States)

Zhang, Xin; Shao, Shuai; Stanley, H. Eugene; Havlin, Shlomo

2014-12-01

Socio-economic networks are of central importance in economic life. We develop a method of identifying and studying motifs in socio-economic networks by focusing on “dynamic motifs,” i.e., evolutionary connection patterns that, because of “node acquaintances” in the network, occur much more frequently than random patterns. We examine two evolving bi-partite networks: i) the world-wide commercial ship chartering market and ii) the ship build-to-order market. We find similar dynamic motifs in both bipartite networks, even though they describe different economic activities. We also find that “influence” and “persistence” are strong factors in the interaction behavior of organizations. When two companies are doing business with the same customer, it is highly probable that another customer who currently only has business relationship with one of these two companies, will become customer of the second in the future. This is the effect of influence. Persistence means that companies with close business ties to customers tend to maintain their relationships over a long period of time.

GNG Motifs Can Replace a GGG Stretch during G-Quadruplex Formation in a Context Dependent Manner.

Directory of Open Access Journals (Sweden)

Kohal Das

Full Text Available G-quadruplexes are one of the most commonly studied non-B DNA structures. Generally, these structures are formed using a minimum of 4, three guanine tracts, with connecting loops ranging from one to seven. Recent studies have reported deviation from this general convention. One such deviation is the involvement of bulges in the guanine tracts. In this study, guanines along with bulges, also referred to as GNG motifs have been extensively studied using recently reported HOX11 breakpoint fragile region I as a model template. By strategic mutagenesis approach we show that the contribution from continuous G-tracts may be dispensible during G-quadruplex formation when such motifs are flanked by GNGs. Importantly, the positioning and number of GNG/GNGNG can also influence the formation of G-quadruplexes. Further, we assessed three genomic regions from HIF1 alpha, VEGF and SHOX gene for G-quadruplex formation using GNG motifs. We show that HIF1 alpha sequence harbouring GNG motifs can fold into intramolecular G-quadruplex. In contrast, GNG motifs in mutant VEGF sequence could not participate in structure formation, suggesting that the usage of GNG is context dependent. Importantly, we show that when two continuous stretches of guanines are flanked by two independent GNG motifs in a naturally occurring sequence (SHOX, it can fold into an intramolecular G-quadruplex. Finally, we show the specific binding of G-quadruplex binding protein, Nucleolin and G-quadruplex antibody, BG4 to SHOX G-quadruplex. Overall, our study provides novel insights into the role of GNG motifs in G-quadruplex structure formation which may have both physiological and pathological implications.

Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

Science.gov (United States)

Petrov, Anton I.; Zirbel, Craig L.; Leontis, Neocles B.

2013-01-01

The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson–Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access. PMID:23970545

A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data.

Science.gov (United States)

Tran, Ngoc Tam L; Huang, Chun-Hsi

2014-02-20

ChIP-Seq (chromatin immunoprecipitation sequencing) has provided the advantage for finding motifs as ChIP-Seq experiments narrow down the motif finding to binding site locations. Recent motif finding tools facilitate the motif detection by providing user-friendly Web interface. In this work, we reviewed nine motif finding Web tools that are capable for detecting binding site motifs in ChIP-Seq data. We showed each motif finding Web tool has its own advantages for detecting motifs that other tools may not discover. We recommended the users to use multiple motif finding Web tools that implement different algorithms for obtaining significant motifs, overlapping resemble motifs, and non-overlapping motifs. Finally, we provided our suggestions for future development of motif finding Web tool that better assists researchers for finding motifs in ChIP-Seq data.

The regulation of ER export and Golgi retention of ST3Gal5 (GM3/GM4 synthase) and B4GalNAcT1 (GM2/GD2/GA2 synthase) by arginine/lysine-based motif adjacent to the transmembrane domain.

Science.gov (United States)

Uemura, Satoshi; Shishido, Fumi; Kashimura, Madoka; Inokuchi, Jin-ichi

2015-12-01

In the Golgi maturation model, the Golgi cisternae dynamically mature along a secretory pathway. In this dynamic process, glycosyltransferases are transported from the endoplasmic reticulum (ER) to the Golgi apparatus where they remain and function. The precise mechanism behind this maturation process remains unclear. We investigated two glycosyltransferases, ST3Gal5 (ST3G5) and B4GalNAcT1 (B4GN1), involved in ganglioside synthesis and examined their signal sequences for ER export and Golgi retention. Reports have suggested that the [R/K](X)[R/K] motif functions as an ER exporting signal; however, this signal sequence is insufficient in stably expressed, full-length ST3G5. Through further analysis, we have clarified that the (2)R(3)R(X)(5) (9)K(X)(3) (13)K sequence in ST3G5 is essential for ER export. We have named the sequence the R/K-based motif. On the other hand, for ER export of B4GN1, the homodimer formation in addition to the R/K-based motif is required for ER export suggesting the importance of unidentified lumenal side interaction. We found that ST3G5 R2A/R3A and K9A/K13A mutants localized not only in Golgi apparatus but also in endosomes. Furthermore, the amounts of mature type asparagine-linked (N)-glycans in ST3G5 R2A/R3A and K9A/K13A mutants were decreased compared with those in wild-type proteins, and the stability of the mutants was lower. These results suggest that the R/K-based motif is necessary for the Golgi retention of ST3G5 and that the retention is involved in the maturation of N-glycans and in stability. Thus, several basic amino acids located on the cytoplasmic tail of ST3G5 play important roles in both ER export and Golgi retention. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Synthesis and photocatalytic activity of CuY{sub y}Fe{sub 2-y}O{sub 4}-CuCo{sub 2}O{sub 4} nanocomposites for H{sub 2} evolution under visible light irradiation

Energy Technology Data Exchange (ETDEWEB)

Yan, Jianhui; Yang, Haihua; Yao, Maohai; Han, Yong [Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Shuyuan Load, Yueyang, Hunan 414000 (China); College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083 (China); Tang, Yougen; Lu, Zhouguang [College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083 (China); Zheng, Shuqin [Department of Chemistry and Chemical Engineering, Hunan Institute of Science and Technology, Shuyuan Load, Yueyang, Hunan 414000 (China)

2009-11-15

Spinel-type CuY{sub y}Fe{sub 2-y}O{sub 4}-CuCo{sub 2}O{sub 4} nanocomposites have been successfully synthesized via a facile citric acid (CA)-assisted sol-gel method. And the as-synthesized nanocomposites have been characterized by techniques of X-ray diffraction (XRD), nitrogen adsorption BET method, and transmission electron microscopy (TEM). The samples are composed of primary ultrafine nanoparticles with nearly spherical morphology and mean particle size of about 80 nm. Moreover, the photocatalytic H{sub 2} evolution activity of the as-obtained samples has been evaluated from aqueous oxalic acid solution under visible light irradiation. The influence of photocatalyst type, calcination temperature, Y{sup 3+} doping content, and the durability of the as-obtained photocatalyst have been investigated in detail. The best photocatalytic H{sub 2} evolution activity was obtained over the as-synthesized CuY{sub 0.08}Fe{sub 1.92}O{sub 4}-CuCo{sub 2}O{sub 4} nanocomposite. (author)

Exposure to widespread environmental endocrine disrupting chemicals and human sperm sex ratio

International Nuclear Information System (INIS)

Jurewicz, Joanna; Radwan, Michał; Sobala, Wojciech; Radwan, Paweł; Jakubowski, Lucjusz; Wielgomas, Bartosz; Ligocka, Danuta; Brzeźnicki, Sławomir; Hanke, Wojciech

2016-01-01

In recent years, a trend toward a declining proportion of male births has been noted in several, but not all, industrialized countries. The underlying reason for the drop in the sex ratio is unclear, but one theory states that widespread environmental endocrine disrupting chemicals affecting the male reproductive system in a negative manner could be part of the explanation. The present study was designed to investigate whether the urinary phthalate, pyrethroids and polycyclic aromatic hydrocarbons metabolites concentrations were associated with sperm Y:X ratio. The study population consisted of 194 men aged under 45 years of age who attended infertility clinic in Lodz, Poland for diagnostic purposes with normal semen concentration of 20–300 mln/ml or with slight oligozoospermia (semen concentration of 15–20 mln/ml) (WHO, 1999). The Y:X ratio was assessed by fluorescent in situ hybridization. Urinary concentrations of 1-hydroxypyrene were measured by high performance liquid chromatography, phthalate metabolites were analyzed using a procedure based on the LC-MS/MS methods and metabolites of synthetic pyrethroids were assessed by gas chromatography ion-tap mass spectrometry method. After adjustment for potential confounders (past diseases, age, abstinence, smoking, alcohol consumption, sperm concentration, motility, morphology) 5OH MEHP, CDCCA to TDCCA and 1-OHP was negatively related to Y:X sperm chromosome ratio (p = 0.033, p < 0.001, p = 0.047 respectively). As this is the first study to elucidate the association between the level of metabolites of widespread environmental endocrine disrupting chemicals (phthalates, synthetic pyrethroids, polycyclic aromatic hydrocarbons) on sex chromosome ratio in sperm therefore, these findings require further replication in other populations. - Highlights: • Urinary phthalate metabolites levels were significantly associated with a decrease in Y/X chromosome bearing sperm. • The levels of 1-hydroxypyrene in urine

Mechanisms of zero-lag synchronization in cortical motifs.

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Leonardo L Gollo

2014-04-01

Full Text Available Zero-lag synchronization between distant cortical areas has been observed in a diversity of experimental data sets and between many different regions of the brain. Several computational mechanisms have been proposed to account for such isochronous synchronization in the presence of long conduction delays: Of these, the phenomenon of "dynamical relaying"--a mechanism that relies on a specific network motif--has proven to be the most robust with respect to parameter mismatch and system noise. Surprisingly, despite a contrary belief in the community, the common driving motif is an unreliable means of establishing zero-lag synchrony. Although dynamical relaying has been validated in empirical and computational studies, the deeper dynamical mechanisms and comparison to dynamics on other motifs is lacking. By systematically comparing synchronization on a variety of small motifs, we establish that the presence of a single reciprocally connected pair--a "resonance pair"--plays a crucial role in disambiguating those motifs that foster zero-lag synchrony in the presence of conduction delays (such as dynamical relaying from those that do not (such as the common driving triad. Remarkably, minor structural changes to the common driving motif that incorporate a reciprocal pair recover robust zero-lag synchrony. The findings are observed in computational models of spiking neurons, populations of spiking neurons and neural mass models, and arise whether the oscillatory systems are periodic, chaotic, noise-free or driven by stochastic inputs. The influence of the resonance pair is also robust to parameter mismatch and asymmetrical time delays amongst the elements of the motif. We call this manner of facilitating zero-lag synchrony resonance-induced synchronization, outline the conditions for its occurrence, and propose that it may be a general mechanism to promote zero-lag synchrony in the brain.

AMP-acetyl CoA synthetase from Leishmania donovani: identification and functional analysis of 'PX4GK' motif.

Science.gov (United States)

Soumya, Neelagiri; Kumar, I Sravan; Shivaprasad, S; Gorakh, Landage Nitin; Dinesh, Neeradi; Swamy, Kayala Kambagiri; Singh, Sushma

2015-04-01

An adenosine monophosphate forming acetyl CoA synthetase (AceCS) which is the key enzyme involved in the conversion of acetate to acetyl CoA has been identified from Leishmania donovani for the first time. Sequence analysis of L. donovani AceCS (LdAceCS) revealed the presence of a 'PX4GK' motif which is highly conserved throughout organisms with higher sequence identity (96%) to lower sequence identity (38%). A ∼ 77 kDa heterologous protein with C-terminal 6X His-tag was expressed in Escherichia coli. Expression of LdAceCS in promastigotes was confirmed by western blot and RT-PCR analysis. Immunolocalization studies revealed that it is a cytosolic protein. We also report the kinetic characterization of recombinant LdAceCS with acetate, adenosine 5'-triphosphate, coenzyme A and propionate as substrates. Site directed mutagenesis of residues in conserved PX4GK motif of LdAceCS was performed to gain insight into its potential role in substrate binding, catalysis and its role in maintaining structural integrity of the protein. P646A, G651A and K652R exhibited more than 90% loss in activity signifying its indispensible role in the enzyme activity. Substitution of other residues in this motif resulted in altered substrate specificity and catalysis. However, none of them had any role in modulation of the secondary structure of the protein except G651A mutant. Copyright © 2015 Elsevier B.V. All rights reserved.

A Role of Sp1 Binding Motifs in Basal and Large T-Antigen-Induced Promoter Activities of Human Polyomavirus HPyV9 and Its Variant UF-1

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Ugo Moens

2017-11-01

Full Text Available Human polyomavirus 9 (HPyV9 was originally detected in the serum of a renal transplant patient. Seroepidemiological studies showed that ~20–50% of the human population have antibodies against this virus. HPyV9 has not yet been associated with any disease and little is known about the route of infection, transmission, host cell tropism, and genomic variability in circulating strains. Recently, the HPyV9 variant UF-1 with an eight base-pair deletion, a thirteen base-pair insertion and with point mutations, creating three putative Sp1 binding sites in the late promoter was isolated from an AIDS patient. Transient transfection studies with a luciferase reporter plasmid driven by HPyV9 or UF1 promoter demonstrated that UF1 early and late promoters were stronger than HPyV9 promoters in most cell lines, and that the UF1 late promoter was more potently activated by HPyV9 large T-antigen (LTAg. Mutation of two Sp1 motifs strongly reduced trans-activation of the late UF1 promoter by HPyV9 LTAg in HeLa cells. In conclusion, the mutations in the UF1 late promoter seem to strengthen its activity and its response to stimulation by HPyV9 LTAg in certain cells. It remains to be investigated whether these promoter changes have an influence on virus replication and affect the possible pathogenic properties of the virus.

Influence of 45S5 Bioglass addition on microstructure and properties of ultrafine grained (Mg-4Y-5.5Dy-0.5Zr) alloy

Energy Technology Data Exchange (ETDEWEB)

Kowalski, K., E-mail: kamil.kowalski@put.poznan.pl [Institute of Materials Science and Engineering, Poznan University of Technology, Jana Pawla II 24, 61-138 Poznan (Poland); Jurczyk, M.U. [Division of Mother’s and Child’s Health, Poznan University of Medical Sciences, Polna 33, 60-535 Poznan (Poland); Wirstlein, P.K. [Department of Gynecology and Obstetrics, Division of Reproduction, Poznan University of Medical Sciences, Polna 33, 60-535 Poznan (Poland); Jakubowicz, J.; Jurczyk, M. [Institute of Materials Science and Engineering, Poznan University of Technology, Jana Pawla II 24, 61-138 Poznan (Poland)

2017-05-15

Highlights: • Ultrafine grained composites were formed by consolidating mechanically alloyed powders. • Mechanical properties were sensitive to the content of 45S5 Bioglass in Mg-4Y-5.5Dy-0.5Zr alloy. • Fluoride treated composites displayed superior corrosion resistance in Ringer solution. • Composites modified with MgF{sub 2} have a higher degree of biocompatibility in comparison with the unmodified reference material. - Abstract: Bulk samples of an ultrafine grained (Mg-4Y-5.5Dy-0.5Zr)-x wt% 45S5 Bioglass (x = 0, 5) and (Mg-4Y-5.5Dy-0.5Zr)-5 wt% 45S5 Bioglass-1 wt% Ag composites have been synthesized by consolidating mechanically alloyed powders. The influence of the chemical composition on the microstructure, mechanical properties and corrosion behavior of bulk composites were studied. The sintering of (Mg-4Y-5.5Dy-0.5Zr)-5 wt% 45S5 Bioglass powders led to the formation of a bulk composite with grain size of approx. 95 nm. The corrosion behavior of Mg-based composites before and after hydrofluoric acid treatment was also investigated. The ultrafine grained (Mg-4Y-5.5Dy-0.5Zr)-5 wt% 45S5 Bioglass composite was more corrosion resistant than the bulk Mg-4Y-5.5Dy-0.5Zr alloy after HF treatment. The in vitro biocompatibility of synthesized composites was evaluated and compared with microcrystalline magnesium. Magnesium, (Mg-4Y-5.5Dy-0.5Zr)-5 wt% 45S5 Bioglass and (Mg-4Y-5.5Dy-0.5Zr)-5 wt% 45S5 Bioglass-1 wt% Ag composites modified with MgF{sub 2} have a higher degree of biocompatibility in comparison with the unmodified reference material.

The tyrosine Y2502.39 in Frizzled 4 defines a conserved motif important for structural integrity of the receptor and recruitment of Disheveled.

Science.gov (United States)

Strakova, Katerina; Matricon, Pierre; Yokota, Chika; Arthofer, Elisa; Bernatik, Ondrej; Rodriguez, David; Arenas, Ernest; Carlsson, Jens; Bryja, Vitezslav; Schulte, Gunnar

2017-10-01

Frizzleds (FZDs) are unconventional G protein-coupled receptors, which activate diverse intracellular signaling pathways via the phosphoprotein Disheveled (DVL) and heterotrimeric G proteins. The interaction interplay of FZDs with DVL and G proteins is complex, involves different regions of FZD and the potential dynamics are poorly understood. In the present study, we aimed to characterize the function of a highly conserved tyrosine (Y250 2.39 ) in the intracellular loop 1 (IL1) of human FZD 4 . We have found Y250 2.39 to be crucial for DVL2 interaction and DVL2 translocation to the plasma membrane. Mutant FZD 4 -Y250 2.39 F, impaired in DVL2 binding, was defective in both β-catenin-dependent and β-catenin-independent WNT signaling induced in Xenopus laevis embryos. The same mutant maintained interaction with the heterotrimeric G proteins Gα 12 and Gα 13 and was able to mediate WNT-induced G protein dissociation and G protein-dependent YAP/TAZ signaling. We conclude from modeling and dynamics simulation efforts that Y250 2.39 is important for the structural integrity of the FZD-DVL, but not for the FZD-G protein interface and hypothesize that the interaction network of Y250 2.39 and H348 4.46 plays a role in specifying downstream signaling pathways induced by the receptor. Copyright © 2017. Published by Elsevier Inc.

Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets.

Science.gov (United States)

Chiu, Yi-Yuan; Lin, Chun-Yu; Lin, Chih-Ta; Hsu, Kai-Cheng; Chang, Li-Zen; Yang, Jinn-Moon

2012-01-01

To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often share similar local binding environments and motifs. As the exponential growth of the number of protein structures, to find the similar structural binding motifs (pharma-motifs) is an emergency task for drug discovery (e.g. side effects and new uses for old drugs) and protein functions. We have developed a Space-Related Pharmamotifs (called SRPmotif) method to recognize the binding motifs by searching against protein structure database. SRPmotif is able to recognize conserved binding environments containing spatially discontinuous pharma-motifs which are often short conserved peptides with specific physico-chemical properties for protein functions. Among 356 pharma-motifs, 56.5% interacting residues are highly conserved. Experimental results indicate that 81.1% and 92.7% polypharmacological targets of each protein-ligand complex are annotated with same biological process (BP) and molecular function (MF) terms, respectively, based on Gene Ontology (GO). Our experimental results show that the identified pharma-motifs often consist of key residues in functional (active) sites and play the key roles for protein functions. The SRPmotif is available at http://gemdock.life.nctu.edu.tw/SRP/. SRPmotif is able to identify similar pharma-interfaces and pharma-motifs sharing similar binding environments for polypharmacological targets by rapidly searching against the protein structure database. Pharma-motifs describe the conservations of binding environments for drug discovery and protein functions. Additionally, these pharma-motifs provide the clues for discovering new sequence-based motifs to predict protein functions from protein sequence databases. We believe that SRPmotif is useful for elucidating protein functions and drug discovery.

Phyloproteomic Analysis of 11780 Six-Residue-Long Motifs Occurrences

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O. V. Galzitskaya

2015-01-01

Full Text Available How is it possible to find good traits for phylogenetic reconstructions? Here, we present a new phyloproteomic criterion that is an occurrence of simple motifs which can be imprints of evolution history. We studied the occurrences of 11780 six-residue-long motifs consisting of two randomly located amino acids in 97 eukaryotic and 25 bacterial proteomes. For all eukaryotic proteomes, with the exception of the Amoebozoa, Stramenopiles, and Diplomonadida kingdoms, the number of proteins containing the motifs from the first group (one of the two amino acids occurs once at the terminal position made about 20%; in the case of motifs from the second (one of two amino acids occurs one time within the pattern and third (the two amino acids occur randomly groups, 30% and 50%, respectively. For bacterial proteomes, this relationship was 10%, 27%, and 63%, respectively. The matrices of correlation coefficients between numbers of proteins where a motif from the set of 11780 motifs appears at least once in 9 kingdoms and 5 phyla of bacteria were calculated. Among the correlation coefficients for eukaryotic proteomes, the correlation between the animal and fungi kingdoms (0.62 is higher than between fungi and plants (0.54. Our study provides support that animals and fungi are sibling kingdoms. Comparison of the frequencies of six-residue-long motifs in different proteomes allows obtaining phylogenetic relationships based on similarities between these frequencies: the Diplomonadida kingdoms are more close to Bacteria than to Eukaryota; Stramenopiles and Amoebozoa are more close to each other than to other kingdoms of Eukaryota.

Motif formation and industry specific topologies in the Japanese business firm network

Science.gov (United States)

Maluck, Julian; Donner, Reik V.; Takayasu, Hideki; Takayasu, Misako

2017-05-01

Motifs and roles are basic quantities for the characterization of interactions among 3-node subsets in complex networks. In this work, we investigate how the distribution of 3-node motifs can be influenced by modifying the rules of an evolving network model while keeping the statistics of simpler network characteristics, such as the link density and the degree distribution, invariant. We exemplify this problem for the special case of the Japanese Business Firm Network, where a well-studied and relatively simple yet realistic evolving network model is available, and compare the resulting motif distribution in the real-world and simulated networks. To better approximate the motif distribution of the real-world network in the model, we introduce both subgraph dependent and global additional rules. We find that a specific rule that allows only for the merging process between nodes with similar link directionality patterns reduces the observed excess of densely connected motifs with bidirectional links. Our study improves the mechanistic understanding of motif formation in evolving network models to better describe the characteristic features of real-world networks with a scale-free topology.

Motif-role-fingerprints: the building-blocks of motifs, clustering-coefficients and transitivities in directed networks.

Directory of Open Access Journals (Sweden)

Mark D McDonnell

Full Text Available Complex networks are frequently characterized by metrics for which particular subgraphs are counted. One statistic from this category, which we refer to as motif-role fingerprints, differs from global subgraph counts in that the number of subgraphs in which each node participates is counted. As with global subgraph counts, it can be important to distinguish between motif-role fingerprints that are 'structural' (induced subgraphs and 'functional' (partial subgraphs. Here we show mathematically that a vector of all functional motif-role fingerprints can readily be obtained from an arbitrary directed adjacency matrix, and then converted to structural motif-role fingerprints by multiplying that vector by a specific invertible conversion matrix. This result demonstrates that a unique structural motif-role fingerprint exists for any given functional motif-role fingerprint. We demonstrate a similar result for the cases of functional and structural motif-fingerprints without node roles, and global subgraph counts that form the basis of standard motif analysis. We also explicitly highlight that motif-role fingerprints are elemental to several popular metrics for quantifying the subgraph structure of directed complex networks, including motif distributions, directed clustering coefficient, and transitivity. The relationships between each of these metrics and motif-role fingerprints also suggest new subtypes of directed clustering coefficients and transitivities. Our results have potential utility in analyzing directed synaptic networks constructed from neuronal connectome data, such as in terms of centrality. Other potential applications include anomaly detection in networks, identification of similar networks and identification of similar nodes within networks. Matlab code for calculating all stated metrics following calculation of functional motif-role fingerprints is provided as S1 Matlab File.

New PAH gene promoter KLF1 and 3'-region C/EBPalpha motifs influence transcription in vitro.

Science.gov (United States)

Klaassen, Kristel; Stankovic, Biljana; Kotur, Nikola; Djordjevic, Maja; Zukic, Branka; Nikcevic, Gordana; Ugrin, Milena; Spasovski, Vesna; Srzentic, Sanja; Pavlovic, Sonja; Stojiljkovic, Maja

2017-02-01

Phenylketonuria (PKU) is a metabolic disease caused by mutations in the phenylalanine hydroxylase (PAH) gene. Although the PAH genotype remains the main determinant of PKU phenotype severity, genotype-phenotype inconsistencies have been reported. In this study, we focused on unanalysed sequences in non-coding PAH gene regions to assess their possible influence on the PKU phenotype. We transiently transfected HepG2 cells with various chloramphenicol acetyl transferase (CAT) reporter constructs which included PAH gene non-coding regions. Selected non-coding regions were indicated by in silico prediction to contain transcription factor binding sites. Furthermore, electrophoretic mobility shift assay (EMSA) and supershift assays were performed to identify which transcriptional factors were engaged in the interaction. We found novel KLF1 motif in the PAH promoter, which decreases CAT activity by 50 % in comparison to basal transcription in vitro. The cytosine at the c.-170 promoter position creates an additional binding site for the protein complex involving KLF1 transcription factor. Moreover, we assessed for the first time the role of a multivariant variable number tandem repeat (VNTR) region located in the 3'-region of the PAH gene. We found that the VNTR3, VNTR7 and VNTR8 constructs had approximately 60 % of CAT activity. The regulation is mediated by the C/EBPalpha transcription factor, present in protein complex binding to VNTR3. Our study highlighted two novel promoter KLF1 and 3'-region C/EBPalpha motifs in the PAH gene which decrease transcription in vitro and, thus, could be considered as PAH expression modifiers. New transcription motifs in non-coding regions will contribute to better understanding of the PKU phenotype complexity and may become important for the optimisation of PKU treatment.

Biomimetic trapping cocktail to screen reactive metabolites: use of an amino acid and DNA motif mixture as light/heavy isotope pairs differing in mass shift.

Science.gov (United States)

Hosaka, Shuto; Honda, Takuto; Lee, Seon Hwa; Oe, Tomoyuki

2018-06-01

Candidate drugs that can be metabolically transformed into reactive electrophilic products, such as epoxides, quinones, and nitroso compounds, are of special concern because subsequent covalent binding to bio-macromolecules can cause adverse drug reactions, such as allergic reactions, hepatotoxicity, and genotoxicity. Several strategies have been reported for screening reactive metabolites, such as a covalent binding assay with radioisotope-labeled drugs and a trapping method followed by LC-MS/MS analyses. Of these, a trapping method using glutathione is the most common, especially at the early stage of drug development. However, the cysteine of glutathione is not the only nucleophilic site in vivo; lysine, histidine, arginine, and DNA bases are also nucleophilic. Indeed, the glutathione trapping method tends to overlook several types of reactive metabolites, such as aldehydes, acylglucuronides, and nitroso compounds. Here, we introduce an alternate way for screening reactive metabolites as follows: A mixture of the light and heavy isotopes of simplified amino acid motifs and a DNA motif is used as a biomimetic trapping cocktail. This mixture consists of [ 2 H 0 ]/[ 2 H 3 ]-1-methylguanidine (arginine motif, Δ 3 Da), [ 2 H 0 ]/[ 2 H 4 ]-2-mercaptoethanol (cysteine motif, Δ 4 Da), [ 2 H 0 ]/[ 2 H 5 ]-4-methylimidazole (histidine motif, Δ 5 Da), [ 2 H 0 ]/[ 2 H 9 ]-n-butylamine (lysine motif, Δ 9 Da), and [ 13 C 0 , 15 N 0 ]/[ 13 C 1 , 15 N 2 ]-2'-deoxyguanosine (DNA motif, Δ 3 Da). Mass tag triggered data-dependent acquisition is used to find the characteristic doublet peaks, followed by specific identification of the light isotope peak using MS/MS. Forty-two model drugs were examined using an in vitro microsome experiment to validate the strategy. Graphical abstract Biomimetic trapping cocktail to screen reactive metabolites.

Spike Pattern Structure Influences Synaptic Efficacy Variability Under STDP and Synaptic Homeostasis. I: Spike Generating Models on Converging Motifs

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Zedong eBi

2016-02-01

Full Text Available In neural systems, synaptic plasticity is usually driven by spike trains. Due to the inherent noises of neurons and synapses as well as the randomness of connection details, spike trains typically exhibit variability such as spatial randomness and temporal stochasticity, resulting in variability of synaptic changes under plasticity, which we call efficacy variability. How the variability of spike trains influences the efficacy variability of synapses remains unclear. In this paper, we try to understand this influence under pair-wise additive spike-timing dependent plasticity (STDP when the mean strength of plastic synapses into a neuron is bounded (synaptic homeostasis. Specifically, we systematically study, analytically and numerically, how four aspects of statistical features, i.e. synchronous firing, burstiness/regularity, heterogeneity of rates and heterogeneity of cross-correlations, as well as their interactions influence the efficacy variability in converging motifs (simple networks in which one neuron receives from many other neurons. Neurons (including the post-synaptic neuron in a converging motif generate spikes according to statistical models with tunable parameters. In this way, we can explicitly control the statistics of the spike patterns, and investigate their influence onto the efficacy variability, without worrying about the feedback from synaptic changes onto the dynamics of the post-synaptic neuron. We separate efficacy variability into two parts: the drift part (DriftV induced by the heterogeneity of change rates of different synapses, and the diffusion part (DiffV induced by weight diffusion caused by stochasticity of spike trains. Our main findings are: (1 synchronous firing and burstiness tend to increase DiffV, (2 heterogeneity of rates induces DriftV when potentiation and depression in STDP are not balanced, and (3 heterogeneity of cross-correlations induces DriftV together with heterogeneity of rates. We anticipate our

Proyecto Youtuber, Influencer en viajes y turismo activo

OpenAIRE

Gálvez Mancheño, María Carmen

2016-01-01

Youtube es una de las grandes plataformas de distribución de contenidos audiovisuales y gracias a ella se han creado nuevas formas de comunicación, como las que han desarrollado los Youtubers. En este trabajo daremos a conocer el importante crecimiento que están teniendo las redes sociales y la evolución de los influencers junto a ellas. Además se ha analizado cómo las marcas y las empresas y sobre todo la industria de turismo cada vez recurren más a estos influencers y a nuevas formas de com...

Parallel motif extraction from very long sequences

KAUST Repository

Sahli, Majed

2013-01-01

Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern applications require mining of motifs in one very long sequence (i.e., in the order of several gigabytes). For this case, there exist statistical approaches that are fast but inaccurate; or combinatorial methods that are sound and complete. Unfortunately, existing combinatorial methods are serial and very slow. Consequently, they are limited to very short sequences (i.e., a few megabytes), small alphabets (typically 4 symbols for DNA sequences), and restricted types of motifs. This paper presents ACME, a combinatorial method for extracting motifs from a single very long sequence. ACME arranges the search space in contiguous blocks that take advantage of the cache hierarchy in modern architectures, and achieves almost an order of magnitude performance gain in serial execution. It also decomposes the search space in a smart way that allows scalability to thousands of processors with more than 90% speedup. ACME is the only method that: (i) scales to gigabyte-long sequences; (ii) handles large alphabets; (iii) supports interesting types of motifs with minimal additional cost; and (iv) is optimized for a variety of architectures such as multi-core systems, clusters in the cloud, and supercomputers. ACME reduces the extraction time for an exact-length query from 4 hours to 7 minutes on a typical workstation; handles 3 orders of magnitude longer sequences; and scales up to 16, 384 cores on a supercomputer. Copyright is held by the owner/author(s).

Crystal structures of NiSO4·9H2O and NiSO4·8H2O: magnetic properties, stability with respect to morenosite (NiSO4·7H2O), the solid-solution series (Mg x Ni1-x )SO4·9H2O

Science.gov (United States)

Fortes, A. D.; Knight, K. S.; Gibbs, A. S.; Wood, I. G.

2018-02-01

Since being discovered initially in mixed-cation systems, a method of forming end-member NiSO4·9H2O and NiSO4·8H2O has been found. We have obtained powder diffraction data from protonated analogues (with X-rays) and deuterated analogues (using neutrons) of these compounds over a range of temperatures, allowing us to determine their crystal structures—including all H-atoms—and to characterise the transitions on warming from 220 to 278 K; glass → 9-hydrate → 8-hydrate + ice → 7-hydrate + ice → partial melt (7-hydrate + liquid). NiSO4·8D2O is triclinic, space-group P\\bar {1} , Z = 2, with unit cell parameters at 150 K, a = 6.12463(8) Å, b = 6.8401(1) Å, c = 12.5339(2) Å, α = 92.846(1)°, β = 97.822(1)°, γ = 96.627(1)° and V = 515.58(1) Å3. The structure consists of two symmetry-inequivalent Ni(D2O)6 octahedra on sites of \\bar {1} symmetry. These are directly joined by a water-water H-bond to form chains of octahedra parallel with the c-axis at x = 0. Two interstitial water molecules serve both to bridge the Ni(D2O)6 octahedral chains in the b-c plane and also to connect with the SO4 2- tetrahedral oxyanion. These tetrahedra are linked by the two interstitial water molecules in a reticular motif to form sheets perpendicular to c. NiSO4·9D2O is monoclinic, space-group P21/c, Z = 4, with unit-cell parameters at 150 K, a = 6.69739(6) Å, b = 11.8628(1) Å, c = 14.5667(1) Å, β = 94.9739(8)° and V = 1152.96(1) Å3. The structure is isotypic with the Mg analogue described elsewhere (Fortes et al., Acta Cryst B 73:47‒64, 2017b). It shares the motif of H-bonded octahedral chains with NiSO4·8D2O, although in the enneahydrate these run parallel with the b-axis at x = 0. Three interstitial water molecules bridge the Ni(D2O)6 octahedra to the SO4 2- tetrahedral oxyanion. The tetrahedra sit at x ≈ 0.5 and are linked by two of the three interstitial water molecules in a pentagonal motif to form ribbons parallel with b. A solid-solution series

LDsplit: screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms.

Science.gov (United States)

Yang, Peng; Wu, Min; Guo, Jing; Kwoh, Chee Keong; Przytycka, Teresa M; Zheng, Jie

2014-02-17

As a fundamental genomic element, meiotic recombination hotspot plays important roles in life sciences. Thus uncovering its regulatory mechanisms has broad impact on biomedical research. Despite the recent identification of the zinc finger protein PRDM9 and its 13-mer binding motif as major regulators for meiotic recombination hotspots, other regulators remain to be discovered. Existing methods for finding DNA sequence motifs of recombination hotspots often rely on the enrichment of co-localizations between hotspots and short DNA patterns, which ignore the cross-individual variation of recombination rates and sequence polymorphisms in the population. Our objective in this paper is to capture signals encoded in genetic variations for the discovery of recombination-associated DNA motifs. Recently, an algorithm called "LDsplit" has been designed to detect the association between single nucleotide polymorphisms (SNPs) and proximal meiotic recombination hotspots. The association is measured by the difference of population recombination rates at a hotspot between two alleles of a candidate SNP. Here we present an open source software tool of LDsplit, with integrative data visualization for recombination hotspots and their proximal SNPs. Applying LDsplit on SNPs inside an established 7-mer motif bound by PRDM9 we observed that SNP alleles preserving the original motif tend to have higher recombination rates than the opposite alleles that disrupt the motif. Running on SNP windows around hotspots each containing an occurrence of the 7-mer motif, LDsplit is able to guide the established motif finding algorithm of MEME to recover the 7-mer motif. In contrast, without LDsplit the 7-mer motif could not be identified. LDsplit is a software tool for the discovery of cis-regulatory DNA sequence motifs stimulating meiotic recombination hotspots by screening and narrowing down to hotspot associated SNPs. It is the first computational method that utilizes the genetic variation of

A single amino-acid change in a highly conserved motif of gp41 elicits HIV-1 neutralization and protects against CD4 depletion.

Science.gov (United States)

Petitdemange, Caroline; Achour, Abla; Dispinseri, Stefania; Malet, Isabelle; Sennepin, Alexis; Ho Tsong Fang, Raphaël; Crouzet, Joël; Marcelin, Anne-Geneviève; Calvez, Vincent; Scarlatti, Gabriella; Debré, Patrice; Vieillard, Vincent

2013-09-01

The induction of neutralizing antibodies against conserved regions of the human immunodeficiency virus type 1 (HIV-1) envelope protein is a major goal of vaccine strategies. We previously identified 3S, a critical conserved motif of gp41 that induces the NKp44L ligand of an activating NK receptor. In vivo, anti-3S antibodies protect against the natural killer (NK) cell-mediated CD4 depletion that occurs without efficient viral neutralization. Specific substitutions within the 3S peptide motif were prepared by directed mutagenesis. Virus production was monitored by measuring the p24 production. Neutralization assays were performed with immune-purified antibodies from immunized mice and a cohort of HIV-infected patients. Expression of NKp44L on CD4(+) T cells and degranulation assay on activating NK cells were both performed by flow cytometry. Here, we show that specific substitutions in the 3S motif reduce viral infection without affecting gp41 production, while decreasing both its capacity to induce NKp44L expression on CD4(+) T cells and its sensitivity to autologous NK cells. Generation of antibodies in mice against the W614 specific position in the 3S motif elicited a capacity to neutralize cross-clade viruses, notable in its magnitude, breadth, and durability. Antibodies against this 3S variant were also detected in sera from some HIV-1-infected patients, demonstrating both neutralization activity and protection against CD4 depletion. These findings suggest that a specific substitution in a 3S-based immunogen might allow the generation of specific antibodies, providing a foundation for a rational vaccine that combine a capacity to neutralize HIV-1 and to protect CD4(+) T cells.

Analisis Unsur Matematika pada Motif Sulam Usus

Directory of Open Access Journals (Sweden)

Fredi Ganda Putra

2017-12-01

Full Text Available Based on interviews with researchers sources said that the beginning of the intestine embroidery is an art of genuine crafts. Called the intestine embroidery because this technique is a technique of combining a strand of cloth resembling the intestine formed according to the pattern by means of embroidered using a thread. Intestinal embroidery techniques were originally used to create a cover of the women's customary wardrobe of Lampung or often referred to as bebe. But not many people in Lampung, especially people who live in Lampung are still many who do not know and recognize the intestine embroidery because most only know tapis only characteristic of Lampung, besides that there are other cultural results that is embroidered intestine. There are still many who do not know that the intestine motif there is a knowledge of mathematics. The researcher's problem formulation is whether there are mathematical elements contained in the intestine embroidery motif based on the concept of geometry. The purpose of this study is to determine whether there are elements of mathematics contained in the intestine motif based on the concept of geometry. Subjects in this study consisted of 4 people obtained by purposive sampling technique. From the results of data analysis conducted by using descriptive analysis and discussion as follows: (1 Intestinal embroidery motif contains the meaning of mathematics and culture or often called Etnomatematika. On the meaning of culture there is a link between the embroidery intestine with a culture that has been there before as the existence of cultural linkage between Hindu belief Buddhism and there are similarities of motifs and decorative patterns contained in the motif embroidery intestine with ornamental variety in Indonesia. (2 The relationship between the intestine with mathematical motifs there are elements of mathematics such as geometry elements in the form of geometry of dimension one and dimension two, and the

THE MOTIF OF THE SECOND COMING IN RUSSIAN FANTASTIC FICTION

Directory of Open Access Journals (Sweden)

Tatyana I. Khoruzhenko

2017-06-01

Full Text Available The motif of the Second Coming of Christ takes a special place in Russian fantastic fiction at the turn of the millennium. In the recent decades allusions to the Gospel topic appears in increasing frequency in the genre of fantasy. The aim of the given article was to analyze the peculiarities of the depiction of the subject of Advent in Russian fantastic fiction. As the basis for the research the novels of Y. Voznesenskaya, N. Perumov, V. Khlumov, S. Lukyanenko and T. Ustimenko are of particular interest. The Advent motif appears in the story line of each of the novels in question. Though, the attitude of the authors to the image of the Savior and his second coming to the world fluctuates: from a respectful expectation (Y. Voznesenskaya, T. Ustimenko, S. Lukyanenko to the depiction of the Savior as a monster (N. Perumov. The possibility of an ambivalent interpretation of the Savior is the eloquent evidence of desacralization of this image. The profaning of the sacred is one of the tendencies of the modern popular culture. The genre of fantastic fiction, as a product of mass culture, has caught this trend quite precisely.

Some New Estimation Methods for Weighted Regression When There are Possible Outliers.

Science.gov (United States)

1985-01-01

about influential points, and to add to our understanding of the structure of the data In Section 2 we show, by considering the influence function , why... influence function lampel; 1968, 1974) for the maximum likelihood esti- mator is proportional to (EP-l)h(x), where £= (y-x’B)exp[-h’(x)e], and is thus...unbounded. Since the influence function for the MLE is quadratic in the residual c, in theory a point with a sufficiently large residual can have an

Thermodynamical and thermoelectric properties of boron doped YPd{sub 3} and YRh{sub 3}

Energy Technology Data Exchange (ETDEWEB)

Dwivedi, Shalini; Sharma, Yamini, E-mail: sharma.yamini62@gmail.com [Theoretical Condensed Matter Physics Laboratory, Dept. of Physics, Feroze Gandhi College, Raebareli-229001 U.P (India); Sharma, Ramesh [Dept. of Physics, Mewar University, Chittorgarh-312901 Rajasthan (India)

2016-05-23

The structural, electronic, thermal, and optical properties of borides of cubic non-magnetic YX{sub 3} (X=Rh, Pd) compounds and their borides which crystallize in the AuCu{sub 3} structure have been studied using the density functional theory (DFT). The flat bands in the vicinity of E{sub F} which are associated with superconductivity appear in YPd{sub 3} and YRh{sub 3} band structures. However, the B s-states enhance the flat band only in YRh{sub 3}B. The optical properties clearly show that boron insertion modifies the absorption and transmittance. The YX{sub 3} alloys and their borides exhibit valuable changes in the thermopower and ZT. It is observed that the properties of the Y-X intermetallics change significantly for the Y-Rh and Y-Pd alloys and the presence of single boron atom modifies the properties to a great extent.

Stability and migration of vacancy in V–4Cr–4Ti alloy: Effects of Al, Si, Y trace elements

International Nuclear Information System (INIS)

Zhang, Chong; Zhang, Pengbo; Li, Ruihuan; Zhao, Jijun; Dong, Chuang

2013-01-01

Addition of trace amounts of Al, Si and Y into V–4Cr–4Ti alloy is beneficial for the mechanical properties under irradiation. It is thus important to investigate the influence of solute/trace elements on stabilities, energetics and diffusion behaviors of vacancy defects. We performed first-principles calculations to evaluate vacancy–solute/trace interaction inside dilute V–X (X = Ti, Cr, Al, Si, Y) and V–4Cr–4Ti–(Al, Si, Y) alloys. With addition of Si and Y, vacancy-based complexes tend to form near Ti–Si and Ti–Y pairs, while the effect of Al is negligible. Moreover, diffusion coefficients of solute/trace element in vanadium were derived using nine-frequency model. With high binding energy and low diffusion coefficient, Si atom is strongly attractive to vacancy in vanadium matrix. Our theoretical results suggest that the interactions between vacancy and solute/trace elements play some role in the evolution of microstructures inside vanadium alloys

Structural and functional studies of a phosphatidic acid-binding antifungal plant defensin MtDef4: Identification of an RGFRRR motif governing fungal cell entry

Energy Technology Data Exchange (ETDEWEB)

Sagaram, Uma S.; El-Mounadi, Kaoutar; Buchko, Garry W.; Berg, Howard R.; Kaur, Jagdeep; Pandurangi, Raghoottama; Smith, Thomas J.; Shah, Dilip

2013-12-04

A highly conserved plant defensin MtDef4 potently inhibits the growth of a filamentous fungus Fusarium graminearum. MtDef4 is internalized by cells of F. graminearum. To determine its mechanism of fungal cell entry and antifungal action, NMR solution structure of MtDef4 has been determined. The analysis of its structure has revealed a positively charged patch on the surface of the protein consisting of arginine residues in its γ-core signature, a major determinant of the antifungal activity of MtDef4. Here, we report functional analysis of the RGFRRR motif of the γ-core signature of MtDef4. The replacement of RGFRRR to AAAARR or to RGFRAA not only abolishes fungal cell entry but also results in loss of the antifungal activity of MtDef4. MtDef4 binds strongly to phosphatidic acid (PA), a precursor for the biosynthesis of membrane phospholipids and a signaling lipid known to recruit cytosolic proteins to membranes. Mutations of RGFRRR which abolish fungal cell entry of MtDef4 also impair its binding to PA. Our results suggest that RGFRRR motif is a translocation signal for entry of MtDef4 into fungal cells and that this positively charged motif likely mediates interaction of this defensin with PA as part of its antifungal action.

Mo{sub 2}B{sub 4}O{sub 9} - connecting borate and metal-cluster chemistry

Energy Technology Data Exchange (ETDEWEB)

Schmitt, Martin K.; Huppertz, Hubert [Institut fuer Allgemeine, Anorganische und Theoretische Chemie, Universitaet Innsbruck (Austria); Janka, Oliver; Poettgen, Rainer [Institut fuer Anorganische und Analytische Chemie, Universitaet Muenster (Germany); Benndorf, Christopher [Institut fuer Anorganische und Analytische Chemie, Universitaet Muenster (Germany); Institut fuer Physikalische Chemie, Universitaet Muenster (Germany); Institut fuer Mineralogie, Kristallographie und Materialwissenschaften, Universitaet Leipzig (Germany); Oliveira, Marcos de Jr. [Sao Carlos Institute of Physics, University of Sao Paulo, Sao Carlos (Brazil); Eckert, Hellmut [Institut fuer Physikalische Chemie, Universitaet Muenster (Germany); Sao Carlos Institute of Physics, University of Sao Paulo, Sao Carlos (Brazil); Pielnhofer, Florian; Tragl, Amadeus-Samuel [Institut fuer Anorganische Chemie, Universitaet Regensburg (Germany); Weihrich, Richard [Institut fuer Materials Resource Management, Universitaet Augsburg (Germany); Joachim, Bastian [Institut fuer Mineralogie und Petrographie, Universitaet Innsbruck (Austria); Johrendt, Dirk [Department Chemie, Ludwig-Maximilians-Universitaet Muenchen (Germany)

2017-06-01

We report on the first thoroughly characterized molybdenum borate, which was synthesized in a high-pressure/high-temperature experiment at 12.3 GPa/1300 C using a Walker-type multianvil apparatus. Mo{sub 2}B{sub 4}O{sub 9} incorporates tetrahedral molybdenum clusters into an anionic borate crystal structure - a structural motif that has never been observed before in the wide field of borate crystal chemistry. The six bonding molecular orbitals of the [Mo{sub 4}] tetrahedron are completely filled with 12 electrons, which are fully delocalized over the four molybdenum atoms. This finding is in agreement with the results of the magnetic measurements, which confirmed the diamagnetic character of Mo{sub 2}B{sub 4}O{sub 9}. The two four-coordinated boron sites can be differentiated in the {sup 11}B MAS-NMR spectrum because of the strongly different degrees of local distortions. Experimentally obtained IR and Raman bands were assigned to vibrational modes based on DFT calculations. (copyright 2017 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

One motif to bind them: A small-XXX-small motif affects transmembrane domain 1 oligomerization, function, localization, and cross-talk between two yeast GPCRs.

Science.gov (United States)

Lock, Antonia; Forfar, Rachel; Weston, Cathryn; Bowsher, Leo; Upton, Graham J G; Reynolds, Christopher A; Ladds, Graham; Dixon, Ann M

2014-12-01

G protein-coupled receptors (GPCRs) are the largest family of cell-surface receptors in mammals and facilitate a range of physiological responses triggered by a variety of ligands. GPCRs were thought to function as monomers, however it is now accepted that GPCR homo- and hetero-oligomers also exist and influence receptor properties. The Schizosaccharomyces pombe GPCR Mam2 is a pheromone-sensing receptor involved in mating and has previously been shown to form oligomers in vivo. The first transmembrane domain (TMD) of Mam2 contains a small-XXX-small motif, overrepresented in membrane proteins and well-known for promoting helix-helix interactions. An ortholog of Mam2 in Saccharomyces cerevisiae, Ste2, contains an analogous small-XXX-small motif which has been shown to contribute to receptor homo-oligomerization, localization and function. Here we have used experimental and computational techniques to characterize the role of the small-XXX-small motif in function and assembly of Mam2 for the first time. We find that disruption of the motif via mutagenesis leads to reduction of Mam2 TMD1 homo-oligomerization and pheromone-responsive cellular signaling of the full-length protein. It also impairs correct targeting to the plasma membrane. Mutation of the analogous motif in Ste2 yielded similar results, suggesting a conserved mechanism for assembly. Using co-expression of the two fungal receptors in conjunction with computational models, we demonstrate a functional change in G protein specificity and propose that this is brought about through hetero-dimeric interactions of Mam2 with Ste2 via the complementary small-XXX-small motifs. This highlights the potential of these motifs to affect a range of properties that can be investigated in other GPCRs. Copyright © 2014. Published by Elsevier B.V.

The MHC motif viewer: a visualization tool for MHC binding motifs

DEFF Research Database (Denmark)

Rapin, Nicolas; Hoof, Ilka; Lund, Ole

2010-01-01

is hampered by the lack of tools for browsing and comparing specificity of these molecules. We have developed a Web server, MHC Motif Viewer, which allows the display of the binding motif for MHC class I proteins for human, chimpanzee, rhesus monkey, mouse, and swine, as well as HLA-DR protein sequences...

OBSERVED VARIABILITY AT 1 and 4 μ m IN THE Y0 BROWN DWARF WISEP J173835.52+273258.9

International Nuclear Information System (INIS)

Leggett, S. K.; Cushing, Michael C.; Hardegree-Ullman, Kevin K.; Trucks, Jesica L.; Marley, M. S.; Morley, Caroline V.; Fortney, J. J.; Saumon, D.; Carey, S. J.; Gelino, C. R.; Kirkpatrick, J. D.; Gizis, J. E.; Mace, G. N.

2016-01-01

We have monitored photometrically the Y0 brown dwarf WISEP J173835.52+273258.9 (W1738) at both near- and mid-infrared wavelengths. This ≲1 Gyr old 400 K dwarf is at a distance of 8 pc and has a mass around 5 M Jupiter . We observed W1738 using two near-infrared filters at λ ≈ 1 μ m, Y and J , on Gemini Observatory and two mid-infrared filters at λ ≈ 4 μ m, [3.6] and [4.5], on the Spitzer observatory. Twenty-four hours were spent on the source by Spitzer on each of 2013 June 30 and October 30 UT. Between these observations, around 5 hr were spent on the source by Gemini on each of 2013 July 17 and August 23 UT. The mid-infrared light curves show significant evolution between the two observations separated by 4 months. We find that a double sinusoid can be fit to the [4.5] data, where one sinusoid has a period of 6.0 ± 0.1 hr and the other a period of 3.0 ± 0.1 hr. The near-infrared observations suggest variability with a ∼3.0 hr period, although only at a ≲2 σ confidence level. We interpret our results as showing that the Y dwarf has a 6.0 ± 0.1 hr rotation period, with one or more large-scale surface features being the source of variability. The peak-to-peak amplitude of the light curve at [4.5] is 3%. The amplitude of the near-infrared variability, if real, may be as high as 5%–30%. Intriguingly, this size of variability and the wavelength dependence can be reproduced by atmospheric models that include patchy KCl and Na 2 S clouds and associated small changes in surface temperature. The small number of large features, as well as the timescale for evolution of the features, is very similar to what is seen in the atmospheres of the solar system gas giants.

OBSERVED VARIABILITY AT 1 and 4 μ m IN THE Y0 BROWN DWARF WISEP J173835.52+273258.9

Energy Technology Data Exchange (ETDEWEB)

Leggett, S. K. [Gemini Observatory, Northern Operations Center, 670 N. A’ohoku Place, Hilo, HI 96720 (United States); Cushing, Michael C.; Hardegree-Ullman, Kevin K.; Trucks, Jesica L. [The University of Toledo, 2801 West Bancroft Street, Mailstop 111, Toledo, OH 43606 (United States); Marley, M. S. [NASA Ames Research Center, Mail Stop 245-3, Moffett Field, CA 94035 (United States); Morley, Caroline V.; Fortney, J. J. [Department of Astronomy and Astrophysics, University of California, Santa Cruz, CA 95064 (United States); Saumon, D. [Los Alamos National Laboratory, P.O. Box 1663, MS F663, Los Alamos, NM 87545 (United States); Carey, S. J. [Spitzer Science Center, CalTech, Pasadena, CA 91125 (United States); Gelino, C. R.; Kirkpatrick, J. D. [IPAC, CalTech, Pasadena, CA 91125 (United States); Gizis, J. E. [University of Delaware, Newark, DE 19716 (United States); Mace, G. N., E-mail: sleggett@gemini.edu [University of Texas, Austin, TX 78712 (United States)

2016-10-20

We have monitored photometrically the Y0 brown dwarf WISEP J173835.52+273258.9 (W1738) at both near- and mid-infrared wavelengths. This ≲1 Gyr old 400 K dwarf is at a distance of 8 pc and has a mass around 5 M {sub Jupiter}. We observed W1738 using two near-infrared filters at λ ≈ 1 μ m, Y and J , on Gemini Observatory and two mid-infrared filters at λ ≈ 4 μ m, [3.6] and [4.5], on the Spitzer observatory. Twenty-four hours were spent on the source by Spitzer on each of 2013 June 30 and October 30 UT. Between these observations, around 5 hr were spent on the source by Gemini on each of 2013 July 17 and August 23 UT. The mid-infrared light curves show significant evolution between the two observations separated by 4 months. We find that a double sinusoid can be fit to the [4.5] data, where one sinusoid has a period of 6.0 ± 0.1 hr and the other a period of 3.0 ± 0.1 hr. The near-infrared observations suggest variability with a ∼3.0 hr period, although only at a ≲2 σ confidence level. We interpret our results as showing that the Y dwarf has a 6.0 ± 0.1 hr rotation period, with one or more large-scale surface features being the source of variability. The peak-to-peak amplitude of the light curve at [4.5] is 3%. The amplitude of the near-infrared variability, if real, may be as high as 5%–30%. Intriguingly, this size of variability and the wavelength dependence can be reproduced by atmospheric models that include patchy KCl and Na{sub 2}S clouds and associated small changes in surface temperature. The small number of large features, as well as the timescale for evolution of the features, is very similar to what is seen in the atmospheres of the solar system gas giants.

Interchannel interaction in orientation and alignment of Kr 4p4mp states in the region of 3d9np resonances

International Nuclear Information System (INIS)

Lagutin, B M; Petrov, I D; Sukhorukov, V L; Werner, L; Klumpp, S; Ehresmann, A; Schartner, K-H; Schmoranzer, H

2009-01-01

The interaction between intermediate channels which influence the population of Kr 4p 4 mp ionic states in the region of the 3d 9 np resonances by the photon-induced Auger decay was investigated. The most important influence on the investigated process stems from 4p 5 ε'l and 3d 9 ε'l channels.

HOXC9-Induced Differentiation in Neuroblastoma Development

Science.gov (United States)

2014-10-01

by HOXC9-binding peaks with the motif-finding program MEME revealed that the most enriched binding motif (T/ATTTAT, E value = 1.6e-35) corresponds to...sequences from predicted peak summits and ran MEME for identify- ing statistically overrepresented motifs. We performed MAST to search motifs in the

On commutativity of right s-unital rings with some polynomial constraints

International Nuclear Information System (INIS)

Khan, M.A.

1994-08-01

We study the commutativity of certain class of rings, namely rings with unity 1 and right s-unital rings under each of the following properties [yx m - x n f(y)x p ,x]=0, [yx m +x n f(y)x p ,x]=0, where f(t) is a polynomial in t 2 Z[t] varying with pair of ring elements x,y and m,n,p are fixed non-negative integers. Moreover, the results have been extended to the case when m and n depend on the choice of x and y and the ring satisfies the Chacron's Theorem. (author). 14 refs

Differential operators associated with Gegenbauer polynomials - 2: The limit-point case

International Nuclear Information System (INIS)

Onyango Otieno, V.P.

1987-10-01

In this paper we study the limit-point case of the Gegenbauer differential equation -((1-x 2 ) υ+1/2 y'(x)) 1 +υ 2 (1-x 2 ) υ-1/2 y(x)=λ(1-x 2 ) υ-1/2 y(x), (x ε (-1,1), λ ε C) in both the so-called right-definite and left-definite cases based partially on a classical approach due to E.C. Titchmarsh. We then link the Titchmarsh approach with operator theoretic results in the spaces L 2 w (-1,1) and H 2 p,q (-1,1). (author). 19 refs

CombiMotif: A new algorithm for network motifs discovery in protein-protein interaction networks

Science.gov (United States)

Luo, Jiawei; Li, Guanghui; Song, Dan; Liang, Cheng

2014-12-01

Discovering motifs in protein-protein interaction networks is becoming a current major challenge in computational biology, since the distribution of the number of network motifs can reveal significant systemic differences among species. However, this task can be computationally expensive because of the involvement of graph isomorphic detection. In this paper, we present a new algorithm (CombiMotif) that incorporates combinatorial techniques to count non-induced occurrences of subgraph topologies in the form of trees. The efficiency of our algorithm is demonstrated by comparing the obtained results with the current state-of-the art subgraph counting algorithms. We also show major differences between unicellular and multicellular organisms. The datasets and source code of CombiMotif are freely available upon request.

Pharmacogenetic Inhibition of eIF4E-Dependent Mmp9 mRNA Translation Reverses Fragile X Syndrome-like Phenotypes

Directory of Open Access Journals (Sweden)

Christos G. Gkogkas

2014-12-01

Full Text Available Summary: Fragile X syndrome (FXS is the leading genetic cause of autism. Mutations in Fmr1 (fragile X mental retardation 1 gene engender exaggerated translation resulting in dendritic spine dysmorphogenesis, synaptic plasticity alterations, and behavioral deficits in mice, which are reminiscent of FXS phenotypes. Using postmortem brains from FXS patients and Fmr1 knockout mice (Fmr1−/y, we show that phosphorylation of the mRNA 5′ cap binding protein, eukaryotic initiation factor 4E (eIF4E, is elevated concomitant with increased expression of matrix metalloproteinase 9 (MMP-9 protein. Genetic or pharmacological reduction of eIF4E phosphorylation rescued core behavioral deficits, synaptic plasticity alterations, and dendritic spine morphology defects via reducing exaggerated translation of Mmp9 mRNA in Fmr1−/y mice, whereas MMP-9 overexpression produced several FXS-like phenotypes. These results uncover a mechanism of regulation of synaptic function by translational control of Mmp-9 in FXS, which opens the possibility of new treatment avenues for the diverse neurological and psychiatric aspects of FXS. : Fragile X syndrome (FXS is caused by dysregulation of translation in the brain. Gkogkas et al. show that phosphorylation of eukaryotic translation initiation factor 4E (eIF4E is increased in FXS postmortem brains and Fmr1−/y mice. Downregulation of eIF4E phosphorylation in Fmr1−/y mice rescues defects in dendritic spine morphology, synaptic plasticity, and social interaction via normalization of MMP-9 expression.

Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters

Directory of Open Access Journals (Sweden)

Farré Domènec

2007-12-01

Full Text Available Abstract Background The arrangement of regulatory motifs in gene promoters, or promoter architecture, is the result of mutation and selection processes that have operated over many millions of years. In mammals, tissue-specific transcriptional regulation is related to the presence of specific protein-interacting DNA motifs in gene promoters. However, little is known about the relative location and spacing of these motifs. To fill this gap, we have performed a systematic search for motifs that show significant bias at specific promoter locations in a large collection of housekeeping and tissue-specific genes. Results We observe that promoters driving housekeeping gene expression are enriched in particular motifs with strong positional bias, such as YY1, which are of little relevance in promoters driving tissue-specific expression. We also identify a large number of motifs that show positional bias in genes expressed in a highly tissue-specific manner. They include well-known tissue-specific motifs, such as HNF1 and HNF4 motifs in liver, kidney and small intestine, or RFX motifs in testis, as well as many potentially novel regulatory motifs. Based on this analysis, we provide predictions for 559 tissue-specific motifs in mouse gene promoters. Conclusion The study shows that motif positional bias is an important feature of mammalian proximal promoters and that it affects both general and tissue-specific motifs. Motif positional constraints define very distinct promoter architectures depending on breadth of expression and type of tissue.

The electronic and optical properties of quaternary GaAs1-x-y N x Bi y alloy lattice-matched to GaAs: a first-principles study.

Science.gov (United States)

Ma, Xiaoyang; Li, Dechun; Zhao, Shengzhi; Li, Guiqiu; Yang, Kejian

2014-01-01

First-principles calculations based on density functional theory have been performed for the quaternary GaAs1-x-y N x Bi y alloy lattice-matched to GaAs. Using the state-of-the-art computational method with the Heyd-Scuseria-Ernzerhof (HSE) hybrid functional, electronic, and optical properties were obtained, including band structures, density of states (DOSs), dielectric function, absorption coefficient, refractive index, energy loss function, and reflectivity. It is found that the lattice constant of GaAs1-x-y N x Bi y alloy with y/x =1.718 can match to GaAs. With the incorporation of N and Bi into GaAs, the band gap of GaAs1-x-y N x Bi y becomes small and remains direct. The calculated optical properties indicate that GaAs1-x-y N x Bi y has higher optical efficiency as it has less energy loss than GaAs. In addition, it is also found that the electronic and optical properties of GaAs1-x-y N x Bi y alloy can be further controlled by tuning the N and Bi compositions in this alloy. These results suggest promising applications of GaAs1-x-y N x Bi y quaternary alloys in optoelectronic devices.

Frequency of MYO9B polymorphisms in celiac patients and controls Frecuencia de polimorfismos del gen MYO9B en pacientes celiacos y en sujetos controles

Directory of Open Access Journals (Sweden)

Tamara Loeff

2012-12-01

Full Text Available Introduction: the MYO9B gene contributes to the maintenance of the intestinal barrier and it has been postulated as a risk factor of celiac disease (CD. The objective of this study was to compare the frequency and association rs2305764, rs2305767and rs1457092 MYO09B polymorphisms in pediatric CD patients from Chile and Argentina. Patients and methods: the study was made in 104 CD pediatric patients (Chilean and Argentineans and 104 controls subjects. MYO9B gene polymorphisms were analyzed by Taqman allelic probes. We evaluated the Hardy-Weinberg equilibrium by means of Chi-square and compared the haplotypes distribution using Fisher test. Results: SNPs rs2305767 and rs1457092 were associated with celiac disease (CD; TT genotype in rs2305767 would be a protective factor (p Introducción: el gen miosina IX B (MYO9B participa en el mantenimiento de la barrera intestinal y se postula que puede aportar riesgo para desarrollar enfermedad celiaca (EC. El objetivo de este estudio fue comparar la frecuencia y la asociación de los polimorfismos rs 2305764, rs 2305767 y rs 1457092 del gen MYO9B en pacientes pediátricos con EC procedentes de Chile y Argentina. Pacientes y métodos: el estudio se realizó en 104 pacientes pediátricos con EC (chilenos y argentinos y en 104 sujetos controles. El análisis de los polimorfismos del gen MYO9B se realizó mediante ensayos Taqman de discriminación alélica. Se evalúo equilibrio de Hardy-Weinberg mediante Chi-cuadrado y comparación de haplotipos según prueba de Fisher. Resultados: los polimorfismos de un solo nucleótido (SNPs rs2305767 y rs1457092 mostraron asociación con la EC. El genotipo TT del rs2305767 sería un factor protector (p < 0,0001, OR = 0,19 IC 0,1-0,4 mientras que el genotipo CT sería un factor de riesgo (p < 0,0001, OR = 4,9 IC 2,2-11,3. En el rs1457092, el genotipo CC resultó también un factor protector frente a esta enfermedad (p < 0,0001, OR = 0,07 IC 0,0-0,3. Conclusión: nuestros

Organofluorine chemistry: synthesis and conformation of vicinal fluoromethylene motifs.

Science.gov (United States)

O'Hagan, David

2012-04-20

The C-F bond is the most polar bond in organic chemistry, and thus the bond has a relatively large dipole moment with a significant -ve charge density on the fluorine atom and correspondingly a +ve charge density on carbon. The electrostatic nature of the bond renders it the strongest one in organic chemistry. However, the fluorine atom itself is nonpolarizable, and thus, despite the charge localization on fluorine, it is a poor hydrogen-bonding acceptor. These properties of the C-F bond make it attractive in the design of nonviscous but polar organic compounds, with a polarity limited to influencing the intramolecular nature of the molecule and less so intermolecular interactions with the immediate environment. In this Perspective, the synthesis of aliphatic chains carrying multivicinal fluoromethylene motifs is described. It emerges that the dipoles of adjacent C-F bonds orientate relative to each other, and thus, individual diastereoisomers display different backbone carbon chain conformations. These conformational preferences recognize the influence of the well-known gauche effect associated with 1,2-difluoroethane but extend to considering 1,3-fluorine-fluorine dipolar repulsions. The synthesis of carbon chains carrying two, three, four, five, and six vicinal fluoromethylene motifs is described, with an emphasis on our own research contributions. These motifs obey almost predictable conformational behavior, and they emerge as candidates for inclusion in the design of performance organic molecules. © 2012 American Chemical Society

A Conserved GPG-Motif in the HIV-1 Nef Core Is Required for Principal Nef-Activities.

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Marta Martínez-Bonet

Full Text Available To find out new determinants required for Nef activity we performed a functional alanine scanning analysis along a discrete but highly conserved region at the core of HIV-1 Nef. We identified the GPG-motif, located at the 121-137 region of HIV-1 NL4.3 Nef, as a novel protein signature strictly required for the p56Lck dependent Nef-induced CD4-downregulation in T-cells. Since the Nef-GPG motif was dispensable for CD4-downregulation in HeLa-CD4 cells, Nef/AP-1 interaction and Nef-dependent effects on Tf-R trafficking, the observed effects on CD4 downregulation cannot be attributed to structure constraints or to alterations on general protein trafficking. Besides, we found that the GPG-motif was also required for Nef-dependent inhibition of ring actin re-organization upon TCR triggering and MHCI downregulation, suggesting that the GPG-motif could actively cooperate with the Nef PxxP motif for these HIV-1 Nef-related effects. Finally, we observed that the Nef-GPG motif was required for optimal infectivity of those viruses produced in T-cells. According to these findings, we propose the conserved GPG-motif in HIV-1 Nef as functional region required for HIV-1 infectivity and therefore with a potential interest for the interference of Nef activity during HIV-1 infection.

Statistical tests to compare motif count exceptionalities

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Vandewalle Vincent

2007-03-01

Full Text Available Abstract Background Finding over- or under-represented motifs in biological sequences is now a common task in genomics. Thanks to p-value calculation for motif counts, exceptional motifs are identified and represent candidate functional motifs. The present work addresses the related question of comparing the exceptionality of one motif in two different sequences. Just comparing the motif count p-values in each sequence is indeed not sufficient to decide if this motif is significantly more exceptional in one sequence compared to the other one. A statistical test is required. Results We develop and analyze two statistical tests, an exact binomial one and an asymptotic likelihood ratio test, to decide whether the exceptionality of a given motif is equivalent or significantly different in two sequences of interest. For that purpose, motif occurrences are modeled by Poisson processes, with a special care for overlapping motifs. Both tests can take the sequence compositions into account. As an illustration, we compare the octamer exceptionalities in the Escherichia coli K-12 backbone versus variable strain-specific loops. Conclusion The exact binomial test is particularly adapted for small counts. For large counts, we advise to use the likelihood ratio test which is asymptotic but strongly correlated with the exact binomial test and very simple to use.

A speedup technique for (l, d-motif finding algorithms

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Dinh Hieu

2011-03-01

Full Text Available Abstract Background The discovery of patterns in DNA, RNA, and protein sequences has led to the solution of many vital biological problems. For instance, the identification of patterns in nucleic acid sequences has resulted in the determination of open reading frames, identification of promoter elements of genes, identification of intron/exon splicing sites, identification of SH RNAs, location of RNA degradation signals, identification of alternative splicing sites, etc. In protein sequences, patterns have proven to be extremely helpful in domain identification, location of protease cleavage sites, identification of signal peptides, protein interactions, determination of protein degradation elements, identification of protein trafficking elements, etc. Motifs are important patterns that are helpful in finding transcriptional regulatory elements, transcription factor binding sites, functional genomics, drug design, etc. As a result, numerous papers have been written to solve the motif search problem. Results Three versions of the motif search problem have been proposed in the literature: Simple Motif Search (SMS, (l, d-motif search (or Planted Motif Search (PMS, and Edit-distance-based Motif Search (EMS. In this paper we focus on PMS. Two kinds of algorithms can be found in the literature for solving the PMS problem: exact and approximate. An exact algorithm identifies the motifs always and an approximate algorithm may fail to identify some or all of the motifs. The exact version of PMS problem has been shown to be NP-hard. Exact algorithms proposed in the literature for PMS take time that is exponential in some of the underlying parameters. In this paper we propose a generic technique that can be used to speedup PMS algorithms. Conclusions We present a speedup technique that can be used on any PMS algorithm. We have tested our speedup technique on a number of algorithms. These experimental results show that our speedup technique is indeed very

Improvement of photoluminescence properties and thermal stability of Y{sub 2.9}Ce{sub 0.1}Al{sub 5−x}Si{sub x}O{sub 12} phosphors with Si{sub 3}N{sub 4} addition

Energy Technology Data Exchange (ETDEWEB)

Zhang, Fangfang [College of Electronic Information and Engineering, Hangzhou Dianzi University, Hangzhou 310018 (China); Song, Kaixin, E-mail: kxsong@hdu.edu.cn [College of Electronic Information and Engineering, Hangzhou Dianzi University, Hangzhou 310018 (China); Jiang, Jun [Ningbo Institute of Materials Technologies and Engineering, Chinese Academy of Sciences, Ningbo 315201 (China); Wu, Song; Zheng, Peng [College of Electronic Information and Engineering, Hangzhou Dianzi University, Hangzhou 310018 (China); Huang, Qingming [Instrument Analysis and Testing Center, Fuzhou University, Fuzhou 350002 (China); Xu, Junming; Qin, Huibin [College of Electronic Information and Engineering, Hangzhou Dianzi University, Hangzhou 310018 (China)

2014-12-05

Highlights: • Y{sub 2.9}Ce{sub 0.1}Al{sub 5−x}Si{sub x}O{sub 12} phosphors were prepared by solid-state reaction in reduced air ambience. • Si{sup 4+} could be incorporated into the host lattice of Y{sub 3}Al{sub 5}O{sub 12} through partial occupation of the Al{sup 3+} sites. • Si{sub 3}N{sub 4} addition can improve photoluminescence efficiency and thermal stability of Y{sub 3}Al{sub 5}O{sub 12}:Ce. - Abstract: A series of Si{sub 3}N{sub 4} doping Y{sub 2.9}Ce{sub 0.1}Al{sub 5−x}Si{sub x}O{sub 12−3x/2}N{sub 4x/3} phosphors were prepared by solid-state reaction in 95%N{sub 2}–5%H{sub 2} reduced air ambience. The XRD characteristics plus Rietveld refinement results shows that the as-sintered powders are unique crystal phase with the same crystal structure of Y{sub 3}Al{sub 5}O{sub 12} (PDF No. 79-1891). The N element was not detected by the analysis of X-ray photoelectron spectroscopy (XPS) and energy dispersive X-ray spectrum (EDS). The photoluminescence spectra (PL and PLE) tests show that the exciting and emitting intensity of PLE and PL gradually increase due to the increase of Si{sub 3}N{sub 4} concentration. Meanwhile, the phosphorescence decay times are prolonged from 45 ns (x = 0) to 78 ns (x = 0.3), under the monitor of 530 nm wavelength. The thermoluminescence tests (TL) confirm the thermal stability of as-phosphors with Si{sub 3}N{sub 4} addition is much better than that of the pristine Y{sub 2.9}Ce{sub 0.1}Al{sub 5}O{sub 12} phosphors.

Relación entre el efecto hidrofóbico superficial de carbones activados y la entalpía de inmersión en soluciones acuosas de fenol, 4-nitro fenol y 3-cloro fenol

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Liliana Giraldo

2009-11-01

Full Text Available Para cinco carbones activados, obtenidos de materiales lignocelulósicos, se determinan las entalpías de inmersión en soluciones fenólicas. Los carbones activados son de carácter básico con valores del pH en el punto de carga cero, pHPZC, entre 7.4 y 9.7. Se determina la entalpía de inmersión de los carbones activados en CCl4 y agua; a partir de estos resultados, se calcula el factor hidrofóbico, fh, que varía entre 2.98 y 6.75. Las entalpías de inmersión de los carbones activados en soluciones de fenol, 4-nitro fenol y 3-cloro fenol están entre 7.6 y 13.9; 12.7 y 20.5; 6.8 y 11.4 Jg-1 respectivamente./For five activated carbons, obtained from lignocellulosic materials the, immersion enthalpies in phenolic solutions are determined. The activated carbons have basic character with values of pH in the point of zero charge, pHPZC, between 7.4 and 9.7. The immersion enthalpies of activated carbons in CCl4 and water are determined, from these results the hydrophobic factor, hf, are calculated, that change between 2.98 and 6.75. The immersion enthalpies of the activated carbons in phenol, 4-nitro phenol and 3-chloro phenol solutions are between 7.6 y 13.9; 12.7 y 20.5; 6.8 y 11.4 Jg-1 respectively

Identity and functions of CxxC-derived motifs.

Science.gov (United States)

Fomenko, Dmitri E; Gladyshev, Vadim N

2003-09-30

Two cysteines separated by two other residues (the CxxC motif) are employed by many redox proteins for formation, isomerization, and reduction of disulfide bonds and for other redox functions. The place of the C-terminal cysteine in this motif may be occupied by serine (the CxxS motif), modifying the functional repertoire of redox proteins. Here we found that the CxxC motif may also give rise to a motif, in which the C-terminal cysteine is replaced with threonine (the CxxT motif). Moreover, in contrast to a view that the N-terminal cysteine in the CxxC motif always serves as a nucleophilic attacking group, this residue could also be replaced with threonine (the TxxC motif), serine (the SxxC motif), or other residues. In each of these CxxC-derived motifs, the presence of a downstream alpha-helix was strongly favored. A search for conserved CxxC-derived motif/helix patterns in four complete genomes representing bacteria, archaea, and eukaryotes identified known redox proteins and suggested possible redox functions for several additional proteins. Catalytic sites in peroxiredoxins were major representatives of the TxxC motif, whereas those in glutathione peroxidases represented the CxxT motif. Structural assessments indicated that threonines in these enzymes could stabilize catalytic thiolates, suggesting revisions to previously proposed catalytic triads. Each of the CxxC-derived motifs was also observed in natural selenium-containing proteins, in which selenocysteine was present in place of a catalytic cysteine.

Formation of YxNd1-xBa2Cu3O7-δ (0≤x≤0.9) superconductors from an undercooled melt via aero-acoustic levitation

International Nuclear Information System (INIS)

Gustafson, D.E.; Hofmeister, W.H.; Bayuzick, R.J.; Nagashio, K.; Kuribayashi, K.

2003-01-01

This paper presents the results of rapid solidification experiments performed on the copper oxide superconductors Y x Nd 1-x Ba 2 Cu 3 O 7-δ (0≤x≤0.9). Spherical rare earth (RE) 123 specimens were levitated in O 2 using aero-acoustic levitation (AAL), melted with a laser, undercooled, and solidified. The peritectic transformation temperature for the reaction RE 2 BaCuO 5 +liquid→REBa 2 Cu 3 O 7-δ corresponding to the maximum recalescence temperature during solidification was determined. RE123 was formed directly from the melt for Y-Nd binary alloy compositions with Nd concentration greater than 20% (Y concentration less than 80%). A minimum in the peritectic transformation temperature for the Nd/Y123 system corresponding to a composition Y 0.3 Nd 0.7 123 was determined at 66 deg. C below the peritectic of pure Nd123

Overlapping ETS and CRE Motifs (G/CCGGAAGTGACGTCA) Preferentially Bound by GABPα and CREB Proteins

Science.gov (United States)

Chatterjee, Raghunath; Zhao, Jianfei; He, Ximiao; Shlyakhtenko, Andrey; Mann, Ishminder; Waterfall, Joshua J.; Meltzer, Paul; Sathyanarayana, B. K.; FitzGerald, Peter C.; Vinson, Charles

2012-01-01

Previously, we identified 8-bps long DNA sequences (8-mers) that localize in human proximal promoters and grouped them into known transcription factor binding sites (TFBS). We now examine split 8-mers consisting of two 4-mers separated by 1-bp to 30-bps (X4-N1-30-X4) to identify pairs of TFBS that localize in proximal promoters at a precise distance. These include two overlapping TFBS: the ETS⇔ETS motif (C/GCCGGAAGCGGAA) and the ETS⇔CRE motif (C/GCGGAAGTGACGTCAC). The nucleotides in bold are part of both TFBS. Molecular modeling shows that the ETS⇔CRE motif can be bound simultaneously by both the ETS and the B-ZIP domains without protein-protein clashes. The electrophoretic mobility shift assay (EMSA) shows that the ETS protein GABPα and the B-ZIP protein CREB preferentially bind to the ETS⇔CRE motif only when the two TFBS overlap precisely. In contrast, the ETS domain of ETV5 and CREB interfere with each other for binding the ETS⇔CRE. The 11-mer (CGGAAGTGACG), the conserved part of the ETS⇔CRE motif, occurs 226 times in the human genome and 83% are in known regulatory regions. In vivo GABPα and CREB ChIP-seq peaks identified the ETS⇔CRE as the most enriched motif occurring in promoters of genes involved in mRNA processing, cellular catabolic processes, and stress response, suggesting that a specific class of genes is regulated by this composite motif. PMID:23050235

Straw enhanced CO2 and CH4 but decreased N2O emissions from flooded paddy soils: Changes in microbial community compositions

Science.gov (United States)

Wang, Ning; Yu, Jian-Guang; Zhao, Ya-Hui; Chang, Zhi-Zhou; Shi, Xiao-Xia; Ma, Lena Q.; Li, Hong-Bo

2018-02-01

To explore microbial mechanisms of straw-induced changes in CO2, CH4, and N2O emissions from paddy field, wheat straw was amended to two paddy soils from Taizhou (TZ) and Yixing (YX), China for 60 d under flooded condition. Illumia sequencing was used to characterize shift in bacterial community compositions. Compared to control, 1-5% straw amendment significantly elevated CO2 and CH4 emissions with higher increase at higher application rates, mainly due to increased soil DOC concentrations. In contrast, straw amendment decreased N2O emission. Considering CO2, CH4, and N2O emissions as a whole, an overall increase in global warming potential was observed with straw amendment. Total CO2 and CH4 emissions from straw-amended soils were significantly higher for YX than TZ soil, suggesting that straw-induced greenhouse gas emissions depended on soil characteristics. The abundance of C-turnover bacteria Firmicutes increased from 28-41% to 54-77% with straw amendment, thereby increasing CO2 and CH4 emissions. However, straw amendment reduced the abundance of denitrifying bacteria Proteobacteria from 18% to 7.2-13% or increased the abundance of N2O reducing bacteria Clostridium from 7.6-11% to 13-30%, thereby decreasing N2O emission. The results suggested straw amendment strongly influenced greenhouse gas emissions via alerting soil properties and bacterial community compositions. Future field application is needed to ascertain the effects of straw return on greenhouse gas emissions.

On the algebraic realization of SU(4) symmetry

International Nuclear Information System (INIS)

Asatryan, G.M.; Zaslavsky, A.N.

1976-01-01

A possibility of nonlinear realization of the symmetry with linearization on the SU(4)xYxC group is discussed. Algebraic properties of SU(4) are restored from the Weinberg condition: amplitudes of goldstone scattering on particles should have a reasonable (as in the Regge theory) asymptotic behaviour. In this case the breaking appears to be minimal. Large values of psi meson masses lead to high-lying charmed trajectories in the SU(4) algebraic realization

DETERMINACIÓN DE PARÁMETROS CINÉTICOS DE DOS INÓCULOS LÁCTICOS: Lactobacillus plantarum A6 Y BACTERIAS ÁCIDO LÁCTICAS DE YOGURT DETERMINAÇÃO DE PARÁMETROS CINÉTICOS DE DOIS INÓCULOS LÁCTICOS: Lactobacillus plantarum A6 E BACTERIAS ÁCIDO LÁCTICAS DE IOGURTE DETERMINARON OF KINETIC PARAMETERS OF TWO LACTIC INOCULUMS: Lactobacillus plantarum A6 AND LACTIC ACID BACTERIAS OF YOGURT

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CLAUDIA AGUDELO

2010-12-01

Full Text Available Se realizó la comparación del comportamiento cinético de dos inóculos de Bacterias Ácido Lácticas (BAL desarrollados a partir de Lactobacillus plantarum A6 y de yogurt comercial. Se incubaron a 35°C durante 48 horas y se repicaron tras 24 horas de fermentación en medio líquido para su posible aplicación en la fermentación de residuos pesqueros. Para cada cepa se midió la biomasa mediante conteo en placa según la NTC 5034 de 2002, el consumo de azúcares totales por el método de antrona y la producción de ácido láctico por titulación bajo la NTC 4978 de 2001, durante el tiempo de incubación. Los resultados mostraron un mejor desarrollo para Lactobacillus plantarum A6 con diferencias significativas (α = 0,05 en los rendimientos Yx/s y Yp/s de 0,401 y 0,34 respectivamente para la primera etapa, y de Yx/s= 0,39 y Yp/s = 0,36 en la segunda etapa, a diferencia de las BAL del yogurt las cuales presentaron rendimientos menores. Otros parámetros cinéticos como la velocidad máxima de crecimiento y tiempo de duplicación para ambas cepas no presentan diferencias significativas (α = 0,05.Foram comparados o comportamento cinético de dois inóculos de Bacterias de Ácido Láctico (BAL desenvolvido a partir de Lactobacillus plantarum A6 e de iogurte comercial. Incubados a 35°C por 48 horas e se repicaram após de 24 horas de fermentação em meio líquido, para possível aplicação na fermentação de residuos de peixe. Para cada amostra se mediu a biomassa mediante contagem em placa acordo com a NTC 5034 de 2002, o consumo de açúcares totais pelo método de antrona e na produção de ácido láctico por titulação sob o NTC 4978 de 2001, durante o tempo de incubação. Os resultados mostraram um melhor desenvolvimento de Lactobacillus plantarum A6 com diferenças significativas (α = 0,05 nos rendimentos Yx/s, Yp/s de 0,401 e 0,34 respectivamente para a primeira fase, e Yx / s = 0,39 e Yp / s = 0,36 na segunda etapa, em contraste

High dielectric constant PrYxOy sensing films electrolyte-insulator-semiconductor pH-sensor for the detection of urea

International Nuclear Information System (INIS)

Wu, Min-Hsien; Lee, Cheng-Da; Pan, Tung-Ming

2009-01-01

In this paper, we describe the structural and sensing properties of high-k PrY x O y sensing films deposited on Si substrates through reactive co-sputtering. Secondary ion mass spectrometry and atomic force microscopy were employed to analyze the compositional and morphological features of these films after annealing at various temperatures. The electrolyte-insulator-semiconductor (EIS) device incorporating a PrY x O y sensing membrane that had been annealed at 800 o C exhibited good sensing characteristics, including a high sensitivity (59.07 mV pH -1 in solutions from pH 2 to 12), a low hysteresis voltage (2.4 mV in the pH loop 7 → 4 → 7 → 10 → 7), and a small drift rate (0.62 mV h -1 in the buffer solution at pH 7). The PrY x O y EIS device also showed a high selective response towards H + . This improvement can be attributed to the small number of crystal defects and the large surface roughness. In addition, the enzymatic EIS-based urea biosensor incorporating a high-k PrY x O y sensing film annealed at 800 o C allowed the potentiometric analysis of urea, at concentrations ranging from 1 to 16 mM, with a sensitivity of 9.59 mV mM -1 .

Short Arginine Motifs Drive Protein Stickiness in the Escherichia coli Cytoplasm.

Science.gov (United States)

Kyne, Ciara; Crowley, Peter B

2017-09-19

Although essential to numerous biotech applications, knowledge of molecular recognition by arginine-rich motifs in live cells remains limited. 1 H, 15 N HSQC and 19 F NMR spectroscopies were used to investigate the effects of C-terminal -GR n (n = 1-5) motifs on GB1 interactions in Escherichia coli cells and cell extracts. While the "biologically inert" GB1 yields high-quality in-cell spectra, the -GR n fusions with n = 4 or 5 were undetectable. This result suggests that a tetra-arginine motif is sufficient to drive interactions between a test protein and macromolecules in the E. coli cytoplasm. The inclusion of a 12 residue flexible linker between GB1 and the -GR 5 motif did not improve detection of the "inert" domain. In contrast, all of the constructs were detectable in cell lysates and extracts, suggesting that the arginine-mediated complexes were weak. Together these data reveal the significance of weak interactions between short arginine-rich motifs and the E. coli cytoplasm and demonstrate the potential of such motifs to modify protein interactions in living cells. These interactions must be considered in the design of (in vivo) nanoscale assemblies that rely on arginine-rich sequences.

Temporal motifs in time-dependent networks

International Nuclear Information System (INIS)

Kovanen, Lauri; Karsai, Márton; Kaski, Kimmo; Kertész, János; Saramäki, Jari

2011-01-01

Temporal networks are commonly used to represent systems where connections between elements are active only for restricted periods of time, such as telecommunication, neural signal processing, biochemical reaction and human social interaction networks. We introduce the framework of temporal motifs to study the mesoscale topological–temporal structure of temporal networks in which the events of nodes do not overlap in time. Temporal motifs are classes of similar event sequences, where the similarity refers not only to topology but also to the temporal order of the events. We provide a mapping from event sequences to coloured directed graphs that enables an efficient algorithm for identifying temporal motifs. We discuss some aspects of temporal motifs, including causality and null models, and present basic statistics of temporal motifs in a large mobile call network

Motif enrichment tool.

Science.gov (United States)

Blatti, Charles; Sinha, Saurabh

2014-07-01

The Motif Enrichment Tool (MET) provides an online interface that enables users to find major transcriptional regulators of their gene sets of interest. MET searches the appropriate regulatory region around each gene and identifies which transcription factor DNA-binding specificities (motifs) are statistically overrepresented. Motif enrichment analysis is currently available for many metazoan species including human, mouse, fruit fly, planaria and flowering plants. MET also leverages high-throughput experimental data such as ChIP-seq and DNase-seq from ENCODE and ModENCODE to identify the regulatory targets of a transcription factor with greater precision. The results from MET are produced in real time and are linked to a genome browser for easy follow-up analysis. Use of the web tool is free and open to all, and there is no login requirement. ADDRESS: http://veda.cs.uiuc.edu/MET/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Far-infrared spectra of yttrium-doped gold clusters Au(n)Y (n=1-9).

Science.gov (United States)

Lin, Ling; Claes, Pieterjan; Gruene, Philipp; Meijer, Gerard; Fielicke, André; Nguyen, Minh Tho; Lievens, Peter

2010-06-21

The geometric, spectroscopic, and electronic properties of neutral yttrium-doped gold clusters Au(n)Y (n=1-9) are studied by far-infrared multiple photon dissociation (FIR-MPD) spectroscopy and quantum chemical calculations. Comparison of the observed and calculated vibrational spectra allows the structures of the isomers present in the molecular beam to be determined. Most of the isomers for which the IR spectra agree best with experiment are calculated to be the energetically most stable ones. Attachment of xenon to the Au(n)Y cluster can cause changes in the IR spectra, which involve band shifts and band splittings. In some cases symmetry changes, as a result of the attachment of xenon atoms, were also observed. All the Au(n)Y clusters considered prefer a low spin state. In contrast to pure gold clusters, which exhibit exclusively planar lowest-energy structures for small sizes, several of the studied species are three-dimensional. This is particularly the case for Au(4)Y and Au(9)Y, while for some other sizes (n=5, 8) the 3D structures have an energy similar to that of their 2D counterparts. Several of the lowest-energy structures are quasi-2D, that is, slightly distorted from planar shapes. For all the studied species the Y atom prefers high coordination, which is different from other metal dopants in gold clusters.

Electrical conductivity and reaction with lithium of LiFe{sub 1-y}Mn{sub y}PO{sub 4} olivine-type cathode materials

Energy Technology Data Exchange (ETDEWEB)

Molenda, J.; Ojczyk, W.; Marzec, J. [Faculty of Materials Science and Ceramics, AGH University of Science and Technology, al. Mickiewicza 30, 30-059 Krakow (Poland)

2007-12-06

Structural, electrical and electrochemical properties of Mn-substituted phospho-olivines LiFe{sub 1-y}Mn{sub y}PO{sub 4} were investigated and compared to those of LiFePO{sub 4}. Rietvield refined XRD patterns taken in the course of delithiation process showed apparent difference between phase compositions of these cathode materials upon lithium extraction. Contrary to the LiFePO{sub 4} and LiMnPO{sub 4} compositions for which a two-phase mechanism of electrochemical lithium extraction/insertion is observed, in case of Mn-substituted LiFe{sub 1-y}Mn{sub y}PO{sub 4} samples a single-phase mechanism of deintercalation was observed in the studied range of lithium concentration. Electrochemical characterization of the cathode materials were performed in Li/Li{sup +}/Li{sub x}Fe{sub 1-y}Mn{sub y}PO{sub 4}-type cells for y = 0.0, 0.25, 0.55, 0.75 and 1.0 compositions. Voltammery studies showed low reversibility of the lithium extraction process in the high-voltage ''manganese'' range, while in the ''iron'' range the reversibility of lithium extraction is high. Impedance measurements of the LiFe{sub 1-y}Mn{sub y}PO{sub 4} cathode materials, which enabled separation of the ionic and electronic components of their entire electrical conductivity, showed distinct influence of Mn content on the electronic part of conductivity. EIS measurements performed at different states of cell charge revealed that the charge-transfer impedance in Li{sub x}Fe{sub 1-y}Mn{sub y}PO{sub 4} is much lower than that of Li{sub x}FePO{sub 4}. (author)

Band metamagnetism and peculiarities of magnetic structure of (Er1-xYx)Co2 compounds

International Nuclear Information System (INIS)

Baranov, N.V.; Kozlov, A.I.; Pirogov, A.N.; Sinitsyn, E.V.

1989-01-01

A study of the magnetization, electric resistance, and thermal expansion as well as neutron diffraction data are used to show that in Er 1-x Y x Co 2 compounds the splitting of the d=zone of cobalt disappears as yttrium concentration grows up to x=0.4 and that simultaneously disordering of the Er subssystem sets in due to a phase transition of the first kind. It is discovered that at x∼0.45 the introduction of a weak external magnetic field with μ 0 H∼0.4 T causes the magnetization of the partially disordered Er subsystem to grow, which is accompanied by an irreversible splitting of the d-zone and an increase in the magnetic moment of cobalt from 0.3μ B to 0.9μ B . The presence of minima on the temperature curves for the electric resistance, observed in Er 1-x Y x Co 2 compounds (.2≤x≤0.6) at temperatures above the magnetic ordering temperature, is related to spin density fluctuations in the Co subsystem

The synthesis and luminescence properties of a novel red-emitting phosphor: Eu3+-doped Ca9La(PO4)7

Science.gov (United States)

Liang, Zehui; Mu, Zhongfei; Wang, Qiang; Zhu, Daoyun; Wu, Fugen

2017-10-01

A series of novel red-emitting phosphors Ca9La1- x (PO4)7: xEu3+ were synthesized by high-temperature solid state reactions. The photoluminescence excitation and photoluminescence spectra of these phosphors were investigated in detail. O2--Eu3+ charge transfer band peaking at about 261 nm is dominant in the PLE spectra of Eu3+-doped Ca9La(PO4)7, indicating that the phosphors are suitable for tricolor fluorescent lamps. The phosphors also show a good absorption in near ultraviolet (around 395 nm) and blue (around 465 nm) spectral region, which indicates that it can be pumped with NUV and blue chips for white light-emitting diodes. The transition of 5D0 → 7F2 of Eu3+ in this lattice can emit bright red light. Ca9La(PO4)7 could accommodate a large amount of Eu3+ with an optimal concentration of 60 mol%. The dipole-dipole interaction between Eu3+ is the dominant mechanism for concentration quenching of Eu3+. The calculated color coordinates lie in red region ( x = 0.64, y = 0.36), which is close to Y2O3: 0.05Eu3+ ( x = 0.65, y = 0.34). The integral emission intensity of Ca9La0.4(PO4)7: 0.6Eu3+ is 1.9 times stronger than that of widely used commercial red phosphor Y2O3: 0.05Eu3+. All these results indicate that Eu3+-doped Ca9La(PO4)7 is a promising red-emitting phosphor which can be used in tricolor fluorescent lamps and white light-emitting diodes.

Identification of helix capping and {beta}-turn motifs from NMR chemical shifts

Energy Technology Data Exchange (ETDEWEB)

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

2012-03-15

We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and {sup 13}C{sup {beta}} chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of {beta}-turns: I, II, I Prime , II Prime and VIII. Using a database of proteins of known structure, the NMR chemical shifts, together with the PDB-extracted amino acid preference of the helix capping and {beta}-turn motifs are used as input data for training an artificial neural network algorithm, which outputs the statistical probability of finding each motif at any given position in the protein. The trained neural networks, contained in the MICS (motif identification from chemical shifts) program, also provide a confidence level for each of their predictions, and values ranging from ca 0.7-0.9 for the Matthews correlation coefficient of its predictions far exceed those attainable by sequence analysis. MICS is anticipated to be useful both in the conventional NMR structure determination process and for enhancing on-going efforts to determine protein structures solely on the basis of chemical shift information, where it can aid in identifying protein database fragments suitable for use in building such structures.

Identification of helix capping and β-turn motifs from NMR chemical shifts

International Nuclear Information System (INIS)

Shen Yang; Bax, Ad

2012-01-01

We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and 13 C β chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of β-turns: I, II, I′, II′ and VIII. Using a database of proteins of known structure, the NMR chemical shifts, together with the PDB-extracted amino acid preference of the helix capping and β-turn motifs are used as input data for training an artificial neural network algorithm, which outputs the statistical probability of finding each motif at any given position in the protein. The trained neural networks, contained in the MICS (motif identification from chemical shifts) program, also provide a confidence level for each of their predictions, and values ranging from ca 0.7–0.9 for the Matthews correlation coefficient of its predictions far exceed those attainable by sequence analysis. MICS is anticipated to be useful both in the conventional NMR structure determination process and for enhancing on-going efforts to determine protein structures solely on the basis of chemical shift information, where it can aid in identifying protein database fragments suitable for use in building such structures.

First principles calculations of the electronic structure and magnetic properties of Y(Fe,M)9.2 and Y(Fe,M)9.2C (M= Si, Ga, Zr)

Science.gov (United States)

Tian, Guang; Zha, Liang; Yang, Wenyun; Qiao, Guanyi; Wang, Changsheng; Yang, Yingchang; Yang, Jinbo

2018-06-01

The preferential site substitution of the Fe by Si, Ga and Zr in the Y(Fe,M)9.2 and Y(Fe,M)9.2C compounds, and the doping effects on the magnetic properties have been studied by the first-principles calculations. It is found that the doping of the Si or Zr can improve the thermodynamic stability of the 1:9 phase, while the substitution of the Fe by Ga makes it unstable. Si atom tends to enter the 3g crystal site and Zr prefers to occupy the 2e site when Y(Fe,M)9.2 and their carbides are synthesized. Although the substitution of the Fe by Si and Zr will reduce the total magnetic moments of the YFe9.2 and their carbides, the volumetric and the d-band narrowing effects caused by the doping can still modify the electron density distributions of the Fe near the Fermi level, improving the magnetic ordering temperature of the non-carbonated compound YFe9.2. The calculated magnetic ordering temperatures of Y(Fe,M)9.2C decrease with the increasing content of the doping elements M due to the stronger hybridization of the d bands in the carbides. For the rare-earth(RE) iron based intermetallics REFe9.2 with the TbCu7-type structure, it is suggested that Zr is able to stabilize the phase and enhance the magnetic ordering temperature, indicating the possible further application in the field of permanent magnets, which has not been reported before.

Influence of Y and La substitution on particle size, structural and magnetic properties of nanosized nickel ferrite prepared by using citrate precursor method

Energy Technology Data Exchange (ETDEWEB)

Anh, Luong Ngoc [International Training Institute for Materials Science (ITIMS), Hanoi University of Science and Technology, 1 Dai Co Viet Road, Hanoi (Viet Nam); Loan, To Thanh, E-mail: totloan@itims.edu.vn [International Training Institute for Materials Science (ITIMS), Hanoi University of Science and Technology, 1 Dai Co Viet Road, Hanoi (Viet Nam); Duong, Nguyen Phuc [International Training Institute for Materials Science (ITIMS), Hanoi University of Science and Technology, 1 Dai Co Viet Road, Hanoi (Viet Nam); Vietnam-Japan International Institute for Science of Technology (VJIIST), Hanoi University of Science and Technology, 1 Dai Co Viet Road, Hanoi (Viet Nam); Soontaranon, Siriwat [Synchrotron Light Research Institute, 111 University Avenue, Suranaree, Muang, Nakhon Ratchasima 30000 (Thailand); Viet Nga, Tran Thi; Hien, Than Duc [International Training Institute for Materials Science (ITIMS), Hanoi University of Science and Technology, 1 Dai Co Viet Road, Hanoi (Viet Nam)

2015-10-25

The compounds with the formulas NiFe{sub 2}O{sub 4}, NiFe{sub 1.9}Y{sub 0.1}O{sub 4} and NiFe{sub 1.9}La{sub 0.1}O{sub 4} were prepared by citrate precursor method and followed by heat treatment in air at 600 °C for 5 h. Crystal structure, valence state, chemical bonding and composition of the samples were studied rigorously by XRD, SXRD, XANES, FTIR and ICP–AES. Rietveld refinement of XRD and SXRD patterns reveals that the samples crystallize in single spinel phase with almost inverted structure in which the substituted ions Y{sup 3+} and La{sup 3+} locate in the octahedral sites and about ten percents of nickel atoms were found at the tetrahedral sites. Morphology and particle size were studied by SEM and TEM. The results show that the samples are composed of clustered nanoparticles with mean particle size decreases approximately from 20 nm in NiFe{sub 2}O{sub 4} sample to 10 nm in the substituted ones. The magnetic measurements were carried out by means of a VSM. Spontaneous magnetization, magnetic coercivity, Curie temperature, superparamagnetic transition temperature, interparticle interaction energy and effective anisotropy were determined and explained on the basis of the surface and finite–size effects and cation distribution. - Highlights: • Y{sup 3+} and La{sup 3+} substituted NiFe{sub 2}O{sub 4} nanoparticles are synthesized by citrate precursor method involving less energy. • XRD, SXRD and FTIR spectra reveal the crystallographic site occupancy of Y{sup 3+} and La{sup 3+}. • Compositions and valence states of cations are verified by ICP-AES and XANES. • Y{sup 3+} and La{sup 3+} substitution decreases the mean particle size to about 10 nm. • Influence of rare earth substitution and finite size in magnetic properties are investigated.

Emerging role of chemokine CC motif ligand 4 related mechanisms in diabetes mellitus and cardiovascular disease: friends or foes?

Science.gov (United States)

Chang, Ting-Ting; Chen, Jaw-Wen

2016-08-24

Chemokines are critical components in pathology. The roles of chemokine CC motif ligand 4 (CCL4) and its receptor are associated with diabetes mellitus (DM) and atherosclerosis cardiovascular diseases. However, due to the complexity of these diseases, the specific effects of CCL4 remain unclear, although recent reports have suggested that multiple pathways are related to CCL4. In this review, we provide an overview of the role and potential mechanisms of CCL4 and one of its major receptors, fifth CC chemokine receptor (CCR5), in DM and cardiovascular diseases. CCL4-related mechanisms, including CCL4 and CCR5, might provide potential therapeutic targets in DM and/or atherosclerosis cardiovascular diseases.

Crystallisation kinetics of amorphous Fe72.5-xCu1Nb4.5Si10+x+yB12-y alloy

International Nuclear Information System (INIS)

Miglierini, M.; Lipka, J.; Sitek, J.

1994-01-01

Fe 73.5 Cu 1 Nb 3 Si 13.5 B 9 and Fe 72.5-x Cu 1 Nb 4.5 Si 10+x+y B 12-y alloys are compared from the point of view of crystallisation behaviour and changes in the short-range order in the amorphous reminder. The increase in Nb to 4.5 at.% in the latter system slows down the formation of nanocrystals to approximately 40% even after 16 hours of anneal at 550 C for x = 0.5, y = 3. Segregation-induced changes in the short-range order are manifested via hyperfine field distributions corresponding to the amorphous reminder. (orig.)

A sialoreceptor binding motif in the Mycoplasma synoviae adhesin VlhA.

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Meghan May

Full Text Available Mycoplasma synoviae depends on its adhesin VlhA to mediate cytadherence to sialylated host cell receptors. Allelic variants of VlhA arise through recombination between an assemblage of promoterless vlhA pseudogenes and a single transcription promoter site, creating lineages of M. synoviae that each express a different vlhA allele. The predicted full-length VlhA sequences adjacent to the promoter of nine lineages of M. synoviae varying in avidity of cytadherence were aligned with that of the reference strain MS53 and with a 60-a.a. hemagglutinating VlhA C-terminal fragment from a Tunisian lineage of strain WVU1853(T. Seven different sequence variants of an imperfectly conserved, single-copy, 12-a.a. candidate cytadherence motif were evident amid the flanking variable residues of the 11 total sequences examined. The motif was predicted to adopt a short hairpin structure in a low-complexity region near the C-terminus of VlhA. Biotinylated synthetic oligopeptides representing four selected variants of the 12-a.a. motif, with the whole synthesized 60-a.a. fragment as a positive control, differed (P<0.01 in the extent they bound to chicken erythrocyte membranes. All bound to a greater extent (P<0.01 than scrambled or irrelevant VlhA domain negative control peptides did. Experimentally introduced branched-chain amino acid (BCAA substitutions Val3Ile and Leu7Ile did not significantly alter binding, whereas fold-destabilizing substitutions Thr4Gly and Ala9Gly tended to reduce it (P<0.05. Binding was also reduced to background levels (P<0.01 when the peptides were exposed to desialylated membranes, or were pre-saturated with free sialic acid before exposure to untreated membranes. From this evidence we conclude that the motif P-X-(BCAA-X-F-X-(BCAA-X-A-K-X-G binds sialic acid and likely mediates VlhA-dependent M. synoviae attachment to host cells. This conserved mechanism retains the potential for fine-scale rheostasis in binding avidity, which could be a

Systematic analysis of phosphotyrosine antibodies recognizing single phosphorylated EPIYA-motifs in CagA of Western-type Helicobacter pylori strains.

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Judith Lind

Full Text Available The clinical outcome of Helicobacter pylori infections is determined by multiple host-pathogen interactions that may develop to chronic gastritis, and sometimes peptic ulcers or gastric cancer. Highly virulent strains encode a type IV secretion system (T4SS that delivers the effector protein CagA into gastric epithelial cells. Translocated CagA undergoes tyrosine phosphorylation at EPIYA-sequence motifs, called A, B and C in Western-type strains, by members of the oncogenic Src and Abl host kinases. Phosphorylated EPIYA-motifs mediate interactions of CagA with host signaling factors--in particular various SH2-domain containing human proteins--thereby hijacking multiple downstream signaling cascades. Observations of tyrosine-phosphorylated CagA are mainly based on the use of commercial phosphotyrosine antibodies, which originally were selected to detect phosphotyrosines in mammalian proteins. Systematic studies of phosphorylated EPIYA-motif detection by the different antibodies would be very useful, but are not yet available. To address this issue, we synthesized phospho- and non-phosphopeptides representing each predominant Western CagA EPIYA-motif, and determined the recognition patterns of seven different phosphotyrosine antibodies in Western blots, and also performed infection studies with diverse representative Western H. pylori strains. Our results show that a total of 9-11 amino acids containing the phosphorylated EPIYA-motifs are necessary and sufficient for specific detection by these antibodies, but revealed great variability in sequence recognition. Three of the antibodies recognized phosphorylated EPIYA-motifs A, B and C similarly well; whereas preferential binding to phosphorylated motif A and motifs A and C was found with two and one antibodies, respectively, and the seventh anti-phosphotyrosine antibody did not recognize any phosphorylated EPIYA-motif. Controls showed that none of the antibodies recognized the corresponding non

Large-scale discovery of promoter motifs in Drosophila melanogaster.

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Thomas A Down

2007-01-01

Full Text Available A key step in understanding gene regulation is to identify the repertoire of transcription factor binding motifs (TFBMs that form the building blocks of promoters and other regulatory elements. Identifying these experimentally is very laborious, and the number of TFBMs discovered remains relatively small, especially when compared with the hundreds of transcription factor genes predicted in metazoan genomes. We have used a recently developed statistical motif discovery approach, NestedMICA, to detect candidate TFBMs from a large set of Drosophila melanogaster promoter regions. Of the 120 motifs inferred in our initial analysis, 25 were statistically significant matches to previously reported motifs, while 87 appeared to be novel. Analysis of sequence conservation and motif positioning suggested that the great majority of these discovered motifs are predictive of functional elements in the genome. Many motifs showed associations with specific patterns of gene expression in the D. melanogaster embryo, and we were able to obtain confident annotation of expression patterns for 25 of our motifs, including eight of the novel motifs. The motifs are available through Tiffin, a new database of DNA sequence motifs. We have discovered many new motifs that are overrepresented in D. melanogaster promoter regions, and offer several independent lines of evidence that these are novel TFBMs. Our motif dictionary provides a solid foundation for further investigation of regulatory elements in Drosophila, and demonstrates techniques that should be applicable in other species. We suggest that further improvements in computational motif discovery should narrow the gap between the set of known motifs and the total number of transcription factors in metazoan genomes.

MHC motif viewer

DEFF Research Database (Denmark)

Rapin, Nicolas Philippe Jean-Pierre; Hoof, Ilka; Lund, Ole

2008-01-01

. Algorithms that predict which peptides MHC molecules bind have recently been developed and cover many different alleles, but the utility of these algorithms is hampered by the lack of tools for browsing and comparing the specificity of these molecules. We have, therefore, developed a web server, MHC motif....... A special viewing feature, MHC fight, allows for display of the specificity of two different MHC molecules side by side. We show how the web server can be used to discover and display surprising similarities as well as differences between MHC molecules within and between different species. The MHC motif...

Influence of the supporting salt concentration on the electrodeposition of ZnO/eosin Y hybrid films

Energy Technology Data Exchange (ETDEWEB)

Boeckler, C.; Oekermann, T. [Institute of Physical Chemistry and Electrochemistry, Leibniz University Hannover (Germany); Saruban, M.; Ichinose, K.; Yoshida, T. [Center of Innovative Photovoltaic Systems (CIPS), Environmental and Renewable Energy Systems (ERES) Division, Graduate School of Engineering, Gifu University (Japan)

2008-10-15

ZnO/eosin Y hybrid films were electrodeposited from O{sub 2}-saturated ZnCl{sub 2}-solution under variation of the concentration of the supporting salt KCl. The supporting salt concentration was found to have a significant influence on the amount of dye loading and the morphology of the ZnO/eosin Y films. By decreasing the supporting salt concentration to 0.01 M KCl, porous films with a high dye loading can be obtained at potentials of -0.8 V vs. SCE at low eosin Y concentrations in the electrodeposition bath, which usually only lead to porous films at potentials where eosin Y is reduced (<-0.9 V vs. SCE). (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Motif discovery in ranked lists of sequences

DEFF Research Database (Denmark)

Nielsen, Morten Muhlig; Tataru, Paula; Madsen, Tobias

2016-01-01

Motif analysis has long been an important method to characterize biological functionality and the current growth of sequencing-based genomics experiments further extends its potential. These diverse experiments often generate sequence lists ranked by some functional property. There is therefore...... advantage of the regular expression feature, including enrichments for combinations of different microRNA seed sites. The method is implemented and made publicly available as an R package and supports high parallelization on multi-core machinery....... a growing need for motif analysis methods that can exploit this coupled data structure and be tailored for specific biological questions. Here, we present an exploratory motif analysis tool, Regmex (REGular expression Motif EXplorer), which offers several methods to evaluate the correlation of motifs...

Scintillation properties of μPD-grown Y{sub 4}Al{sub 2}O{sub 9}:Pr (YAM:Pr) crystals

Energy Technology Data Exchange (ETDEWEB)

Drozdowski, Winicjusz, E-mail: wind@fizyka.umk.pl [Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun (Poland); Brylew, Kamil [Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun (Poland); Malinowski, Michał [Institute of Microelectronics and Optoelectronics, Koszykowa 75, 00-662 Warsaw (Poland); Turczyński, Sebastian [Institute of Electronic Materials Technology, Wolczynska 133, 01-919 Warsaw (Poland)

2015-05-25

Highlights: • YAM:Pr crystals do scintillate and as such deserve further interest. • Fast d–f luminescence of Pr{sup 3+} ions appears in X-ray excited spectra. • Two components (24 and 790 ns) constitute scintillation time profiles. - Abstract: Y{sub 4}Al{sub 2}O{sub 9}:Pr (YAM:Pr) crystals have been grown by the micro-pulling-down method and their scintillation properties have been investigated. YAM:0.1%Pr displays a light yield of about 2000 ph/MeV and its scintillation time profile contains a prompt component with a decay time of 23.5 ns and a contribution of 20%. Radioluminescence spectra show both fast d–f and slow f–f praseodymium emissions. Low temperature glow curves are complex, consisting of discrete peaks and broad bands related to quasi-continuous trap distributions. Overall scintillation performance of YAM:Pr deteriorates with increasing praseodymium concentration.

Deciphering functional glycosaminoglycan motifs in development.

Science.gov (United States)

Townley, Robert A; Bülow, Hannes E

2018-03-23

Glycosaminoglycans (GAGs) such as heparan sulfate, chondroitin/dermatan sulfate, and keratan sulfate are linear glycans, which when attached to protein backbones form proteoglycans. GAGs are essential components of the extracellular space in metazoans. Extensive modifications of the glycans such as sulfation, deacetylation and epimerization create structural GAG motifs. These motifs regulate protein-protein interactions and are thereby repsonsible for many of the essential functions of GAGs. This review focusses on recent genetic approaches to characterize GAG motifs and their function in defined signaling pathways during development. We discuss a coding approach for GAGs that would enable computational analyses of GAG sequences such as alignments and the computation of position weight matrices to describe GAG motifs. Copyright © 2018 Elsevier Ltd. All rights reserved.

Fitness for synchronization of network motifs

DEFF Research Database (Denmark)

Vega, Y.M.; Vázquez-Prada, M.; Pacheco, A.F.

2004-01-01

We study the synchronization of Kuramoto's oscillators in small parts of networks known as motifs. We first report on the system dynamics for the case of a scale-free network and show the existence of a non-trivial critical point. We compute the probability that network motifs synchronize, and fi...... that the fitness for synchronization correlates well with motifs interconnectedness and structural complexity. Possible implications for present debates about network evolution in biological and other systems are discussed....

The position of the Gly-xxx-Gly motif in transmembrane segments modulates dimer affinity.

Science.gov (United States)

Johnson, Rachel M; Rath, Arianna; Deber, Charles M

2006-12-01

Although the intrinsic low solubility of membrane proteins presents challenges to their high-resolution structure determination, insight into the amino acid sequence features and forces that stabilize their folds has been provided through study of sequence-dependent helix-helix interactions between single transmembrane (TM) helices. While the stability of helix-helix partnerships mediated by the Gly-xxx-Gly (GG4) motif is known to be generally modulated by distal interfacial residues, it has not been established whether the position of this motif, with respect to the ends of a given TM segment, affects dimer affinity. Here we examine the relationship between motif position and affinity in the homodimers of 2 single-spanning membrane protein TM sequences: glycophorin A (GpA) and bacteriophage M13 coat protein (MCP). Using the TOXCAT assay for dimer affinity on a series of GpA and MCP TM segments that have been modified with either 4 Leu residues at each end or with 8 Leu residues at the N-terminal end, we show that in each protein, centrally located GG4 motifs are capable of stronger helix-helix interactions than those proximal to TM helix ends, even when surrounding interfacial residues are maintained. The relative importance of GG4 motifs in stabilizing helix-helix interactions therefore must be considered not only in its specific residue context but also in terms of the location of the interactive surface relative to the N and C termini of alpha-helical TM segments.

Aplikasi Ornamen Khas Maluku untuk Pengembangan Desain Motif Batik

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Masiswo Masiswo

2016-04-01

Full Text Available ABSTRAKMaluku memiliki banyak ragam hias budaya warisan nilai leluhur berupa ornamen etnis yang merupakan kesenian dan keterampilan kerajinan. Hasil warisan tersebut sampai saat ini masih lestari hidup serta dapat dinikmati sebagai konsumsi rohani yang memuaskan manusia. Berkaitan dengan keberlangsungan nilai-nilai tradisi etnis yang berwujud pada ornamen-ornamen daerah Maluku, maka dikembangkan untuk kebutuhan manusia berupa motif batik pada kain. Pengembangan ornamen ini lebih menekankan pada representasi akan bentuk-bentuk ornamen yang diterapkan pada kerajinan batik berupa motif khas Maluku. Pengembangan alternatif desain motif batik dibuat tiga variasi yang bersumber dari ornamen khas Maluku dibuat prototipe produknya dan diuji ketahanan luntur warnanya. Hasil uji ketahanan luntur warna terhadap gosokan basah dari tiga prototipe produk berpredikat baik sekali terdapat pada “Motif Siwa” dan predikat baik pada motif “Siwa Talang” dan motif “Matahari Siwa Talang”.Kata kunci: desain, Maluku, motif batik, ornamenABSTRACTMaluku has much decorative ancestral cultural heritage value in the form of ornament ethnic arts and crafts skills. The result of the legacy is still sustainable living can be enjoyed as well as satisfying spiritual human consumption.Related to the sustainability of traditional values in the form of ethnic ornaments Maluku, it was developed for human needs in the form of batik cloth . The development of these ornaments will be more emphasis on the representation forms of ornamentation that is applied to a batik motif Maluku. Development of alternative design motif made three variations. The development of three alternative design motifs derived from the Maluku ornaments made and tested a prototype product color fastness. The test results of color fastness to wet rubbing of the three prototypes are excellent products predicated on the "Motif Siwa" and a good rating on the motif "Siwa Talang" and motif "Matahari Siwa

The limits of de novo DNA motif discovery.

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David Simcha

Full Text Available A major challenge in molecular biology is reverse-engineering the cis-regulatory logic that plays a major role in the control of gene expression. This program includes searching through DNA sequences to identify "motifs" that serve as the binding sites for transcription factors or, more generally, are predictive of gene expression across cellular conditions. Several approaches have been proposed for de novo motif discovery-searching sequences without prior knowledge of binding sites or nucleotide patterns. However, unbiased validation is not straightforward. We consider two approaches to unbiased validation of discovered motifs: testing the statistical significance of a motif using a DNA "background" sequence model to represent the null hypothesis and measuring performance in predicting membership in gene clusters. We demonstrate that the background models typically used are "too null," resulting in overly optimistic assessments of significance, and argue that performance in predicting TF binding or expression patterns from DNA motifs should be assessed by held-out data, as in predictive learning. Applying this criterion to common motif discovery methods resulted in universally poor performance, although there is a marked improvement when motifs are statistically significant against real background sequences. Moreover, on synthetic data where "ground truth" is known, discriminative performance of all algorithms is far below the theoretical upper bound, with pronounced "over-fitting" in training. A key conclusion from this work is that the failure of de novo discovery approaches to accurately identify motifs is basically due to statistical intractability resulting from the fixed size of co-regulated gene clusters, and thus such failures do not necessarily provide evidence that unfound motifs are not active biologically. Consequently, the use of prior knowledge to enhance motif discovery is not just advantageous but necessary. An implementation of

Peptide-binding motifs of two common equine class I MHC molecules in Thoroughbred horses.

Science.gov (United States)

Bergmann, Tobias; Lindvall, Mikaela; Moore, Erin; Moore, Eugene; Sidney, John; Miller, Donald; Tallmadge, Rebecca L; Myers, Paisley T; Malaker, Stacy A; Shabanowitz, Jeffrey; Osterrieder, Nikolaus; Peters, Bjoern; Hunt, Donald F; Antczak, Douglas F; Sette, Alessandro

2017-05-01

Quantitative peptide-binding motifs of MHC class I alleles provide a valuable tool to efficiently identify putative T cell epitopes. Detailed information on equine MHC class I alleles is still very limited, and to date, only a single equine MHC class I allele, Eqca-1*00101 (ELA-A3 haplotype), has been characterized. The present study extends the number of characterized ELA class I specificities in two additional haplotypes found commonly in the Thoroughbred breed. Accordingly, we here report quantitative binding motifs for the ELA-A2 allele Eqca-16*00101 and the ELA-A9 allele Eqca-1*00201. Utilizing analyses of endogenously bound and eluted ligands and the screening of positional scanning combinatorial libraries, detailed and quantitative peptide-binding motifs were derived for both alleles. Eqca-16*00101 preferentially binds peptides with aliphatic/hydrophobic residues in position 2 and at the C-terminus, and Eqca-1*00201 has a preference for peptides with arginine in position 2 and hydrophobic/aliphatic residues at the C-terminus. Interestingly, the Eqca-16*00101 motif resembles that of the human HLA A02-supertype, while the Eqca-1*00201 motif resembles that of the HLA B27-supertype and two macaque class I alleles. It is expected that the identified motifs will facilitate the selection of candidate epitopes for the study of immune responses in horses.

Isopiestic Investigation of the Osmotic and Activity Coefficients of {yMgCl2 + (1 - y)MgSO4}(aq) and the Osmotic Coefficients of Na2SO4.MgSO4(aq) at 298.15 K

Energy Technology Data Exchange (ETDEWEB)

Miladinovic, J; Ninkovic, R; Todorovic, M; Rard, J A

2007-06-06

Isopiestic vapor pressure measurements were made for {l_brace}yMgCl{sub 2} + (1-y)MgSO{sub 4}{r_brace}(aq) solutions with MgCl{sub 2} ionic strength fractions of y = 0, 0.1997, 0.3989, 0.5992, 0.8008, and (1) at the temperature 298.15 K, using KCl(aq) as the reference standard. These measurements for the mixtures cover the ionic strength range I = 0.9794 to 9.4318 mol {center_dot} kg{sup -1}. In addition, isopiestic measurements were made with NaCl(aq) as reference standard for mixtures of {l_brace}xNa{sub 2}SO{sub 4} + (1-x)MgSO{sub 4}{r_brace}(aq) with the molality fraction x = 0.50000 that correspond to solutions of the evaporite mineral bloedite (astrakanite), Na{sub 2}Mg(SO{sub 4}){sub 2} {center_dot} 4H{sub 2}O(cr). The total molalities, m{sub T} = m(Na{sub 2}SO{sub 4}) + m(MgSO{sub 4}), range from m{sub T} = 1.4479 to 4.4312 mol {center_dot} kg{sup -1} (I = 5.0677 to 15.509 mol {center_dot} kg{sup -1}), where the uppermost concentration is the highest oversaturation molality that could be achieved by isothermal evaporation of the solvent at 298.15 K. The parameters of an extended ion-interaction (Pitzer) model for MgCl2(aq) at 298.15 K, which were required for an analysis of the {l_brace}yMgCl{sub 2} + (1-y)MgSO{sub 4}{r_brace}(aq) mixture results, were evaluated up to I = 12.025 mol {center_dot} kg{sup -1} from published isopiestic data together with the six new osmotic coefficients obtained in this study. Osmotic coefficients of {l_brace}yMgCl{sub 2} + (1-y)MgSO{sub 4}{r_brace}(aq) solutions from the present study, along with critically-assessed values from previous studies, were used to evaluate the mixing parameters of the extended ion-interaction model.

PENGARUH KEBUTUHAN TERHADAP MOTIF PENGGUNAAN KARTU DEBET BANK CENTRAL ASIA (BCA DI KALANGAN MAHASISWA AKTIF FAKULTAS EKONOMI UNIVERSITAS KRISTEN PETRA SURABAYA

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Hatane Semuel

2003-01-01

Full Text Available This research is conducted to the students of class 1999, 2000, and 2001 of Economics Faculty of Petra Christian University. This research focuses on cognitive and affective motive of those subjects in using BCA's debit card, assuming that consumers tend to use objective and subjective factors in considering to purchase certain product. The result of this research shows that achievement needs, power needs, and affiliation needs simultaneously influence the motive of the subjects in using BCA's debit card, in which 46% of the influence can be explained by the model. Achievement needs have more dominant influence compared to power needs. Besides that, education factor (study duration found to influence the cognitive motive, which is shown by the motive difference among class 1999, 2000, and 2001. Abstract in Bahasa Indonesia : Penelitian dilakukan terhadap mahasiswa Fakultas ekonomi Universitas Kristen PETRA Surabaya angkatan 1999, 2000, dan 2001. Fokus penelitian pada motif kognitif dan afektif dalam menggunakan produk kartu debet BCA, dengan asumsi bahwa konsumen dalam mempertimbangkan pembelian suatu produk lebih didasarkan pada faktor obyektif dan subyektif. Hasil penelitian mengungkapkan kebutuhan yang diukur melalui, achievement needs, power needs, affiliation needs ternyata secara serempak berpengaruh terhadap motif penggunaan kartu debet BCA di kalangan mahasiswa Fakultas Ekonomi Universitas Kristen PETRA Surabaya, dengan kemampuan 46% dapat dijelaskan dari dalam model. Achievement needs mempunyai pengaruh lebih dominan dibandingkan power needs. Selain itu faktor pendidikan (lama studi mempunyai dampak terhadap motif kognitif, hal ini terungkap dari adanya perbedaan motif tersebut pada angkatan 1999 dengan angkatan 2000 maupun angkatan 2001. Kata kunci: motif, achievement, power, needs.

Enrichment of Circular Code Motifs in the Genes of the Yeast Saccharomyces cerevisiae

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Christian J. Michel

2017-12-01

Full Text Available A set X of 20 trinucleotides has been found to have the highest average occurrence in the reading frame, compared to the two shifted frames, of genes of bacteria, archaea, eukaryotes, plasmids and viruses. This set X has an interesting mathematical property, since X is a maximal C 3 self-complementary trinucleotide circular code. Furthermore, any motif obtained from this circular code X has the capacity to retrieve, maintain and synchronize the original (reading frame. Since 1996, the theory of circular codes in genes has mainly been developed by analysing the properties of the 20 trinucleotides of X , using combinatorics and statistical approaches. For the first time, we test this theory by analysing the X motifs, i.e., motifs from the circular code X , in the complete genome of the yeast Saccharomyces cerevisiae. Several properties of X motifs are identified by basic statistics (at the frequency level, and evaluated by comparison to R motifs, i.e., random motifs generated from 30 different random codes R . We first show that the frequency of X motifs is significantly greater than that of R motifs in the genome of S. cerevisiae. We then verify that no significant difference is observed between the frequencies of X and R motifs in the non-coding regions of S. cerevisiae, but that the occurrence number of X motifs is significantly higher than R motifs in the genes (protein-coding regions. This property is true for all cardinalities of X motifs (from 4 to 20 and for all 16 chromosomes. We further investigate the distribution of X motifs in the three frames of S. cerevisiae genes and show that they occur more frequently in the reading frame, regardless of their cardinality or their length. Finally, the ratio of X genes, i.e., genes with at least one X motif, to non- X genes, in the set of verified genes is significantly different to that observed in the set of putative or dubious genes with no experimental evidence. These results, taken together

Enrichment of Circular Code Motifs in the Genes of the Yeast Saccharomyces cerevisiae.

Science.gov (United States)

Michel, Christian J; Ngoune, Viviane Nguefack; Poch, Olivier; Ripp, Raymond; Thompson, Julie D

2017-12-03

A set X of 20 trinucleotides has been found to have the highest average occurrence in the reading frame, compared to the two shifted frames, of genes of bacteria, archaea, eukaryotes, plasmids and viruses. This set X has an interesting mathematical property, since X is a maximal C3 self-complementary trinucleotide circular code. Furthermore, any motif obtained from this circular code X has the capacity to retrieve, maintain and synchronize the original (reading) frame. Since 1996, the theory of circular codes in genes has mainly been developed by analysing the properties of the 20 trinucleotides of X, using combinatorics and statistical approaches. For the first time, we test this theory by analysing the X motifs, i.e., motifs from the circular code X, in the complete genome of the yeast Saccharomyces cerevisiae . Several properties of X motifs are identified by basic statistics (at the frequency level), and evaluated by comparison to R motifs, i.e., random motifs generated from 30 different random codes R. We first show that the frequency of X motifs is significantly greater than that of R motifs in the genome of S. cerevisiae . We then verify that no significant difference is observed between the frequencies of X and R motifs in the non-coding regions of S. cerevisiae , but that the occurrence number of X motifs is significantly higher than R motifs in the genes (protein-coding regions). This property is true for all cardinalities of X motifs (from 4 to 20) and for all 16 chromosomes. We further investigate the distribution of X motifs in the three frames of S. cerevisiae genes and show that they occur more frequently in the reading frame, regardless of their cardinality or their length. Finally, the ratio of X genes, i.e., genes with at least one X motif, to non-X genes, in the set of verified genes is significantly different to that observed in the set of putative or dubious genes with no experimental evidence. These results, taken together, represent the first

Dielectric Study of the Phase Transitions in [P(CH3)4]2CuY4 (Y = Cl, Br)

Science.gov (United States)

Gesi, Kazuo

2002-05-01

Phase transitions in [P(CH3)4]2CuY4 (Y = Cl, Br) have been studied by dielectric measurements. In [P(CH3)4]2CuCl4, a slight break and a discontinuous jump on the dielectric constant vs. temperature curve are seen at the normal-incommensurate and the incommensurate-commensurate phase transitions, respectively. A small peak of dielectric constant along the b-direction exists just above the incommensurate-to-commensurate transition temperature. The anisotropic dielectric anomalies of [P(CH3)4]2CuBr4 at phase transitions were measured along the three crystallographic axes. The pressure-temperature phase diagram of [P(CH3)4]2CuCl4 was determined. The initial pressure coefficients of the normal-to-incommensurate and the incommensurate-to-commensurate transition temperatures are 0.19 K/MPa and 0.27 K/MPa, respectively. The incommensurate phase in [P(CH3)4]2CuCl4 disappears at a triple point which exists at 335 MPa and 443 K. The stability and the pressure effects of the incommensurate phases are much different among the four [Z(CH3)4]2CuY4 crystals (Z = N, P; Y = Cl, Br).

Parole, Sintagmatik, dan Paradigmatik Motif Batik Mega Mendung

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Rudi - Nababan

2012-04-01

Full Text Available ABSTRACT   Discussing traditional batik is related a lot to the organization system of fine arts element ac- companying it, either the pattern of the motif or the technique of the making. In this case, the motif of Mega Mendung Cirebon certainly has patterns and rules which are traditionally different from the other motifs in other areas. Through  semiotics analysis especially with Saussure and Pierce concept, it can be traced that batik with Cirebon motif, in this case Mega Mendung motif, has parole and langue system, as unique fine arts language in batik, and structure of visual syntagmatic and paradigmatic. In the context of batik motif as fine arts language, it is surely related to sign system as symbol and icon.       Keywords: visual semiotic, Cirebon’s batik.

Synthesis, crystal structure and photoluminescent properties of Eu{sup 3+} ion-activated R{sub 4}MoO{sub 9} (R = Y, Gd, and Lu)

Energy Technology Data Exchange (ETDEWEB)

Li, Huaiyong [Department of Materials Science and Engineering, Liaocheng University, Liaocheng 252059 (China); Moon, Byung Kee; Choi, Byung Chun [Department of Physics, Pukyong National University, Busan 608-737 (Korea, Republic of); Jeong, Jung Hyun, E-mail: jhjeong@pknu.ac.kr [Department of Physics, Pukyong National University, Busan 608-737 (Korea, Republic of); Yang, Hyun Kyoung [Jeju Global Research Center, Korea Institute of Energy Research, Jeju 695-971 (Korea, Republic of); Jang, Kiwan; Lee, Ho Sueb [Department of Physics, Changwon National University, Changwon 641-773 (Korea, Republic of); Yi, Soung Soo [Department of Electronic Material Engineering, Silla University, Busan 617-736 (Korea, Republic of)

2013-05-15

Rare earth molybdates R{sub 4}MoO{sub 9} (R = Y, Gd, and Lu) with Eu{sup 3+} ion-doped were synthesized by solid-state reaction. The phase structure, optical absorption and photoluminescence properties of the as-prepared powder samples were studied. The powder X-ray diffraction patterns indicated that all the compounds crystallized in a hexagonal structure, and the lattice parameters reduced in the order of the ionic radii of R. The UV–visible diffuse reflectance spectra revealed that the compounds had a strong absorption of near-UV light due to the excitation of MoO{sub 6} groups in the host lattices. The energy absorbed by the host lattices could then be transferred to doped Eu{sup 3+} ions, resulting in red emission due to the f–f transitions of Eu{sup 3+} ions. The optical absorption and photoluminescence properties of the compounds indicated that they might be candidates as the color-conversion red phosphors for solid-state lighting. - Highlights: ► Structure, optical and photoluminescence properties of Eu{sup 3+} ion-activated R{sub 4}MoO{sub 9} were studied. ► Energy transfer from MoO{sub x} to Eu{sup 3+} can be used to convert near-UV to red light. ► R{sub 4}MoO{sub 9}:Eu might be candidate for color-conversion red phosphors excited by near-UV light.

Dipeptide frequency/bias analysis identifies conserved sites of nonrandomness shared by cysteine-rich motifs.

Science.gov (United States)

Campion, S R; Ameen, A S; Lai, L; King, J M; Munzenmaier, T N

2001-08-15

This report describes the application of a simple computational tool, AAPAIR.TAB, for the systematic analysis of the cysteine-rich EGF, Sushi, and Laminin motif/sequence families at the two-amino acid level. Automated dipeptide frequency/bias analysis detects preferences in the distribution of amino acids in established protein families, by determining which "ordered dipeptides" occur most frequently in comprehensive motif-specific sequence data sets. Graphic display of the dipeptide frequency/bias data revealed family-specific preferences for certain dipeptides, but more importantly detected a shared preference for employment of the ordered dipeptides Gly-Tyr (GY) and Gly-Phe (GF) in all three protein families. The dipeptide Asn-Gly (NG) also exhibited high-frequency and bias in the EGF and Sushi motif families, whereas Asn-Thr (NT) was distinguished in the Laminin family. Evaluation of the distribution of dipeptides identified by frequency/bias analysis subsequently revealed the highly restricted localization of the G(F/Y) and N(G/T) sequence elements at two separate sites of extreme conservation in the consensus sequence of all three sequence families. The similar employment of the high-frequency/bias dipeptides in three distinct protein sequence families was further correlated with the concurrence of these shared molecular determinants at similar positions within the distinctive scaffolds of three structurally divergent, but similarly employed, motif modules.

A Comparative Study on the Origin and Variety of Motifs in Shahsavan Salt Bags and Caucasian Textiles

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Siamak Egharloo

2017-12-01

Full Text Available Shahsavan tribes of Iran and the Caucasus region have had considerable and often inevitable intercourse and associations during the history due to their common borders and special geographical locations. The result of this has been manifested in different forms of intermingled factors and elements, specifically the textiles of tribes and ethnic groups. The interactions of the mentioned realm, i.e. textile industry, have best been appeared in patterns, motifs, colors and compositions and weaving of the hand-woven textiles among which Shahsavan "salt bags" (NAMAKDᾹN are a case in point. According to the facts and the importance of this subject, we can propose some questions as follows: What influences have the field of weaving had in these two regions as a result of their interactions and historical background? What are the motifs and their classifications in these two regions and which ones share common patterns? And which ones abound? Having been done in analytical and comparative method, the present research has examined the field of weaving in Shahsavan tribe with emphasis on its salt bags together with other Caucasian textiles (salt bags, etc.. The objectives of the research have been the study of the influences and interactions between the two regions and the recognition of patterns and motifs on their textiles. Finally, we can infer that the certain location of Iran and its common borders with the Caucasus besides tribal distribution of groups in northern and southern areas could be considered the reasons for cultural influences in the mentioned regions. The dominant motifs to be noticed here are dragons (S shape, diamonds and stars, crab-like and cross motifs as well as negative and positive spaces.

Temperature-compensated Love wave based gas sensor on waveguide structure of SiO2/36° YX LiTaO3

International Nuclear Information System (INIS)

Wang, Wen; Xie, Xiao; Chen, Gui; Liu, Jiuling; He, Shitang

2015-01-01

A temperature-compensated Love wave device was proposed for gas sensing utilizing a waveguide structure of SiO 2 /36° YX LiTaO 3 . Significant improvement in the temperature stability of the hybrid Love wave device was implemented by varying the guiding layer thickness. The optimal values yielding low cross-sensitivity to temperature and high mass sensitivity in gas sorption were determined theoretically by solving the coupled electromechanical field equation in layered media. The theoretical analysis was confirmed experimentally in dimethylmethylphosphonate (DMMP) detection by using a fluoroalcoholpolysiloxane (SXFA) coated Love wave sensor. The experimental results indicate that better sensitivity and excellent temperature stability were obtained from the developed Love wave gas sensor over the Rayleigh surface acoustic wave (R-SAW) sensors. (paper)

Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae

Science.gov (United States)

Fauteux, François; Strömvik, Martina V

2009-01-01

Background Accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of cis-regulatory motifs. Results We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP) gene promoters from three plant families, namely Brassicaceae (mustards), Fabaceae (legumes) and Poaceae (grasses) using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (Arabidopsis thaliana (L.) Heynh.), soybean (Glycine max (L.) Merr.) and rice (Oryza sativa L.) respectively. We have identified three conserved motifs (two RY-like and one ACGT-like) in Brassicaceae and Fabaceae SSP gene promoters that are similar to experimentally characterized seed-specific cis-regulatory elements. Fabaceae SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in Poaceae SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins. Conclusion Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination of conserved motifs

Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae

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Fauteux François

2009-10-01

Full Text Available Abstract Background Accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of cis-regulatory motifs. Results We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP gene promoters from three plant families, namely Brassicaceae (mustards, Fabaceae (legumes and Poaceae (grasses using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (Arabidopsis thaliana (L. Heynh., soybean (Glycine max (L. Merr. and rice (Oryza sativa L. respectively. We have identified three conserved motifs (two RY-like and one ACGT-like in Brassicaceae and Fabaceae SSP gene promoters that are similar to experimentally characterized seed-specific cis-regulatory elements. Fabaceae SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in Poaceae SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins. Conclusion Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination

Motif statistics and spike correlations in neuronal networks

International Nuclear Information System (INIS)

Hu, Yu; Shea-Brown, Eric; Trousdale, James; Josić, Krešimir

2013-01-01

Motifs are patterns of subgraphs of complex networks. We studied the impact of such patterns of connectivity on the level of correlated, or synchronized, spiking activity among pairs of cells in a recurrent network of integrate and fire neurons. For a range of network architectures, we find that the pairwise correlation coefficients, averaged across the network, can be closely approximated using only three statistics of network connectivity. These are the overall network connection probability and the frequencies of two second order motifs: diverging motifs, in which one cell provides input to two others, and chain motifs, in which two cells are connected via a third intermediary cell. Specifically, the prevalence of diverging and chain motifs tends to increase correlation. Our method is based on linear response theory, which enables us to express spiking statistics using linear algebra, and a resumming technique, which extrapolates from second order motifs to predict the overall effect of coupling on network correlation. Our motif-based results seek to isolate the effect of network architecture perturbatively from a known network state. (paper)

Bayesian centroid estimation for motif discovery.

Science.gov (United States)

Carvalho, Luis

2013-01-01

Biological sequences may contain patterns that signal important biomolecular functions; a classical example is regulation of gene expression by transcription factors that bind to specific patterns in genomic promoter regions. In motif discovery we are given a set of sequences that share a common motif and aim to identify not only the motif composition, but also the binding sites in each sequence of the set. We propose a new centroid estimator that arises from a refined and meaningful loss function for binding site inference. We discuss the main advantages of centroid estimation for motif discovery, including computational convenience, and how its principled derivation offers further insights about the posterior distribution of binding site configurations. We also illustrate, using simulated and real datasets, that the centroid estimator can differ from the traditional maximum a posteriori or maximum likelihood estimators.

Bayesian centroid estimation for motif discovery.

Directory of Open Access Journals (Sweden)

Luis Carvalho

Full Text Available Biological sequences may contain patterns that signal important biomolecular functions; a classical example is regulation of gene expression by transcription factors that bind to specific patterns in genomic promoter regions. In motif discovery we are given a set of sequences that share a common motif and aim to identify not only the motif composition, but also the binding sites in each sequence of the set. We propose a new centroid estimator that arises from a refined and meaningful loss function for binding site inference. We discuss the main advantages of centroid estimation for motif discovery, including computational convenience, and how its principled derivation offers further insights about the posterior distribution of binding site configurations. We also illustrate, using simulated and real datasets, that the centroid estimator can differ from the traditional maximum a posteriori or maximum likelihood estimators.

eso-na-nceij-ui-y-19-9-7

Indian Academy of Sciences (India)

Page 1. Science Smiles. RKLaxman. It saves a lot of bother, If you programme it, it goes about on its own taking pictures of tourist and historical interests, and returns. R -E-S-O-NA-N-C-E-I-J-UI-Y-19-9-7----~-------~~-------------------. 5.

Sobrepeso, obesidad y desnutrición crónica en niños de 6 a 9 años en Perú, 2009-2010

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Jaime Pajuelo-Ramírez

Full Text Available Objetivos. Determinar la prevalencia de sobrepeso, obesidad y desnutrición crónica en niños de 6 a 9 años en Perú. Materiales y métodos . Estudio transversal utilizando la Encuesta Nacional de Hogares del 2009 al 2010. Se analizó la relación talla/edad con referencias del National Center for Health Statistic (NCSH y de la Organización Mundial de la Salud (OMS, considerando debajo de menos dos desviaciones estándar para desnutrición crónica (DC; y las tablas de referencias de Must y de la OMS para medir el índice de masa corporal con valores percentiles entre 85 y 95 para sobrepeso y por encima del percentil 95 para obesidad. Resultados. Utilizando como referencia Must el sobrepeso fue 12,1% y la obesidad 9,4%, y de acuerdo a la OMS el sobrepeso y la obesidad fueron 10,2 y 11,3% respectivamente. La prevalencia de DC según referencias de la NCSH y OMS es 15,4 y 17,8% respectivamente. Mayor prevalencia de DC se encuentran en la sierra norte (25,2%, sierra centro (22,9% y sierra sur (19%, mientras que la obesidad está más presente en la costa sur (28%, Lima Metropolitana (22,8% y costa centro (22,5%. De los niños con DC el 6,5% tiene sobrepeso y 1,2% obesidad. Conclusiones. La DC está disminuyendo por cuanto los promedios de talla han mejorado, sin embargo la obesidad se ha duplicado. La presencia de DC y obesidad en niños de 6 a 9 años en diferentes regiones del Perú propone un reto en la planificación de políticas de alimentación y nutrición

Asymptotics for a special solution to the second member of the Painleve I hierarchy

International Nuclear Information System (INIS)

Claeys, T

2010-01-01

We study the asymptotic behavior of a special smooth solution y(x, t) to the second member of the Painleve I hierarchy. This solution arises in random matrix theory and in the study of the Hamiltonian perturbations of hyperbolic equations. The asymptotic behavior of y(x, t) if x → ±∞ (for fixed t) is known and relatively simple, but it turns out to be more subtle when x and t tend to infinity simultaneously. We distinguish a region of algebraic asymptotic behavior and a region of elliptic asymptotic behavior, and we obtain rigorous asymptotics in both regions. We also discuss two critical transitional asymptotic regimes.

Structural changes of Bi1.8Sr2(Ca1-xYx)Cu2.2Oz ceramics with yttrium content studied by electron diffraction and high-resolution electron microscopy

Science.gov (United States)

Onozuka, Takashi; Iwabuchi, Yoshihiro; Fukase, Tetsuo; Sato, Hiroshi; Mitchell, Terence E.

1991-06-01

The mode of the incommensurate modulation in the b direction of the Bi1.8Sr2(Ca1-xYx)Cu2.2Oz (0.054.5b0 and 5b0 or 4.5b0 and 4b0, thus creating periods of b=4.75b0-4.0b0. The fundamental orthorhombic lattice has dimensions of a~=b~=b0 (0.54 nm) and c~=c0 (3.1 nm). The change of the mixing mode from one to the other mentioned above occurs just in the yttrium concentration range, 0.454.5b0/2 and 5b0/2 or 4.5b0/2 and 4b0/2 in high-resolution lattice images. These images are reproduced well by a multislice computer-simulation technique.

GROWTH AND COMPOSITION OF Arthrospira (Spirulina platensis IN A TUBULAR PHOTOBIOREACTOR USING AMMONIUM NITRATE AS THE NITROGEN SOURCE IN A FED-BATCH PROCESS

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C. Cruz-Martínez

2015-06-01

Full Text Available AbstractNH4NO3 simultaneously provides a readily assimilable nitrogen source (ammonia and a reserve of nitrogen (nitrate, allowing for an increase in Arthrospira platensis biomass production while reducing the cost of the cultivation medium. In this study, a 22plus star central composite experimental design combined with response surface methodology was employed to analyze the influence of light intensity (I and the total amount of added NH4NO3 (Mt on a bench-scale tubular photobioreactor for fed-batch cultures. The maximum cell concentration (Xm, cell productivity (PX and biomass yield on nitrogen (YX/N were evaluated, as were the protein and lipid contents. Under optimized conditions (I = 148 μmol·photons·m-2·s-1 and Mt = 9.7 mM NH4NO3, Xm = 4710 ±34.4 mg·L-1, PX = 478.9 ±3.8 mg·L-1·d-1 and YX/N = 15.87 ±0.13 mg·mg-1 were obtained. The best conditions for protein content in the biomass (63.2% were not the same as those that maximized cell growth (I = 180 μmol·photons·m-2·s-1 and Mt = 22.5 mM NH4NO3. Based on these results, it is possible to conclude that ammonium nitrate is an interesting alternate nitrogen source for the cultivation of A. platensisin a fed-batch process and could be used for other photosynthetic microorganisms.

CONTEMPORARY USAGE OF TRADITIONAL TURKISH MOTIFS IN PRODUCT DESIGNS

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Tulay Gumuser

2012-12-01

Full Text Available The aim of this study is to identify the traditional Turkish motifs and its relations among present industrial designs. Traditional Turkish motifs played a very important role in 16th century onwards. The arts of the Ottoman Empire were used because of their symbolic meanings and unique styles. When we examine these motifs we encounter; Tiger Stripe, Three Spot (Çintemani, Rumi, Hatayi, Penç, Cloud, Crescent, Star, Crown, Hyacinth, Tulip and Carnation motifs. Nowadays, Turkish designers have begun to use these traditional Turkish motifs in their designs so as to create differences and awareness in the world design. The examples of these industrial designs, using the Turkish motifs, have survived and have Ottoman heritage and historical value. In this study, the Turkish motifs will be examined along with their focus on contemporary Turkish industrial designs used today.

SIMuLLDA : a Multilingual Lexical Database Application using a Structured Interlingua

NARCIS (Netherlands)

Janssen, M.

2002-01-01

It is commonly accepted that there are about five to six thousand languages. For many pairs of languages Y>, there is no dictionary X->Y or Y->X, there are only dictionaries for the pairs X->English/French/Spanish, and English/French/Spanish->Y. There is a clear need for

RNA motif search with data-driven element ordering.

Science.gov (United States)

Rampášek, Ladislav; Jimenez, Randi M; Lupták, Andrej; Vinař, Tomáš; Brejová, Broňa

2016-05-18

In this paper, we study the problem of RNA motif search in long genomic sequences. This approach uses a combination of sequence and structure constraints to uncover new distant homologs of known functional RNAs. The problem is NP-hard and is traditionally solved by backtracking algorithms. We have designed a new algorithm for RNA motif search and implemented a new motif search tool RNArobo. The tool enhances the RNAbob descriptor language, allowing insertions in helices, which enables better characterization of ribozymes and aptamers. A typical RNA motif consists of multiple elements and the running time of the algorithm is highly dependent on their ordering. By approaching the element ordering problem in a principled way, we demonstrate more than 100-fold speedup of the search for complex motifs compared to previously published tools. We have developed a new method for RNA motif search that allows for a significant speedup of the search of complex motifs that include pseudoknots. Such speed improvements are crucial at a time when the rate of DNA sequencing outpaces growth in computing. RNArobo is available at http://compbio.fmph.uniba.sk/rnarobo .

Influencing the selectivity of zeolite Y for triglycine adsorption

NARCIS (Netherlands)

Wijntje, R.; Bosch, H.; Haan, A.B. de; Bussmann, P.J.T.

2007-01-01

In prior work we studied the adsorption of triglycine on zeolite Y under reference conditions. This study aims to solve the question of which adsorbent properties and process conditions influence the adsorption triglycine from an aqueous solution by zeolite Y. Relevant zeolite parameters to study

T cell receptor zeta allows stable expression of receptors containing the CD3gamma leucine-based receptor-sorting motif

DEFF Research Database (Denmark)

Dietrich, J; Geisler, C

1998-01-01

The leucine-based motif in the T cell receptor (TCR) subunit CD3gamma constitutes a strong internalization signal. In fully assembled TCR this motif is inactive unless phosphorylated. In contrast, the motif is constitutively active in CD4/CD3gamma and Tac/CD3gamma chimeras independently of phosph......The leucine-based motif in the T cell receptor (TCR) subunit CD3gamma constitutes a strong internalization signal. In fully assembled TCR this motif is inactive unless phosphorylated. In contrast, the motif is constitutively active in CD4/CD3gamma and Tac/CD3gamma chimeras independently...... of phosphorylation and leads to rapid internalization and sorting of these chimeras to lysosomal degradation. Because the TCRzeta chain rescues incomplete TCR complexes from lysosomal degradation and allows stable surface expression of fully assembled TCR, we addressed the question whether TCRzeta has the potential...... to mask the CD3gamma leucine-based motif. By studying CD4/CD3gamma and CD16/CD3gamma chimeras, we found that CD16/CD3gamma chimeras associated with TCRzeta. The CD16/CD3gamma-TCRzeta complexes were stably expressed at the cell surface and had a low spontaneous internalization rate, indicating...

22 CFR 9a.4 - Classification.

Science.gov (United States)

2010-04-01

... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Classification. 9a.4 Section 9a.4 Foreign... ENERGY PROGRAMS; RELATED MATERIAL § 9a.4 Classification. (a) Section 1 of E.O. 11932, August 4, 1976.... If the officer determines that the information or material warrants classification, he shall assign...

UV photolysis of 4-iodo-, 4-bromo-, and 4-chlorophenol: Competition between C–Y (Y = halogen) and O–H bond fission

International Nuclear Information System (INIS)

Sage, Alan G.; Oliver, Thomas A. A.; King, Graeme A.; Murdock, Daniel; Harvey, Jeremy N.; Ashfold, Michael N. R.

2013-01-01

The wavelength dependences of C–Y and O–H bond fission following ultraviolet photoexcitation of 4-halophenols (4-YPhOH) have been investigated using a combination of velocity map imaging, H Rydberg atom photofragment translational spectroscopy, and high level spin-orbit resolved electronic structure calculations, revealing a systematic evolution in fragmentation behaviour across the series Y = I, Br, Cl (and F). All undergo O–H bond fission following excitation at wavelengths λ≲ 240 nm, on repulsive ((n/π)σ*) potential energy surfaces (PESs), yielding fast H atoms with mean kinetic energies ∼11 000 cm −1 . For Y = I and Br, this process occurs in competition with prompt C–I and C–Br bond cleavage on another (n/π)σ* PES, but no Cl/Cl* products unambiguously attributable to one photon induced C–Cl bond fission are observed from 4-ClPhOH. Differences in fragmentation behaviour at longer excitation wavelengths are more marked. Prompt C–I bond fission is observed following excitation of 4-IPhOH at all λ≤ 330 nm; the wavelength dependent trends in I/I* product branching ratio, kinetic energy release, and recoil anisotropy suggest that (with regard to C–I bond fission) 4-IPhOH behaves like a mildly perturbed iodobenzene. Br atoms are observed when exciting 4-BrPhOH at long wavelengths also, but their velocity distributions suggest that dissociation occurs after internal conversion to the ground state. O–H bond fission, by tunnelling (as in phenol), is observed only in the cases of 4-FPhOH and, more weakly, 4-ClPhOH. These observed differences in behaviour can be understood given due recognition of (i) the differences in the vertical excitation energies of the C–Y centred (n/π)σ* potentials across the series Y = I < Br < Cl and the concomitant reduction in C–Y bond strength, cf. that of the rival O–H bond, and (ii) the much increased spin-orbit coupling in, particularly, 4-IPhOH. The present results provide (another) reminder of the

Identification of sequence motifs significantly associated with antisense activity

Directory of Open Access Journals (Sweden)

Peek Andrew S

2007-06-01

Full Text Available Abstract Background Predicting the suppression activity of antisense oligonucleotide sequences is the main goal of the rational design of nucleic acids. To create an effective predictive model, it is important to know what properties of an oligonucleotide sequence associate significantly with antisense activity. Also, for the model to be efficient we must know what properties do not associate significantly and can be omitted from the model. This paper will discuss the results of a randomization procedure to find motifs that associate significantly with either high or low antisense suppression activity, analysis of their properties, as well as the results of support vector machine modelling using these significant motifs as features. Results We discovered 155 motifs that associate significantly with high antisense suppression activity and 202 motifs that associate significantly with low suppression activity. The motifs range in length from 2 to 5 bases, contain several motifs that have been previously discovered as associating highly with antisense activity, and have thermodynamic properties consistent with previous work associating thermodynamic properties of sequences with their antisense activity. Statistical analysis revealed no correlation between a motif's position within an antisense sequence and that sequences antisense activity. Also, many significant motifs existed as subwords of other significant motifs. Support vector regression experiments indicated that the feature set of significant motifs increased correlation compared to all possible motifs as well as several subsets of the significant motifs. Conclusion The thermodynamic properties of the significantly associated motifs support existing data correlating the thermodynamic properties of the antisense oligonucleotide with antisense efficiency, reinforcing our hypothesis that antisense suppression is strongly associated with probe/target thermodynamics, as there are no enzymatic

Influence of the sintering temperature on the Sr content in a Ca_(_1_−_x_−_y_)Ce_xSr_yAl_zTi_(_1_−_z_)O_3 perovskite (x = 0.04–0.16) co-doped with Ce

International Nuclear Information System (INIS)

Kamel, Nour-el-hayet; Mouheb, Yasmina; Kamel, Ziane; Moudir, Dalila; Aouchiche, Fairouz; Arabi, Azeddine

2016-01-01

A Sr-Ce co-doped perovskite, with the chemical formula: Ca_(_1_−_x_−_y_)Ce_xSr_yAl_zTi_(_1_−_z_)O_3 (y = 0.04, 0.08, 0.12 and 0.16, x = 0.05) is synthesized by sol–gel process. The influence of the sintering temperature, Ts, on the rate of inserted Sr was investigated at 1223, 1373 and 1473 K. The Sr amount sequestered in the perovskite reaches 85% (y = 0.16, 9.50 wt%) for Ts = 1373 K, giving sintering densities between 3.520 and 4.400. XRD analysis reveals an orthorhombic CaTiO_3 structure. The lattice parameters obey to Vegard’s law for Ts = 1373 and 1473 K. SEM analysis shows orthorhombic grains of 0.514 μm × 1 μm mean dimensions. MCC1 and MCC2 tests, performed on minerals sintered at 1373 K, indicate that the most durable one is that containing 9.50 wt% Sr. MCC1 test gave 6.998·10"−"6 g/cm"2 d of Sr, and MCC2 2.143·10"−"4 g/cm"2 d of Ce. The temperature favors the Sr dissolution to the detriment of Ce. The Ca dissolution rate reaches 1.002·10"−"6 to 2.005·10"−"6 g/cm"2 d. - Highlights: • Ca_(_1_−_x_−_y_)Ce_xSr_yAl_zTi_(_1_−_z_)O_3 perovskite is synthesized by sol–gel. • The influence of the sintering temperature, Ts, on the rate of inserted Sr was investigated at 1223, 1373 and 1473 K. • 85% of total Sr was sequestered in the perovskite for Ts = 1373 K. • MCC1 and MCC2 leach tests indicate that the most durable mineral is that containing 9.50 wt.% Sr. • MCC1 test gave 8.10 10"−"1"0 kg/m"2.d Sr. The lower is the leaching temperature the higher is the mineral durability.

22 CFR 9.4 - Original classification.

Science.gov (United States)

2010-04-01

... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Original classification. 9.4 Section 9.4 Foreign Relations DEPARTMENT OF STATE GENERAL SECURITY INFORMATION REGULATIONS § 9.4 Original classification. (a) Definition. Original classification is the initial determination that certain information...

Do motifs reflect evolved function?--No convergent evolution of genetic regulatory network subgraph topologies.

Science.gov (United States)

Knabe, Johannes F; Nehaniv, Chrystopher L; Schilstra, Maria J

2008-01-01

Methods that analyse the topological structure of networks have recently become quite popular. Whether motifs (subgraph patterns that occur more often than in randomized networks) have specific functions as elementary computational circuits has been cause for debate. As the question is difficult to resolve with currently available biological data, we approach the issue using networks that abstractly model natural genetic regulatory networks (GRNs) which are evolved to show dynamical behaviors. Specifically one group of networks was evolved to be capable of exhibiting two different behaviors ("differentiation") in contrast to a group with a single target behavior. In both groups we find motif distribution differences within the groups to be larger than differences between them, indicating that evolutionary niches (target functions) do not necessarily mold network structure uniquely. These results show that variability operators can have a stronger influence on network topologies than selection pressures, especially when many topologies can create similar dynamics. Moreover, analysis of motif functional relevance by lesioning did not suggest that motifs were of greater importance to the functioning of the network than arbitrary subgraph patterns. Only when drastically restricting network size, so that one motif corresponds to a whole functionally evolved network, was preference for particular connection patterns found. This suggests that in non-restricted, bigger networks, entanglement with the rest of the network hinders topological subgraph analysis.

Lesion Orientation of O4-Alkylthymidine Influences Replication by Human DNA Polymerase η

OpenAIRE

O’Flaherty, D. K.; Patra, A.; Su, Y.; Guengerich, F. P.; Egli, M.; Wilds, C. J.

2016-01-01

DNA lesions that elude repair may undergo translesion synthesis catalyzed by Y-family DNA polymerases. O4-Alkylthymidines, persistent adducts that can result from carcinogenic agents, may be encountered by DNA polymerases. The influence of lesion orientation around the C4-O4 bond on processing by human DNA polymerase η (hPol η) was studied for oligonucleotides containing O4-methylthymidine, O4-ethylthymidine, and analogs restricting the O4-methylene group in an anti-orientation. Primer extens...

Barro y matemáticas: 9 sucesiones y una escala

OpenAIRE

Lluis, Josep; Pol, Catalina; Triay, Maria

2009-01-01

El objeto de este artículo es presentar el cartel didáctico que relaciona matemáticas y cerámica titulado La successió del fang (La sucesión del barro) y las actividades que entorno a él se han realizado en el marco de la Fira del Fang (Feria del Barro) que organiza el Ayuntamiento de Marratxí (Mallorca). En esta ocasión, el cartel didáctico ha corrido a cargo de la Societat Balear de Matemàtiques SBM-XEIX. El público escolar al que va dirigido abarca principalmente edades desde 4 a 12 años....

Cave acoustics in prehistory: Exploring the association of Palaeolithic visual motifs and acoustic response.

Science.gov (United States)

Fazenda, Bruno; Scarre, Chris; Till, Rupert; Pasalodos, Raquel Jiménez; Guerra, Manuel Rojo; Tejedor, Cristina; Peredo, Roberto Ontañón; Watson, Aaron; Wyatt, Simon; Benito, Carlos García; Drinkall, Helen; Foulds, Frederick

2017-09-01

During the 1980 s, acoustic studies of Upper Palaeolithic imagery in French caves-using the technology then available-suggested a relationship between acoustic response and the location of visual motifs. This paper presents an investigation, using modern acoustic measurement techniques, into such relationships within the caves of La Garma, Las Chimeneas, La Pasiega, El Castillo, and Tito Bustillo in Northern Spain. It addresses methodological issues concerning acoustic measurement at enclosed archaeological sites and outlines a general framework for extraction of acoustic features that may be used to support archaeological hypotheses. The analysis explores possible associations between the position of visual motifs (which may be up to 40 000 yrs old) and localized acoustic responses. Results suggest that motifs, in general, and lines and dots, in particular, are statistically more likely to be found in places where reverberation is moderate and where the low frequency acoustic response has evidence of resonant behavior. The work presented suggests that an association of the location of Palaeolithic motifs with acoustic features is a statistically weak but tenable hypothesis, and that an appreciation of sound could have influenced behavior among Palaeolithic societies of this region.

15 CFR 4.9 - Business Information.

Science.gov (United States)

2010-01-01

... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false Business Information. 4.9 Section 4.9... of Information Act § 4.9 Business Information. (a) In general. Business information obtained by the... the purposes of this section: (1) Business information means commercial or financial information...

Male homosexuality and maternal immune responsivity to the Y-linked protein NLGN4Y.

Science.gov (United States)

Bogaert, Anthony F; Skorska, Malvina N; Wang, Chao; Gabrie, José; MacNeil, Adam J; Hoffarth, Mark R; VanderLaan, Doug P; Zucker, Kenneth J; Blanchard, Ray

2018-01-09

We conducted a direct test of an immunological explanation of the finding that gay men have a greater number of older brothers than do heterosexual men. This explanation posits that some mothers develop antibodies against a Y-linked protein important in male brain development, and that this effect becomes increasingly likely with each male gestation, altering brain structures underlying sexual orientation in their later-born sons. Immune assays targeting two Y-linked proteins important in brain development-protocadherin 11 Y-linked (PCDH11Y) and neuroligin 4 Y-linked (NLGN4Y; isoforms 1 and 2)-were developed. Plasma from mothers of sons, about half of whom had a gay son, along with additional controls (women with no sons, men) was analyzed for male protein-specific antibodies. Results indicated women had significantly higher anti-NLGN4Y levels than men. In addition, after statistically controlling for number of pregnancies, mothers of gay sons, particularly those with older brothers, had significantly higher anti-NLGN4Y levels than did the control samples of women, including mothers of heterosexual sons. The results suggest an association between a maternal immune response to NLGN4Y and subsequent sexual orientation in male offspring. Copyright © 2018 the Author(s). Published by PNAS.

Motif signatures of transcribed enhancers

KAUST Repository

Kleftogiannis, Dimitrios

2017-09-14

In mammalian cells, transcribed enhancers (TrEn) play important roles in the initiation of gene expression and maintenance of gene expression levels in spatiotemporal manner. One of the most challenging questions in biology today is how the genomic characteristics of enhancers relate to enhancer activities. This is particularly critical, as several recent studies have linked enhancer sequence motifs to specific functional roles. To date, only a limited number of enhancer sequence characteristics have been investigated, leaving space for exploring the enhancers genomic code in a more systematic way. To address this problem, we developed a novel computational method, TELS, aimed at identifying predictive cell type/tissue specific motif signatures. We used TELS to compile a comprehensive catalog of motif signatures for all known TrEn identified by the FANTOM5 consortium across 112 human primary cells and tissues. Our results confirm that distinct cell type/tissue specific motif signatures characterize TrEn. These signatures allow discriminating successfully a) TrEn from random controls, proxy of non-enhancer activity, and b) cell type/tissue specific TrEn from enhancers expressed and transcribed in different cell types/tissues. TELS codes and datasets are publicly available at http://www.cbrc.kaust.edu.sa/TELS.

UV photolysis of 4-iodo-, 4-bromo-, and 4-chlorophenol: Competition between C-Y (Y = halogen) and O-H bond fission

Science.gov (United States)

Sage, Alan G.; Oliver, Thomas A. A.; King, Graeme A.; Murdock, Daniel; Harvey, Jeremy N.; Ashfold, Michael N. R.

2013-04-01

The wavelength dependences of C-Y and O-H bond fission following ultraviolet photoexcitation of 4-halophenols (4-YPhOH) have been investigated using a combination of velocity map imaging, H Rydberg atom photofragment translational spectroscopy, and high level spin-orbit resolved electronic structure calculations, revealing a systematic evolution in fragmentation behaviour across the series Y = I, Br, Cl (and F). All undergo O-H bond fission following excitation at wavelengths λ ≲ 240 nm, on repulsive ((n/π)σ*) potential energy surfaces (PESs), yielding fast H atoms with mean kinetic energies ˜11 000 cm-1. For Y = I and Br, this process occurs in competition with prompt C-I and C-Br bond cleavage on another (n/π)σ* PES, but no Cl/Cl* products unambiguously attributable to one photon induced C-Cl bond fission are observed from 4-ClPhOH. Differences in fragmentation behaviour at longer excitation wavelengths are more marked. Prompt C-I bond fission is observed following excitation of 4-IPhOH at all λ ≤ 330 nm; the wavelength dependent trends in I/I* product branching ratio, kinetic energy release, and recoil anisotropy suggest that (with regard to C-I bond fission) 4-IPhOH behaves like a mildly perturbed iodobenzene. Br atoms are observed when exciting 4-BrPhOH at long wavelengths also, but their velocity distributions suggest that dissociation occurs after internal conversion to the ground state. O-H bond fission, by tunnelling (as in phenol), is observed only in the cases of 4-FPhOH and, more weakly, 4-ClPhOH. These observed differences in behaviour can be understood given due recognition of (i) the differences in the vertical excitation energies of the C-Y centred (n/π)σ* potentials across the series Y = I increased spin-orbit coupling in, particularly, 4-IPhOH. The present results provide (another) reminder of the risks inherent in extrapolating photochemical behaviour measured for one molecule at one wavelength to other (related) molecules and to

Insertion of tetracysteine motifs into dopamine transporter extracellular domains.

Directory of Open Access Journals (Sweden)

Deanna M Navaroli

Full Text Available The neuronal dopamine transporter (DAT is a major determinant of extracellular dopamine (DA levels and is the primary target for a variety of addictive and therapeutic psychoactive drugs. DAT is acutely regulated by protein kinase C (PKC activation and amphetamine exposure, both of which modulate DAT surface expression by endocytic trafficking. In order to use live imaging approaches to study DAT endocytosis, methods are needed to exclusively label the DAT surface pool. The use of membrane impermeant, sulfonated biarsenic dyes holds potential as one such approach, and requires introduction of an extracellular tetracysteine motif (tetraCys; CCPGCC to facilitate dye binding. In the current study, we took advantage of intrinsic proline-glycine (Pro-Gly dipeptides encoded in predicted DAT extracellular domains to introduce tetraCys motifs into DAT extracellular loops 2, 3, and 4. [(3H]DA uptake studies, surface biotinylation and fluorescence microscopy in PC12 cells indicate that tetraCys insertion into the DAT second extracellular loop results in a functional transporter that maintains PKC-mediated downregulation. Introduction of tetraCys into extracellular loops 3 and 4 yielded DATs with severely compromised function that failed to mature and traffic to the cell surface. This is the first demonstration of successful introduction of a tetracysteine motif into a DAT extracellular domain, and may hold promise for use of biarsenic dyes in live DAT imaging studies.

Ternary gallides RE_4Rh_9Ga_5, RE_5Rh_1_2Ga_7 and RE_7Rh_1_8Ga_1_1 (RE=Y, La-Nd, Sm, Gd, Tb). Intergrowth structures with MgCu_2 and CaCu_5 related slabs

International Nuclear Information System (INIS)

Seidel, Stefan; Rodewald, Ute C.; Poettgen, Rainer; Janka, Oliver

2017-01-01

Fourteen ternary gallides RE_4Rh_9Ga_5, RE_5Rh_1_2Ga_7 and RE_7Rh_1_8Ga_1_1 (RE=Y, La-Nd, Sm, Gd, Tb) were synthesized from the elements by arc-melting, followed by different annealing sequences either in muffle or induction furnaces. The samples were characterized through Guinier powder patterns and the crystal structures of Ce_4Rh_9Ga_5, Ce_5Rh_1_2Ga_7, Ce_7Rh_1_8Ga_1_1, Nd_5Rh_1_0_._4_4_(_4_)Ga_8_._5_6_(_4_), Nd_4Rh_9Ga_5 and Gd_4Rh_9Ga_5 were refined from single crystal X-ray diffractometer data. The new gallides are the n=2, 3 and 5 members of the RE_2_+_n Rh_3_+_3_n Ga_1_+_2_n structure series in the Parthe intergrowth concept. The slabs of these intergrowth structures derive from the cubic Laves phase MgCu_2 (Mg_2Ni_3Si as ternary variant) and CaCu_5 (CeCo_3B_2 as ternary variant). Only the Nd_5Rh_1_0_._4_4_(_4_)Ga_8_._5_6_(_4_) crystal shows Rh/Ga mixing within the Laves type slabs. Magnetic susceptibility measurements reveal Pauli paramagnetism for Y_4Rh_9Ga_5 and Curie-Weiss paramagnetism for Gd_4Rh_9Ga_5 and Tb_4Rh_9Ga_5. Low-temperature data show ferromagnetic ordering at T_C=78.1 (Gd_4Rh_9Ga_5) and 55.8 K (Tb_4Rh_9Ga_5).

STUDYING THE INFLUENCE OF THE PYRENE INTERCALATOR TINA ON THE STABILITY OF DNA i-MOTIFS

DEFF Research Database (Denmark)

El-Sayed, Ahmed A.; Pedersen, Erik Bjerregaard; Khaireldin, Nahid A.

2012-01-01

Certain cytosine-rich (C-rich) DNA sequences can fold into secondary structures as four-stranded i-motifs with hemiprotonated base pairs. Here we synthesized C-rich TINA-intercalating oligonucleotides by inserting a nonnucleotide pyrene moiety between two C-rich regions. The stability of their i-...

El 9 de Abril y su contexto internacional

Directory of Open Access Journals (Sweden)

Pierre Gilhodes

1986-01-01

Full Text Available Los acontecimientos del 9 de abril de 1948 en Bogotá son vistos no tanto en sus aspectos internos, sino que se les muestra con las posibles conexiones e influencias de la situación social de agitación existente en otros países latinoamericanos y la guerra fría a nivel mundial.

Calibration setting numbers for dose calibrators for the PET isotopes "5"2Mn, "6"4Cu, "7"6Br, "8"6Y, "8"9Zr, "1"2"4I

International Nuclear Information System (INIS)

Wooten, A. Lake; Lewis, Benjamin C.; Szatkowski, Daniel J.; Sultan, Deborah H.; Abdin, Kinda I.; Voller, Thomas F.; Liu, Yongjian; Lapi, Suzanne E.

2016-01-01

For PET radionuclides, the radioactivity of a sample can be conveniently measured by a dose calibrator. These devices depend on a “calibration setting number”, but many recommended settings from manuals were interpolated based on standard sources of other radionuclide(s). We conducted HPGe gamma-ray spectroscopy, resulting in a reference for determining settings in two types of vessels containing one of several PET radionuclides. Our results reiterate the notion that in-house, experimental calibrations are recommended for different radionuclides and vessels. - Highlights: • Dose calibrators measure radioactivity by ionization of gas from emitted radiation. • Accuracy of dose calibrators depends on “calibration setting numbers” for isotopes. • Many manufacturer settings are interpolated from emissions of other radionuclides. • As a high-precision reference, HPGe gamma-ray spectroscopy was conducted. • New calibrations were found for PET isotopes "5"2Mn, "6"4Cu, "7"6Br, "8"6Y, "8"9Zr, and "1"2"4I.

Direct AUC optimization of regulatory motifs.

Science.gov (United States)

Zhu, Lin; Zhang, Hong-Bo; Huang, De-Shuang

2017-07-15

The discovery of transcription factor binding site (TFBS) motifs is essential for untangling the complex mechanism of genetic variation under different developmental and environmental conditions. Among the huge amount of computational approaches for de novo identification of TFBS motifs, discriminative motif learning (DML) methods have been proven to be promising for harnessing the discovery power of accumulated huge amount of high-throughput binding data. However, they have to sacrifice accuracy for speed and could fail to fully utilize the information of the input sequences. We propose a novel algorithm called CDAUC for optimizing DML-learned motifs based on the area under the receiver-operating characteristic curve (AUC) criterion, which has been widely used in the literature to evaluate the significance of extracted motifs. We show that when the considered AUC loss function is optimized in a coordinate-wise manner, the cost function of each resultant sub-problem is a piece-wise constant function, whose optimal value can be found exactly and efficiently. Further, a key step of each iteration of CDAUC can be efficiently solved as a computational geometry problem. Experimental results on real world high-throughput datasets illustrate that CDAUC outperforms competing methods for refining DML motifs, while being one order of magnitude faster. Meanwhile, preliminary results also show that CDAUC may also be useful for improving the interpretability of convolutional kernels generated by the emerging deep learning approaches for predicting TF sequences specificities. CDAUC is available at: https://drive.google.com/drive/folders/0BxOW5MtIZbJjNFpCeHlBVWJHeW8 . dshuang@tongji.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

A numerical solution to the radial equation of the tidal wave propagation

International Nuclear Information System (INIS)

Makarious, S.H.

1981-08-01

The tidal wave function y(x) is a solution to an inhomogeneous, linear, second-order differential equation with variable coefficient. Numerical values for the height-dependence terms, in the observed tides, have been utilized in finding y(x) as a solution to an initial-value problem. Complex Fast Fourier Transform technique is also used to obtain the solution in a complex form. Based on a realistic temperature structure, the atmosphere - below 110 km - has been divided into layers with distinct characteristics, and thus the technique of propagation in stratified media has been applied. The reduced homogeneous equation assumes the form of Helmholtz equation and with initial conditions the general solution is obtained. (author)

Low temperature features of the local structure of Sm1-xYxS

International Nuclear Information System (INIS)

Menushenkov, A. P.; Chernikov, R. V.; Sidorov, V. V.; Klementiev, K. V.; Alekseev, P. A.; Rybina, A. V.

2007-01-01

The particular features of the local electronic and local crystal structures of the mixed-valence compound Sm 1-x Y x S are studied by the XAFS spectroscopy methods in the temperature range 20-300 K for the yttrium concentration x = 0.17, 0.25, 0.33, and 0.45. The temperature behavior of the valence of Sm, as well as of the lengths and the Debye-Waller factors of the bonds Sm-S, Sm-Sm(Y), Y-S, and Y-Sm(Y), has been determined. The violation of the Vegard law has been observed. A model for the estimation of the energy width of the 4f level and of its position with respect to the Fermi level is proposed

The influence of yttrium (Y) on the corrosion of Mg-Y binary alloys

International Nuclear Information System (INIS)

Liu Ming; Schmutz, Patrik; Uggowitzer, Peter J.; Song Guangling; Atrens, Andrej

2010-01-01

Research highlights: → The Y-intermetallic can accelerate corrosion and Y can increase the protectiveness of the surface layer. → In 0.1 M NaCl, the corrosion rate of Mg-Y alloys increased with increasing Y due to the Y intermetallic. → In 0.1 M NaCl, there was filiform corrosion. → In 0.1 M Na 2 SO 4 , the corrosion rate of Mg-Y alloys decreased with increasing Y in the range 3-7%Y. → Hydrogen evolution was observed from particular parts of the alloy surface. - Abstract: Corrosion of Mg-Y alloys was studied using electrochemical evaluations, immersion tests and direct observations. There were two important effects. In 0.1 M NaCl, the corrosion rate increased with increasing Y content due to increasing amounts of the Y-containing intermetallic. In 0.1 M Na 2 SO 4 , the corrosion rate decreased with increasing Y content above 3%, attributed to a more protective surface film, despite the intermetallic. The corrosion rate evaluated by electrochemical impedance spectroscopy was somewhat smaller than that evaluated from H evolution as expected from the Mg corrosion mechanism. A mechanism is proposed for filiform corrosion. Direct in situ corrosion observations revealed that a predominant feature was hydrogen evolution from particular parts of the alloy surface.

Neoanalysis, Orality, and Intertextuality: An Examination of Homeric Motif Transference

Directory of Open Access Journals (Sweden)

Jonathan Burgess

2006-03-01

Full Text Available In Homeric studies scholars have speculated on the influence of (non-surviving preHomeric material on the Iliad. This article expands this line of argument from an oralist perspective, with reference to modern intertextual theory. It concludes that preHomeric and nonHomeric motifs from oral traditions were transferred into the epic poem, creating an intertextually allusive poetics that would have been recognizable to an early Greek audience informed of mythological traditions.

Estudio comparativo de cuatro sistemas de propagación de levadura cervecera por lote alimentado Comparative study of four fed-batch propagation systems of beer yeast

Directory of Open Access Journals (Sweden)

Hoyos H.

1998-06-01

Full Text Available

Se realizó la propagación por lotes de levadura cervecera y con base en estos resultados se ajustó un modelo matemático. Se llevaron a cabo cuatro fermentaciones con diferentes técnicas de alimentación y se confrontaron los resultados mediante simulación. Las técnicas estudiadas fueron alimentación puntual, alimentación continua-puntual y de alta densidad. La mayor concentración celular y factor de propagación se presentó con el cultivo de alta densidad. La simulación demostró que la alimentación continua o puntual afecta el comportamiento celular, ya sea sobre la velocidad específica y/o el factor estequiométrico Yx/s . Se encontró que la técnica de alta densidad aumenta el factor estequiométrico Yx/s.

DMINDA: an integrated web server for DNA motif identification and analyses.

Science.gov (United States)

Ma, Qin; Zhang, Hanyuan; Mao, Xizeng; Zhou, Chuan; Liu, Bingqiang; Chen, Xin; Xu, Ying

2014-07-01

DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

der(4)t(Y;4): Three-generation transmission and sperm meiotic segregation analysis.

Science.gov (United States)

Vozdova, Miluse; Horinova, Vera; Wernerova, Vendula; Skalikova, Romana; Rybar, Roman; Prinosilova, Petra; Oracova, Eva; Rubes, Jiri

2011-05-01

We present a family where five members (three males and two females) are carriers of der(4)t(Y;4)(q11.23;p16.3). The adult carriers are phenotypicaly normal and fertile; the boy shows macrocephaly, psychomotor retardation, and atypical autism. The FISH on cultured lymphocytes confirmed that the redundant Yq heterochromatin was attached to the 4p-subtelomeric region maintained on the der(4). Sperm FISH analysis performed in a normospermic der(4) carrier showed a significant distortion of the expected 1:1 ratio of the X- and Y-bearing spermatozoa in favor of the X chromosome and significant lack of Y,der(4)spermatozoa. The overall lack of Y spermatozoa was not balanced even by a relative excess of Y,4 sperm. The analysis of X, Y, 7, 8, 18, and 21 sperm disomy and diploidy did not indicate any interchromosomal effect. The chromosome 4 disomy was significantly increased but still very low to be of considerable reproductive significance. The neurodevelomental phenotype of the boy was probably caused by a gene mutation. The coincidental occurrence of such chromosomal aberration and boy's phenotype might lead to misinterpretation of the causal relationship between these findings. It is necessary to consider the results of chromosomal analysis and clinical records of relatives for provide genetic counseling in such families. Copyright © 2011 Wiley-Liss, Inc.

Synthesis, characterization and electrochemical performance of ...

Indian Academy of Sciences (India)

2017-09-06

Sep 6, 2017 ... devices (e.g., PC and laptop computers, wireless and mobile phones, camcorders, etc.) .... axis is approximately equal to the charge transfer resistance. (Rct). .... [16] Li Y-X, Gong Z L and Yang Y 2007 J. Power Sour. 174 528.

Efficient motif finding algorithms for large-alphabet inputs

Directory of Open Access Journals (Sweden)

Pavlovic Vladimir

2010-10-01

Full Text Available Abstract Background We consider the problem of identifying motifs, recurring or conserved patterns, in the biological sequence data sets. To solve this task, we present a new deterministic algorithm for finding patterns that are embedded as exact or inexact instances in all or most of the input strings. Results The proposed algorithm (1 improves search efficiency compared to existing algorithms, and (2 scales well with the size of alphabet. On a synthetic planted DNA motif finding problem our algorithm is over 10× more efficient than MITRA, PMSPrune, and RISOTTO for long motifs. Improvements are orders of magnitude higher in the same setting with large alphabets. On benchmark TF-binding site problems (FNP, CRP, LexA we observed reduction in running time of over 12×, with high detection accuracy. The algorithm was also successful in rapidly identifying protein motifs in Lipocalin, Zinc metallopeptidase, and supersecondary structure motifs for Cadherin and Immunoglobin families. Conclusions Our algorithm reduces computational complexity of the current motif finding algorithms and demonstrate strong running time improvements over existing exact algorithms, especially in important and difficult cases of large-alphabet sequences.

A tryptophan-rich motif in the human parainfluenza virus type 2 V protein is critical for the blockade of toll-like receptor 7 (TLR7)- and TLR9-dependent signaling.

Science.gov (United States)

Kitagawa, Yoshinori; Yamaguchi, Mayu; Zhou, Min; Komatsu, Takayuki; Nishio, Machiko; Sugiyama, Tsuyoshi; Takeuchi, Kenji; Itoh, Masae; Gotoh, Bin

2011-05-01

Plasmacytoid dendritic cells (pDCs) do not produce alpha interferon (IFN-α) unless viruses cause a systemic infection or overcome the first-line defense provided by conventional DCs and macrophages. We show here that even paramyxoviruses, whose infections are restricted to the respiratory tract, have a V protein able to prevent Toll-like receptor 7 (TLR7)- and TLR9-dependent IFN-α induction specific to pDCs. Mutational analysis of human parainfluenza virus type 2 demonstrates that the second Trp residue of the Trp-rich motif (Trp-X(3)-Trp-X(9)-Trp) in the C-terminal domain unique to V, a determinant for IRF7 binding, is critical for the blockade of TLR7/9-dependent signaling.

RMOD: a tool for regulatory motif detection in signaling network.

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Jinki Kim

Full Text Available Regulatory motifs are patterns of activation and inhibition that appear repeatedly in various signaling networks and that show specific regulatory properties. However, the network structures of regulatory motifs are highly diverse and complex, rendering their identification difficult. Here, we present a RMOD, a web-based system for the identification of regulatory motifs and their properties in signaling networks. RMOD finds various network structures of regulatory motifs by compressing the signaling network and detecting the compressed forms of regulatory motifs. To apply it into a large-scale signaling network, it adopts a new subgraph search algorithm using a novel data structure called path-tree, which is a tree structure composed of isomorphic graphs of query regulatory motifs. This algorithm was evaluated using various sizes of signaling networks generated from the integration of various human signaling pathways and it showed that the speed and scalability of this algorithm outperforms those of other algorithms. RMOD includes interactive analysis and auxiliary tools that make it possible to manipulate the whole processes from building signaling network and query regulatory motifs to analyzing regulatory motifs with graphical illustration and summarized descriptions. As a result, RMOD provides an integrated view of the regulatory motifs and mechanism underlying their regulatory motif activities within the signaling network. RMOD is freely accessible online at the following URL: http://pks.kaist.ac.kr/rmod.

A role for non-covalent SUMO interaction motifs in Pc2/CBX4 E3 activity.

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Jacqueline C Merrill

2010-01-01

Full Text Available Modification of proteins by the small ubiquitin like modifier (SUMO is an essential process in mammalian cells. SUMO is covalently attached to lysines in target proteins via an enzymatic cascade which consists of E1 and E2, SUMO activating and conjugating enzymes. There is also a variable requirement for non-enzymatic E3 adapter like proteins, which can increase the efficiency and specificity of the sumoylation process. In addition to covalent attachment of SUMO to target proteins, specific non-covalent SUMO interaction motifs (SIMs that are generally short hydrophobic peptide motifs have been identified.Intriguingly, consensus SIMs are present in most SUMO E3s, including the polycomb protein, Pc2/Cbx4. However, a role for SIMs in SUMO E3 activity remains to be shown. We show that Pc2 contains two functional SIMs, both of which contribute to full E3 activity in mammalian cells, and are also required for sumoylation of Pc2 itself. Pc2 forms distinct sub-nuclear foci, termed polycomb bodies, and can recruit partner proteins, such as the corepressor CtBP. We demonstrate that mutation of the SIMs in Pc2 prevents Pc2-dependent CtBP sumoylation, and decreases enrichment of SUMO1 and SUMO2 at polycomb foci. Furthermore, mutational analysis of both SUMO1 and SUMO2 reveals that the SIM-interacting residues of both SUMO isoforms are required for Pc2-mediated sumoylation and localization to polycomb foci.This work provides the first clear evidence for a role for SIMs in SUMO E3 activity.

Transport properties of partially-filled Ce{sub y}Co{sub 4}Sb{sub 12}

Energy Technology Data Exchange (ETDEWEB)

Uher, C; Chen, B; Hu, S; Morelli, D T; Meisner, G P

1997-07-01

The authors have investigated the magnetic and transport properties of Ce{sub y}Co{sub 4}Sb{sub 12} filled skutterudites with the filling fraction y {le} 0.1. These compounds are n-type materials that develop a magnetic moment upon the presence of trivalent cerium. Cerium has a strong influence on all transport properties and even in small amounts it drastically reduces the lattice thermal conductivity. The resulting figures of merit are comparable to the values established previously for the p-type filled skutterudites.

Different Effects of Androgen on the Expression of Fut1, Fut2, Fut4 and Fut9 in Male Mouse Reproductive Tract

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Chun-Mei Wang

2013-11-01

Full Text Available The α-(1,2 fucosyltransferases (Fut1 and Fut2 and α-(1,3 fucosyltransferases (Fut4, Fut9 are responsible for the synthesis of Lewis X (LeX and Lewis Y (LeY conjugated to glycoproteins. We recently reported that these fucosyltransferases were differentially expressed in the reproductive tract of male mouse. Here, we studied the effect of androgen on fucosyltransferase expression through the use of mouse castration models. We found that Fut1 mRNA and Fut4 mRNA were upregulated, while Fut2 mRNA and Fut9 mRNA were downregulated by androgen in the caput epididymis. However, in the vas deferens and prostate, only Fut4 mRNA and Fut2 mRNA were respectively upregulated following exposure to androgen. In the seminal vesicle, all fucosyltransferases, with the exception of Fut9, were upregulated. We identified the androgen receptor binding sites (ARBSs of Fut2, Fut4 and Fut9 in the caput epididymis. Luciferase assay for these ARBSs is able to provide an indication as to why Fut4 and Fut9 are differently expressed and regulated by androgen, although they catalyze the same α-(1,3 fucose linkage. Our study showed that androgen could differentially regulate the expression of these fucosyltransferases and provided an insight into the characteristic distribution of each fucosyltransferase responsible for LeX/LeY biosynthesis in the male reproductive tract.

Pr:Ca1-xRxF2+x (R=Y or Gd) crystals: Modulated blue, orange and red emission spectra with the proportion of R3+ ions

Science.gov (United States)

Yu, Hao; Qian, Xiaobo; Guo, Linyang; Jiang, Dapeng; Wu, Qinghui; Tang, Fei; Su, Liangbi; Ju, Qiangwen; Wang, Jingya; Xu, Jun

2018-04-01

The spectroscopic properties of 0.6at.%:Pr:Ca1-xRxF2+x (R = Y, Gd; x = 0,0.006, 0.012, 0.03, 0.06) crystals were investigated and compared. The XRD tests were conducted and the cell dimensions of the crystals were calculated. Room temperature absorption spectra have been registered and analyzed. The emission spectra and decay curves of the crystals were obtained at room temperature. Increasing the proportion of the lattice regulators of Y3+ or Gd3+ ions could significantly enhance the luminescence intensity of all visible emission bands with different ratios. Particularly, the emission intensity ratio of orange to red increased from 0.15 to 1.9 in Pr:Ca1-xYxF2+x crystals and to 1.02 in Pr:Ca1-xGdxF2+x crystals, respectively. Furthermore, Pr:Ca1-xGdxF2+x crystals have substantially strong emission at orange and red region of 580-660 nm, comparable with blue light at 482 nm. The quantum efficiency of the crystals increased rapidly with the increment of R3+ concentration, and finally tend to be 100%.

Analysis of alkaptonuria (AKU) mutations and polymorphisms reveals that the CCC sequence motif is a mutational hot spot in the homogentisate 1,2 dioxygenase gene (HGO).

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Beltrán-Valero de Bernabé, D; Jimenez, F J; Aquaron, R; Rodríguez de Córdoba, S

1999-01-01

We recently showed that alkaptonuria (AKU) is caused by loss-of-function mutations in the homogentisate 1,2 dioxygenase gene (HGO). Herein we describe haplotype and mutational analyses of HGO in seven new AKU pedigrees. These analyses identified two novel single-nucleotide polymorphisms (INV4+31A-->G and INV11+18A-->G) and six novel AKU mutations (INV1-1G-->A, W60G, Y62C, A122D, P230T, and D291E), which further illustrates the remarkable allelic heterogeneity found in AKU. Reexamination of all 29 mutations and polymorphisms thus far described in HGO shows that these nucleotide changes are not randomly distributed; the CCC sequence motif and its inverted complement, GGG, are preferentially mutated. These analyses also demonstrated that the nucleotide substitutions in HGO do not involve CpG dinucleotides, which illustrates important differences between HGO and other genes for the occurrence of mutation at specific short-sequence motifs. Because the CCC sequence motifs comprise a significant proportion (34.5%) of all mutated bases that have been observed in HGO, we conclude that the CCC triplet is a mutational hot spot in HGO. PMID:10205262

UV photolysis of 4-iodo-, 4-bromo-, and 4-chlorophenol: competition between C-Y (Y = halogen) and O-H bond fission.

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Sage, Alan G; Oliver, Thomas A A; King, Graeme A; Murdock, Daniel; Harvey, Jeremy N; Ashfold, Michael N R

2013-04-28

The wavelength dependences of C-Y and O-H bond fission following ultraviolet photoexcitation of 4-halophenols (4-YPhOH) have been investigated using a combination of velocity map imaging, H Rydberg atom photofragment translational spectroscopy, and high level spin-orbit resolved electronic structure calculations, revealing a systematic evolution in fragmentation behaviour across the series Y = I, Br, Cl (and F). All undergo O-H bond fission following excitation at wavelengths λ ≲ 240 nm, on repulsive ((n∕π)σ∗) potential energy surfaces (PESs), yielding fast H atoms with mean kinetic energies ∼11,000 cm(-1). For Y = I and Br, this process occurs in competition with prompt C-I and C-Br bond cleavage on another (n∕π)σ∗ PES, but no Cl∕Cl∗ products unambiguously attributable to one photon induced C-Cl bond fission are observed from 4-ClPhOH. Differences in fragmentation behaviour at longer excitation wavelengths are more marked. Prompt C-I bond fission is observed following excitation of 4-IPhOH at all λ ≤ 330 nm; the wavelength dependent trends in I∕I∗ product branching ratio, kinetic energy release, and recoil anisotropy suggest that (with regard to C-I bond fission) 4-IPhOH behaves like a mildly perturbed iodobenzene. Br atoms are observed when exciting 4-BrPhOH at long wavelengths also, but their velocity distributions suggest that dissociation occurs after internal conversion to the ground state. O-H bond fission, by tunnelling (as in phenol), is observed only in the cases of 4-FPhOH and, more weakly, 4-ClPhOH. These observed differences in behaviour can be understood given due recognition of (i) the differences in the vertical excitation energies of the C-Y centred (n∕π)σ∗ potentials across the series Y = I bond strength, cf. that of the rival O-H bond, and (ii) the much increased spin-orbit coupling in, particularly, 4-IPhOH. The present results provide (another) reminder of the risks inherent in extrapolating photochemical

Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation.

Science.gov (United States)

Michael, Sushama; Travé, Gilles; Ramu, Chenna; Chica, Claudia; Gibson, Toby J

2008-02-15

KEN-box-mediated target selection is one of the mechanisms used in the proteasomal destruction of mitotic cell cycle proteins via the APC/C complex. While annotating the Eukaryotic Linear Motif resource (ELM, http://elm.eu.org/), we found that KEN motifs were significantly enriched in human protein entries with cell cycle keywords in the UniProt/Swiss-Prot database-implying that KEN-boxes might be more common than reported. Matches to short linear motifs in protein database searches are not, per se, significant. KEN-box enrichment with cell cycle Gene Ontology terms suggests that collectively these motifs are functional but does not prove that any given instance is so. Candidates were surveyed for native disorder prediction using GlobPlot and IUPred and for motif conservation in homologues. Among >25 strong new candidates, the most notable are human HIPK2, CHFR, CDC27, Dab2, Upf2, kinesin Eg5, DNA Topoisomerase 1 and yeast Cdc5 and Swi5. A similar number of weaker candidates were present. These proteins have yet to be tested for APC/C targeted destruction, providing potential new avenues of research.

48 CFR 9.106-4 - Reports.

Science.gov (United States)

2010-10-01

... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Reports. 9.106-4 Section 9... CONTRACTOR QUALIFICATIONS Responsible Prospective Contractors 9.106-4 Reports. (a) The surveying activity... performance. The narrative shall report any persistent pattern of need for costly and burdensome Government...

Target motifs affecting natural immunity by a constitutive CRISPR-Cas system in Escherichia coli.

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Cristóbal Almendros

Full Text Available Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR and CRISPR associated (cas genes conform the CRISPR-Cas systems of various bacteria and archaea and produce degradation of invading nucleic acids containing sequences (protospacers that are complementary to repeat intervening spacers. It has been demonstrated that the base sequence identity of a protospacer with the cognate spacer and the presence of a protospacer adjacent motif (PAM influence CRISPR-mediated interference efficiency. By using an original transformation assay with plasmids targeted by a resident spacer here we show that natural CRISPR-mediated immunity against invading DNA occurs in wild type Escherichia coli. Unexpectedly, the strongest activity is observed with protospacer adjoining nucleotides (interference motifs that differ from the PAM both in sequence and location. Hence, our results document for the first time native CRISPR activity in E. coli and demonstrate that positions next to the PAM in invading DNA influence their recognition and degradation by these prokaryotic immune systems.

Intervalos de referencia para concentraciones séricas de T3 y T4. Estudio preliminar

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Cecilia Miranda Pantoja

2013-12-01

Full Text Available Fundamento: la determinación cuantitativa de las hormonas tiroideas T3 y T4 reviste gran importancia en el diagnóstico y la evaluación del hipertiroidismo, en especial del hipertiroidismo aislado causado por T3.Objetivo: establecer los intervalos de referencia de T3 y T4 en el laboratorio de medicina nuclear del Hospital General Universitario Dr. Gustavo Aldereguía Lima de Cienfuegos. Métodos: estudio descriptivo y prospectivo realizado mediante el método de radioinmunoanálisis, competencia que se establece entre la T3 y T4 sin marcar, y la marcada por un número limitado de los sitios de unión del anticuerpo específico. Al hacer reaccionar una cantidad fija de trazador y anticuerpo con diferentes cantidades del ligando sin marcar, la cantidad de trazador unido por el anticuerpo será inversamente proporcional a la concentración del ligando sin marcar. Resultados: los valores obtenidos se describen según una distribución gaussiana (media aritmética = 117, desviación estándar =31 para T4; media aritmética = 2,64, desviación estándar = 0,64 para T3, comprobado mediante un test de Chi cuadrado. Los rangos de valores normales obtenidos fueron de de 55 – 178 nmol/L y 1,4 – 3,9 nmol/L para T4 y T3 respectivamente. Conclusiones: los intervalos de referencia obtenidos resultaron más amplios que los propuestos por el productor, sobre todo en el caso de T4.

Nanopowders Y{sub 1−y}Nd{sub y}V{sub 1−x}Cr{sub x}O{sub 4} with y=0 and 1; x=0, 0.1, 0.2 and 0.5 synthesized by a sol–gel process. Relationship between morphological characteristics and optical properties

Energy Technology Data Exchange (ETDEWEB)

Alcaraz, L. [Departamento de Química Inorgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n, 28040 Madrid (Spain); Isasi, J., E-mail: isasi@quim.ucm.es [Departamento de Química Inorgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n, 28040 Madrid (Spain); Caballero, A.C. [Departamento de Electrocerámica, Instituto de Cerámica y Vidrio (CSIC), Kelsen, 5, 28049 Madrid (Spain); Izquierdo, J.G.; Bañares, L. [Departamento de Química Física I and Centro de Láseres Ultrarrápidos, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria s/n, 28040 Madrid (Spain)

2015-05-15

Y{sub 1−y}Nd{sub y}V{sub 1−x}Cr{sub x}O{sub 4} nanopowders with y=0 and 0.1; x=0, 0.1, 0.2 and 0.5, have been synthetized by a sol–gel process followed by heating in an oxygen flow. This second treatment was done only in the case of samples containing chromium. The samples have been characterized by X-ray diffraction (XRD), Fourier Transform Infrared (FTIR) spectroscopy, scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The structural analysis revealed that when chromium was inserted at vanadium-sites in Y{sub 0.9}Nd{sub 0.1}VO{sub 4}, the host retained the tetragonal symmetry corresponding to a zircon-type structure, attributed to the space group I4{sub 1}/amd. In addition, a loss of crystallinity was observed when chromium substitutes vanadium into the Y{sub 0.9}Nd{sub 0.1}VO{sub 4} host. The morphological studies revealed agglomerates of spherical particles whose size is increased with the Cr content and confirmed the composition of all synthetized samples. FTIR spectra of these samples exhibit a broadening and a slight shift of the bands around 830 cm{sup −1} towards higher values of frequency when the chromium content increases. The effect of vanadium substitution by chromium on the optical properties was also evaluated by UV–vis absorption and photoluminescence (PL) spectroscopies. The broad UV band absorption is due to the presence of Cr{sup 5+}. A decrease of PL emission is found when chromium substitutes vanadium in the YVO{sub 4} host. - Highlights: • Nanophosphors Y{sub 1−y}Nd{sub y}V{sub 1−x}Cr{sub x}O{sub 4} with y=0, 0.1 and x=0, 0.1, 0.2 and 0.5 have been synthesized. • Structural analysis reveals structural distortions associated to chromium insertion. • Morphological studies confirm the nanocristalline size and the stoichiometry of synthesized samples. • Chromium insertion causes a decrease of the PL emission intensity.

The crystal structure of the Sox4 HMG domain-DNA complex suggests a mechanism for positional interdependence in DNA recognition.

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Jauch, Ralf; Ng, Calista K L; Narasimhan, Kamesh; Kolatkar, Prasanna R

2012-04-01

It has recently been proposed that the sequence preferences of DNA-binding TFs (transcription factors) can be well described by models that include the positional interdependence of the nucleotides of the target sites. Such binding models allow for multiple motifs to be invoked, such as principal and secondary motifs differing at two or more nucleotide positions. However, the structural mechanisms underlying the accommodation of such variant motifs by TFs remain elusive. In the present study we examine the crystal structure of the HMG (high-mobility group) domain of Sox4 [Sry (sex-determining region on the Y chromosome)-related HMG box 4] bound to DNA. By comparing this structure with previously solved structures of Sox17 and Sox2, we observed subtle conformational differences at the DNA-binding interface. Furthermore, using quantitative electrophoretic mobility-shift assays we validated the positional interdependence of two nucleotides and the presence of a secondary Sox motif in the affinity landscape of Sox4. These results suggest that a concerted rearrangement of two interface amino acids enables Sox4 to accommodate primary and secondary motifs. The structural adaptations lead to altered dinucleotide preferences that mutually reinforce each other. These analyses underline the complexity of the DNA recognition by TFs and provide an experimental validation for the conceptual framework of positional interdependence and secondary binding motifs.

Promoter motifs required for c-mpl gene expression induced by thrombopoietin in CMK cells.

Science.gov (United States)

Sunohara, Masataka; Sato, Iwao; Morikawa, Shigeru

2017-11-30

Thrombopoietin (TPO) and its receptor, c-Mpl, are the central regulators of megakaryocyte development and platelet production and are also crucial to regulate megakaryocytopoiesis. TPO remarkably elevated c-mpl promoter activity, while the protein kinase C (PKC) inhibitors, GF109203, H7 and Calphostin C, clearly reduced the steady level of its promoter activity.  In the present study, motifs crucial for c-mpl promoter activity induced by TPO treatment have been analyzed using a human megakaryoblastic cell line, CMK. Destruction of the -107Sp1 and the -57Sp1 sites in the c-mpl promoter enhancer region resulted in decrease of the promoter activity by 53.1% and 64.4%, respectively, and destruction of -69Ets and -28Ets elements dramatically decreased the promoter activity by 96.4% and 87.8%, respectively, while mutation of -77GATA moderately reduced the activity by 31.4%. The result was in agreement with our previous report that showed the crucial motifs in the c-mpl promoter for the promoter activity induced by PMA-treatment. This indicates that TPO-induced activation of the c-mpl promoter activity is fully modulated by transcription through a PKC-dependent pathway and the two Sp1 and two Ets motifs are crucial for the activation of the c-mpl promoter activity rather than a GATA motif in the c-mpl promoter of CMK cells.

DNA motif alignment by evolving a population of Markov chains.

Science.gov (United States)

Bi, Chengpeng

2009-01-30

Deciphering cis-regulatory elements or de novo motif-finding in genomes still remains elusive although much algorithmic effort has been expended. The Markov chain Monte Carlo (MCMC) method such as Gibbs motif samplers has been widely employed to solve the de novo motif-finding problem through sequence local alignment. Nonetheless, the MCMC-based motif samplers still suffer from local maxima like EM. Therefore, as a prerequisite for finding good local alignments, these motif algorithms are often independently run a multitude of times, but without information exchange between different chains. Hence it would be worth a new algorithm design enabling such information exchange. This paper presents a novel motif-finding algorithm by evolving a population of Markov chains with information exchange (PMC), each of which is initialized as a random alignment and run by the Metropolis-Hastings sampler (MHS). It is progressively updated through a series of local alignments stochastically sampled. Explicitly, the PMC motif algorithm performs stochastic sampling as specified by a population-based proposal distribution rather than individual ones, and adaptively evolves the population as a whole towards a global maximum. The alignment information exchange is accomplished by taking advantage of the pooled motif site distributions. A distinct method for running multiple independent Markov chains (IMC) without information exchange, or dubbed as the IMC motif algorithm, is also devised to compare with its PMC counterpart. Experimental studies demonstrate that the performance could be improved if pooled information were used to run a population of motif samplers. The new PMC algorithm was able to improve the convergence and outperformed other popular algorithms tested using simulated and biological motif sequences.

Systematic study of spin crossover and structure in [Co(terpyRX)2](Y)2 systems (terpyRX = 4'-alkoxy-2,2':6',2''-terpyridine, X = 4, 8, 12, Y = BF4(-), ClO4(-), PF6(-), BPh4(-))

DEFF Research Database (Denmark)

Nielsen, Pia; Nielsen, Hans Toftlund; Bond, Andrew

2009-01-01

A family of spin crossover cobalt(II) complexes of the type [Co(terpyRX)(2)](Y)(2) x nH(2)O (X = 4, 8, 12 and Y = BF(4)(-), ClO(4)(-), PF(6)(-), BPh(4)(-)) has been synthesized, whereby the alkyl chain length, RX, and counteranion, Y, have been systematically varied. The structural (single crystal...

Okul yöneticileri ve öğretmenlerin 4+4+4 eğitim sistemine yönelik tutumlarının incelenmesi [Determining the attitudes of school administrators and teachers on 4+4+4 education system

Directory of Open Access Journals (Sweden)

Ahmet ÜSTÜN

2014-04-01

Full Text Available Bu araştırmanın amacı, eğitim sisteminde 4+4+4 olarak bilinen yeni düzenlemenin etkililiği hakkında yönetici ve öğretmenlerin görüşünü belirlemektir. Araştırma ilişkisel tarama modelinde bir çalışma olup, veriler okul müdürlerine ve öğretmenlere anket uygulanarak elde edilmiştir. Araştırmanın evrenini, Amasya İli Merkezinde bulunan ilkokul ve ortaokullarda görev yapan yönetici ve öğretmenler, örneklemini ise on ilkokul ve on ortaokulda görev yapan ve amaçlı örneklem yöntemine göre seçilen yönetici ve öğretmenler oluşturmaktadır. Uygulama yapılırken, farklı sosyo-ekonomik yapıya, öğrenci sayısına, yerleşim yerlerine ve farklı okul tipine sahip okul müdürleri ve farklı branşlardan öğretmenler bir arada bulunarak çalışılmıştır. Bu çalışmada 4+4+4 Eğitim Sistemine Yönelik Tutum Ölçeği kullanılmıştır. Araştırma sonucunda, yönetici ve öğretmenlerin 4+4+4 eğitim sistemine yönelik tutumlarında cinsiyete, yaşa ve kıdeme göre farklılıklar olduğu, kadınların ve mesleki kıdemi az yönetici ve öğretmenlerin tereddütlerinin olduğu ve geleceğe yönelik olumlu beklentiye sahip olmadıkları sonucuna ulaşılmıştır.

DNA motif elucidation using belief propagation.

Science.gov (United States)

Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

2013-09-01

Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k=8∼10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors' websites: e.g. http://www.cs.toronto.edu/∼wkc/kmerHMM.

DNA motif elucidation using belief propagation

KAUST Repository

Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

2013-01-01

Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ?10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors' websites: e.g. http://www.cs.toronto.edu/?wkc/kmerHMM. 2013 The Author(s).

DNA motif elucidation using belief propagation

KAUST Repository

Wong, Ka-Chun

2013-06-29

Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ?10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors\\' websites: e.g. http://www.cs.toronto.edu/?wkc/kmerHMM. 2013 The Author(s).

Near-Infrared Spectroscopy of the Y0 WISEP J173835.52+273258.9 and the Y1 WISE J035000.32-565830.2: the Importance of Non-Equilibrium Chemistry

Science.gov (United States)

Leggett, S. K.; Tremblin, P.; Saumon, D.; Marley, M. S.; Morley, Caroline V.; Amundsen, D. S.; Baraffe, I.; Chabrier, G.

2016-01-01

We present new near-infrared spectra, obtained at Gemini Observatory, for two Y dwarfs: WISE J035000.32-565830.2 (W0350) and WISEP J173835.52+273258.9 (W1738). A FLAMINGOS-2 R = 540 spectrum was obtained for W0350, covering 1.0 < ? micrometer < 1.7, and a cross-dispersed GNIRS R = 2800 spectrum was obtained for W1738, covering 0.993 - 1.087 micrometer, 1.191 - 1.305 micrometer, 1.589 - 1.631 micrometer, and 1.985 - 2.175 micrometer, in four orders. We also present revised Y JH photometry for W1738, using new NIRI Y and J imaging, and a re-analysis of the previously published NIRI H band images. We compare these data, together with previously published data for late-T and Y dwarfs, to cloud-free models of solar metallicity, calculated both in chemical equilibrium and with disequilibrium driven by vertical transport. We find that for the Y dwarfs the non-equilibrium models reproduce the near-infrared data better than the equilibrium models. The remaining discrepancies suggest that fine-tuning the CH4/CO and NH3/N2 balance is needed. Improved trigonometric parallaxes would improve the analysis. Despite the uncertainties and discrepancies, the models reproduce the observed near-infrared spectra well. We find that for the Y0, W1738, T(sub eff) = 425 +/- 25K and log g = 4.0 +/- 0.25, and for the Y1, W0350, T(sub eff) = 350 +/- 25K and log g = 4.0 +/- 0.25. W1738 may be metal-rich. Based on evolutionary models, these temperatures and gravities correspond to a mass range for both Y dwarfs of 3 - 9 Jupiter masses, with W0350 being a cooler, slightly older, version of W1738; the age of W0350 is 0.3 - 3 Gyr, and the age of W1738 is 0.15 - 1 Gyr.

The identification of functional motifs in temporal gene expression analysis

Directory of Open Access Journals (Sweden)

Michael G. Surette

2005-01-01

Full Text Available The identification of transcription factor binding sites is essential to the understanding of the regulation of gene expression and the reconstruction of genetic regulatory networks. The in silico identification of cis-regulatory motifs is challenging due to sequence variability and lack of sufficient data to generate consensus motifs that are of quantitative or even qualitative predictive value. To determine functional motifs in gene expression, we propose a strategy to adopt false discovery rate (FDR and estimate motif effects to evaluate combinatorial analysis of motif candidates and temporal gene expression data. The method decreases the number of predicted motifs, which can then be confirmed by genetic analysis. To assess the method we used simulated motif/expression data to evaluate parameters. We applied this approach to experimental data for a group of iron responsive genes in Salmonella typhimurium 14028S. The method identified known and potentially new ferric-uptake regulator (Fur binding sites. In addition, we identified uncharacterized functional motif candidates that correlated with specific patterns of expression. A SAS code for the simulation and analysis gene expression data is available from the first author upon request.

Imprinting of CCR9 on CD4 T cells requires IL-4 signaling on mesenteric lymph node dendritic cells.

Science.gov (United States)

Elgueta, Raul; Sepulveda, Fernando E; Vilches, Felipe; Vargas, Leonardo; Mora, J Rodrigo; Bono, Maria Rosa; Rosemblatt, Mario

2008-05-15

It has recently been shown that IL-4 can educate dendritic cells (DC) to differentially affect T cell effector activity. In this study, we show that IL-4 can also act upon DC to instruct naive T cells to express the gut-associated homing receptor CCR9. Thus, effector T cells generated after coculture with mesenteric lymph node (MLN)-DC show a higher expression of CCR9 when activated in the presence of IL-4. In contrast, IL-4 had no effect on CCR9 expression when naive T cells were polyclonally activated in the absence of MLN-DC, suggesting that the effect of IL-4 on CCR9 expression passed through DC. Indeed, T cells activated by MLN-DC from IL-4Ralpha(-/-) mice showed a much lower CCR9 expression and a greatly reduced migration to the small intestine than T cells activated by wild-type MLN-DC even in the presence of IL-4. Consistent with the finding that the vitamin A metabolite retinoic acid (RA) induces gut-homing molecules on T cells, we further demonstrate that IL-4 up-regulated retinaldehyde dehydrogenase 2 mRNA on MLN-DC, a critical enzyme involved in the synthesis of RA. Moreover, LE135, a RA receptor antagonist, blocked the increased expression of CCR9 driven by IL-4-treated MLN-DC. Thus, besides the direct effect of RA on T cell gut tropism, our results show that the induction of a gut-homing phenotype on CD4(+) T cells is also influenced by the effect of IL-4 on gut-associated DC.

Resolution and evolution of the duck-billed platypus karyotype with an X1Y1X2Y2X3Y3X4Y4X5Y5 male sex chromosome constitution.

Science.gov (United States)

Rens, Willem; Grützner, Frank; O'brien, Patricia C M; Fairclough, Helen; Graves, Jennifer A M; Ferguson-Smith, Malcolm A

2004-11-16

The platypus (2n = 52) has a complex karyotype that has been controversial over the last three decades. The presence of unpaired chromosomes and an unknown sex-determining system especially has defied attempts at conventional analysis. This article reports on the preparation of chromosome-specific probes from flow-sorted chromosomes and their application in the identification and classification of all platypus chromosomes. This work reveals that the male karyotype has 21 pairs of chromosomes and 10 unpaired chromosomes (E1-E10), which are linked by short regions of homology to form a multivalent chain in meiosis. The female karyotype differs in that five of these unpaired elements (E1, E3, E5, E7, and E9) are each present in duplicate, whereas the remaining five unpaired elements (E2, E4, E6, E8, and E10) are absent. This finding indicates that sex is determined by the alternate segregation of the chain of 10 during spermatogenesis so that equal numbers of sperm bear either one of the two groups of five elements, i.e., five X and five Y chromosomes. Chromosome painting reveals that these X and Y chromosomes contain pairing (XY shared) and differential (X- or Y-specific) segments. Y differential regions must contain male-determining genes, and X differential regions should be dosage-compensated in the female. Two models for the evolution of the sex-determining system are presented. The resolution of the longstanding debate over the platypus karyotype is an important step toward the understanding of mechanisms of sex determination, dosage compensation, and karyotype evolution.

Modulation of i-motif thermodynamic stability by the introduction of UNA (unlocked nucleic acid) monomers

DEFF Research Database (Denmark)

Pasternak, Anna; Wengel, Jesper

2011-01-01

The influence of acyclic RNA derivatives, UNA (unlocked nucleic acid) monomers, on i-DNA thermodynamic stability has been investigated. The 22 nt human telomeric fragment was chosen as the model sequence for stability studies. UNA monomers modulate i-motif stability in a position-depending manner...

Sintésis y propiedades fotofísicas de compuestos de platino y paladio con ligandos (fluoren-9-iliden) metanoditiolato

OpenAIRE

Pérez Cadenas, María

2007-01-01

En este trabajo se ha realizado la síntesis y caracterización estructural de complejos de platino y paladio con el ligando (fluoren-9-iliden) metanoditiolato y sus derivados 2,7-disustituídos. Se ha estudiado la influencia del carácter fuertemente dador de los nuevos ligandos en las estructuras, reactividades, comportamiento redox y propiedades fotofísicas de sus complejos metálicos, así como las posibilidades de agregación de centros metálicos adicionales y su influencia en las propiedades f...

Arrestin scaffolds NHERF1 to the P2Y12 receptor to regulate receptor internalization.

Science.gov (United States)

Nisar, Shaista P; Cunningham, Margaret; Saxena, Kunal; Pope, Robert J; Kelly, Eamonn; Mundell, Stuart J

2012-07-13

We have recently shown in a patient with mild bleeding that the PDZ-binding motif of the platelet G protein-coupled P2Y(12) receptor (P2Y(12)R) is required for effective receptor traffic in human platelets. In this study we show for the first time that the PDZ motif-binding protein NHERF1 exerts a major role in potentiating G protein-coupled receptor (GPCR) internalization. NHERF1 interacts with the C-tail of the P2Y(12)R and unlike many other GPCRs, NHERF1 interaction is required for effective P2Y(12)R internalization. In vitro and prior to agonist stimulation P2Y(12)R/NHERF1 interaction requires the intact PDZ binding motif of this receptor. Interestingly on receptor stimulation NHERF1 no longer interacts directly with the receptor but instead binds to the receptor via the endocytic scaffolding protein arrestin. These findings suggest a novel model by which arrestin can serve as an adaptor to promote NHERF1 interaction with a GPCR to facilitate effective NHERF1-dependent receptor internalization.

The human CD8β M-4 isoform dominant in effector memory T cells has distinct cytoplasmic motifs that confer unique properties.

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Deepshi Thakral

Full Text Available The CD8 co-receptor influences T cell recognition and responses in both anti-tumor and anti-viral immunity. During evolution in the ancestor of humans and chimpanzees, the CD8B gene acquired two additional exons. As a result, in humans, there are four CD8β splice variants (M1 to M4 that differ in their cytoplasmic tails. The M-1 isoform which is the equivalent of murine CD8β, is predominantly expressed in naïve T cells, whereas, the M-4 isoform is predominantly expressed in effector memory T cells. The characteristics of the M-4 isoform conferred by its unique 36 amino acid cytoplasmic tail are not known. In this study, we identified a dihydrophobic leucine-based receptor internalization motif in the cytoplasmic tail of M-4 that regulated its cell surface expression and downregulation after activation. Further the M-4 cytoplasmic tail was able to associate with ubiquitinated targets in 293T cells and mutations in the amino acids NPW, a potential EH domain binding site, either enhanced or inhibited the interaction. In addition, the M-4 tail was itself mono-ubiquitinated on a lysine residue in both 293T cells and a human T cell line. When peripheral blood human T cells expressed CD8αβ M-4, the frequency of MIP-1β secreting cells responding to antigen presenting cells was two-fold higher as compared to CD8αβ M-1 expressing T cells. Thus, the cytoplasmic tail of the CD8β M-4 isoform has unique characteristics, which likely contributed to its selective expression and function in human effector memory T cells.

Inmunohistoquímica de la proteína p16INK4a en biopsias y extendidos cervicovaginales y su relación con HPV por PCR Immunohistochemistry of p16INK4a in biopsies and cervicovaginal smears, and its correlation with HPV detected by PCR

Directory of Open Access Journals (Sweden)

Alejandro García

2008-12-01

Full Text Available Estudios recientes sugieren que la sobreexpresión de p16, determinada por inmunohistoquímica, sería un marcador específico de células escamosas displásicas y neoplásicas con alta asociación con HPV de alto riesgo. Nuestro objetivo fue correlacionar los hallazgos cito/histológicos con la expresión de p16 y el subtipo de HPV por PCR. Seleccionamos 95 biopsias de cuello uterino y 4 legrados endocervicales de 99 individuos, y 30 extendidos cervicovaginales de otros 30 individuos, que se dividieron según el diagnóstico morfológico. Inmunomarcamos cortes del material incluido en parafina y los extendidos con el kit CINtecT p16INK4a (DAKO. Evaluamos HPV por PCR utilizando 25/99 biopsias con lesión intraepitelial escamosa de bajo grado. Observamos marcación positiva para p16 en 1/35 biopsias (2.9% y 1/11 extendidos (9% en los grupos sin HPV ni displasia; 16/25 biopsias (64% y 6/10 extendidos (60% en aquellos con lesión de bajo grado y 38/39 biopsias (97.4% y 8/9 extendidos (89% en los grupos con lesión de alto grado y carcinoma escamoso. Todas las muestras con HPV-6/11 fueron negativas o positivas focales para p16, en tanto que aquellas con HPV-18 u otros subtipos fueron mayoritariamente positivas de tipo difuso. Concluimos que la expresión de p16 presenta alta correlación con el diagnóstico cito/histológico y alta asociación entre la marcación difusa y la presencia de HPV de alto riesgo, aportando mayor objetividad en casos dudosos y ayudando a seleccionar grupos de individuos con riesgo de progresión de enfermedad, con un costo aceptable para estudiar grandes grupos.Recent studies suggest that p16 overexpression determined by immunohistochemistry would be a specific marker for neoplastic and dysplastic squamous cells associated with high-risk HPV. The purpose of this study was to assess the correlation between cyto-histological findings, p16 expression and HPV subtype. A total of 99 biopsies were selected, 4 endocervical

Comparison of second and third orders Runge-Kutta methods for ...

African Journals Online (AJOL)

This work is concerned with the analysis of second and third orders Runge- Kutta formulae capable of solving initial value problems in Ordinary Differential Equations of the form: y1 = f(x, y), y(x0) = y0, a £ x £ b. The intention is to find out which of these two orders can improve the performance of results when implemented ...

Hybrid DNA i-motif: Aminoethylprolyl-PNA (pC5) enhance the stability of DNA (dC5) i-motif structure.

Science.gov (United States)

Gade, Chandrasekhar Reddy; Sharma, Nagendra K

2017-12-15

This report describes the synthesis of C-rich sequence, cytosine pentamer, of aep-PNA and its biophysical studies for the formation of hybrid DNA:aep-PNAi-motif structure with DNA cytosine pentamer (dC 5 ) under acidic pH conditions. Herein, the CD/UV/NMR/ESI-Mass studies strongly support the formation of stable hybrid DNA i-motif structure with aep-PNA even near acidic conditions. Hence aep-PNA C-rich sequence cytosine could be considered as potential DNA i-motif stabilizing agents in vivo conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Automatic annotation of protein motif function with Gene Ontology terms

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Gopalakrishnan Vanathi

2004-09-01

Full Text Available Abstract Background Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern searching algorithms and programs exist foridentifying candidate protein motifs at the whole genome level. However, amuch needed and importanttask is to determine the functions of the newly identified protein motifs. The Gene Ontology (GO project is an endeavor to annotate the function of genes or protein sequences with terms from a dynamic, controlled vocabulary and these annotations serve well as a knowledge base. Results This paperpresents methods to mine the GO knowledge base and use the association between the GO terms assigned to a sequence and the motifs matched by the same sequence as evidence for predicting the functions of novel protein motifs automatically. The task of assigning GO terms to protein motifsis viewed as both a binary classification and information retrieval problem, where PROSITE motifs are used as samples for mode training and functional prediction. The mutual information of a motif and aGO term association isfound to be a very useful feature. We take advantageof the known motifs to train a logistic regression classifier, which allows us to combine mutual information with other frequency-based features and obtain a probability of correctassociation. The trained logistic regression model has intuitively meaningful and logically plausible parameter values, and performs very well empirically according to our evaluation criteria. Conclusions In this research, different methods for automatic annotation of protein motifs have been investigated. Empirical result demonstrated that the methods have a great potential for detecting and augmenting information about thefunctions of newly discovered candidate protein motifs.

Verification of the MOTIF code version 3.0

International Nuclear Information System (INIS)

Chan, T.; Guvanasen, V.; Nakka, B.W.; Reid, J.A.K.; Scheier, N.W.; Stanchell, F.W.

1996-12-01

As part of the Canadian Nuclear Fuel Waste Management Program (CNFWMP), AECL has developed a three-dimensional finite-element code, MOTIF (Model Of Transport In Fractured/ porous media), for detailed modelling of groundwater flow, heat transport and solute transport in a fractured rock mass. The code solves the transient and steady-state equations of groundwater flow, solute (including one-species radionuclide) transport, and heat transport in variably saturated fractured/porous media. The initial development was completed in 1985 (Guvanasen 1985) and version 3.0 was completed in 1986. This version is documented in detail in Guvanasen and Chan (in preparation). This report describes a series of fourteen verification cases which has been used to test the numerical solution techniques and coding of MOTIF, as well as demonstrate some of the MOTIF analysis capabilities. For each case the MOTIF solution has been compared with a corresponding analytical or independently developed alternate numerical solution. Several of the verification cases were included in Level 1 of the International Hydrologic Code Intercomparison Project (HYDROCOIN). The MOTIF results for these cases were also described in the HYDROCOIN Secretariat's compilation and comparison of results submitted by the various project teams (Swedish Nuclear Power Inspectorate 1988). It is evident from the graphical comparisons presented that the MOTIF solutions for the fourteen verification cases are generally in excellent agreement with known analytical or numerical solutions obtained from independent sources. This series of verification studies has established the ability of the MOTIF finite-element code to accurately model the groundwater flow and solute and heat transport phenomena for which it is intended. (author). 20 refs., 14 tabs., 32 figs

Resistivity and Hall effect in Y9Co7

International Nuclear Information System (INIS)

Ali, N.; Datars, W.R.; Kozlowski, G.; Woods, S.B.

1987-01-01

The temperature dependence of the resistivity and Hall effect of Y 9 Co 7 has been measured from room temperature to 1.6 K. The saturation of the resistivity at high temperature is similar to that of A15 compounds and can be interpreted in terms of a localised phonon mode formation as shown by Yu and Anderson for A15 compounds. A T 2 -dependence of the resistivity is observed for temperatures below approx.= 25 K. A similar T 2 -dependence at low temperatures is always observed in A15 compounds as well and is not fully understood. However, a T 2 -dependence below 10 K does not seem to be due to itinerant ferromagnetism in Y 9 Co 7 as concluded recently by Kolodziejczyk and Spalek. The observation of a peak at approx.= 25 K in the Hall coefficient suggests a spin glass type of freezing at low temperatures which possibly can account for the T 2 -dependence of the resistivity below approx.= 10 K. (author)

Nanopowders Y1−yNdyV1−xCrxO4 with y=0 and 1; x=0, 0.1, 0.2 and 0.5 synthesized by a sol–gel process. Relationship between morphological characteristics and optical properties

International Nuclear Information System (INIS)

Alcaraz, L.; Isasi, J.; Caballero, A.C.; Izquierdo, J.G.; Bañares, L.

2015-01-01

Y 1−y Nd y V 1−x Cr x O 4 nanopowders with y=0 and 0.1; x=0, 0.1, 0.2 and 0.5, have been synthetized by a sol–gel process followed by heating in an oxygen flow. This second treatment was done only in the case of samples containing chromium. The samples have been characterized by X-ray diffraction (XRD), Fourier Transform Infrared (FTIR) spectroscopy, scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The structural analysis revealed that when chromium was inserted at vanadium-sites in Y 0.9 Nd 0.1 VO 4 , the host retained the tetragonal symmetry corresponding to a zircon-type structure, attributed to the space group I4 1 /amd. In addition, a loss of crystallinity was observed when chromium substitutes vanadium into the Y 0.9 Nd 0.1 VO 4 host. The morphological studies revealed agglomerates of spherical particles whose size is increased with the Cr content and confirmed the composition of all synthetized samples. FTIR spectra of these samples exhibit a broadening and a slight shift of the bands around 830 cm −1 towards higher values of frequency when the chromium content increases. The effect of vanadium substitution by chromium on the optical properties was also evaluated by UV–vis absorption and photoluminescence (PL) spectroscopies. The broad UV band absorption is due to the presence of Cr 5+ . A decrease of PL emission is found when chromium substitutes vanadium in the YVO 4 host. - Highlights: • Nanophosphors Y 1−y Nd y V 1−x Cr x O 4 with y=0, 0.1 and x=0, 0.1, 0.2 and 0.5 have been synthesized. • Structural analysis reveals structural distortions associated to chromium insertion. • Morphological studies confirm the nanocristalline size and the stoichiometry of synthesized samples. • Chromium insertion causes a decrease of the PL emission intensity

Purification and functional motifs of the recombinant ATPase of orf virus.

Science.gov (United States)

Lin, Fong-Yuan; Chan, Kun-Wei; Wang, Chi-Young; Wong, Min-Liang; Hsu, Wei-Li

2011-10-01

Our previous study showed that the recombinant ATPase encoded by the A32L gene of orf virus displayed ATP hydrolysis activity as predicted from its amino acids sequence. This viral ATPase contains four known functional motifs (motifs I-IV) and a novel AYDG motif; they are essential for ATP hydrolysis reaction by binding ATP and magnesium ions. The motifs I and II correspond with the Walker A and B motifs of the typical ATPase, respectively. To examine the biochemical roles of these five conserved motifs, recombinant ATPases of five deletion mutants derived from the Taiping strain were expressed and purified. Their ATPase functions were assayed and compared with those of two wild type strains, Taiping and Nantou isolated in Taiwan. Our results showed that deletions at motifs I-III or IV exhibited lower activity than that of the wild type. Interestingly, deletion of AYDG motif decreased the ATPase activity more significantly than those of motifs I-IV deletions. Divalent ions such as magnesium and calcium were essential for ATPase activity. Moreover, our recombinant proteins of orf virus also demonstrated GTPase activity, though weaker than the original ATPase activity. Copyright © 2011 Elsevier Inc. All rights reserved.

Crystallisation kinetics of amorphous Fe{sub 72.5-x}Cu{sub 1}Nb{sub 4.5}Si{sub 10+x+y}B{sub 12-y} alloy

Energy Technology Data Exchange (ETDEWEB)

Miglierini, M. [Komenskeho Univ., Bratislava (Czechoslovakia). Dept. of Nuclear Physics and Technics; Lipka, J. [Komenskeho Univ., Bratislava (Czechoslovakia). Dept. of Nuclear Physics and Technics; Sitek, J. [Komenskeho Univ., Bratislava (Czechoslovakia). Dept. of Nuclear Physics and Technics

1994-11-01

Fe{sub 73.5}Cu{sub 1}Nb{sub 3}Si{sub 13.5}B{sub 9} and Fe{sub 72.5-x}Cu{sub 1}Nb{sub 4.5}Si{sub 10+x+y}B{sub 12-y} alloys are compared from the point of view of crystallisation behaviour and changes in the short-range order in the amorphous reminder. The increase in Nb to 4.5 at.% in the latter system slows down the formation of nanocrystals to approximately 40% even after 16 hours of anneal at 550 C for x = 0.5, y = 3. Segregation-induced changes in the short-range order are manifested via hyperfine field distributions corresponding to the amorphous reminder. (orig.)

Mild hydrothermal synthesis, crystal structure, spectroscopic and magnetic properties of the [MxIIM2.5-xIII(H2O)2(HPIIIO3)y(PVO4)2-yF] [M=Fe, x=2.08, y=1.58; M=Co, Ni, x=2.5, y=2] compounds

International Nuclear Information System (INIS)

Orive, Joseba; Mesa, Jose L.; Legarra, Estibaliz; Plazaola, Fernando; Arriortua, Maria I.; Rojo, Teofilo

2009-01-01

The [M x II M 2.5-x III (H 2 O) 2 (HP III O 3 ) y (P V O 4 ) 2-y F] [M=Fe (1), x=2.08, y=1.58; M=Co (2), x=2.5, y=2; Ni (3), x=2.5, y=2] compounds have been synthesized using mild hydrothermal conditions at 170 deg. C during five days. Single-crystals of (1) and (2), and polycrystalline sample of (3) were obtained. These isostructural compounds crystallize in the orthorhombic system, space group Aba2, with a=9.9598(2), b=18.8149(4) and c=8.5751(2) A for (1), a=9.9142(7), b=18.570(1) and c=8.4920(5) A for (2) and a=9.8038(2), b=18.2453(2) and c=8.4106(1) A for (3), with Z=8 in the three phases. An X-ray diffraction study reveals that the crystal structure is composed of a three-dimensional skeleton formed by [MO 5 F] and [MO 4 F 2 ] (M=Fe, Co and Ni) octahedra and [HPO 3 ] tetrahedra, partially substituted by [PO 4 ] tetrahedra in phase (1). The IR spectra show the vibrational modes of the water molecules and those of the (HPO 3 ) 2- tetrahedral oxoanions. The thermal study indicates that the limit of thermal stability of these phases is 195 deg. C for (1) and 315 deg. C for (2) and (3). The electronic absorption spectroscopy shows the characteristic bands of the Fe(II), Co(II) and Ni(II) high-spin cations in slightly distorted octahedral geometry. Magnetic measurements indicate the existence of global antiferromagnetic interactions between the metallic centers with a ferromagnetic transition in the three compounds at 28, 14 and 21 K for (1), (2) and (3), respectively. Compound (1) exhibits a hysteresis loop with remnant magnetization and coercive field values of 0.72 emu/mol and 880 Oe, respectively. - Abstract: Polyhedral view of the crystal structure of the [M x II M 2.5-x III (H 2 O) 2 (HP III O 3 ) y (P IV O 4 ) 2-y F] [M=Fe, x=2.08, y=1.58; M=Co, Ni, x=2.5, y=2] compounds showing the sheets along the [001] direction.

An experimental test of a fundamental food web motif.

Science.gov (United States)

Rip, Jason M K; McCann, Kevin S; Lynn, Denis H; Fawcett, Sonia

2010-06-07

Large-scale changes to the world's ecosystem are resulting in the deterioration of biostructure-the complex web of species interactions that make up ecological communities. A difficult, yet crucial task is to identify food web structures, or food web motifs, that are the building blocks of this baroque network of interactions. Once identified, these food web motifs can then be examined through experiments and theory to provide mechanistic explanations for how structure governs ecosystem stability. Here, we synthesize recent ecological research to show that generalist consumers coupling resources with different interaction strengths, is one such motif. This motif amazingly occurs across an enormous range of spatial scales, and so acts to distribute coupled weak and strong interactions throughout food webs. We then perform an experiment that illustrates the importance of this motif to ecological stability. We find that weak interactions coupled to strong interactions by generalist consumers dampen strong interaction strengths and increase community stability. This study takes a critical step by isolating a common food web motif and through clear, experimental manipulation, identifies the fundamental stabilizing consequences of this structure for ecological communities.

Highly scalable Ab initio genomic motif identification

KAUST Repository

Marchand, Benoit; Bajic, Vladimir B.; Kaushik, Dinesh

2011-01-01

We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.

OSR1 regulates a subset of inward rectifier potassium channels via a binding motif variant.

Science.gov (United States)

Taylor, Clinton A; An, Sung-Wan; Kankanamalage, Sachith Gallolu; Stippec, Steve; Earnest, Svetlana; Trivedi, Ashesh T; Yang, Jonathan Zijiang; Mirzaei, Hamid; Huang, Chou-Long; Cobb, Melanie H

2018-04-10

The with-no-lysine (K) (WNK) signaling pathway to STE20/SPS1-related proline- and alanine-rich kinase (SPAK) and oxidative stress-responsive 1 (OSR1) kinase is an important mediator of cell volume and ion transport. SPAK and OSR1 associate with upstream kinases WNK 1-4, substrates, and other proteins through their C-terminal domains which interact with linear R-F-x-V/I sequence motifs. In this study we find that SPAK and OSR1 also interact with similar affinity with a motif variant, R-x-F-x-V/I. Eight of 16 human inward rectifier K + channels have an R-x-F-x-V motif. We demonstrate that two of these channels, Kir2.1 and Kir2.3, are activated by OSR1, while Kir4.1, which does not contain the motif, is not sensitive to changes in OSR1 or WNK activity. Mutation of the motif prevents activation of Kir2.3 by OSR1. Both siRNA knockdown of OSR1 and chemical inhibition of WNK activity disrupt NaCl-induced plasma membrane localization of Kir2.3. Our results suggest a mechanism by which WNK-OSR1 enhance Kir2.1 and Kir2.3 channel activity by increasing their plasma membrane localization. Regulation of members of the inward rectifier K + channel family adds functional and mechanistic insight into the physiological impact of the WNK pathway.

Photoluminescence properties of Eu2+-activated Ca2Y2Si2O9 phosphor

NARCIS (Netherlands)

Zhang, Zhijun; Delsing, A.C.A.; Notten, P.H.L.; Zhao, Jingtai; Hintzen, H.T.J.M.

2012-01-01

Eu2+-activated Ca2Y2Si2O9 phosphors with different Eu2+ concentrations have been prepared by a solid-state reaction method at high temperature and their photoluminescence (PL) properties were investigated. Photoluminescence results show that Eu2+-doped Ca2Y2Si2O9 can be efficiently excited by

Dimensionality of social networks using motifs and eigenvalues.

Directory of Open Access Journals (Sweden)

Anthony Bonato

Full Text Available We consider the dimensionality of social networks, and develop experiments aimed at predicting that dimension. We find that a social network model with nodes and links sampled from an m-dimensional metric space with power-law distributed influence regions best fits samples from real-world networks when m scales logarithmically with the number of nodes of the network. This supports a logarithmic dimension hypothesis, and we provide evidence with two different social networks, Facebook and LinkedIn. Further, we employ two different methods for confirming the hypothesis: the first uses the distribution of motif counts, and the second exploits the eigenvalue distribution.

Transduction motif analysis of gastric cancer based on a human signaling network

Energy Technology Data Exchange (ETDEWEB)

Liu, G.; Li, D.Z.; Jiang, C.S.; Wang, W. [Fuzhou General Hospital of Nanjing Command, Department of Gastroenterology, Fuzhou, China, Department of Gastroenterology, Fuzhou General Hospital of Nanjing Command, Fuzhou (China)

2014-04-04

To investigate signal regulation models of gastric cancer, databases and literature were used to construct the signaling network in humans. Topological characteristics of the network were analyzed by CytoScape. After marking gastric cancer-related genes extracted from the CancerResource, GeneRIF, and COSMIC databases, the FANMOD software was used for the mining of gastric cancer-related motifs in a network with three vertices. The significant motif difference method was adopted to identify significantly different motifs in the normal and cancer states. Finally, we conducted a series of analyses of the significantly different motifs, including gene ontology, function annotation of genes, and model classification. A human signaling network was constructed, with 1643 nodes and 5089 regulating interactions. The network was configured to have the characteristics of other biological networks. There were 57,942 motifs marked with gastric cancer-related genes out of a total of 69,492 motifs, and 264 motifs were selected as significantly different motifs by calculating the significant motif difference (SMD) scores. Genes in significantly different motifs were mainly enriched in functions associated with cancer genesis, such as regulation of cell death, amino acid phosphorylation of proteins, and intracellular signaling cascades. The top five significantly different motifs were mainly cascade and positive feedback types. Almost all genes in the five motifs were cancer related, including EPOR, MAPK14, BCL2L1, KRT18, PTPN6, CASP3, TGFBR2, AR, and CASP7. The development of cancer might be curbed by inhibiting signal transductions upstream and downstream of the selected motifs.

Multiple TPR motifs characterize the Fanconi anemia FANCG protein.

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Blom, Eric; van de Vrugt, Henri J; de Vries, Yne; de Winter, Johan P; Arwert, Fré; Joenje, Hans

2004-01-05

The genome protection pathway that is defective in patients with Fanconi anemia (FA) is controlled by at least eight genes, including BRCA2. A key step in the pathway involves the monoubiquitylation of FANCD2, which critically depends on a multi-subunit nuclear 'core complex' of at least six FANC proteins (FANCA, -C, -E, -F, -G, and -L). Except for FANCL, which has WD40 repeats and a RING finger domain, no significant domain structure has so far been recognized in any of the core complex proteins. By using a homology search strategy comparing the human FANCG protein sequence with its ortholog sequences in Oryzias latipes (Japanese rice fish) and Danio rerio (zebrafish) we identified at least seven tetratricopeptide repeat motifs (TPRs) covering a major part of this protein. TPRs are degenerate 34-amino acid repeat motifs which function as scaffolds mediating protein-protein interactions, often found in multiprotein complexes. In four out of five TPR motifs tested (TPR1, -2, -5, and -6), targeted missense mutagenesis disrupting the motifs at the critical position 8 of each TPR caused complete or partial loss of FANCG function. Loss of function was evident from failure of the mutant proteins to complement the cellular FA phenotype in FA-G lymphoblasts, which was correlated with loss of binding to FANCA. Although the TPR4 mutant fully complemented the cells, it showed a reduced interaction with FANCA, suggesting that this TPR may also be of functional importance. The recognition of FANCG as a typical TPR protein predicts this protein to play a key role in the assembly and/or stabilization of the nuclear FA protein core complex.

Armadillo motifs involved in vesicular transport.

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Harald Striegl

Full Text Available Armadillo (ARM repeat proteins function in various cellular processes including vesicular transport and membrane tethering. They contain an imperfect repeating sequence motif that forms a conserved three-dimensional structure. Recently, structural and functional insight into tethering mediated by the ARM-repeat protein p115 has been provided. Here we describe the p115 ARM-motifs for reasons of clarity and nomenclature and show that both sequence and structure are highly conserved among ARM-repeat proteins. We argue that there is no need to invoke repeat types other than ARM repeats for a proper description of the structure of the p115 globular head region. Additionally, we propose to define a new subfamily of ARM-like proteins and show lack of evidence that the ARM motifs found in p115 are present in other long coiled-coil tethering factors of the golgin family.

Lesion Orientation of O4-Alkylthymidine Influences Replication by Human DNA Polymerase η.

Science.gov (United States)

O'Flaherty, D K; Patra, A; Su, Y; Guengerich, F P; Egli, M; Wilds, C J

2016-08-01

DNA lesions that elude repair may undergo translesion synthesis catalyzed by Y-family DNA polymerases. O 4 -Alkylthymidines, persistent adducts that can result from carcinogenic agents, may be encountered by DNA polymerases. The influence of lesion orientation around the C4- O 4 bond on processing by human DNA polymerase η (hPol η ) was studied for oligonucleotides containing O 4 -methylthymidine, O 4 -ethylthymidine, and analogs restricting the O 4 -methylene group in an anti -orientation. Primer extension assays revealed that the O 4 -alkyl orientation influences hPol η bypass. Crystal structures of hPol η •DNA•dNTP ternary complexes with O 4 -methyl- or O 4 -ethylthymidine in the template strand showed the nucleobase of the former lodged near the ceiling of the active site, with the syn - O 4 -methyl group engaged in extensive hydrophobic interactions. This unique arrangement for O 4 -methylthymidine with hPol η , inaccessible for the other analogs due to steric/conformational restriction, is consistent with differences observed for nucleotide incorporation and supports the concept that lesion conformation influences extension across DNA damage. Together, these results provide mechanistic insights on the mutagenicity of O 4 MedT and O 4 EtdT when acted upon by hPol η .

Characterizing Motif Dynamics of Electric Brain Activity Using Symbolic Analysis

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Massimiliano Zanin

2014-10-01

Full Text Available Motifs are small recurring circuits of interactions which constitute the backbone of networked systems. Characterizing motif dynamics is therefore key to understanding the functioning of such systems. Here we propose a method to define and quantify the temporal variability and time scales of electroencephalogram (EEG motifs of resting brain activity. Given a triplet of EEG sensors, links between them are calculated by means of linear correlation; each pattern of links (i.e., each motif is then associated to a symbol, and its appearance frequency is analyzed by means of Shannon entropy. Our results show that each motif becomes observable with different coupling thresholds and evolves at its own time scale, with fronto-temporal sensors emerging at high thresholds and changing at fast time scales, and parietal ones at low thresholds and changing at slower rates. Finally, while motif dynamics differed across individuals, for each subject, it showed robustness across experimental conditions, indicating that it could represent an individual dynamical signature.

Discriminative motif discovery via simulated evolution and random under-sampling.

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Tao Song

Full Text Available Conserved motifs in biological sequences are closely related to their structure and functions. Recently, discriminative motif discovery methods have attracted more and more attention. However, little attention has been devoted to the data imbalance problem, which is one of the main reasons affecting the performance of the discriminative models. In this article, a simulated evolution method is applied to solve the multi-class imbalance problem at the stage of data preprocessing, and at the stage of Hidden Markov Models (HMMs training, a random under-sampling method is introduced for the imbalance between the positive and negative datasets. It is shown that, in the task of discovering targeting motifs of nine subcellular compartments, the motifs found by our method are more conserved than the methods without considering data imbalance problem and recover the most known targeting motifs from Minimotif Miner and InterPro. Meanwhile, we use the found motifs to predict protein subcellular localization and achieve higher prediction precision and recall for the minority classes.

Discriminative motif discovery via simulated evolution and random under-sampling.

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Song, Tao; Gu, Hong

2014-01-01

Conserved motifs in biological sequences are closely related to their structure and functions. Recently, discriminative motif discovery methods have attracted more and more attention. However, little attention has been devoted to the data imbalance problem, which is one of the main reasons affecting the performance of the discriminative models. In this article, a simulated evolution method is applied to solve the multi-class imbalance problem at the stage of data preprocessing, and at the stage of Hidden Markov Models (HMMs) training, a random under-sampling method is introduced for the imbalance between the positive and negative datasets. It is shown that, in the task of discovering targeting motifs of nine subcellular compartments, the motifs found by our method are more conserved than the methods without considering data imbalance problem and recover the most known targeting motifs from Minimotif Miner and InterPro. Meanwhile, we use the found motifs to predict protein subcellular localization and achieve higher prediction precision and recall for the minority classes.

The synthesis and luminescence properties of a novel red-emitting phosphor. Eu{sup 3+}-doped Ca{sub 9}La(PO{sub 4}){sub 7}

Energy Technology Data Exchange (ETDEWEB)

Liang, Zehui [Guangdong University of Technology, Experimental Teaching Department, Guangzhou (China); Guangdong University of Technology, School of Chemical Engineering and Light Industry, Guangzhou (China); Mu, Zhongfei; Zhu, Daoyun [Guangdong University of Technology, Experimental Teaching Department, Guangzhou (China); Wang, Qiang; Wu, Fugen [Guangdong University of Technology, School of Materials and Energy, Guangzhou (China)

2017-10-15

A series of novel red-emitting phosphors Ca{sub 9}La{sub 1-x}(PO{sub 4}){sub 7}: xEu{sup 3+} were synthesized by high-temperature solid state reactions. The photoluminescence excitation and photoluminescence spectra of these phosphors were investigated in detail. O{sup 2-}-Eu{sup 3+} charge transfer band peaking at about 261 nm is dominant in the PLE spectra of Eu{sup 3+}-doped Ca{sub 9}La(PO{sub 4}){sub 7}, indicating that the phosphors are suitable for tricolor fluorescent lamps. The phosphors also show a good absorption in near ultraviolet (around 395 nm) and blue (around 465 nm) spectral region, which indicates that it can be pumped with NUV and blue chips for white light-emitting diodes. The transition of {sup 5}D{sub 0} → {sup 7}F{sub 2} of Eu{sup 3+} in this lattice can emit bright red light. Ca{sub 9}La(PO{sub 4}){sub 7} could accommodate a large amount of Eu{sup 3+} with an optimal concentration of 60 mol%. The dipole-dipole interaction between Eu{sup 3+} is the dominant mechanism for concentration quenching of Eu{sup 3+}. The calculated color coordinates lie in red region (x = 0.64, y = 0.36), which is close to Y{sub 2}O{sub 3}: 0.05Eu{sup 3+} (x = 0.65, y = 0.34). The integral emission intensity of Ca{sub 9}La{sub 0.4}(PO{sub 4}){sub 7}: 0.6Eu{sup 3+} is 1.9 times stronger than that of widely used commercial red phosphor Y{sub 2}O{sub 3}: 0.05Eu{sup 3+}. All these results indicate that Eu{sup 3+}-doped Ca{sub 9}La(PO{sub 4}){sub 7} is a promising red-emitting phosphor which can be used in tricolor fluorescent lamps and white light-emitting diodes. (orig.)

PCSK-9: papel en las hipercolesterolemias y anticuerpos monoclonales específicos inhibitorios

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Álvaro J. Ruiz

2017-11-01

Los anticuerpos monoclonales contra PCSK9, evolocumab y alirocumab, son una novedosa herramienta terapéutica de gran utilidad en los casos de hipercolesterolemia familiar heterocigota, en algunos casos de hipercolesterolemia familiar homocigota y de personas con alto riesgo cardiovascular, cuyos niveles de cLDL no pueden ser controlados con dosis máximas toleradas de las estatinas de mayor efectividad, además de ezetimibe y cambios en el estilo de vida.

Análisis y estudio del radar Ramet AD9

OpenAIRE

López Jiménez, José Manuel

2009-01-01

El proyecto está basado en un estudio completo y detallado del radar RAMET modelo AD9. Las autoridades de tráfico catalanas, a través del Servei Català del Trànsit, están introduciendo en nuestras carreteras este tipo de cinemómetro desde el año 2007, para el control de tráfico en carretera. El hecho de ser una novedad dentro de nuestro entorno hace que su desconocimiento sobre su composición y sus peculiaridades respecto a otro tipo de radares sea interesante realizar este estudio....

Expanding CRISPR/Cas9 Genome Editing Capacity in Zebrafish Using SaCas9

OpenAIRE

Feng, Yan; Chen, Cheng; Han, Yuxiang; Chen, Zelin; Lu, Xiaochan; Liang, Fang; Li, Song; Qin, Wei; Lin, Shuo

2016-01-01

The type II CRISPR/Cas9 system has been used widely for genome editing in zebrafish. However, the requirement for the 5′-NGG-3′ protospacer-adjacent motif (PAM) of Cas9 from Streptococcus pyogenes (SpCas9) limits its targeting sequences. Here, we report that a Cas9 ortholog from Staphylococcus aureus (SaCas9), and its KKH variant, successfully induced targeted mutagenesis with high frequency in zebrafish. Confirming previous findings, the SpCas9 variant, VQR, can also induce targeted mutation...

CRECIMIENTO, ACUMULACIÓN DE MACRONUTRIENTES Y PRODUCCIÓN DE MELÓN CANTALOUPO Y AMARILLO

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JUAN WALDIR MENDOZA-CORTEZ

2014-01-01

Full Text Available Fueron conducidos dos experimentos individuales en el municipio de Mossoró, Rio Grande do Norte, Brazil. Se empleó dos cultivares de melón, ‘Olimpic express’ (del tipo Cantaloupo e ‘Iracema’ (del tipo Amarillo, para evaluar el crecimiento y la acumulación de macronutrientes, bajo el diseño de bloques al azar con siete tratamientos (épocas de muestreo y tres repeticiones. Los muestreos de plantas fueron realizados a los 14, 21, 28, 35, 42, 49 y 56 días después del trasplante (DDT. El crecimiento fue lento hasta 28 DDT en ambos cultivares evaluados, intensificándose en el periodo siguiente, alcanzando a los 56 DDT, 246.4g planta-1, en ‘Olimpic express’,y 266.9 g planta-1, en ‘Iracema’, siendo la materia seca (MS de los frutos correspondientes a 60% y 64% de la MS total, respectivamente. Mayores acumulaciones de N, P y K fueron obtenidos en los frutos, mientras de Ca, Mg y S en las hojas. Al final del ciclo, en ‘Olimpic express’, cuya productividad fue de 32 t ha-1, fueron acumulados 173.4, 110.1, 101.1, 26.9, 15.6 y 13.5 kg ha-1 de K, Ca, N, Mg, S y P, respectivamente, y en ‘Iracema’, cuya productividad fue de 38 t ha-1, fueron acumulados 136.0, 93.9, 84.1, 22.6, 15.4 y 9.5 kg ha-1 de K, N, Ca, Mg, S y P, respectivamente. En relación al total acumulado, las exportaciones de N, P, K, Ca, Mg y S en los frutos fueron de 61, 73, 66, 9, 35 y 39% (‘Olimpic express’y 58, 70, 55, 6, 33 y 41% (‘Iracema’. Con una menor producción de frutos y una mayor acumulación de nutrientes, ‘Olimpic express’ ha demostrado ser menos eficiente en el uso de nutrientes que ‘Iracema’.

Computational analyses of synergism in small molecular network motifs.

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Yili Zhang

2014-03-01

Full Text Available Cellular functions and responses to stimuli are controlled by complex regulatory networks that comprise a large diversity of molecular components and their interactions. However, achieving an intuitive understanding of the dynamical properties and responses to stimuli of these networks is hampered by their large scale and complexity. To address this issue, analyses of regulatory networks often focus on reduced models that depict distinct, reoccurring connectivity patterns referred to as motifs. Previous modeling studies have begun to characterize the dynamics of small motifs, and to describe ways in which variations in parameters affect their responses to stimuli. The present study investigates how variations in pairs of parameters affect responses in a series of ten common network motifs, identifying concurrent variations that act synergistically (or antagonistically to alter the responses of the motifs to stimuli. Synergism (or antagonism was quantified using degrees of nonlinear blending and additive synergism. Simulations identified concurrent variations that maximized synergism, and examined the ways in which it was affected by stimulus protocols and the architecture of a motif. Only a subset of architectures exhibited synergism following paired changes in parameters. The approach was then applied to a model describing interlocked feedback loops governing the synthesis of the CREB1 and CREB2 transcription factors. The effects of motifs on synergism for this biologically realistic model were consistent with those for the abstract models of single motifs. These results have implications for the rational design of combination drug therapies with the potential for synergistic interactions.

Synthesis and characterization of the novel rare earth orthophosphates Y0.5Er0.5PO4 and Y0.5Yb0.5PO4

International Nuclear Information System (INIS)

Schildhammer, Daniel; Petschnig, Lucas L.; Fuhrmann, Gerda; Heymann, Gunter; Schottenberger, Herwig; Huppertz, Hubert; Tribus, Martina

2016-01-01

The new mixed rare earth (RE) orthophosphates Y 0.5 Er 0.5 PO 4 and Y 0.5 Yb 0.5 PO 4 were synthesized by a classical solid state reaction in an electrical furnace at 1200 C. As starting materials, the corresponding rare earth oxides and diammonium hydrogen phosphate were used. The powder diffraction analyses revealed that the new compounds Y 0.5 Er 0.5 PO 4 and Y 0.5 Yb 0.5 PO 4 crystallize in a zircon-type structure being isostructural with the rare earth orthophosphate YPO 4 . Y 0.5 Er 0.5 PO 4 and Y 0.5 Yb 0.5 PO 4 crystallize in the tetragonal space group I4 1 /amd (no. 141) with four formula units in the unit cell. The structural parameters based on Rietveld refinements are a = 687.27(2), c = 601.50(2) pm, V = 0.28412(1) nm 3 , R p = 0.0143, and R wp = 0.0186 (all data) for Y 0.5 Er 0.5 PO 4 and a = 684.61(2), c = 599.31(2) pm, V = 0.28089(2) nm 3 , R p = 0.0242, and R wp = 0.0313 (all data) for Y 0.5 Yb 0.5 PO 4 . Furthermore, the structure of Y 0.5 Er 0.5 PO 4 was refined from single-crystal X-ray diffraction data: a = 687.78(5), c = 601.85(4) pm, V = 0.28470(5) nm 3 , R 1 = 0.0165, and wR 2 = 0.0385 (all data). In both compounds, the rare earth metal ions are eightfold coordinated by oxygen atoms, forming two unique interlocking tetrahedra with two individual RE-O distances. The tetrahedral phosphate groups [PO 4 ] 3- are slightly distorted in both compounds. The individual rare earth ions share a common position (Wyckoff site 4a). The presence of two rare earth ions in the structures of the new orthophosphates Y 0.5 Er 0.5 PO 4 and Y 0.5 Yb 0.5 PO 4 was additionally confirmed by single-crystal EDX spectroscopy revealing a ratio of 1:1.

Structural motifs of pre-nucleation clusters.

Science.gov (United States)

Zhang, Y; Türkmen, I R; Wassermann, B; Erko, A; Rühl, E

2013-10-07

Structural motifs of pre-nucleation clusters prepared in single, optically levitated supersaturated aqueous aerosol microparticles containing CaBr2 as a model system are reported. Cluster formation is identified by means of X-ray absorption in the Br K-edge regime. The salt concentration beyond the saturation point is varied by controlling the humidity in the ambient atmosphere surrounding the 15-30 μm microdroplets. This leads to the formation of metastable supersaturated liquid particles. Distinct spectral shifts in near-edge spectra as a function of salt concentration are observed, in which the energy position of the Br K-edge is red-shifted by up to 7.1 ± 0.4 eV if the dilute solution is compared to the solid. The K-edge positions of supersaturated solutions are found between these limits. The changes in electronic structure are rationalized in terms of the formation of pre-nucleation clusters. This assumption is verified by spectral simulations using first-principle density functional theory and molecular dynamics calculations, in which structural motifs are considered, explaining the experimental results. These consist of solvated CaBr2 moieties, rather than building blocks forming calcium bromide hexahydrates, the crystal system that is formed by drying aqueous CaBr2 solutions.

APOE epsilon4 and Alzheimer's disease: positive association in a Colombian clinical series and review of the Latin-American studies Asociación positiva entre APOE épsilon4 y demencia de Alzheimer en una serie clinica en Bogotá (Colombia y revision de los estudios latinoamericanos

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Martine Jacquier

2001-03-01

Full Text Available OBJECTIVE: As the strength of the association between the APOE epsilon4 allele and Alzheimer's disease (AD varies across ethnic groups, we studied if there was such an association in Colombian patients. METHOD: We performed apolipoprotein E (APOE genotyping in a clinical sample of 83 unrelated AD patients, predominantly late-onset (>65 yrs including familial ( n =30 and sporadic AD cases (n= 53 diagnosed according to NINCDS-ADRDA criteria and assessed by a multi-disciplinary team. Control subjects (n = 44 had no significant cognitive impairment by medical interview and neuro-psychological testing. RESULTS: We found a high association (OR= 5.1 95%CI 1.9 -13.6 between APOE epsilon4 and AD, in this series with predominantly late-onset cases with familial aggregation in 24 cases (28.9%. A significant negative association was found between epsilon2 and AD (OR= 0.2 95% CI 0.05-0.75. CONCLUSION: Further population-based surveys in Colombia are warranted to precise a possible dose effect of APOE epsilon4.OBJETIVO: Como la fortaleza de la asociación entre el alelo épsilon4 del gen APOE y la enfermedad de Alzheimer (EA difiere entre grupos étnicos, quisimos evaluar si esta asociación existe en pacientes colombianos. MÉTODOS: Realizamos una genotipificación para el gen de la apolipoproteina E (APOE en una muestra clínica de 83 pacientes con EA no relacionados, de inicio predominantemente tardío (> 65 años, incluyendo casos familiares (n=30 y esporádicos (n=53 diagnosticados según los criterios del NINCDS-ADRDA y evaluados por un equipo multi-disciplinario. Los sujetos control (n= 44 no presentaban deterioro cognoscitivo de acuerdo con la entrevista médica y la evaluación neuropsicológica. RESULTADOS: Hallamos una alta asociación (OR= 5.1; IC95% 1.9- 13.6 entre APOE épsilon4 y EA en la serie de casos de inicio tardío y con agregación familiar en 24 sujetos (28.9%. Una asociación negativa, estadísticamente significativa, fue encontrada

Characterization of Novel Calmodulin Binding Domains within IQ Motifs of IQGAP1

Science.gov (United States)

Jang, Deok-Jin; Ban, Byungkwan; Lee, Jin-A

2011-01-01

IQ motif-containing GTPase-activating protein 1 (IQGAP1), which is a well-known calmodulin (CaM) binding protein, is involved in a wide range of cellular processes including cell proliferation, tumorigenesis, adhesion, and migration. Interaction of IQGAP1 with CaM is important for its cellular functions. Although each IQ domain of IQGAP1 for CaM binding has been characterized in a Ca2+-dependent or -independent manner, it was not clear which IQ motifs are physiologically relevant for CaM binding in the cells. In this study, we performed immunoprecipitation using 3xFLAGhCaM in mammalian cell lines to characterize the domains of IQGAP1 that are key for CaM binding under physiological conditions. Interestingly, using this method, we identified two novel domains, IQ(2.7-3) and IQ(3.5-4.4), within IQGAP1 that were involved in Ca2+-independent or -dependent CaM binding, respectively. Mutant analysis clearly showed that the hydrophobic regions within IQ(2.7-3) were mainly involved in apoCaM binding, while the basic amino acids and hydrophobic region of IQ(3.5-4.4) were required for Ca2+/CaM binding. Finally, we showed that IQ(2.7-3) was the main apoCaM binding domain and both IQ(2.7-3) and IQ(3.5-4.4) were required for Ca2+/CaM binding within IQ(1- 2-3-4). Thus, we identified and characterized novel direct CaM binding motifs essential for IQGAP1. This finding indicates that IQGAP1 plays a dynamic role via direct interactions with CaM in a Ca2+-dependent or -independent manner. PMID:22080369

Two actinide-organic frameworks constructed by a tripodal flexible ligand: Occurrence of infinite ((UO{sub 2})O{sub 2}(OH){sub 3}){sub 4n} and hexanuclear (Th{sub 6}O{sub 4}(OH){sub 4}) motifs

Energy Technology Data Exchange (ETDEWEB)

Liang, Lingling; Zhang, Ronglan [College of Chemistry and Materials, Shaanxi Key Laboratory of Physico-Inorganic Chemistry, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of education, Northwest University, Xi’an 710069 (China); Zhao, Jianshe, E-mail: jszhao@nwu.edu.cn [College of Chemistry and Materials, Shaanxi Key Laboratory of Physico-Inorganic Chemistry, Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of education, Northwest University, Xi’an 710069 (China); Liu, Chiyang, E-mail: lcy@nwu.edu.cn [Department of Geology, Northwest University, Xi’an 710069 (China); Weng, Ng Seik [The University of Nottingham Malaysia Campus, 43500 Semenyih, Selangor Darul Ehsan (Malaysia)

2016-11-15

Two new actinide metal-organic frameworks were constructed by using a tripodal flexible ligand tris (2-carboxyethyl) isocyanurate (H{sub 3}tci) under hydrothermal condition. The combination of H{sub 3}tci and uranyl nitrate hexahydrate in aqueous solution leads to the isolation of [(UO{sub 2}){sub 2}(H{sub 2}O){sub 4}]{sub 0.5}(tci){sub 2}(UO{sub 2}){sub 4}(OH){sub 4}·18H{sub 2}O (1), which contains two distinct UO{sub 2}{sup 2+} coordination environments. Four uranyl cations, linked through μ{sub 3}-OH respectively, result in the edge-sharing ribbons. Then, the layer structure is constructed by U-O clusters linked through other eight-coordinated uranyl unions, giving rise to a porous structure in the space. Topological analysis reveals that complex 1 belongs to a (4, 8)-connected net with a schläfli symbol of (3{sup 4.}2{sup 6.}3){sub 2}(3{sup 4.}4{sup 6.}5{sup 6.}6{sup 8.}7{sup 3.}8). Th{sub 3}(tci){sub 2}O{sub 2}(OH){sub 2}(H{sub 2}O){sub 3}·12H{sub 2}O (2) generated by the reaction of H{sub 3}tci and thorium nitrate tetrahydrate, possesses nine-fold coodinated Th(IV) centers with a monocapped square antiprismatic geometry. The hexamers “Th{sub 6}O{sub 4}(OH){sub 4}” motifs are connected together by the carboxylate groups, showing a three-dimensional structures. Complex 2 takes on an 8-connected architecture and the point symbol is (4{sup 24.}6{sup 4}). - Graphical abstract: Two new 3D actinide metal-organic frameworks were constructed by using a tripodal flexible ligand tris (2-carboxyethyl) isocyanurate (H3tci) and their topological structures were displayed. The infinite ((UO{sub 2})O{sub 2}(OH){sub 3}){sub 4n} and hexanuclear (Th{sub 6}O{sub 4}(OH){sub 4}) motifs were found in the title actinides networks.

Convergent evolution and mimicry of protein linear motifs in host-pathogen interactions.

Science.gov (United States)

Chemes, Lucía Beatriz; de Prat-Gay, Gonzalo; Sánchez, Ignacio Enrique

2015-06-01

Pathogen linear motif mimics are highly evolvable elements that facilitate rewiring of host protein interaction networks. Host linear motifs and pathogen mimics differ in sequence, leading to thermodynamic and structural differences in the resulting protein-protein interactions. Moreover, the functional output of a mimic depends on the motif and domain repertoire of the pathogen protein. Regulatory evolution mediated by linear motifs can be understood by measuring evolutionary rates, quantifying positive and negative selection and performing phylogenetic reconstructions of linear motif natural history. Convergent evolution of linear motif mimics is widespread among unrelated proteins from viral, prokaryotic and eukaryotic pathogens and can also take place within individual protein phylogenies. Statistics, biochemistry and laboratory models of infection link pathogen linear motifs to phenotypic traits such as tropism, virulence and oncogenicity. In vitro evolution experiments and analysis of natural sequences suggest that changes in linear motif composition underlie pathogen adaptation to a changing environment. Copyright © 2015 Elsevier Ltd. All rights reserved.

Luminescent properties of red-emitting LiSr4B3O(9−3x/2)Nx:Eu2+ phosphor for white-LEDs

International Nuclear Information System (INIS)

Yu Hua; Deng Degang; Xu Shiqing; Yu Cuiping; Yin Haoyong; Nie Qiulin

2012-01-01

An Eu 2+ -activated oxynitride LiSr (4−y) B 3 O (9−3x/2) N x :yEu 2+ red-emitting phosphor was synthesized by solid-state reactions. The synthesized phosphor crystallized in a cubic system with space group Ia–3d. The LiSr 4 B 3 O (9−3x/2) N x :Eu 2+ phosphors exhibited a broad red emission band with a peak at 610 nm and a full width at half maximum of 106 nm under 410 nm excitation, which is ascribed to the 4f 6 5d 1 →4f 7 transition of Eu 2+ . The optimal doped nitrogen concentration was observed to be x=0.75. The average decay times of two different emission centers were estimated to be 568 and 489 ns in the LiSr 3.99 B 3 O 8.25 N 0.5 :0.01Eu 2+ phosphors, respectively. Concentration quenching of Eu 2+ ions occurred at y=0.07, and the critical distance was determined as 17.86 Å. The non-radiative transitions via dipole–dipole interactions resulted in the concentration quenching of Eu 2+ -site emission centers in the LiSr 4 B 3 O 9 host. These results indicate LiSr 4 B 3 O (9−3x/2) N x :Eu 2+ phosphor is promising for application in white near-UV LEDs. - Highlights: ► An oxynitride LiSr 4 B 3 O 9 N:Eu 2+ red-emitting phosphor was prepared at low synthesis temperature. ► The introduced nitrogen improved the excitation and emission intensity of the phosphor. ► The wide excitation band matches well with near-UV LED chips. ► The emission spectrum of the phosphor showed a broad full width at half maximum of about 106 nm.

The Verrucomicrobia LexA-binding Motif: Insights into the Evolutionary Dynamics of the SOS Response

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Ivan Erill

2016-07-01

Full Text Available The SOS response is the primary bacterial mechanism to address DNA damage, coordinating multiple cellular processes that include DNA repair, cell division and translesion synthesis. In contrast to other regulatory systems, the composition of the SOS genetic network and the binding motif of its transcriptional repressor, LexA, have been shown to vary greatly across bacterial clades, making it an ideal system to study the co-evolution of transcription factors and their regulons. Leveraging comparative genomics approaches and prior knowledge on the core SOS regulon, here we define the binding motif of the Verrucomicrobia, a recently described phylum of emerging interest due to its association with eukaryotic hosts. Site directed mutagenesis of the Verrucomicrobium spinosum recA promoter confirms that LexA binds a 14 bp palindromic motif with consensus sequence TGTTC-N4-GAACA. Computational analyses suggest that recognition of this novel motif is determined primarily by changes in base-contacting residues of the third alpha helix of the LexA helix-turn-helix DNA binding motif. In conjunction with comparative genomics analysis of the LexA regulon in the Verrucomicrobia phylum, electrophoretic shift assays reveal that LexA binds to operators in the promoter region of DNA repair genes and a mutagenesis cassette in this organism, and identify previously unreported components of the SOS response. The identification of tandem LexA-binding sites generating instances of other LexA-binding motifs in the lexA gene promoter of Verrucomicrobia species leads us to postulate a novel mechanism for LexA-binding motif evolution. This model, based on gene duplication, successfully addresses outstanding questions in the intricate co-evolution of the LexA protein, its binding motif and the regulatory network it controls.

The Verrucomicrobia LexA-Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response.

Science.gov (United States)

Erill, Ivan; Campoy, Susana; Kılıç, Sefa; Barbé, Jordi

2016-01-01

The SOS response is the primary bacterial mechanism to address DNA damage, coordinating multiple cellular processes that include DNA repair, cell division, and translesion synthesis. In contrast to other regulatory systems, the composition of the SOS genetic network and the binding motif of its transcriptional repressor, LexA, have been shown to vary greatly across bacterial clades, making it an ideal system to study the co-evolution of transcription factors and their regulons. Leveraging comparative genomics approaches and prior knowledge on the core SOS regulon, here we define the binding motif of the Verrucomicrobia, a recently described phylum of emerging interest due to its association with eukaryotic hosts. Site directed mutagenesis of the Verrucomicrobium spinosum recA promoter confirms that LexA binds a 14 bp palindromic motif with consensus sequence TGTTC-N4-GAACA. Computational analyses suggest that recognition of this novel motif is determined primarily by changes in base-contacting residues of the third alpha helix of the LexA helix-turn-helix DNA binding motif. In conjunction with comparative genomics analysis of the LexA regulon in the Verrucomicrobia phylum, electrophoretic shift assays reveal that LexA binds to operators in the promoter region of DNA repair genes and a mutagenesis cassette in this organism, and identify previously unreported components of the SOS response. The identification of tandem LexA-binding sites generating instances of other LexA-binding motifs in the lexA gene promoter of Verrucomicrobia species leads us to postulate a novel mechanism for LexA-binding motif evolution. This model, based on gene duplication, successfully addresses outstanding questions in the intricate co-evolution of the LexA protein, its binding motif and the regulatory network it controls.

Estabilidad Fisicoquímica y Funcional de Uchuva (Physalis peruviana L. Impregnada a Vacío con Calcio y Vitaminas B9, D y E, Durante el Almacenamiento Refrigerado / Phisicochemical and Functional Stability of Cape Gooseberry (Physalis peruviana L. Vacuu

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Peña Correa Ruth Fabiola

2013-08-01

Full Text Available Resumen. Debido a la creciente demanda de alimentossaludables, la industria alimentaria está mejorando el valornutritivo de estos, modificando su composición nutricional.Las frutas tropicales son ampliamente aceptadas por losconsumidores y a la vez representan una alternativa ideal para la obtención de alimentos funcionales a través de la incorporación de vitaminas y minerales. El objetivo de este estudio fue evaluar, en el transcurso del tiempo, variaciones en las propiedades fisicoquímicas, el contenido de vitaminas (C, B9, D y E y calcio, y la capacidad antioxidante (Folin, DPPH• y ABTS•+, de un producto de uchuva mínimamente procesado, fortificado por la técnica de impregnación a vacío (IV. Los resultados indican que una porción de 200 g de uchuva fortificada aporta el 81,6%; 72,3%; 38,9% y 50,2% de los valores diarios de referencia (VDR respectivos de las vitaminas B9, C, D y E, y el 15,4% de los de calcio. Durante el almacenamiento se encontró disminución de la concentración de las vitaminas B9 y E. Un comportamiento similar al de la vitamina E se presentó en la capacidad antioxidante (CA medida en la fracción liposoluble. La incorporación de componentes fisiológicamente activos en el interior de la estructura de las uchuvas mediante la técnica de IV, le confieren a la fruta mejores propiedades antioxidantes yfuncionales respecto a las uchuvas frescas. / Abstract. Due to the increasing demand of healthy foods, the food industry is improving the nutritional value of these by changing their nutritional composition. Tropical fruits are widelyaccepted by consumers and are an ideal alternative for obtaining functional foods through the addition of vitamins and minerals. The aim of this study was to evaluate, over time, variations in the physicochemical properties, vitamins (C, B9, D and E and calcium, and the antioxidant capacity (Folin, DPPH• and ABTS•+, in a cape gooseberry minimally processed product, fortified by

Methods and statistics for combining motif match scores.

Science.gov (United States)

Bailey, T L; Gribskov, M

1998-01-01

Position-specific scoring matrices are useful for representing and searching for protein sequence motifs. A sequence family can often be described by a group of one or more motifs, and an effective search must combine the scores for matching a sequence to each of the motifs in the group. We describe three methods for combining match scores and estimating the statistical significance of the combined scores and evaluate the search quality (classification accuracy) and the accuracy of the estimate of statistical significance of each. The three methods are: 1) sum of scores, 2) sum of reduced variates, 3) product of score p-values. We show that method 3) is superior to the other two methods in both regards, and that combining motif scores indeed gives better search accuracy. The MAST sequence homology search algorithm utilizing the product of p-values scoring method is available for interactive use and downloading at URL http:/(/)www.sdsc.edu/MEME.

Influence of the sintering temperature on the Sr content in a Ca{sub (1−x−y)}Ce{sub x}Sr{sub y}Al{sub z}Ti{sub (1−z)}O{sub 3} perovskite (x = 0.04–0.16) co-doped with Ce

Energy Technology Data Exchange (ETDEWEB)

Kamel, Nour-el-hayet; Mouheb, Yasmina, E-mail: mouhebyascrna@hotmail.com; Kamel, Ziane; Moudir, Dalila; Aouchiche, Fairouz; Arabi, Azeddine

2016-08-15

A Sr-Ce co-doped perovskite, with the chemical formula: Ca{sub (1−x−y)}Ce{sub x}Sr{sub y}Al{sub z}Ti{sub (1−z)}O{sub 3} (y = 0.04, 0.08, 0.12 and 0.16, x = 0.05) is synthesized by sol–gel process. The influence of the sintering temperature, Ts, on the rate of inserted Sr was investigated at 1223, 1373 and 1473 K. The Sr amount sequestered in the perovskite reaches 85% (y = 0.16, 9.50 wt%) for Ts = 1373 K, giving sintering densities between 3.520 and 4.400. XRD analysis reveals an orthorhombic CaTiO{sub 3} structure. The lattice parameters obey to Vegard’s law for Ts = 1373 and 1473 K. SEM analysis shows orthorhombic grains of 0.514 μm × 1 μm mean dimensions. MCC1 and MCC2 tests, performed on minerals sintered at 1373 K, indicate that the most durable one is that containing 9.50 wt% Sr. MCC1 test gave 6.998·10{sup −6} g/cm{sup 2} d of Sr, and MCC2 2.143·10{sup −4} g/cm{sup 2} d of Ce. The temperature favors the Sr dissolution to the detriment of Ce. The Ca dissolution rate reaches 1.002·10{sup −6} to 2.005·10{sup −6} g/cm{sup 2} d. - Highlights: • Ca{sub (1−x−y)}Ce{sub x}Sr{sub y}Al{sub z}Ti{sub (1−z)}O{sub 3} perovskite is synthesized by sol–gel. • The influence of the sintering temperature, Ts, on the rate of inserted Sr was investigated at 1223, 1373 and 1473 K. • 85% of total Sr was sequestered in the perovskite for Ts = 1373 K. • MCC1 and MCC2 leach tests indicate that the most durable mineral is that containing 9.50 wt.% Sr. • MCC1 test gave 8.10 10{sup −10} kg/m{sup 2}.d Sr. The lower is the leaching temperature the higher is the mineral durability.

MOCCS: Clarifying DNA-binding motif ambiguity using ChIP-Seq data.

Science.gov (United States)

Ozaki, Haruka; Iwasaki, Wataru

2016-08-01

As a key mechanism of gene regulation, transcription factors (TFs) bind to DNA by recognizing specific short sequence patterns that are called DNA-binding motifs. A single TF can accept ambiguity within its DNA-binding motifs, which comprise both canonical (typical) and non-canonical motifs. Clarification of such DNA-binding motif ambiguity is crucial for revealing gene regulatory networks and evaluating mutations in cis-regulatory elements. Although chromatin immunoprecipitation sequencing (ChIP-seq) now provides abundant data on the genomic sequences to which a given TF binds, existing motif discovery methods are unable to directly answer whether a given TF can bind to a specific DNA-binding motif. Here, we report a method for clarifying the DNA-binding motif ambiguity, MOCCS. Given ChIP-Seq data of any TF, MOCCS comprehensively analyzes and describes every k-mer to which that TF binds. Analysis of simulated datasets revealed that MOCCS is applicable to various ChIP-Seq datasets, requiring only a few minutes per dataset. Application to the ENCODE ChIP-Seq datasets proved that MOCCS directly evaluates whether a given TF binds to each DNA-binding motif, even if known position weight matrix models do not provide sufficient information on DNA-binding motif ambiguity. Furthermore, users are not required to provide numerous parameters or background genomic sequence models that are typically unavailable. MOCCS is implemented in Perl and R and is freely available via https://github.com/yuifu/moccs. By complementing existing motif-discovery software, MOCCS will contribute to the basic understanding of how the genome controls diverse cellular processes via DNA-protein interactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

4,5,7,8,17-Pentahydroxy-14,18-dimethyl-6-methylene-3,10-dioxapentacyclo[9.8.0.01,7.04,19.013,18]nonadec-14-ene-9,16-dione methanol solvate dihydrate

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Chin Hoe Teh

2009-04-01

Full Text Available The title quassinoid compound, C20H24O9·CH3OH·2H2O, is a natural eurycomanone isolated from the roots of Eurycoma longifolia. The molecules contain a fused five-ring system, with one tetrahydrofuran ring adopting an envelope conformation, one tetrahydropyran-2-one ring in a screw boat conformation, one cyclohexenone ring in a half-chair conformation and two cyclohexane rings in chair conformations. Intramolecular C—H...O interactions generate S(5 ring motifs and an O—H...O interaction generates an S(7 ring motif. In the crystal, molecules are linked via intermolecular O—H...O interactions along the b axis and further stacked along a axis. The absolute configuration of the title compound was inferred from previously solved structures of its analogues.

Design of potent inhibitors of human RAD51 recombinase based on BRC motifs of BRCA2 protein: modeling and experimental validation of a chimera peptide.

KAUST Repository

Nomme, Julian; Renodon-Corniè re, Axelle; Asanomi, Yuya; Sakaguchi, Kazuyasu; Stasiak, Alicja Z; Stasiak, Andrzej; Norden, Bengt; Tran, Vinh; Takahashi, Masayuki

2010-01-01

We have previously shown that a 28-amino acid peptide derived from the BRC4 motif of BRCA2 tumor suppressor inhibits selectively human RAD51 recombinase (HsRad51). With the aim of designing better inhibitors for cancer treatment, we combined an in silico docking approach with in vitro biochemical testing to construct a highly efficient chimera peptide from eight existing human BRC motifs. We built a molecular model of all BRC motifs complexed with HsRad51 based on the crystal structure of the BRC4 motif-HsRad51 complex, computed the interaction energy of each residue in each BRC motif, and selected the best amino acid residue at each binding position. This analysis enabled us to propose four amino acid substitutions in the BRC4 motif. Three of these increased the inhibitory effect in vitro, and this effect was found to be additive. We thus obtained a peptide that is about 10 times more efficient in inhibiting HsRad51-ssDNA complex formation than the original peptide.

Design of potent inhibitors of human RAD51 recombinase based on BRC motifs of BRCA2 protein: modeling and experimental validation of a chimera peptide.

KAUST Repository

Nomme, Julian

2010-08-01

We have previously shown that a 28-amino acid peptide derived from the BRC4 motif of BRCA2 tumor suppressor inhibits selectively human RAD51 recombinase (HsRad51). With the aim of designing better inhibitors for cancer treatment, we combined an in silico docking approach with in vitro biochemical testing to construct a highly efficient chimera peptide from eight existing human BRC motifs. We built a molecular model of all BRC motifs complexed with HsRad51 based on the crystal structure of the BRC4 motif-HsRad51 complex, computed the interaction energy of each residue in each BRC motif, and selected the best amino acid residue at each binding position. This analysis enabled us to propose four amino acid substitutions in the BRC4 motif. Three of these increased the inhibitory effect in vitro, and this effect was found to be additive. We thus obtained a peptide that is about 10 times more efficient in inhibiting HsRad51-ssDNA complex formation than the original peptide.

Low-dimensional morphospace of topological motifs in human fMRI brain networks

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Sarah E. Morgan

2018-06-01

Full Text Available We present a low-dimensional morphospace of fMRI brain networks, where axes are defined in a data-driven manner based on the network motifs. The morphospace allows us to identify the key variations in healthy fMRI networks in terms of their underlying motifs, and we observe that two principal components (PCs can account for 97% of the motif variability. The first PC of the motif distribution is correlated with efficiency and inversely correlated with transitivity. Hence this axis approximately conforms to the well-known economical small-world trade-off between integration and segregation in brain networks. Finally, we show that the economical clustering generative model proposed by Vértes et al. (2012 can approximately reproduce the motif morphospace of the real fMRI brain networks, in contrast to other generative models. Overall, the motif morphospace provides a powerful way to visualize the relationships between network properties and to investigate generative or constraining factors in the formation of complex human brain functional networks. Motifs have been described as the building blocks of complex networks. Meanwhile, a morphospace allows networks to be placed in a common space and can reveal the relationships between different network properties and elucidate the driving forces behind network topology. We combine the concepts of motifs and morphospaces to create the first motif morphospace of fMRI brain networks. Crucially, the morphospace axes are defined by the motifs, in a data-driven manner. We observe strong correlations between the networks’ positions in morphospace and their global topological properties, suggesting that motif morphospaces are a powerful way to capture the topology of networks in a low-dimensional space and to compare generative models of brain networks. Motif morphospaces could also be used to study other complex networks’ topologies.

Two-dimensional hydrogen-bonded polymers in the crystal structures of the ammonium salts of phenoxyacetic acid, (4-fluorophenoxyacetic acid and (4-chloro-2-methylphenoxyacetic acid

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Graham Smith

2014-12-01

Full Text Available The structures of the ammonium salts of phenoxyacetic acid, NH4+·C8H6O3−, (I, (4-fluorophenoxyacetic acid, NH4+·C8H5FO3−, (II, and the herbicidally active (4-chloro-2-methylphenoxyacetic acid (MCPA, NH4+·C9H8ClO3−·0.5H2O, (III have been determined. All have two-dimensional layered structures based on inter-species ammonium N—H...O hydrogen-bonding associations, which give core substructures consisting primarily of conjoined cyclic motifs. The crystals of (I and (II are isomorphous with the core comprising R12(5, R12(4 and centrosymmetric R42(8 ring motifs, giving two-dimensional layers lying parallel to (100. In (III, the water molecule of solvation lies on a crystallographic twofold rotation axis and bridges two carboxyl O atoms in an R44(12 hydrogen-bonded motif, creating two R43(10 rings, which together with a conjoined centrosymmetric R42(8 ring incorporating both ammonium cations, generate two-dimensional layers lying parallel to (100. No π–π ring associations are present in any of the structures.

The N-terminal leucine-zipper motif in PTRF/cavin-1 is essential and sufficient for its caveolae-association

Energy Technology Data Exchange (ETDEWEB)

Wei, Zhuang [State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China); Laboratory of System Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China); Zou, Xinle [State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China); Wang, Hongzhong; Lei, Jigang; Wu, Yuan [State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China); Laboratory of System Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China); Liao, Kan, E-mail: kliao@sibs.ac.cn [State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China); Laboratory of System Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China)

2015-01-16

Highlight: • The N-terminal leucine-zipper motif in PTRF/cavin-1 determines caveolar association. • Different cellular localization of PTRF/cavin-1 influences its serine 389 and 391 phosphorylation state. • PTRF/cavin-1 regulates cell motility via its caveolar association. - Abstract: PTRF/cavin-1 is a protein of two lives. Its reported functions in ribosomal RNA synthesis and in caveolae formation happen in two different cellular locations: nucleus vs. plasma membrane. Here, we identified that the N-terminal leucine-zipper motif in PTRF/cavin-1 was essential for the protein to be associated with caveolae in plasma membrane. It could counteract the effect of nuclear localization sequence in the molecule (AA 235–251). Deletion of this leucine-zipper motif from PTRF/cavin-1 caused the mutant to be exclusively localized in nuclei. The fusion of this leucine-zipper motif with histone 2A, which is a nuclear protein, could induce the fusion protein to be exported from nucleus. Cell migration was greatly inhibited in PTRF/cavin-1{sup −/−} mouse embryonic fibroblasts (MEFs). The inhibited cell motility could only be rescued by exogenous cavin-1 but not the leucine-zipper motif deleted cavin-1 mutant. Plasma membrane dynamics is an important factor in cell motility control. Our results suggested that the membrane dynamics in cell migration is affected by caveolae associated PTRF/cavin-1.

The N-terminal leucine-zipper motif in PTRF/cavin-1 is essential and sufficient for its caveolae-association

International Nuclear Information System (INIS)

Wei, Zhuang; Zou, Xinle; Wang, Hongzhong; Lei, Jigang; Wu, Yuan; Liao, Kan

2015-01-01

Highlight: • The N-terminal leucine-zipper motif in PTRF/cavin-1 determines caveolar association. • Different cellular localization of PTRF/cavin-1 influences its serine 389 and 391 phosphorylation state. • PTRF/cavin-1 regulates cell motility via its caveolar association. - Abstract: PTRF/cavin-1 is a protein of two lives. Its reported functions in ribosomal RNA synthesis and in caveolae formation happen in two different cellular locations: nucleus vs. plasma membrane. Here, we identified that the N-terminal leucine-zipper motif in PTRF/cavin-1 was essential for the protein to be associated with caveolae in plasma membrane. It could counteract the effect of nuclear localization sequence in the molecule (AA 235–251). Deletion of this leucine-zipper motif from PTRF/cavin-1 caused the mutant to be exclusively localized in nuclei. The fusion of this leucine-zipper motif with histone 2A, which is a nuclear protein, could induce the fusion protein to be exported from nucleus. Cell migration was greatly inhibited in PTRF/cavin-1 −/− mouse embryonic fibroblasts (MEFs). The inhibited cell motility could only be rescued by exogenous cavin-1 but not the leucine-zipper motif deleted cavin-1 mutant. Plasma membrane dynamics is an important factor in cell motility control. Our results suggested that the membrane dynamics in cell migration is affected by caveolae associated PTRF/cavin-1

Memetic algorithms for de novo motif-finding in biomedical sequences.

Science.gov (United States)

Bi, Chengpeng

2012-09-01

The objectives of this study are to design and implement a new memetic algorithm for de novo motif discovery, which is then applied to detect important signals hidden in various biomedical molecular sequences. In this paper, memetic algorithms are developed and tested in de novo motif-finding problems. Several strategies in the algorithm design are employed that are to not only efficiently explore the multiple sequence local alignment space, but also effectively uncover the molecular signals. As a result, there are a number of key features in the implementation of the memetic motif-finding algorithm (MaMotif), including a chromosome replacement operator, a chromosome alteration-aware local search operator, a truncated local search strategy, and a stochastic operation of local search imposed on individual learning. To test the new algorithm, we compare MaMotif with a few of other similar algorithms using simulated and experimental data including genomic DNA, primary microRNA sequences (let-7 family), and transmembrane protein sequences. The new memetic motif-finding algorithm is successfully implemented in C++, and exhaustively tested with various simulated and real biological sequences. In the simulation, it shows that MaMotif is the most time-efficient algorithm compared with others, that is, it runs 2 times faster than the expectation maximization (EM) method and 16 times faster than the genetic algorithm-based EM hybrid. In both simulated and experimental testing, results show that the new algorithm is compared favorably or superior to other algorithms. Notably, MaMotif is able to successfully discover the transcription factors' binding sites in the chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) data, correctly uncover the RNA splicing signals in gene expression, and precisely find the highly conserved helix motif in the transmembrane protein sequences, as well as rightly detect the palindromic segments in the primary micro

G-Quadruplexes influence pri-microRNA processing.

Science.gov (United States)

Rouleau, Samuel G; Garant, Jean-Michel; Bolduc, François; Bisaillon, Martin; Perreault, Jean-Pierre

2018-02-01

RNA G-Quadruplexes (G4) have been shown to possess many biological functions, including the regulation of microRNA (miRNA) biogenesis and function. However, their impact on pri-miRNA processing remains unknown. We identified G4 located near the Drosha cleavage site in three distinct pri-miRNAs: pri-mir200c, pri-mir451a, and pri-mir497. The folding of the potential G4 motifs was determined in solution. Subsequently, mutations disrupting G4 folding led to important changes in the mature miRNAs levels in cells. Moreover, using small antisense oligonucleotides binding to the pri-miRNA, it was possible to modulate, either positively or negatively, the mature miRNA levels. Together, these data demonstrate that G4 motifs could contribute to the regulation of pri-mRNA processing, a novel role for G4. Considering that bio-informatics screening indicates that between 9% and 50% of all pri-miRNAs contain a putative G4, these structures possess interesting potential as future therapeutic targets.

Discovering Motifs in Biological Sequences Using the Micron Automata Processor.

Science.gov (United States)

Roy, Indranil; Aluru, Srinivas

2016-01-01

Finding approximately conserved sequences, called motifs, across multiple DNA or protein sequences is an important problem in computational biology. In this paper, we consider the (l, d) motif search problem of identifying one or more motifs of length l present in at least q of the n given sequences, with each occurrence differing from the motif in at most d substitutions. The problem is known to be NP-complete, and the largest solved instance reported to date is (26,11). We propose a novel algorithm for the (l,d) motif search problem using streaming execution over a large set of non-deterministic finite automata (NFA). This solution is designed to take advantage of the micron automata processor, a new technology close to deployment that can simultaneously execute multiple NFA in parallel. We demonstrate the capability for solving much larger instances of the (l, d) motif search problem using the resources available within a single automata processor board, by estimating run-times for problem instances (39,18) and (40,17). The paper serves as a useful guide to solving problems using this new accelerator technology.

PISMA: A Visual Representation of Motif Distribution in DNA Sequences

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Rogelio Alcántara-Silva

2017-03-01

Full Text Available Background: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code–like, as a gene-map–like, and as a transcript scheme. Results: We obtained graphical schemes of the CpG site distribution from 91 human papillomavirus genomes. Also, we present 2 analyses: one of DNA motifs associated with either methylation-resistant or methylation-sensitive CpG islands and another analysis of motifs associated with exosome RNA secretion. Availability and Implementation: PISMA is developed in Java; it is executable in any type of hardware and in diverse operating systems. PISMA is freely available to noncommercial users. The English version and the User Manual are provided in Supplementary Files 1 and 2, and a Spanish version is available at www.biomedicas.unam.mx/wp-content/software/pisma.zip and www.biomedicas.unam.mx/wp-content/pdf/manual/pisma.pdf .

Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network

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Barabási Albert-László

2004-01-01

Full Text Available Abstract Background Transcriptional regulation of cellular functions is carried out through a complex network of interactions among transcription factors and the promoter regions of genes and operons regulated by them.To better understand the system-level function of such networks simplification of their architecture was previously achieved by identifying the motifs present in the network, which are small, overrepresented, topologically distinct regulatory interaction patterns (subgraphs. However, the interaction of such motifs with each other, and their form of integration into the full network has not been previously examined. Results By studying the transcriptional regulatory network of the bacterium, Escherichia coli, we demonstrate that the two previously identified motif types in the network (i.e., feed-forward loops and bi-fan motifs do not exist in isolation, but rather aggregate into homologous motif clusters that largely overlap with known biological functions. Moreover, these clusters further coalesce into a supercluster, thus establishing distinct topological hierarchies that show global statistical properties similar to the whole network. Targeted removal of motif links disintegrates the network into small, isolated clusters, while random disruptions of equal number of links do not cause such an effect. Conclusion Individual motifs aggregate into homologous motif clusters and a supercluster forming the backbone of the E. coli transcriptional regulatory network and play a central role in defining its global topological organization.

Interaction between Y chromosome haplogroup O3* and 4-n-octylphenol exposure reduces the susceptibility to spermatogenic impairment in Han Chinese.

Science.gov (United States)

Hu, Weiyue; Chen, Minjian; Ji, Juan; Qin, Yufeng; Zhang, Feng; Xu, Miaofei; Wu, Wei; Du, Guizhen; Wu, Di; Han, Xiumei; Jin, Li; Xia, Yankai; Lu, Chuncheng; Wang, Xinru

2017-10-01

Certain genetic background (mainly Y chromosome haplogroups, Y-hg) may modify the susceptibility of certain environmental exposure to some diseases. Compared with respective main effects of genetic background or environmental exposure, interactions between them reflect more realistic combined effects on the susceptibility to a disease. To identify the interactions on spermatogenic impairment, we performed Y chromosome haplotyping and measurement of 9 urinary phenols concentrations in 774 infertile males and 520 healthy controls in a Han Chinese population, and likelihood ratio tests were used to examine the interactions between Y-hgs and phenols. Originally, we observed that Y-hg C and Y-hg F * might modify the susceptibility to male infertility with urinary 4-n-octylphenol (4-n-OP) level (P inter = 0.005 and 0.019, respectively). Subsequently, based on our results, two panels were tested to identify the possible protective sub-branches of Y-hg F * to 4-n-OP exposure, and Y-hg O3 * was uncovered to interact with 4-n-OP (P inter = 0.019). In conclusion, while 4-n-OP shows an adverse effect on spermatogenesis, Y-hg O3 * makes individuals more adaptive to such an effect for maintaining basic reproductive capacity. Copyright © 2017 Elsevier Inc. All rights reserved.

MODA: an efficient algorithm for network motif discovery in biological networks.

Science.gov (United States)

Omidi, Saeed; Schreiber, Falk; Masoudi-Nejad, Ali

2009-10-01

In recent years, interest has been growing in the study of complex networks. Since Erdös and Rényi (1960) proposed their random graph model about 50 years ago, many researchers have investigated and shaped this field. Many indicators have been proposed to assess the global features of networks. Recently, an active research area has developed in studying local features named motifs as the building blocks of networks. Unfortunately, network motif discovery is a computationally hard problem and finding rather large motifs (larger than 8 nodes) by means of current algorithms is impractical as it demands too much computational effort. In this paper, we present a new algorithm (MODA) that incorporates techniques such as a pattern growth approach for extracting larger motifs efficiently. We have tested our algorithm and found it able to identify larger motifs with more than 8 nodes more efficiently than most of the current state-of-the-art motif discovery algorithms. While most of the algorithms rely on induced subgraphs as motifs of the networks, MODA is able to extract both induced and non-induced subgraphs simultaneously. The MODA source code is freely available at: http://LBB.ut.ac.ir/Download/LBBsoft/MODA/

The influence of {gamma}-irradiation on electrophysical properties of spinel-based oxide ceramics

Energy Technology Data Exchange (ETDEWEB)

Kovalskiy, A.P.; Shpotyuk, O.I. E-mail: karat@ipm.lviv.ua; Hadzaman, I.V.; Mrooz, O.Ya.; Vakiv, M.M

2000-05-02

The influence of {sup 60}Co {gamma}-irradiation with 1.25 MeV average energy and 1 MGy absorbed dose on electrophysical properties of Cu-, Ni-, Co- and Mn-based spinel ceramic materials in the Cu{sub x}Ni{sub 1-x-y}Co{sub 2y}Mn{sub 2-y}O{sub 4} (0,1{<=}x{<=}0,8;0,1{<=}y{<=}0,9-x) system is investigated. The {gamma}-induced increasing of the electrical resistance is observed for the investigated samples of various compositions. It is supposed that these changes are explained by cationic redistribution in the spinel sublattices of the ceramics.

9 CFR 355.4 - Application.

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2010-01-01

... CERTIFICATION CERTIFIED PRODUCTS FOR DOGS, CATS, AND OTHER CARNIVORA; INSPECTION, CERTIFICATION, AND... 9 Animals and Animal Products 2 2010-01-01 2010-01-01 false Application. 355.4 Section 355.4 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE AGENCY...

Assessing local structure motifs using order parameters for motif recognition, interstitial identification, and diffusion path characterization

Science.gov (United States)

Zimmermann, Nils E. R.; Horton, Matthew K.; Jain, Anubhav; Haranczyk, Maciej

2017-11-01

Structure-property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells) of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal closed packed-like environments. Here, we showcase the usefulness of local order parameters to identify these basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP) database (61,422 compounds) for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT) facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO2-spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.

CITOGENETICA DE HIBRIDOS ENTRE TURNERA GRANDIDENTATA (4x Y T. SUBULATA Y T. SCABRA (2x (TURNERACEAE

Directory of Open Access Journals (Sweden)

Aveliano Fernández

1993-01-01

Full Text Available Turnera subulata y T.scabra, 2n = 2x = 10, se cruzaron con T.grandidentata, 2n = 4x = 20, y los híbridos obtenidos se estudiaron citológicamente para determinar la relación entre estas especies. Todos los híbridos presentaron 2n = 3x = 15 y meiosis irregular. En T.subulata x T.grandidentata se hallo una asociación cromosómica media de 4,28 univalentes, 4,16 bivalentes y 0,73 trivalentes. T.scabra x T.grandidentata tuvieron una asociación cromosómica media de 4,53 univalentes, 4,42 bivalentes, 0,53 trivalentes y 0.03 cuadrivalents. El estudio citogenético de estos híbridos indica que estas tres especies tienen el mismo genoma básico. Las fórmulas genómicas Asu Asu para T.subulata, Asc Asc para T.scabra y AgAgArAr para T.grandidentata fueron propuestas en trabajos anteriores. Las asociaciones y las configuraciones que se encuentran en los híbridos analizados en éste estudio avalan las fórmulas genómicas propuestas.

9 CFR 4.11 - Stipulations.

Science.gov (United States)

2010-01-01

... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Stipulations. 4.11 Section 4.11 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE ANIMAL WELFARE RULES OF PRACTICE GOVERNING PROCEEDINGS UNDER THE ANIMAL WELFARE ACT Supplemental Rules of...

A specific A/T polymorphism in Western tyrosine phosphorylation B-motifs regulates Helicobacter pylori CagA epithelial cell interactions.

Directory of Open Access Journals (Sweden)

Xue-Song Zhang

2015-02-01

Full Text Available Helicobacter pylori persistently colonizes the human stomach, with mixed roles in human health. The CagA protein, a key host-interaction factor, is translocated by a type IV secretion system into host epithelial cells, where its EPIYA tyrosine phosphorylation motifs (TPMs are recognized by host cell kinases, leading to multiple host cell signaling cascades. The CagA TPMs have been described as type A, B, C or D, each with a specific conserved amino acid sequence surrounding EPIYA. Database searching revealed strong non-random distribution of the B-motifs (including EPIYA and EPIYT in Western H. pylori isolates. In silico analysis of Western H. pylori CagA sequences provided evidence that the EPIYT B-TPMs are significantly less associated with gastric cancer than the EPIYA B-TPMs. By generating and using a phosphorylated CagA B-TPM-specific antibody, we demonstrated the phosphorylated state of the CagA B-TPM EPIYT during H. pylori co-culture with host cells. We also showed that within host cells, CagA interaction with phosphoinositol 3-kinase (PI3-kinase was B-TPM tyrosine-phosphorylation-dependent, and the recombinant CagA with EPIYT B-TPM had higher affinity to PI3-kinase and enhanced induction of AKT than the isogenic CagA with EPIYA B-TPM. Structural modeling of the CagA B-TPM motif bound to PI3-kinase indicated that the threonine residue at the pY+1 position forms a side-chain hydrogen bond to N-417 of PI3-kinase, which cannot be formed by alanine. During co-culture with AGS cells, an H. pylori strain with a CagA EPIYT B-TPM had significantly attenuated induction of interleukin-8 and hummingbird phenotype, compared to the isogenic strain with B-TPM EPIYA. These results suggest that the A/T polymorphisms could regulate CagA activity through interfering with host signaling pathways related to carcinogenesis, thus influencing cancer risk.

Disabling Cas9 by an anti-CRISPR DNA mimic.

Science.gov (United States)

Shin, Jiyung; Jiang, Fuguo; Liu, Jun-Jie; Bray, Nicolas L; Rauch, Benjamin J; Baik, Seung Hyun; Nogales, Eva; Bondy-Denomy, Joseph; Corn, Jacob E; Doudna, Jennifer A

2017-07-01

CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 gene editing technology is derived from a microbial adaptive immune system, where bacteriophages are often the intended target. Natural inhibitors of CRISPR-Cas9 enable phages to evade immunity and show promise in controlling Cas9-mediated gene editing in human cells. However, the mechanism of CRISPR-Cas9 inhibition is not known, and the potential applications for Cas9 inhibitor proteins in mammalian cells have not been fully established. We show that the anti-CRISPR protein AcrIIA4 binds only to assembled Cas9-single-guide RNA (sgRNA) complexes and not to Cas9 protein alone. A 3.9 Å resolution cryo-electron microscopy structure of the Cas9-sgRNA-AcrIIA4 complex revealed that the surface of AcrIIA4 is highly acidic and binds with a 1:1 stoichiometry to a region of Cas9 that normally engages the DNA protospacer adjacent motif. Consistent with this binding mode, order-of-addition experiments showed that AcrIIA4 interferes with DNA recognition but has no effect on preformed Cas9-sgRNA-DNA complexes. Timed delivery of AcrIIA4 into human cells as either protein or expression plasmid allows on-target Cas9-mediated gene editing while reducing off-target edits. These results provide a mechanistic understanding of AcrIIA4 function and demonstrate that inhibitors can modulate the extent and outcomes of Cas9-mediated gene editing.

INFLUENCIA DE LA QUÍMICA SUPERFICIAL EN LA ENTALPÍA DE INMERSIÓN DE CARBONES ACTIVADOS EN SOLUCIONES ACUOSAS DE FENOL Y 4-NITRO FENOL

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Luisa Fernanda Navarrete

2008-04-01

Full Text Available Se estudian las interacciones de cinco muestras de carbón activado obtenidas a partir de diferentes materiales lignocelulósicos, con diferente grado de activación alrededor de 20%, con soluciones acuosas de fenol y 4-nitro fenol mediante la determinación de las entalpías de inmersión. Se establece que los carbones activados obtenidos son de carácter básico y presentan valores para el punto de carga cero (PZC, que varían entre 7,4 y 9,7, y contenidos de basicidad total mayores en todos los casos que los valores obtenidos para la acidez total. Se determina la entalpía de inmersión de los carbones activados en soluciones de NaOH y HCl con valores mayores para la entalpía de inmersión en HCl que se encuentran entre 32,6 y 68,3 Jg-1. Las entalpías de inmersión en solución de fenol se hallan entre 7,6 y 13,9 Jg-1, y para el caso del 4-nitro fenol se encuentran entre 12,7 y 20,5 Jg-1; con valores mayores para todas las muestras para la inmersión en el segundo compuesto.

Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins

Science.gov (United States)

Kinjo, Akira R.; Nakamura, Haruki

2012-01-01

Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs that represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures. PMID:22347478

Probing structural changes of self assembled i-motif DNA

KAUST Repository

Lee, Iljoon; Patil, Sachin; Fhayli, Karim; Alsaiari, Shahad K.; Khashab, Niveen M.

2015-01-01

We report an i-motif structural probing system based on Thioflavin T (ThT) as a fluorescent sensor. This probe can discriminate the structural changes of RET and Rb i-motif sequences according to pH change. This journal is

Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated

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Down Thomas A

2010-09-01

Full Text Available Abstract Background DNA methylation can regulate gene expression by modulating the interaction between DNA and proteins or protein complexes. Conserved consensus motifs exist across the human genome ("predicted transcription factor binding sites": "predicted TFBS" but the large majority of these are proven by chromatin immunoprecipitation and high throughput sequencing (ChIP-seq not to be biological transcription factor binding sites ("empirical TFBS". We hypothesize that DNA methylation at conserved consensus motifs prevents promiscuous or disorderly transcription factor binding. Results Using genome-wide methylation maps of the human heart and sperm, we found that all conserved consensus motifs as well as the subset of those that reside outside CpG islands have an aggregate profile of hyper-methylation. In contrast, empirical TFBS with conserved consensus motifs have a profile of hypo-methylation. 40% of empirical TFBS with conserved consensus motifs resided in CpG islands whereas only 7% of all conserved consensus motifs were in CpG islands. Finally we further identified a minority subset of TF whose profiles are either hypo-methylated or neutral at their respective conserved consensus motifs implicating that these TF may be responsible for establishing or maintaining an un-methylated DNA state, or whose binding is not regulated by DNA methylation. Conclusions Our analysis supports the hypothesis that at least for a subset of TF, empirical binding to conserved consensus motifs genome-wide may be controlled by DNA methylation.

9 CFR 89.4 - Watering.

Science.gov (United States)

2010-01-01

... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Watering. 89.4 Section 89.4 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE INTERSTATE TRANSPORTATION OF ANIMALS (INCLUDING POULTRY) AND ANIMAL PRODUCTS STATEMENT OF POLICY UNDER THE TWENTY-EIGHT HOUR...

Planck intermediate results I. Further validation of new Planck clusters with XMM-Newton

DEFF Research Database (Denmark)

Aghanim, N.; Collaboration, Planck; Arnaud, M.

2012-01-01

of candidates previously confirmed with XMM-Newton. The X-ray and optical redshifts for a total of 20 clusters are found to be in excellent agreement. We also show that useful lower limits can be put on cluster redshifts using X-ray data only via the use of the Y-X vs. Y-SZ and X-ray flux F-X vs. Y-SZ relations....

Thermoelectric Properties of the Chemically Doped Ca3Co4O9 System: A Structural Perspective

Science.gov (United States)

Wu, Tao; Tyson, Trevor; Wang, Hsin; Li, Qiang

2010-03-01

Cu doped and Y doped [Ca2CoO3][CoO2]1.61 (referred to as Ca3Co4O9) were prepared by solid state reaction. Temperature dependent thermoelectric properties, resistivity (ρ), Seeback coefficient (S) and thermal conductivity (κ), were measured. As seen before, it is found that doping by Cu and Y significantly enhances the thermoelectric properties. In order to understand the origin of these changes in properties in terms of the atomic structure, synchrotron x-ray diffraction and x-ray absorption spectroscopy were applied to probe the change in the average structure and the location of the dopants. The details of the location and coordination of Co and Y in the host lattice and the effect on the figure of merit are discussed. This work is supported by DOE Grant DE-FG02-07ER46402.

El impacto del 9 de abril en Cali y el Valle del Cauca

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Carlos Andrés Charry Joya

2009-12-01

Full Text Available DESDE UNA PERSPECTIVA PROCESUAL, ESTE ARTÍcULO EXPLORA y ANALIZA LAS formas de configuración social de poder regional durante los años previos al asesinato de Jorge Eliécer Gaitán y el impacto que el magnicidio tuvo en dicho proceso. El autor destaca el mejor posicionamiento logrado por los grupos sociales marginados como consecuencia de las transformaciones sociopoliticas ocurridas en la década de 1930 y 1940, señala las tensiones que esto generó entre los sectores establecidos y, tras el 9 de abril de 1948, nota un cambio considerable en los equilibrios de poder entre los sectores sociales que contraviene la tendencia antes mencionada.

Molecular and clinical description of a girl with a 46,X,t(Y;4)(q11.2;p16)/45,X,der(4)t(Y;4)(q11.2;p16) karyotype and a small cryptic 4p subtelomeric deletion.

Science.gov (United States)

Zahed, Laila; Sismani, Carolina; Ioannides, M; Saleh, Monzer; Koumbaris, G; Kenj, Mazen; Abdallah, Amal; Ayyache, Maya; Patsalis, Philippos

2008-04-01

We report on a 13-year-old female with short stature, minimal axillary and pubic hair, no breast development, absence of uterus and ovaries, with the following karyotype on lymphocyte cultures: 46,X,t(Y;4)(q11.2;p16)[40]/45,X,der(4)t(Y;4)(q11.2;p16)[10]. Loss of the small derivative Y chromosome in 20% of the cells was also confirmed in skin fibroblast cultures. FISH analyses using Y centromere, SRY, subtelomere XpYp/XqYq, Y and 4 painting probes, confirmed the cytogenetic findings. High-resolution STS analyses using 40 markers covering the Y chromosome did not identify any deletion on the Y. However, de novo absence of the 4p subtelomeric region was noted by FISH, although this deletion was not revealed by Array-CGH at 1 Mb resolution, the last array clone being 0.35 or 1 Mb distal to the 4p FISH probe. The female phenotype of this patient must be due to the loss of the derivative Y chromosomes in some of her cells, especially the gonads, while the 4p subtelomeric deletion does not seem to contribute to her phenotype. Copyright 2008 Wiley-Liss, Inc.

BlockLogo: Visualization of peptide and sequence motif conservation

DEFF Research Database (Denmark)

Olsen, Lars Rønn; Kudahl, Ulrich Johan; Simon, Christian

2013-01-01

BlockLogo is a web-server application for the visualization of protein and nucleotide fragments, continuous protein sequence motifs, and discontinuous sequence motifs using calculation of block entropy from multiple sequence alignments. The user input consists of a multiple sequence alignment, se...

Desigualdades educacionales en mortalidad y supervivencia de mujeres y hombres de las Américas, 1990-2010

Directory of Open Access Journals (Sweden)

Mariana Haeberer

2015-08-01

Full Text Available OBJETIVO: Analizar la magnitud y tendencias de las desigualdades educacionales en mortalidad y supervivencia de mujeres y hombres entre países de las Américas. MÉTODOS: Se calcularon métricas de brecha y gradiente de desigualdad en mortalidad adulta, edad promedio de muerte, esperanza de vida y esperanza de vida saludable, según nivel educativo entre países en hombres y mujeres para 1990 y 2010. RESULTADOS: Entre 1990-2010 el promedio de años de escolaridad aumentó de 8 a 10 sin diferencia entre sexos. La tasa de mortalidad adulta (15-59 años no cambió: 1,9 por 1 000 mujeres y 3,7 por 1 000 hombres. El índice de desigualdad de la pendiente aumentó de -1,0 a -2,0 por 1 000 mujeres y de -1,2 a -4,4 por 1 000 hombres. La esperanza de vida aumentó de 75,6 a 78,7 años en mujeres y de 68,9 a 72,4 en hombres; la desigualdad absoluta disminuyó de 7,8 a 7,2 años en mujeres y aumentó de 7,2 a 9,2 años en hombres. La esperanza de vida saludable aumentó de 63,7 a 65,9 años en mujeres y de 59,5 a 62,5 años en hombres; el índice de desigualdad de la pendiente se redujo de 6,9 a 5,8 años en mujeres y aumentó de 6,9 a 7,8 años en hombres. CONCLUSIONES: Entre países de las Américas, los hombres tienen mayor riesgo de morir, mueren más tempranamente y viven menos años libres de enfermedad y discapacidad que las mujeres; el nivel educativo es un determinante de la mortalidad y la sobrevida en ambos sexos y las desigualdades educacionales son más pronunciadas y ascendentes entre hombres y desproporcionadamente concentradas en las poblaciones socialmente más desaventajadas.

Dicty_cDB: VFN152 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available A: rk*eiis*iiq***lsklfinf*ss*tl**s*sfixx*kfi*siirfhfxy**ksxxnlm nkl*silin*qlninqfqlpplplplppll*ly*mlikvkkfinxriqkxxnxmk*xiix kqxlxxx...xxxxxxgxxxxxxxxxxxx--- ---irefksk*ig*nd**y*nnnsc*rw****m...yhyhylhyfsfikc**k*rnl*ixefksxxxg*ndx*yx nnxsxxxxxxxxxxxxxxxxxxxxxx--- ---LENSKASKLDEMIDNIETTTLVKDGDDSEWVILKL

A self-assembling peptide RADA16-I integrated with spider fibroin uncrystalline motifs

Directory of Open Access Journals (Sweden)

Sun L

2012-02-01

Full Text Available Lijuan Sun1,2, Xiaojun Zhao1,31West China Hospital Laboratory of Nanomedicine and Institute for Nanobiomedical Technology and Membrane Biology, Sichuan University, Chengdu 610041, Sichuan, China; 2Dept of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, Guangdong, China; 3Center for Biomedical Engineering NE47-378, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USAAbstract: Mechanical strength of nanofiber scaffolds formed by the self-assembling peptide RADA16-I or its derivatives is not very good and limits their application. To address this problem, we inserted spidroin uncrystalline motifs, which confer incomparable elasticity and hydrophobicity to spider silk GGAGGS or GPGGY, into the C-terminus of RADA16-I to newly design two peptides: R3 (n-RADARADARADARADA-GGAGGS-c and R4 (n-RADARADARADARADA-GPGGY-c, and then observed the effect of these motifs on biophysical properties of the peptide. Atomic force microscopy, transmitting electron microscopy, and circular dichroism spectroscopy confirm that R3 and R4 display ß-sheet structure and self-assemble into long nanofibers. Compared with R3, the ß-sheet structure and nanofibers formed by R4 are more stable; they change to random coil and unordered aggregation at higher temperature. Rheology measurements indicate that novel peptides form hydrogel when induced by DMEM, and the storage modulus of R3 and R4 hydrogel is 0.5 times and 3 times higher than that of RADA16-I, respectively. Furthermore, R4 hydrogel remarkably promotes growth of liver cell L02 and liver cancer cell SMCC7721 compared with 2D culture, determined by MTT assay. Novel peptides still have potential as hydrophobic drug carriers; they can stabilize pyrene microcrystals in aqueous solution and deliver this into a lipophilic environment, identified by fluorescence emission spectra. Altogether, the spider fibroin motif GPGGY most effectively enhances mechanical

Osmotic and activity coefficients of {y Na2SO4 + (1 - y) ZnSO4}(aq) at T = 298.15 K

International Nuclear Information System (INIS)

Marjanovic, V.; Ninkovic, R.; Miladinovic, J.; Todorovic, M.; Pavicevic, V.

2005-01-01

The osmotic coefficients of the mixed electrolyte solution {y Na 2 SO 4 + (1 - y) ZnSO 4 }(aq) have been measured by the isopiestic method, at T = 298.5 K. The experimental results were treated by Scatchard's, Pitzer-Kim's and Clegg-Pitzer-Brimblecombe's methods for mixed-electrolyte solutions. By these methods, the activity coefficients for Na 2 SO 4 and ZnSO 4 were calculated and compared. The Scatchard interaction parameters are used for calculation of the excess Gibbs free energy as a function of ionic strength and ionic-strength fraction of Na 2 SO 4 . Also, the Zdanovskii's rule of linearity is tested

RegRNA: an integrated web server for identifying regulatory RNA motifs and elements

OpenAIRE

Huang, Hsi-Yuan; Chien, Chia-Hung; Jen, Kuan-Hua; Huang, Hsien-Da

2006-01-01

Numerous regulatory structural motifs have been identified as playing essential roles in transcriptional and post-transcriptional regulation of gene expression. RegRNA is an integrated web server for identifying the homologs of regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs and structural homologs of regulatory RNA motifs can be recognized. The regulatory RNA motifs supported in RegRNA are categorized into several classes: (i) motifs in mRNA 5′-untra...

Assessing Local Structure Motifs Using Order Parameters for Motif Recognition, Interstitial Identification, and Diffusion Path Characterization

Directory of Open Access Journals (Sweden)

Nils E. R. Zimmermann

2017-11-01

Full Text Available Structure–property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors, as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal close packed-like environments. Here, we showcase the usefulness of local order parameters to identify these basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP database (61,422 compounds for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO2-spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.

Isothermal vapour-liquid equilibria data of methanol + propan-2-OL ...

African Journals Online (AJOL)

methylpropan-2-ol binary mixtures are investigated at 333.15k, using gas chromatographic technique. ... The y-x plots reveals that the mixtures methanol + propan-2-ol and methanol +2-methylpropan-2-ol deviate strongly from ideal solution behaviour.

Creation of Hybrid Nanorods From Sequences of Natural Trimeric Fibrous Proteins Using the Fibritin Trimerization Motif

Science.gov (United States)

Papanikolopoulou, Katerina; van Raaij, Mark J.; Mitraki, Anna

Stable, artificial fibrous proteins that can be functionalized open new avenues in fields such as bionanomaterials design and fiber engineering. An important source of inspiration for the creation of such proteins are natural fibrous proteins such as collagen, elastin, insect silks, and fibers from phages and viruses. The fibrous parts of this last class of proteins usually adopt trimeric, β-stranded structural folds and are appended to globular, receptor-binding domains. It has been recently shown that the globular domains are essential for correct folding and trimerization and can be successfully substituted by a very small (27-amino acid) trimerization motif from phage T4 fibritin. The hybrid proteins are correctly folded nanorods that can withstand extreme conditions. When the fibrous part derives from the adenovirus fiber shaft, different tissue-targeting specificities can be engineered into the hybrid proteins, which therefore can be used as gene therapy vectors. The integration of such stable nanorods in devices is also a big challenge in the field of biomechanical design. The fibritin foldon domain is a versatile trimerization motif and can be combined with a variety of fibrous motifs, such as coiled-coil, collagenous, and triple β-stranded motifs, provided the appropriate linkers are used. The combination of different motifs within the same fibrous molecule to create stable rods with multiple functions can even be envisioned. We provide a comprehensive overview of the experimental procedures used for designing, creating, and characterizing hybrid fibrous nanorods using the fibritin trimerization motif.

Structural Properties and Sensing Performance of CeYxOy Sensing Films for Electrolyte-Insulator-Semiconductor pH Sensors.

Science.gov (United States)

Pan, Tung-Ming; Wang, Chih-Wei; Chen, Ching-Yi

2017-06-07

In this study we developed CeY x O y sensing membranes displaying super-Nernstian pH-sensitivity for use in electrolyte-insulator-semiconductor (EIS) pH sensors. We examined the effect of thermal annealing on the structural properties and sensing characteristics of the CeY x O y sensing membranes deposited through reactive co-sputtering onto Si substrates. X-ray diffraction, atomic force microscopy, and X-ray photoelectron spectroscopy revealed the structural, morphological, and chemical features, respectively, of the CeY x O y films after their annealing at 600-900 °C. Among the tested systems, the CeY x O y EIS device prepared with annealing at 800 °C exhibited the highest sensitivity (78.15 mV/pH), the lowest hysteresis voltage (1.4 mV), and the lowest drift rate (0.85 mV/h). Presumably, these annealing conditions optimized the stoichiometry of (CeY)O 2 in the film and its surface roughness while suppressing silicate formation at the CeY x O y -Si interface. We attribute the super-Nernstian pH-sensitivity to the incorporation of Y ions in the Ce framework, thereby decreasing the oxidation state Ce (Ce 4+  → Ce 3+ ) and resulting in less than one electron transferred per proton in the redox reaction.

{sup 4}He channelling studies of U{sub 4}O{sub 9}

Energy Technology Data Exchange (ETDEWEB)

Garrido, Frederico [Centre de Spectrometrie Nucleaire et de Spectrometrie de Masse, CNRS-IN2P3-Universite Paris-Sud, Batiments 104-108, 91405 Orsay (France)]. E-mail: garrido@csnsm.in2p3.fr; Nowicki, Lech [The Andrzej Soltan Institute for Nuclear Studies, Hoza 69, 00-681 Warsaw (Poland); Stonert, Anna [Andrzej Soltan Institute for Nuclear Studies, Hoza 69, 00-681 Warsaw (Poland); Pietraszko, Adam [Institute for Low Temperature and Structural Research, Polish Academy of Science, 50-422 Wroclaw (Poland); Wendler, Elke [Institut fuer Festkoerperphysik, Friedrich-Schiller Universitaet Jena, 07743 Jena (Germany)

2006-08-15

UO{sub 2} and U{sub 4}O{sub 9} single crystals were investigated by means of the {sup 4}He backscattering/channelling technique and the use of the 3032-keV elastic scattering resonance on {sup 16}O. Angular scans obtained for U{sub 4}O{sub 9} were interpreted in the framework of a recently published U{sub 4}O{sub 9} model. It was shown that the U{sub 4}O{sub 9} channelling data can be explained by the aggregation of some O atoms in cuboctahedral clusters, and the displacement of other (U and O) atoms from the UO{sub 2}-type sites. Basing on the combined use of the channelling technique and Monte Carlo simulations we suggest that the displacements of U atoms from their fluorite sites are larger than those determined by the neutron diffraction analysis.

Evolutionarily conserved bias of amino-acid usage refines the definition of PDZ-binding motif

Directory of Open Access Journals (Sweden)

Launey Thomas

2011-06-01

Full Text Available Abstract Background The interactions between PDZ (PSD-95, Dlg, ZO-1 domains and PDZ-binding motifs play central roles in signal transductions within cells. Proteins with PDZ domains bind to PDZ-binding motifs almost exclusively when the motifs are located at the carboxyl (C- terminal ends of their binding partners. However, it remains little explored whether PDZ-binding motifs show any preferential location at the C-terminal ends of proteins, at genome-level. Results Here, we examined the distribution of the type-I (x-x-S/T-x-I/L/V or type-II (x-x-V-x-I/V PDZ-binding motifs in proteins encoded in the genomes of five different species (human, mouse, zebrafish, fruit fly and nematode. We first established that these PDZ-binding motifs are indeed preferentially present at their C-terminal ends. Moreover, we found specific amino acid (AA bias for the 'x' positions in the motifs at the C-terminal ends. In general, hydrophilic AAs were favored. Our genomics-based findings confirm and largely extend the results of previous interaction-based studies, allowing us to propose refined consensus sequences for all of the examined PDZ-binding motifs. An ontological analysis revealed that the refined motifs are functionally relevant since a large fraction of the proteins bearing the motif appear to be involved in signal transduction. Furthermore, co-precipitation experiments confirmed two new protein interactions predicted by our genomics-based approach. Finally, we show that influenza virus pathogenicity can be correlated with PDZ-binding motif, with high-virulence viral proteins bearing a refined PDZ-binding motif. Conclusions Our refined definition of PDZ-binding motifs should provide important clues for identifying functional PDZ-binding motifs and proteins involved in signal transduction.

Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs

LENUS (Irish Health Repository)

Casey, Fergal

2011-08-22

Abstract Background Gene and protein interactions are commonly represented as networks, with the genes or proteins comprising the nodes and the relationship between them as edges. Motifs, or small local configurations of edges and nodes that arise repeatedly, can be used to simplify the interpretation of networks. Results We examined triplet motifs in a network of quantitative epistatic genetic relationships, and found a non-random distribution of particular motif classes. Individual motif classes were found to be associated with different functional properties, suggestive of an underlying biological significance. These associations were apparent not only for motif classes, but for individual positions within the motifs. As expected, NNN (all negative) motifs were strongly associated with previously reported genetic (i.e. synthetic lethal) interactions, while PPP (all positive) motifs were associated with protein complexes. The two other motif classes (NNP: a positive interaction spanned by two negative interactions, and NPP: a negative spanned by two positives) showed very distinct functional associations, with physical interactions dominating for the former but alternative enrichments, typical of biochemical pathways, dominating for the latter. Conclusion We present a model showing how NNP motifs can be used to recognize supportive relationships between protein complexes, while NPP motifs often identify opposing or regulatory behaviour between a gene and an associated pathway. The ability to use motifs to point toward underlying biological organizational themes is likely to be increasingly important as more extensive epistasis mapping projects in higher organisms begin.

Fingerprint motifs of phytases | Fan | African Journal of Biotechnology

African Journals Online (AJOL)

Among the total of potential 173 phytases gained in 11 plant genomes through MAST, PAPhys are the major phytases, and HAPhys are the minor, and other phytase groups are not found in planta. Keywords: Phytase, fingerprint motif, multiple EM for motif elicitation (MEME), MAST African Journal of Biotechnology Vol.

Microstructural changes of Y-doped V-4Cr-4Ti alloys after ion and neutron irradiation

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H. Watanabe

2016-12-01

Full Text Available High-purity Y-doped V-4Cr-4Ti alloys (0.1–0.2wt. % Y, manufactured by the National Institute for Fusion Science (NIFS, were used for this study. Heavy-ion and fission-neutron irradiation was carried out at temperatures 673–873K. During the ion irradiation at 873K, the microstructure was controlled by the formation of Ti(C,O,N precipitates lying on the (100 plane. Y addition effectively suppressed the growth of Ti(C,O,N precipitates, especially at lower dose irradiation to up to 4 dpa. However, at higher dose levels (12.0 dpa, the number density was almost at the same levels irrespective of the presence of Y. After neutron irradiation at 873K, fine titanium oxides were also observed in all V alloys. However, smaller oxide sizes were observed in the Y-doped samples under the same irradiation conditions. The detailed analysis of EDS showed that the center of the Ti(C,O,N precipitates was mainly enriched by nitrogen. The results showed that the contribution of not only oxygen atoms picked up from the irradiation environment but also nitrogen atoms is essential to understand the microstructural evolution of V-4Cr-4Ti-Y alloys.

Nitrogen Removal Characteristics of Pseudomonas putida Y-9 Capable of Heterotrophic Nitrification and Aerobic Denitrification at Low Temperature

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Yi Xu

2017-01-01

Full Text Available The cold-adapted bacterium Pseudomonas putida Y-9 was investigated and exhibited excellent capability for nitrogen removal at 15°C. The strain capable of heterotrophic nitrification and aerobic denitrification could efficiently remove ammonium, nitrate, and nitrite at an average removal rate of 2.85 mg, 1.60 mg, and 1.83 mg NL−1 h−1, respectively. Strain Y-9 performed nitrification in preference to denitrification when ammonium and nitrate or ammonium and nitrite coexisted in the solution. Meantime, the presence of nitrate had no effect on the ammonium removal rate of strain Y-9, and yet the presence of high concentration of nitrite would inhibit the cell growth and decrease the nitrification rate. The experimental results indicate that P. putida Y-9 has potential application for the treatment of wastewater containing high concentrations of ammonium along with its oxidation products at low temperature.

The atomic arrangement of iimoriite-(Y), Y2(SiO4)(CO3)

Science.gov (United States)

Hughes, J.M.; Foord, E.E.; Jai-Nhuknan, J.; Bell, J.M.

1996-01-01

Iimoriite-(Y) from Bokan Mountain, Prince of Wales Island, Alaska has been studied using single-crystal X-ray-diffraction techniques. The mineral, ideally Y2(SiO4)(CO3), crystallizes in space group P1, with a 6.5495(13), b 6.6291(14), c 6.4395(11)A??, ?? 116.364(15), ?? 92.556(15) and ?? 95.506(17)??. The atomic arrangement has been solved and refined to an R value of 0.019. The arrangement of atoms consists of alternating (011) slabs of orthosilicate groups and carbonate groups, with no sharing of oxygen atoms between anionic complexes in adjacent slabs. Y1 atoms separate adjacent tetrahedra along [100] within the orthosilicate slab, and Y2 atoms separate adjacent carbonate groups along [100] within the carbonate slab. Adjacent orthosilicate and carbonate slabs are linked in (100) by bonding Y atoms from each slab to oxygen atoms of adjacent slabs, in the form of YO8 polyhedra. The Y1 atoms exist in Y12O14 dimers in the orthosilicate slab, and the Y2 atoms exist in continuous [011] ribbons of edge-sharing Y2O8 polyhedra in the carbonate slab.

Effect of Yttrium Addition on Glass-Forming Ability and Magnetic Properties of Fe–Co–B–Si–Nb Bulk Metallic Glass

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Teruo Bitoh

2015-06-01

Full Text Available The glass-forming ability (GFA and the magnetic properties of the [(Fe0.5Co0.50.75B0.20Si0.05]96Nb4−xYx bulk metallic glasses (BMGs have been studied. The partial replacement of Nb by Y improves the thermal stability of the glass against crystallization. The saturation mass magnetization (σs exhibits a maximum around 2 at. % Y, and the value of σs of the alloy with 2 at. % Y is 6.5% larger than that of the Y-free alloy. The coercivity shows a tendency to decrease with increasing Y content. These results indicate that the partial replacement of Nb by Y in the Fe–Co–B–Si–Nb BMGs is useful to simultaneous achievement of high GFA, high σs, and good soft magnetic properties.

Discovery of novel interacting partners of PSMD9, a proteasomal chaperone: Role of an Atypical and versatile PDZ-domain motif interaction and identification of putative functional modules

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Nikhil Sangith

2014-01-01

Full Text Available PSMD9 (Proteasome Macropain non-ATPase subunit 9, a proteasomal assembly chaperone, harbors an uncharacterized PDZ-like domain. Here we report the identification of five novel interacting partners of PSMD9 and provide the first glimpse at the structure of the PDZ-domain, including the molecular details of the interaction. We based our strategy on two propositions: (a proteins with conserved C-termini may share common functions and (b PDZ domains interact with C-terminal residues of proteins. Screening of C-terminal peptides followed by interactions using full-length recombinant proteins, we discovered hnRNPA1 (an RNA binding protein, S14 (a ribosomal protein, CSH1 (a growth hormone, E12 (a transcription factor and IL6 receptor as novel PSMD9-interacting partners. Through multiple techniques and structural insights, we clearly demonstrate for the first time that human PDZ domain interacts with the predicted Short Linear Sequence Motif (SLIM at the C-termini of the client proteins. These interactions are also recapitulated in mammalian cells. Together, these results are suggestive of the role of PSMD9 in transcriptional regulation, mRNA processing and editing, hormone and receptor activity and protein translation. Our proof-of-principle experiments endorse a novel and quick method for the identification of putative interacting partners of similar PDZ-domain proteins from the proteome and for discovering novel functions.

4s24p3--4s4p4 and 4s24p3--4s2fp25s transitions in Y VII, Zr VIII, Nb IX, and MoX

International Nuclear Information System (INIS)

Reader, J.; Acquista, N.

1981-01-01

Spectra of ionized Y, Zr, Nb, and Mo have been observed in sliding-spark and triggered-spark discharges on 10.7-m normal- and grazing-incidence spectrographs at the National Bureau of Standards in Washington, D. C. From these observations the 4s 2 4p 3 --4s4p 4 transitions in Y VII, Zr VIII, Nb IX, and Mo X have been identified. The 4s 2 4p 3 --4s 2 4p 2 5s transitions in Y VII-Mo X, previously identified by Rahimullah et al. [Phys. Scr. 14, 221--223 (1976); 18, 96--106 (1978)], have been confirmed. In Y VII the 4s 2 4p 3 --4s 2 4p 2 6s and 4s4p 4 --4p 5 transition also have been found. The parameters obtained from least-squares fits to the energy levels are compared with Hartree--Fock calculations. Preliminary values of the ionization energies have been determined as 110.02 +- 0.15 eV for Y VII, 133.7 +- 0.5 eV for Zr VIII, 159.2 +- 0.7 eV for Nb IX, and 186.4 +- 1.2 eV for Mo X

Indides RE{sub 3}T{sub 2}In{sub 4} (RE = Y, Gd-Tm, Lu; T = Ni, Ru, Rh) with a ZrNiAl superstructure

Energy Technology Data Exchange (ETDEWEB)

Heying, Birgit; Niehaus, Oliver; Rodewald, Ute C.; Poettgen, Rainer [Univ. Muenster (Germany). Inst. fuer Anorganische und Analytische Chemie

2016-07-01

Three series of rare earth-transition metal-indides RE{sub 3}T{sub 2}In{sub 4} (RE=Y, Gd-Tm, Lu; T=Ni, Ru, Rh) were synthesized from arc-melted RE{sub 3}T{sub 2} precursor compounds and indium tear shot in sealed niobium ampoules using different annealing sequences. The new indides crystallize with the hexagonal Lu{sub 3}Co{sub 2}In{sub 4}-type structure, space group P anti 6. All samples were characterized on the basis of Guinier powder patterns and six structures were refined from single crystal X-ray diffractometer data. The RE{sub 3}T{sub 2}In{sub 4} structures are derived from the ZrNiAl type through RE/In ordering, paralleled by a symmetry reduction from P anti 62m to P anti 6. This induces twinning for some of the investigated crystals. The main crystal chemical motifs of the RE{sub 3}T{sub 2}In{sub 4} structures are trigonal prisms of rare earth, respectively indium atoms that are filled by the transition metals.

Anion induced conformational preference of Cα NN motif residues in functional proteins.

Science.gov (United States)

Patra, Piya; Ghosh, Mahua; Banerjee, Raja; Chakrabarti, Jaydeb

2017-12-01

Among different ligand binding motifs, anion binding C α NN motif consisting of peptide backbone atoms of three consecutive residues are observed to be important for recognition of free anions, like sulphate or biphosphate and participate in different key functions. Here we study the interaction of sulphate and biphosphate with C α NN motif present in different proteins. Instead of total protein, a peptide fragment has been studied keeping C α NN motif flanked in between other residues. We use classical force field based molecular dynamics simulations to understand the stability of this motif. Our data indicate fluctuations in conformational preferences of the motif residues in absence of the anion. The anion gives stability to one of these conformations. However, the anion induced conformational preferences are highly sequence dependent and specific to the type of anion. In particular, the polar residues are more favourable compared to the other residues for recognising the anion. © 2017 Wiley Periodicals, Inc.

Gene regulatory and signaling networks exhibit distinct topological distributions of motifs

Science.gov (United States)

Ferreira, Gustavo Rodrigues; Nakaya, Helder Imoto; Costa, Luciano da Fontoura

2018-04-01

The biological processes of cellular decision making and differentiation involve a plethora of signaling pathways and gene regulatory circuits. These networks in turn exhibit a multitude of motifs playing crucial parts in regulating network activity. Here we compare the topological placement of motifs in gene regulatory and signaling networks and observe that it suggests different evolutionary strategies in motif distribution for distinct cellular subnetworks.

Finding a Leucine in a Haystack: Searching the Proteome for ambigous Leucine-Aspartic Acid motifs

KAUST Repository

Arold, Stefan T.

2016-01-25

Leucine-aspartic acid (LD) motifs are short helical protein-protein interaction motifs involved in cell motility, survival and communication. LD motif interactions are also implicated in cancer metastasis and are targeted by several viruses. LD motifs are notoriously difficult to detect because sequence pattern searches lead to an excessively high number of false positives. Hence, despite 20 years of research, only six LD motif–containing proteins are known in humans, three of which are close homologues of the paxillin family. To enable the proteome-wide discovery of LD motifs, we developed LD Motif Finder (LDMF), a web tool based on machine learning that combines sequence information with structural predictions to detect LD motifs with high accuracy. LDMF predicted 13 new LD motifs in humans. Using biophysical assays, we experimentally confirmed in vitro interactions for four novel LD motif proteins. Thus, LDMF allows proteome-wide discovery of LD motifs, despite a highly ambiguous sequence pattern. Functional implications will be discussed.

A proposed vestigial translation initiation motif in VP1 of hepatitis A virus.

Science.gov (United States)

Kang, Jeong-Ah; Funkhouser, Ann W

2002-07-01

The internal ribosome entry site (IRES) of picornaviruses has a 3' polypyrimidine tract (PPT) 16-24 bases upstream of an AUG triplet (PPT/AUG motif). This motif is critical in determining the efficiency of cap-independent translation. HAV has a conserved PPT/AUG motif consisting of a nine base sequence (AGGUUUUUC) 23 bases upstream of the preferred AUG start codon. This HAV-specific PPT/AUG motif is repeated and conserved in VP1 of HAV, but not of other picornaviruses. We proposed that the PPT/AUG motif in the open reading frame initiated translation and/or had an impact on the life cycle of the virus. In vitro translation of mutant bicistronic mRNAs and growth in cell culture of mutant viruses provided no evidence that the VP1 PPT/AUG motif had any impact on either translation or growth. HAV differs from other picornaviruses in its inefficient growth in cell culture. Since the HAV-specific PPT/AUG motif is found in only 1 in 300,000 reported viral sequences outside the hepatovirus genus, this motif may be a vestigial translation initiation element and may have played a role in determining the unusual phenotype of HAV.

Identification of high-efficiency 3′GG gRNA motifs in indexed FASTA files with ngg2

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Elisha D. Roberson

2015-11-01

Full Text Available CRISPR/Cas9 is emerging as one of the most-used methods of genome modification in organisms ranging from bacteria to human cells. However, the efficiency of editing varies tremendously site-to-site. A recent report identified a novel motif, called the 3′GG motif, which substantially increases the efficiency of editing at all sites tested in C. elegans. Furthermore, they highlighted that previously published gRNAs with high editing efficiency also had this motif. I designed a Python command-line tool, ngg2, to identify 3′GG gRNA sites from indexed FASTA files. As a proof-of-concept, I screened for these motifs in six model genomes: Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Mus musculus, and Homo sapiens. I also scanned the genomes of pig (Sus scrofa and African elephant (Loxodonta africana to demonstrate the utility in non-model organisms. I identified more than 60 million single match 3′GG motifs in these genomes. Greater than 61% of all protein coding genes in the reference genomes had at least one unique 3′GG gRNA site overlapping an exon. In particular, more than 96% of mouse and 93% of human protein coding genes have at least one unique, overlapping 3′GG gRNA. These identified sites can be used as a starting point in gRNA selection, and the ngg2 tool provides an important ability to identify 3′GG editing sites in any species with an available genome sequence.

77 FR 45558 - 4.9 GHz Band

Science.gov (United States)

2012-08-01

..., our rules currently require 4.9 GHz licensees to ``cooperate in the selection and use of channels in... directional and thus can be represented as narrow paths on a coordination map; in contrast, they note, the low-power, less- directional, geographically-dispersed links in a 4.9 GHz network must be represented as a...

CMD: A Database to Store the Bonding States of Cysteine Motifs with Secondary Structures

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Hamed Bostan

2012-01-01

Full Text Available Computational approaches to the disulphide bonding state and its connectivity pattern prediction are based on various descriptors. One descriptor is the amino acid sequence motifs flanking the cysteine residue motifs. Despite the existence of disulphide bonding information in many databases and applications, there is no complete reference and motif query available at the moment. Cysteine motif database (CMD is the first online resource that stores all cysteine residues, their flanking motifs with their secondary structure, and propensity values assignment derived from the laboratory data. We extracted more than 3 million cysteine motifs from PDB and UniProt data, annotated with secondary structure assignment, propensity value assignment, and frequency of occurrence and coefficiency of their bonding status. Removal of redundancies generated 15875 unique flanking motifs that are always bonded and 41577 unique patterns that are always nonbonded. Queries are based on the protein ID, FASTA sequence, sequence motif, and secondary structure individually or in batch format using the provided APIs that allow remote users to query our database via third party software and/or high throughput screening/querying. The CMD offers extensive information about the bonded, free cysteine residues, and their motifs that allows in-depth characterization of the sequence motif composition.

9 CFR 117.4 - Test animals.

Science.gov (United States)

2010-01-01

... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Test animals. 117.4 Section 117.4 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE VIRUSES, SERUMS, TOXINS, AND ANALOGOUS PRODUCTS; ORGANISMS AND VECTORS ANIMALS AT LICENSED ESTABLISHMENTS § 117.4...