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Sample records for residues highly conserved

  1. Highly conserved small subunit residues influence rubisco large subunit catalysis.

    Science.gov (United States)

    Genkov, Todor; Spreitzer, Robert J

    2009-10-30

    The chloroplast enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes the rate-limiting step of photosynthetic CO(2) fixation. With a deeper understanding of its structure-function relationships and competitive inhibition by O(2), it may be possible to engineer an increase in agricultural productivity and renewable energy. The chloroplast-encoded large subunits form the active site, but the nuclear-encoded small subunits can also influence catalytic efficiency and CO(2)/O(2) specificity. To further define the role of the small subunit in Rubisco function, the 10 most conserved residues in all small subunits were substituted with alanine by transformation of a Chlamydomonas reinhardtii mutant that lacks the small subunit gene family. All the mutant strains were able to grow photosynthetically, indicating that none of the residues is essential for function. Three of the substitutions have little or no effect (S16A, P19A, and E92A), one primarily affects holoenzyme stability (L18A), and the remainder affect catalysis with or without some level of associated structural instability (Y32A, E43A, W73A, L78A, P79A, and F81A). Y32A and E43A cause decreases in CO(2)/O(2) specificity. Based on the x-ray crystal structure of Chlamydomonas Rubisco, all but one (Glu-92) of the conserved residues are in contact with large subunits and cluster near the amino- or carboxyl-terminal ends of large subunit alpha-helix 8, which is a structural element of the alpha/beta-barrel active site. Small subunit residues Glu-43 and Trp-73 identify a possible structural connection between active site alpha-helix 8 and the highly variable small subunit loop between beta-strands A and B, which can also influence Rubisco CO(2)/O(2) specificity.

  2. A highly Conserved Aspartic Acid Residue of the Chitosanase from Bacillus Sp. TS Is Involved in the Substrate Binding.

    Science.gov (United States)

    Zhou, Zhanping; Zhao, Shuangzhi; Liu, Yang; Chang, Zhengying; Ma, Yanhe; Li, Jian; Song, Jiangning

    2016-11-01

    The chitosanase from Bacillus sp. TS (CsnTS) is an enzyme belonging to the glycoside hydrolase family 8. The sequence of CsnTS shares 98 % identity with the chitosanase from Bacillus sp. K17. Crystallography analysis and site-direct mutagenesis of the chitosanase from Bacillus sp. K17 identified the important residues involved in the catalytic interaction and substrate binding. However, despite progress in understanding the catalytic mechanism of the chitosanase from the family GH8, the functional roles of some residues that are highly conserved throughout this family have not been fully elucidated. This study focused on one of these residues, i.e., the aspartic acid residue at position 318. We found that apart from asparagine, mutation of Asp318 resulted in significant loss of enzyme activity. In-depth investigations showed that mutation of this residue not only impaired enzymatic activity but also affected substrate binding. Taken together, our results showed that Asp318 plays an important role in CsnTS activity.

  3. Highly conserved serine residue 40 in HIV-1 p6 regulates capsid processing and virus core assembly

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    Solbak Sara MØ

    2011-02-01

    Full Text Available Abstract Background The HIV-1 p6 Gag protein regulates the final abscission step of nascent virions from the cell membrane by the action of two late assembly (L- domains. Although p6 is located within one of the most polymorphic regions of the HIV-1 gag gene, the 52 amino acid peptide binds at least to two cellular budding factors (Tsg101 and ALIX, is a substrate for phosphorylation, ubiquitination, and sumoylation, and mediates the incorporation of the HIV-1 accessory protein Vpr into viral particles. As expected, known functional domains mostly overlap with several conserved residues in p6. In this study, we investigated the importance of the highly conserved serine residue at position 40, which until now has not been assigned to any known function of p6. Results Consistently with previous data, we found that mutation of Ser-40 has no effect on ALIX mediated rescue of HIV-1 L-domain mutants. However, the only feasible S40F mutation that preserves the overlapping pol open reading frame (ORF reduces virus replication in T-cell lines and in human lymphocyte tissue cultivated ex vivo. Most intriguingly, L-domain mediated virus release is not dependent on the integrity of Ser-40. However, the S40F mutation significantly reduces the specific infectivity of released virions. Further, it was observed that mutation of Ser-40 selectively interferes with the cleavage between capsid (CA and the spacer peptide SP1 in Gag, without affecting cleavage of other Gag products. This deficiency in processing of CA, in consequence, led to an irregular morphology of the virus core and the formation of an electron dense extra core structure. Moreover, the defects induced by the S40F mutation in p6 can be rescued by the A1V mutation in SP1 that generally enhances processing of the CA-SP1 cleavage site. Conclusions Overall, these data support a so far unrecognized function of p6 mediated by Ser-40 that occurs independently of the L-domain function, but selectively

  4. Highly Conserved Arg Residue of ERFNIN Motif of Pro-Domain is Important for pH-Induced Zymogen Activation Process in Cysteine Cathepsins K and L.

    Science.gov (United States)

    Aich, Pulakesh; Biswas, Sampa

    2018-06-01

    Pro-domain of a cysteine cathepsin contains a highly conserved Ex 2 Rx 2 Fx 2 Nx 3 Ix 3 N (ERFNIN) motif. The zymogen structure of cathepsins revealed that the Arg(R) residue of the motif is a central residue of a salt-bridge/H-bond network, stabilizing the scaffold of the pro-domain. Importance of the arginine is also demonstrated in studies where a single mutation (Arg → Trp) in human lysosomal cathepsin K (hCTSK) is linked to a bone-related genetic disorder "Pycnodysostosis". In the present study, we have characterized in vitro Arg → Trp mutant of hCTSK and the same mutant of hCTSL. The R → W mutant of hCTSK revealed that this mutation leads to an unstable zymogen that is spontaneously activated and auto-proteolytically degraded rapidly. In contrast, the same mutant of hCTSL is sufficiently stable and has proteolytic activity almost like its wild-type counterpart; however it shows an altered zymogen activation condition in terms of pH, temperature and time. Far and near UV circular dichroism and intrinsic tryptophan fluorescence experiments have revealed that the mutation has minimal effect on structure of the protease hCTSL. Molecular modeling studies shows that the mutated Trp31 in hCTSL forms an aromatic cluster with Tyr23 and Trp30 leading to a local stabilization of pro-domain and supplements the loss of salt-bridge interaction mediated by Arg31 in wild-type. In hCTSK-R31W mutant, due to presence of a non-aromatic Ser30 residue such interaction is not possible and may be responsible for local instability. These differences may cause detrimental effects of R31W mutation on the regulation of hCTSK auto-activation process compared to altered activation process in hCTSL.

  5. On the relationship between residue structural environment and sequence conservation in proteins.

    Science.gov (United States)

    Liu, Jen-Wei; Lin, Jau-Ji; Cheng, Chih-Wen; Lin, Yu-Feng; Hwang, Jenn-Kang; Huang, Tsun-Tsao

    2017-09-01

    Residues that are crucial to protein function or structure are usually evolutionarily conserved. To identify the important residues in protein, sequence conservation is estimated, and current methods rely upon the unbiased collection of homologous sequences. Surprisingly, our previous studies have shown that the sequence conservation is closely correlated with the weighted contact number (WCN), a measure of packing density for residue's structural environment, calculated only based on the C α positions of a protein structure. Moreover, studies have shown that sequence conservation is correlated with environment-related structural properties calculated based on different protein substructures, such as a protein's all atoms, backbone atoms, side-chain atoms, or side-chain centroid. To know whether the C α atomic positions are adequate to show the relationship between residue environment and sequence conservation or not, here we compared C α atoms with other substructures in their contributions to the sequence conservation. Our results show that C α positions are substantially equivalent to the other substructures in calculations of various measures of residue environment. As a result, the overlapping contributions between C α atoms and the other substructures are high, yielding similar structure-conservation relationship. Take the WCN as an example, the average overlapping contribution to sequence conservation is 87% between C α and all-atom substructures. These results indicate that only C α atoms of a protein structure could reflect sequence conservation at the residue level. © 2017 Wiley Periodicals, Inc.

  6. Combining specificity determining and conserved residues improves functional site prediction

    Directory of Open Access Journals (Sweden)

    Gelfand Mikhail S

    2009-06-01

    Full Text Available Abstract Background Predicting the location of functionally important sites from protein sequence and/or structure is a long-standing problem in computational biology. Most current approaches make use of sequence conservation, assuming that amino acid residues conserved within a protein family are most likely to be functionally important. Most often these approaches do not consider many residues that act to define specific sub-functions within a family, or they make no distinction between residues important for function and those more relevant for maintaining structure (e.g. in the hydrophobic core. Many protein families bind and/or act on a variety of ligands, meaning that conserved residues often only bind a common ligand sub-structure or perform general catalytic activities. Results Here we present a novel method for functional site prediction based on identification of conserved positions, as well as those responsible for determining ligand specificity. We define Specificity-Determining Positions (SDPs, as those occupied by conserved residues within sub-groups of proteins in a family having a common specificity, but differ between groups, and are thus likely to account for specific recognition events. We benchmark the approach on enzyme families of known 3D structure with bound substrates, and find that in nearly all families residues predicted by SDPsite are in contact with the bound substrate, and that the addition of SDPs significantly improves functional site prediction accuracy. We apply SDPsite to various families of proteins containing known three-dimensional structures, but lacking clear functional annotations, and discusse several illustrative examples. Conclusion The results suggest a better means to predict functional details for the thousands of protein structures determined prior to a clear understanding of molecular function.

  7. Reverse Conservation Analysis Reveals the Specificity Determining Residues of Cytochrome P450 Family 2 (CYP 2

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    Tai-Sung Lee

    2008-01-01

    Full Text Available The concept of conservation of amino acids is widely used to identify important alignment positions of orthologs. The assumption is that important amino acid residues will be conserved in the protein family during the evolutionary process. For paralog alignment, on the other hand, the opposite concept can be used to identify residues that are responsible for specificity. Assuming that the function-specific or ligand-specific residue positions will have higher diversity since they are under evolutionary pressure to fit the target specificity, these function-specific or ligand-specific residues positions will have a lower degree of conservation than other positions in a highly conserved paralog alignment. This study assessed the ability of reverse conservation analysis to identify function-specific and ligand-specific residue positions in closely related paralog. Reverse conservation analysis of paralog alignments successfully identified all six previously reported substrate recognition sites (SRSs in cytochrome P450 family 2 (CYP 2. Further analysis of each subfamily identified the specificity-determining residues (SDRs that have been experimentally found. New potential SDRs were also predicted and await confirmation by further experiments or modeling calculations. This concept may be also applied to identify SDRs in other protein families.

  8. Residual distribution for general time-dependent conservation laws

    International Nuclear Information System (INIS)

    Ricchiuto, Mario; Csik, Arpad; Deconinck, Herman

    2005-01-01

    We consider the second-order accurate numerical solution of general time-dependent hyperbolic conservation laws over unstructured grids in the framework of the Residual Distribution method. In order to achieve full conservation of the linear, monotone and first-order space-time schemes of (Csik et al., 2003) and (Abgrall et al., 2000), we extend the conservative residual distribution (CRD) formulation of (Csik et al., 2002) to prismatic space-time elements. We then study the design of second-order accurate and monotone schemes via the nonlinear mapping of the local residuals of linear monotone schemes. We derive sufficient and necessary conditions for the well-posedness of the mapping. We prove that the schemes obtained with the CRD formulation satisfy these conditions by construction. Thus the nonlinear schemes proposed in this paper are always well defined. The performance of the linear and nonlinear schemes are evaluated on a series of test problems involving the solution of the Euler equations and of a two-phase flow model. We consider the resolution of strong shocks and complex interacting flow structures. The results demonstrate the robustness, accuracy and non-oscillatory character of the proposed schemes. d schemes

  9. Relationships between residue Voronoi volume and sequence conservation in proteins.

    Science.gov (United States)

    Liu, Jen-Wei; Cheng, Chih-Wen; Lin, Yu-Feng; Chen, Shao-Yu; Hwang, Jenn-Kang; Yen, Shih-Chung

    2018-02-01

    Functional and biophysical constraints can cause different levels of sequence conservation in proteins. Previously, structural properties, e.g., relative solvent accessibility (RSA) and packing density of the weighted contact number (WCN), have been found to be related to protein sequence conservation (CS). The Voronoi volume has recently been recognized as a new structural property of the local protein structural environment reflecting CS. However, for surface residues, it is sensitive to water molecules surrounding the protein structure. Herein, we present a simple structural determinant termed the relative space of Voronoi volume (RSV); it uses the Voronoi volume and the van der Waals volume of particular residues to quantify the local structural environment. RSV (range, 0-1) is defined as (Voronoi volume-van der Waals volume)/Voronoi volume of the target residue. The concept of RSV describes the extent of available space for every protein residue. RSV and Voronoi profiles with and without water molecules (RSVw, RSV, VOw, and VO) were compared for 554 non-homologous proteins. RSV (without water) showed better Pearson's correlations with CS than did RSVw, VO, or VOw values. The mean correlation coefficient between RSV and CS was 0.51, which is comparable to the correlation between RSA and CS (0.49) and that between WCN and CS (0.56). RSV is a robust structural descriptor with and without water molecules and can quantitatively reflect evolutionary information in a single protein structure. Therefore, it may represent a practical structural determinant to study protein sequence, structure, and function relationships. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Ranking multiple docking solutions based on the conservation of inter-residue contacts

    KAUST Repository

    Oliva, Romina M.; Vangone, Anna; Cavallo, Luigi

    2013-01-01

    ) conformations in the top positions is still an open problem. Herein we present CONSRANK, a simple and effective tool to rank multiple docking solutions, which relies on the conservation of inter-residue contacts in the analyzed decoys ensemble. First

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

    Science.gov (United States)

    Ito, Ryousuke; Nakada, Chika; Hoshino, Tsutomu

    2017-01-18

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

  12. Conserved Aromatic Residue Confers Cation Selectivity in Claudin-2 and Claudin-10b*

    Science.gov (United States)

    Li, Jiahua; Zhuo, Min; Pei, Lei; Yu, Alan S. L.

    2013-01-01

    In tight junctions, both claudin-2 and claudin-10b form paracellular cation-selective pores by the interaction of the first ECL 1 with permeating ions. We hypothesized that a highly conserved aromatic residue near the pore selectivity filter of claudins contributes to cation selectivity by cation-π interaction with the permeating cation. To test this, we generated MDCK I Tet-off cells stably transfected with claudin-2 Tyr67 mutants. The Y67L mutant showed reduced cation selectivity compared with wild-type claudin-2 due to a decrease in Na+ permeability, without affecting the Cl− permeability. The Y67A mutant enlarged the pore size and further decreased the charge selectivity due to an increase in Cl− permeability. The Y67F mutant restored the Na+ permeability, Cl− permeability, and pore size back to wild-type. The accessibility of Y67C to methanethiosulfonate modification indicated that its side chain faces the lumen of the pore. In claudin-10b, the F66L mutant reduced cation selectivity, and the F66A mutant lost pore conductance. We conclude that the conserved aromatic residue near the cation pore domain of claudins contributes to cation selectivity by a dual role of cation-π interaction and a luminal steric effect. Our findings provide new insight into how ion selectivity is achieved in the paracellular pore. PMID:23760508

  13. Substitution of cysteine for a conserved alanine residue in the catalytic center of type II iodothyronine deiodinase alters interaction with reducing cofactor

    NARCIS (Netherlands)

    W. Klootwijk (Willem); T.J. Visser (Theo); G.G.J.M. Kuiper (George)

    2002-01-01

    textabstractHuman type II iodothyronine deiodinase (D2) catalyzes the activation of T(4) to T(3). The D2 enzyme, like the type I (D1) and type III (D3) deiodinases, contains a selenocysteine (SeC) residue (residue 133 in D2) in the highly conserved catalytic center. Remarkably, all

  14. Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue

    KAUST Repository

    Da, Lin-Tai

    2016-04-19

    The dynamics of the RNA polymerase II (Pol II) backtracking process is poorly understood. We built a Markov State Model from extensive molecular dynamics simulations to identify metastable intermediate states and the dynamics of backtracking at atomistic detail. Our results reveal that Pol II backtracking occurs in a stepwise mode where two intermediate states are involved. We find that the continuous bending motion of the Bridge helix (BH) serves as a critical checkpoint, using the highly conserved BH residue T831 as a sensing probe for the 3′-terminal base paring of RNA:DNA hybrid. If the base pair is mismatched, BH bending can promote the RNA 3′-end nucleotide into a frayed state that further leads to the backtracked state. These computational observations are validated by site-directed mutagenesis and transcript cleavage assays, and provide insights into the key factors that regulate the preferences of the backward translocation.

  15. Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue

    KAUST Repository

    Da, Lin-Tai; Pardo-Avila, Fá tima; Xu, Liang; Silva, Daniel-Adriano; Zhang, Lu; Gao, Xin; Wang, Dong; Huang, Xuhui

    2016-01-01

    The dynamics of the RNA polymerase II (Pol II) backtracking process is poorly understood. We built a Markov State Model from extensive molecular dynamics simulations to identify metastable intermediate states and the dynamics of backtracking at atomistic detail. Our results reveal that Pol II backtracking occurs in a stepwise mode where two intermediate states are involved. We find that the continuous bending motion of the Bridge helix (BH) serves as a critical checkpoint, using the highly conserved BH residue T831 as a sensing probe for the 3′-terminal base paring of RNA:DNA hybrid. If the base pair is mismatched, BH bending can promote the RNA 3′-end nucleotide into a frayed state that further leads to the backtracked state. These computational observations are validated by site-directed mutagenesis and transcript cleavage assays, and provide insights into the key factors that regulate the preferences of the backward translocation.

  16. A conserved residue of l-alanine dehydrogenase from Bacillus pseudofirmus, Lys-73, participates in the catalytic reaction through hydrogen bonding.

    Science.gov (United States)

    He, Guangzheng; Xu, Shujing; Wang, Shanshan; Zhang, Qing; Liu, Dong; Chen, Yuling; Ju, Jiansong; Zhao, Baohua

    2018-03-01

    A multiple protein sequence alignment of l-alanine dehydrogenases from different bacterial species revealed that five highly conserved amino acid residues Arg-15, Lys-73, Lys-75, His-96 and Asp-269 are potential catalytic residues of l-alanine dehydrogenase from Bacillus pseudofirmus OF4. In this study, recombinant OF4Ald and its mutants of five conserved residues were constructed, expressed in Escherichia coli, purified by His 6 -tag affinity column and gel filtration chromatography, structure homology modeling, and characterized. The purified protein OF4Ald displayed high specificity to l-alanine (15Umg -1 ) with an optimal temperature and pH of 40°C and 10.5, respectively. Enzymatic assay and activity staining in native gels showed that mutations at four conserved residue Arg-15, Lys-75, His-96 and Asp-269 (except residue Lys-73) resulted in a complete loss in enzymatic activity, which signified that these predicted active sites are indispensable for OF4Ald activity. In contrast, the mutant K73A resulted in 6-fold improvement in k cat /K m towards l-alanine as compared to the wild type protein. Further research of the residue Lys-73 substituted by various amino acids and structural modeling revealed that residue Lys-73 might be involved in the catalytic reaction of the enzyme by influencing the enzyme-substrate binding through the hydrogen-bonding interaction with conserved residue Lys-75. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Ranking multiple docking solutions based on the conservation of inter-residue contacts

    KAUST Repository

    Oliva, Romina M.

    2013-06-17

    Molecular docking is the method of choice for investigating the molecular basis of recognition in a large number of functional protein complexes. However, correctly scoring the obtained docking solutions (decoys) to rank native-like (NL) conformations in the top positions is still an open problem. Herein we present CONSRANK, a simple and effective tool to rank multiple docking solutions, which relies on the conservation of inter-residue contacts in the analyzed decoys ensemble. First it calculates a conservation rate for each inter-residue contact, then it ranks decoys according to their ability to match the more frequently observed contacts. We applied CONSRANK to 102 targets from three different benchmarks, RosettaDock, DOCKGROUND, and Critical Assessment of PRedicted Interactions (CAPRI). The method performs consistently well, both in terms of NL solutions ranked in the top positions and of values of the area under the receiver operating characteristic curve. Its ideal application is to solutions coming from different docking programs and procedures, as in the case of CAPRI targets. For all the analyzed CAPRI targets where a comparison is feasible, CONSRANK outperforms the CAPRI scorers. The fraction of NL solutions in the top ten positions in the RosettaDock, DOCKGROUND, and CAPRI benchmarks is enriched on average by a factor of 3.0, 1.9, and 9.9, respectively. Interestingly, CONSRANK is also able to specifically single out the high/medium quality (HMQ) solutions from the docking decoys ensemble: it ranks 46.2 and 70.8% of the total HMQ solutions available for the RosettaDock and CAPRI targets, respectively, within the top 20 positions. © 2013 Wiley Periodicals, Inc.

  18. The Influence of Repeat Surgery and Residual Disease on Recurrence After Breast-Conserving Surgery

    DEFF Research Database (Denmark)

    Bodilsen, Anne; Bjerre, Karsten; Offersen, Birgitte V

    2015-01-01

    BACKGROUND: A significant proportion of women who have breast-conserving surgery (BCS) subsequently undergo re-excision or proceed to mastectomy. This study aimed to identify factors associated with residual disease after repeat surgery and to determine their effect on ipsilateral breast tumor re...

  19. Functional identification of conserved residues involved in Lactobacillus rhamnosus strain GG sortase specificity and pilus biogenesis.

    Science.gov (United States)

    Douillard, François P; Rasinkangas, Pia; von Ossowski, Ingemar; Reunanen, Justus; Palva, Airi; de Vos, Willem M

    2014-05-30

    In Gram-positive bacteria, sortase-dependent pili mediate the adhesion of bacteria to host epithelial cells and play a pivotal role in colonization, host signaling, and biofilm formation. Lactobacillus rhamnosus strain GG, a well known probiotic bacterium, also displays on its cell surface mucus-binding pilus structures, along with other LPXTG surface proteins, which are processed by sortases upon specific recognition of a highly conserved LPXTG motif. Bioinformatic analysis of all predicted LPXTG proteins encoded by the L. rhamnosus GG genome revealed a remarkable conservation of glycine residues juxtaposed to the canonical LPXTG motif. Here, we investigated and defined the role of this so-called triple glycine (TG) motif in determining sortase specificity during the pilus assembly and anchoring. Mutagenesis of the TG motif resulted in a lack or an alteration of the L. rhamnosus GG pilus structures, indicating that the TG motif is critical in pilus assembly and that they govern the pilin-specific and housekeeping sortase specificity. This allowed us to propose a regulatory model of the L. rhamnosus GG pilus biogenesis. Remarkably, the TG motif was identified in multiple pilus gene clusters of other Gram-positive bacteria, suggesting that similar signaling mechanisms occur in other, mainly pathogenic, species. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  20. Case studies in residual use and energy conservation at wastewater treatment plants

    Energy Technology Data Exchange (ETDEWEB)

    Stewart, D. [Science Applications International Corp., Los Altos, CA (United States)

    1995-06-01

    The US Environmental Protection Agency (EPA) and the National Renewable Energy Laboratory (NREL) for the US Department of Energy (DOE) funded a study to document energy conservation activities and their effects on operation costs, regulatory compliance, and process optimization at several wastewater treatment plants (WWTPS). The purpose of this report is to review the efforts of wastewater treatment Facilities that use residuals as fuels. Case histories are presented for facilities that have taken measures to reduce energy consumption during wastewater treatment. Most of the WWTPs discussed in this report have retrofitted existing facilities to achieve energy conservation. The case studies of energy conservation measures found no effects on the facilities` ability to comply with NPDES permits. Indeed, energy conservation activities enhance environmental compliance in several ways.

  1. Conserved residues of the human mitochondrial holocytochrome c synthase mediate interactions with heme.

    Science.gov (United States)

    Babbitt, Shalon E; San Francisco, Brian; Bretsnyder, Eric C; Kranz, Robert G

    2014-08-19

    C-type cytochromes are distinguished by the covalent attachment of a heme cofactor, a modification that is typically required for its subsequent folding, stability, and function. Heme attachment takes place in the mitochondrial intermembrane space and, in most eukaryotes, is mediated by holocytochrome c synthase (HCCS). HCCS is the primary component of the eukaryotic cytochrome c biogenesis pathway, known as System III. The catalytic function of HCCS depends on its ability to coordinate interactions between its substrates: heme and cytochrome c. Recent advancements in the recombinant expression and purification of HCCS have facilitated comprehensive analyses of the roles of conserved residues in HCCS, as demonstrated in this study. Previously, we proposed a four-step model describing HCCS-mediated cytochrome c assembly, identifying a conserved histidine residue (His154) as an axial ligand to the heme iron. In this study, we performed a systematic mutational analysis of 17 conserved residues in HCCS, and we provide evidence that the enzyme contains two heme-binding domains. Our data indicate that heme contacts mediated by residues within these domains modulate the dynamics of heme binding and contribute to the stability of the HCCS-heme-cytochrome c steady state ternary complex. While some residues are essential for initial heme binding (step 1), others impact the subsequent release of the holocytochrome c product (step 4). Certain HCCS mutants that were defective in heme binding were corrected for function by exogenous aminolevulinic acid (ALA, the precursor to heme). This chemical "correction" supports the proposed role of heme binding for the corresponding residues.

  2. Residue management practices and planter attachments for corn production in a conservation agriculture system

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    J. Nejadi

    2013-11-01

    Full Text Available Seed placement and failure to establish a uniform plant stand are critical problems associated with production of corn (Zea mays following wheat (Triticum aestivum in a conservation agriculture system in Iran. Our objectives were to evaluate the performance of a corn row- crop planter equipped with two planter attachments (smooth/toothed coulters at six wheat residue management systems (three tillage systems and two levels of surface residue at two forward speeds of 5 and 7 km h-1. Residue retained after planting, seeding depth, emergence rate index (ERI and seed spacing indices were determined. The baled residue plots tilled by chisel plow followed by disc harrow (BRCD resulted in minimum residue after planting as compared to other residue treatments. Furthermore, the maximum values of the ERI and uniformity of plant spacing pertained to this treatment. Other results showed that the ERI increased up to 18% for the toothed coulter as compared to the smooth coulter. The toothed coulter also established a deeper seed placement as compared to the smooth coulter. Planting at forward speed of 5 km h-1 resulted in deeper seeding depth as compared to a forward speed of 7 km h-1. However, lower values of miss and precision indices were obtained at forward speed of 7 km h-1, indicating a more uniformity of plant spacing. Results of this study showed that equipping the conventional planter with toothed coulter and planting in soil prepared under the BRCD residue management system can result in a satisfactory conservation crop production system.

  3. Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis.

    Science.gov (United States)

    Du, Yushen; Wu, Nicholas C; Jiang, Lin; Zhang, Tianhao; Gong, Danyang; Shu, Sara; Wu, Ting-Ting; Sun, Ren

    2016-11-01

    Identification and annotation of functional residues are fundamental questions in protein sequence analysis. Sequence and structure conservation provides valuable information to tackle these questions. It is, however, limited by the incomplete sampling of sequence space in natural evolution. Moreover, proteins often have multiple functions, with overlapping sequences that present challenges to accurate annotation of the exact functions of individual residues by conservation-based methods. Using the influenza A virus PB1 protein as an example, we developed a method to systematically identify and annotate functional residues. We used saturation mutagenesis and high-throughput sequencing to measure the replication capacity of single nucleotide mutations across the entire PB1 protein. After predicting protein stability upon mutations, we identified functional PB1 residues that are essential for viral replication. To further annotate the functional residues important to the canonical or noncanonical functions of viral RNA-dependent RNA polymerase (vRdRp), we performed a homologous-structure analysis with 16 different vRdRp structures. We achieved high sensitivity in annotating the known canonical polymerase functional residues. Moreover, we identified a cluster of noncanonical functional residues located in the loop region of the PB1 β-ribbon. We further demonstrated that these residues were important for PB1 protein nuclear import through the interaction with Ran-binding protein 5. In summary, we developed a systematic and sensitive method to identify and annotate functional residues that are not restrained by sequence conservation. Importantly, this method is generally applicable to other proteins about which homologous-structure information is available. To fully comprehend the diverse functions of a protein, it is essential to understand the functionality of individual residues. Current methods are highly dependent on evolutionary sequence conservation, which is

  4. A conserved residue cluster that governs kinetics of ATP-dependent gating of Kir6.2 potassium channels

    DEFF Research Database (Denmark)

    Zhang, Roger S; Wright, Jordan; Pless, Stephan Alexander

    2015-01-01

    modest effects on gating kinetics despite significant changes in ATP sensitivity and open probability. However, we identified a pair of highly conserved neighboring amino acids (Trp68, Lys170) that control the rate of channel opening and inhibition in response to ATP. Paradoxically, mutations of Trp68...... or Lys170 markedly slow the kinetics of channel opening (500 ms and 700 ms for Trp68Leu and Lys170Asn, respectively), while increasing channel open probability. Examining the functional effects of these residues using phi-value analysis revealed a steep negative slope. This finding implies...

  5. The formation of a native-like structure containing eight conserved hydrophobic residues is rate limiting in two-state protein folding of ACBP

    DEFF Research Database (Denmark)

    Kragelund, Birthe Brandt; Osmark, Peter; Neergaard, Thomas B.

    1999-01-01

    The acyl-coenzyme A-binding proteins (ACBPs) contain 26 highly conserved sequence positions. The majority of these have been mutated in the bovine protein, and their influence on the rate of two-state folding and unfolding has been measured. The results identify eight sequence positions, out of 24...... probed, that are critical for fast productive folding. The residues are all hydrophobic and located in the interface between the N- and C-terminal helices. The results suggest that one specific site dominated by conserved hydrophobic residues forms the structure of the productive rate-determining folding...... step and that a sequential framework model can describe the protein folding reaction....

  6. Importance of uncharged polar residues and proline in the proximal two-thirds (Pro107–Ser128 of the highly conserved region of mouse ileal Na+-dependent bile acid transporter, Slc10a2, in transport activity and cellular expression

    Directory of Open Access Journals (Sweden)

    Saeki Tohru

    2013-02-01

    Full Text Available Abstract Background SLC10A2-mediated reabsorption of bile acids at the distal end of the ileum is the first step in enterohepatic circulation. Because bile acids act not only as detergents but also as signaling molecules in lipid metabolism and energy production, SLC10A2 is important as the key transporter for understanding the in vivo kinetics of bile acids. SLC10A family members and the homologous genes of various species share a highly conserved region corresponding to Gly104–Pro142 of SLC10A2. The functional importance of this region has not been fully elucidated. Results To elucidate the functional importance of this region, we previously performed mutational analysis of the uncharged polar residues and proline in the distal one-third (Thr130–Pro142 of the highly conserved region in mouse Slc10a2. In this study, proline and uncharged polar residues in the remaining two-thirds of this region in mouse Slc10a2 were subjected to mutational analysis, and taurocholic acid uptake and cell surface localization were examined. Cell surface localization of Slc10a2 is necessary for bile acid absorption. Mutants in which Asp or Leu were substituted for Pro107 (P107N or P107L were abundantly expressed, but their cell surface localization was impaired. The S126A mutant was completely impaired in cellular expression. The T110A and S128A mutants exhibited remarkably enhanced membrane expression. The S112A mutant was properly expressed at the cell surface but transport activity was completely lost. Replacement of Tyr117 with various amino acids resulted in reduced transport activity. The degree of reduction roughly depended on the van der Waals volume of the side chains. Conclusions The functional importance of proline and uncharged polar residues in the highly conserved region of mouse Slc10a2 was determined. This information will contribute to the design of bile acid-conjugated prodrugs for efficient drug delivery or SLC10A2 inhibitors for

  7. Using a consensus approach based on the conservation of inter-residue contacts to rank CAPRI models

    KAUST Repository

    Vangone, Anna; Cavallo, Luigi; Oliva, Romina M.

    2013-01-01

    Herein we propose the use of a consensus approach, CONSRANK, for ranking CAPRI models. CONSRANK relies on the conservation of inter-residue contacts in the analyzed decoys ensemble. Models are ranked according to their ability to match the most

  8. Networks of High Mutual Information Define the Structural Proximity of Catalytic Sites: Implications for Catalytic Residue Identification

    DEFF Research Database (Denmark)

    Buslje, Cristina Marino; Teppa, Elin; Di Doménico, Tomas

    2010-01-01

    other non-functional conserved residues. Using a data set of 434 Pfam families included in the catalytic site atlas (CSA) database, we tested this hypothesis and demonstrated that MI can complement amino acid conservation scores to detect CR. The Kullback-Leibler (KL) conservation measurement was shown.......90, the Cls method was found to have a sensitivity of 0.816. In summary, we demonstrate that networks of residues with high MI provide a distinct signature on CR and propose that such a signature should be present in other classes of functional residues where the requirement to maintain a particular function...

  9. Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction

    DEFF Research Database (Denmark)

    Teppa, Elin; Wilkins, Angela D.; Nielsen, Morten

    2012-01-01

    Background: A large panel of methods exists that aim to identify residues with critical impact on protein function based on evolutionary signals, sequence and structure information. However, it is not clear to what extent these different methods overlap, and if any of the methods have higher...... predictive potential compared to others when it comes to, in particular, the identification of catalytic residues (CR) in proteins. Using a large set of enzymatic protein families and measures based on different evolutionary signals, we sought to break up the different components of the information content......-value Evolutionary Trace (rvET) methods and conservation, another containing mutual information (MI) methods, and the last containing methods designed explicitly for the identification of specificity determining positions (SDPs): integer-value Evolutionary Trace (ivET), SDPfox, and XDET. In terms of prediction of CR...

  10. Molecular Basis for Enzymatic Sulfite Oxidation -- HOW THREE CONSERVED ACTIVE SITE RESIDUES SHAPE ENZYME ACTIVITY

    Energy Technology Data Exchange (ETDEWEB)

    Bailey, Susan; Rapson, Trevor; Johnson-Winters, Kayunta; Astashkin, Andrei; Enemark, John; Kappler, Ulrike

    2008-11-10

    Sulfite dehydrogenases (SDHs) catalyze the oxidation and detoxification of sulfite to sulfate, a reaction critical to all forms of life. Sulfite-oxidizing enzymes contain three conserved active site amino acids (Arg-55, His-57, and Tyr-236) that are crucial for catalytic competency. Here we have studied the kinetic and structural effects of two novel and one previously reported substitution (R55M, H57A, Y236F) in these residues on SDH catalysis. Both Arg-55 and His-57 were found to have key roles in substrate binding. An R55M substitution increased Km(sulfite)(app) by 2-3 orders of magnitude, whereas His-57 was required for maintaining a high substrate affinity at low pH when the imidazole ring is fully protonated. This effect may be mediated by interactions of His-57 with Arg-55 that stabilize the position of the Arg-55 side chain or, alternatively, may reflect changes in the protonation state of sulfite. Unlike what is seen for SDHWT and SDHY236F, the catalytic turnover rates of SDHR55M and SDHH57A are relatively insensitive to pH (~;;60 and 200 s-1, respectively). On the structural level, striking kinetic effects appeared to correlate with disorder (in SDHH57A and SDHY236F) or absence of Arg-55 (SDHR55M), suggesting that Arg-55 and the hydrogen bonding interactions it engages in are crucial for substrate binding and catalysis. The structure of SDHR55M has sulfate bound at the active site, a fact that coincides with a significant increase in the inhibitory effect of sulfate in SDHR55M. Thus, Arg-55 also appears to be involved in enabling discrimination between the substrate and product in SDH.

  11. Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis

    Directory of Open Access Journals (Sweden)

    Yushen Du

    2016-11-01

    Full Text Available Identification and annotation of functional residues are fundamental questions in protein sequence analysis. Sequence and structure conservation provides valuable information to tackle these questions. It is, however, limited by the incomplete sampling of sequence space in natural evolution. Moreover, proteins often have multiple functions, with overlapping sequences that present challenges to accurate annotation of the exact functions of individual residues by conservation-based methods. Using the influenza A virus PB1 protein as an example, we developed a method to systematically identify and annotate functional residues. We used saturation mutagenesis and high-throughput sequencing to measure the replication capacity of single nucleotide mutations across the entire PB1 protein. After predicting protein stability upon mutations, we identified functional PB1 residues that are essential for viral replication. To further annotate the functional residues important to the canonical or noncanonical functions of viral RNA-dependent RNA polymerase (vRdRp, we performed a homologous-structure analysis with 16 different vRdRp structures. We achieved high sensitivity in annotating the known canonical polymerase functional residues. Moreover, we identified a cluster of noncanonical functional residues located in the loop region of the PB1 β-ribbon. We further demonstrated that these residues were important for PB1 protein nuclear import through the interaction with Ran-binding protein 5. In summary, we developed a systematic and sensitive method to identify and annotate functional residues that are not restrained by sequence conservation. Importantly, this method is generally applicable to other proteins about which homologous-structure information is available.

  12. Residue conservation and dimer-interface analysis of olfactory receptor molecular models

    Directory of Open Access Journals (Sweden)

    Ramanathan Sowdhamini

    2012-10-01

    Full Text Available Olfactory Receptors (ORs are members of the Class A rhodopsin like G-protein coupled receptors (GPCRs which are the initial players in the signal transduction cascade, leading to the generation of nerve impulses transmitted to the brain and resulting in the detection of odorant molecules. Despite the accumulation of thousands of olfactory receptor sequences, no crystal structures of ORs are known tο date. However, the recent availability of crystallographic models of a few GPCRs allows us to generate homology models of ORs and analyze their amino acid patterns, as there is a huge diversity in OR sequences. In this study, we have generated three-dimensional models of 100 representative ORs from Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans and Sacharomyces cerevisiae which were selected on the basis of a composite classification scheme and phylogenetic analysis. The crystal structure of bovine rhodopsin was used as a template and it was found that the full-length models have more than 90% of their residues in allowed regions of the Ramachandran plot. The structures were further used for analysis of conserved residues in the transmembrane and extracellular loop regions in order to identify functionally important residues. Several ORs are known to be functional as dimers and hence dimer interfaces were predicted for OR models to analyse their oligomeric functional state.

  13. Role of conserved cysteine residues in Herbaspirillum seropedicae NifA activity.

    Science.gov (United States)

    Oliveira, Marco A S; Baura, Valter A; Aquino, Bruno; Huergo, Luciano F; Kadowaki, Marco A S; Chubatsu, Leda S; Souza, Emanuel M; Dixon, Ray; Pedrosa, Fábio O; Wassem, Roseli; Monteiro, Rose A

    2009-01-01

    Herbaspirillum seropedicae is an endophytic diazotrophic bacterium that associates with economically important crops. NifA protein, the transcriptional activator of nif genes in H. seropedicae, binds to nif promoters and, together with RNA polymerase-sigma(54) holoenzyme, catalyzes the formation of open complexes to allow transcription initiation. The activity of H. seropedicae NifA is controlled by ammonium and oxygen levels, but the mechanisms of such control are unknown. Oxygen sensitivity is attributed to a conserved motif of cysteine residues in NifA that spans the central AAA+ domain and the interdomain linker that connects the AAA+ domain to the C-terminal DNA binding domain. Here we mutagenized this conserved motif of cysteines and assayed the activity of mutant proteins in vivo. We also purified the mutant variants of NifA and tested their capacity to bind to the nifB promoter region. Chimeric proteins between H. seropedicae NifA, an oxygen-sensitive protein, and Azotobacter vinelandii NifA, an oxygen-tolerant protein, were constructed and showed that the oxygen response is conferred by the central AAA+ and C-terminal DNA binding domains of H. seropedicae NifA. We conclude that the conserved cysteine motif is essential for NifA activity, although single cysteine-to-serine mutants are still competent at binding DNA.

  14. Identification of conserved regions and residues within Hedgehog acyltransferase critical for palmitoylation of Sonic Hedgehog.

    Directory of Open Access Journals (Sweden)

    John A Buglino

    2010-06-01

    Full Text Available Sonic hedgehog (Shh is a palmitoylated protein that plays key roles in mammalian development and human cancers. Palmitoylation of Shh is required for effective long and short range Shh-mediated signaling. Attachment of palmitate to Shh is catalyzed by Hedgehog acyltransferase (Hhat, a member of the membrane bound O-acyl transferase (MBOAT family of multipass membrane proteins. The extremely hydrophobic composition of MBOAT proteins has limited their biochemical characterization. Except for mutagenesis of two conserved residues, there has been no structure-function analysis of Hhat, and the regions of the protein required for Shh palmitoylation are unknown.Here we undertake a systematic approach to identify residues within Hhat that are required for protein stability and/or enzymatic activity. We also identify a second, novel MBOAT homology region (residues 196-234 that is required for Hhat activity. In total, ten deletion mutants and eleven point mutants were generated and analyzed. Truncations at the N- and C-termini of Hhat yielded inactive proteins with reduced stability. Four Hhat mutants with deletions within predicted loop regions and five point mutants retained stability but lost palmitoylation activity. We purified two point mutants, W378A and H379A, with defective Hhat activity. Kinetic analyses revealed alterations in apparent K(m and V(max for Shh and/or palmitoyl CoA, changes that likely explain the catalytic defects observed for these mutants.This study has pinpointed specific regions and multiple residues that regulate Hhat stability and catalysis. Our findings should be applicable to other MBOAT proteins that mediate lipid modification of Wnt proteins and ghrelin, and should serve as a model for understanding how secreted morphogens are modified by palmitoyl acyltransferases.

  15. Intragenic suppressor of Osiaa23 revealed a conserved tryptophan residue crucial for protein-protein interactions.

    Directory of Open Access Journals (Sweden)

    Jun Ni

    Full Text Available The Auxin/Indole-3-Acetic Acid (Aux/IAA and Auxin Response Factor (ARF are two important families that play key roles in auxin signal transduction. Both of the families contain a similar carboxyl-terminal domain (Domain III/IV that facilitates interactions between these two families. In spite of the importance of protein-protein interactions among these transcription factors, the mechanisms involved in these interactions are largely unknown. In this study, we isolated six intragenic suppressors of an auxin insensitive mutant, Osiaa23. Among these suppressors, Osiaa23-R5 successfully rescued all the defects of the mutant. Sequence analysis revealed that an amino acid substitution occurred in the Tryptophan (W residue in Domain IV of Osiaa23. Yeast two-hybrid experiments showed that the mutation in Domain IV prevents the protein-protein interactions between Osiaa23 and OsARFs. Phylogenetic analysis revealed that the W residue is conserved in both OsIAAs and OsARFs. Next, we performed site-specific amino acid substitutions within Domain IV of OsARFs, and the conserved W in Domain IV was exchanged by Serine (S. The mutated OsARF(WSs can be released from the inhibition of Osiaa23 and maintain the transcriptional activities. Expression of OsARF(WSs in Osiaa23 mutant rescued different defects of the mutant. Our results suggest a previously unknown importance of Domain IV in both families and provide an indirect way to investigate functions of OsARFs.

  16. FragKB: structural and literature annotation resource of conserved peptide fragments and residues.

    Directory of Open Access Journals (Sweden)

    Ashish V Tendulkar

    Full Text Available BACKGROUND: FragKB (Fragment Knowledgebase is a repository of clusters of structurally similar fragments from proteins. Fragments are annotated with information at the level of sequence, structure and function, integrating biological descriptions derived from multiple existing resources and text mining. METHODOLOGY: FragKB contains approximately 400,000 conserved fragments from 4,800 representative proteins from PDB. Literature annotations are extracted from more than 1,700 articles and are available for over 12,000 fragments. The underlying systematic annotation workflow of FragKB ensures efficient update and maintenance of this database. The information in FragKB can be accessed through a web interface that facilitates sequence and structural visualization of fragments together with known literature information on the consequences of specific residue mutations and functional annotations of proteins and fragment clusters. FragKB is accessible online at http://ubio.bioinfo.cnio.es/biotools/fragkb/. SIGNIFICANCE: The information presented in FragKB can be used for modeling protein structures, for designing novel proteins and for functional characterization of related fragments. The current release is focused on functional characterization of proteins through inspection of conservation of the fragments.

  17. A case of postirradiation angiosarcoma developed in the residual breast after breast-conserving surgery

    International Nuclear Information System (INIS)

    Nomura, Shinji; Okazaki, Yoshikazu; Fujii, Masakazu; Akiyama, Norio; Tomozawa, Naofumi; Morishige, Ichiro

    2008-01-01

    The patient was a 50-year-old woman who had undergone breast-conserving surgery for right breast cancer (C area, Bp+Ax, T2N0M0, Stage I, and scirrhous carcinoma), followed by irradiation at a total dose of 50 Gy in 1998. When 6 years 5 months had elapsed after the operation, redness and induration developed in the A area of the right breast. A biopsy via wedge resection was performed and the histopathological diagnosis was angiosarcoma. We could not rule out a possibility of positive surgical stump, and performed additional resection+skin grafting. No sarcoma remnant was demonstrated in the material resected additionally, but 2 years later, the patient experienced recurrence. Thus mastectomy+extended resection of the full thickness of the skin+skin grafting were performed. Postirradiation sarcoma involving the skin and vessels is a rare entity and occurs in 0.03-0.8% of all cases after radiation therapy. It metastasizes to the distant organs in an early stage and carries poor prognosis. No standard therapy for the disease has been established as yet. Early detection and extended resection are considered to contribute to an improvement of the prognosis. This paper deals with such a rare entity as postirradiation angiosarcoma developed in the residual breast after breast-conserving surgery. (author)

  18. Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification.

    Directory of Open Access Journals (Sweden)

    Cristina Marino Buslje

    Full Text Available Identification of catalytic residues (CR is essential for the characterization of enzyme function. CR are, in general, conserved and located in the functional site of a protein in order to attain their function. However, many non-catalytic residues are highly conserved and not all CR are conserved throughout a given protein family making identification of CR a challenging task. Here, we put forward the hypothesis that CR carry a particular signature defined by networks of close proximity residues with high mutual information (MI, and that this signature can be applied to distinguish functional from other non-functional conserved residues. Using a data set of 434 Pfam families included in the catalytic site atlas (CSA database, we tested this hypothesis and demonstrated that MI can complement amino acid conservation scores to detect CR. The Kullback-Leibler (KL conservation measurement was shown to significantly outperform both the Shannon entropy and maximal frequency measurements. Residues in the proximity of catalytic sites were shown to be rich in shared MI. A structural proximity MI average score (termed pMI was demonstrated to be a strong predictor for CR, thus confirming the proposed hypothesis. A structural proximity conservation average score (termed pC was also calculated and demonstrated to carry distinct information from pMI. A catalytic likeliness score (Cls, combining the KL, pC and pMI measures, was shown to lead to significantly improved prediction accuracy. At a specificity of 0.90, the Cls method was found to have a sensitivity of 0.816. In summary, we demonstrate that networks of residues with high MI provide a distinct signature on CR and propose that such a signature should be present in other classes of functional residues where the requirement to maintain a particular function places limitations on the diversification of the structural environment along the course of evolution.

  19. Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification.

    Science.gov (United States)

    Marino Buslje, Cristina; Teppa, Elin; Di Doménico, Tomas; Delfino, José María; Nielsen, Morten

    2010-11-04

    Identification of catalytic residues (CR) is essential for the characterization of enzyme function. CR are, in general, conserved and located in the functional site of a protein in order to attain their function. However, many non-catalytic residues are highly conserved and not all CR are conserved throughout a given protein family making identification of CR a challenging task. Here, we put forward the hypothesis that CR carry a particular signature defined by networks of close proximity residues with high mutual information (MI), and that this signature can be applied to distinguish functional from other non-functional conserved residues. Using a data set of 434 Pfam families included in the catalytic site atlas (CSA) database, we tested this hypothesis and demonstrated that MI can complement amino acid conservation scores to detect CR. The Kullback-Leibler (KL) conservation measurement was shown to significantly outperform both the Shannon entropy and maximal frequency measurements. Residues in the proximity of catalytic sites were shown to be rich in shared MI. A structural proximity MI average score (termed pMI) was demonstrated to be a strong predictor for CR, thus confirming the proposed hypothesis. A structural proximity conservation average score (termed pC) was also calculated and demonstrated to carry distinct information from pMI. A catalytic likeliness score (Cls), combining the KL, pC and pMI measures, was shown to lead to significantly improved prediction accuracy. At a specificity of 0.90, the Cls method was found to have a sensitivity of 0.816. In summary, we demonstrate that networks of residues with high MI provide a distinct signature on CR and propose that such a signature should be present in other classes of functional residues where the requirement to maintain a particular function places limitations on the diversification of the structural environment along the course of evolution.

  20. Conserved Residues Lys57 and Lys401 of Protein Disulfide Isomerase Maintain an Active Site Conformation for Optimal Activity: Implications for Post-Translational Regulation

    Directory of Open Access Journals (Sweden)

    Cody Caba

    2018-02-01

    Full Text Available Despite its study since the 1960's, very little is known about the post-translational regulation of the multiple catalytic activities performed by protein disulfide isomerase (PDI, the primary protein folding catalyst of the cell. This work identifies a functional role for the highly conserved CxxC-flanking residues Lys57 and Lys401 of human PDI in vitro. Mutagenesis studies have revealed these residues as modulating the oxidoreductase activity of PDI in a pH-dependent manner. Non-conservative amino acid substitutions resulted in enzyme variants upwards of 7-fold less efficient. This attenuated activity was found to translate into a 2-fold reduction of the rate of electron shuttling between PDI and the intraluminal endoplasmic reticulum oxidase, ERO1α, suggesting a functional significance to oxidative protein folding. In light of this, the possibility of lysine acetylation at residues Lys57 and Lys401 was assessed by in vitro treatment using acetylsalicylic acid (aspirin. A total of 28 acetyllysine residues were identified, including acLys57 and acLys401. The kinetic behavior of the acetylated protein form nearly mimicked that obtained with a K57/401Q double substitution variant providing an indication that acetylation of the active site-flanking lysine residues can act to reversibly modulate PDI activity.

  1. Conserved Residues Lys57 and Lys401 of Protein Disulfide Isomerase Maintain an Active Site Conformation for Optimal Activity: Implications for Post-Translational Regulation.

    Science.gov (United States)

    Caba, Cody; Ali Khan, Hyder; Auld, Janeen; Ushioda, Ryo; Araki, Kazutaka; Nagata, Kazuhiro; Mutus, Bulent

    2018-01-01

    Despite its study since the 1960's, very little is known about the post-translational regulation of the multiple catalytic activities performed by protein disulfide isomerase (PDI), the primary protein folding catalyst of the cell. This work identifies a functional role for the highly conserved CxxC-flanking residues Lys 57 and Lys 401 of human PDI in vitro . Mutagenesis studies have revealed these residues as modulating the oxidoreductase activity of PDI in a pH-dependent manner. Non-conservative amino acid substitutions resulted in enzyme variants upwards of 7-fold less efficient. This attenuated activity was found to translate into a 2-fold reduction of the rate of electron shuttling between PDI and the intraluminal endoplasmic reticulum oxidase, ERO1α, suggesting a functional significance to oxidative protein folding. In light of this, the possibility of lysine acetylation at residues Lys 57 and Lys 401 was assessed by in vitro treatment using acetylsalicylic acid (aspirin). A total of 28 acetyllysine residues were identified, including acLys 57 and acLys 401 . The kinetic behavior of the acetylated protein form nearly mimicked that obtained with a K57/401Q double substitution variant providing an indication that acetylation of the active site-flanking lysine residues can act to reversibly modulate PDI activity.

  2. Alanine substitution of conserved residues in the cytoplasmic tail of herpes simplex virus gB can enhance or abolish cell fusion activity and viral entry

    International Nuclear Information System (INIS)

    Ruel, Nancy; Zago, Anna; Spear, Patricia G.

    2006-01-01

    Herpes simplex virus (HSV) glycoprotein B (gB) is one of the four viral glycoproteins required for viral entry and cell fusion and is highly conserved among herpesviruses. Mutants of HSV type 2 gB were generated by substituting conserved residues in the cytoplasmic tail with alanine or by deleting 41 amino acids from the C-terminus. Some of the mutations abolished cell fusion activity and also prevented transport of gB to the cell surface, identifying residues in the gB cytoplasmic tail that are critical for intracellular transport of this glycoprotein. These mutations also prevented production of infectious virus, possibly because the mutant forms of gB were not transported to the site of envelopment. Other mutations, particularly the deletion, significantly enhanced cell fusion activity. These mutations, as well as others described previously, identify regions of the gB cytoplasmic domain that modulate cell fusion activity

  3. Readings in Wildlife and Fish Conservation, High School Conservation Curriculum Project.

    Science.gov (United States)

    Ensminger, Jack

    This publication is a tentative edition of readings on Wildlife and Fish Conservation in Louisiana, and as such it forms part of one of the four units of study designed for an experimental high school course, the "High School Conservation Curriculum Project." The other three units are concerned with Forest Conervation, Soil and Water…

  4. Contributions of conserved residues at the gating interface of glycine receptors

    DEFF Research Database (Denmark)

    Pless, Stephan Alexander; Leung, Ada W Y; Galpin, Jason D

    2011-01-01

    and the in vivo nonsense suppression method to incorporate unnatural amino acids to probe the electrostatic and hydrophobic contributions of five highly conserved side chains near the interface, Glu-53, Phe-145, Asp-148, Phe-187, and Arg-218. Our results suggest a salt bridge between Asp-148 in loop 7 and Arg-218......Glycine receptors (GlyRs) are chloride channels that mediate fast inhibitory neurotransmission and are members of the pentameric ligand-gated ion channel (pLGIC) family. The interface between the ligand binding domain and the transmembrane domain of pLGICs has been proposed to be crucial...

  5. Automatic residue removal for high-NA extreme illumination

    Science.gov (United States)

    Moon, James; Nam, Byong-Sub; Jeong, Joo-Hong; Kong, Dong-Ho; Nam, Byung-Ho; Yim, Dong Gyu

    2007-10-01

    An epidemic for smaller node has been that, as the device architecture shrinks, lithography process requires high Numerical Aperture (NA), and extreme illumination system. This, in turn, creates many lithography problems such as low lithography process margin (Depth of Focus, Exposure Latitude), unstable Critical Dimension (CD) uniformity and restricted guideline for device design rule and so on. Especially for high NA, extreme illumination such as immersion illumination systems, above all the related problems, restricted design rule due to forbidden pitch is critical and crucial issue. This forbidden pitch is composed of numerous optical effects but majority of these forbidden pitch compose of photo resist residue and these residue must be removed to relieve some room for already tight design rule. In this study, we propose automated algorithm to remove photo resist residue due to high NA and extreme illumination condition. This algorithm automatically self assembles assist patterns based on the original design layout, therefore insuring the safety and simplicity of the generated assist pattern to the original design and removes any resist residue created by extreme illumination condition. Also we tested our automated algorithm on full chip FLASH memory device and showed the residue removal effect by using commercial verification tools as well as on actual test wafer.

  6. The conserved glycine residues in the transmembrane domain of the Semliki Forest virus fusion protein are not required for assembly and fusion

    International Nuclear Information System (INIS)

    Liao Maofu; Kielian, Margaret

    2005-01-01

    The alphavirus Semliki Forest virus (SFV) infects cells via a low pH-triggered fusion reaction mediated by the viral E1 protein. Both the E1 fusion peptide and transmembrane (TM) domain are essential for membrane fusion, but the functional requirements for the TM domain are poorly understood. Here we explored the role of the five TM domain glycine residues, including the highly conserved glycine pair at E1 residues 415/416. SFV mutants with alanine substitutions for individual or all five glycine residues (5G/A) showed growth kinetics and fusion pH dependence similar to those of wild-type SFV. Mutants with increasing substitution of glycine residues showed an increasingly more stringent requirement for cholesterol during fusion. The 5G/A mutant showed decreased fusion kinetics and extent in fluorescent lipid mixing assays. TM domain glycine residues thus are not required for efficient SFV fusion or assembly but can cause subtle effects on the properties of membrane fusion

  7. Entropy Viscosity Method for High-Order Approximations of Conservation Laws

    KAUST Repository

    Guermond, J. L.

    2010-09-17

    A stabilization technique for conservation laws is presented. It introduces in the governing equations a nonlinear dissipation function of the residual of the associated entropy equation and bounded from above by a first order viscous term. Different two-dimensional test cases are simulated - a 2D Burgers problem, the "KPP rotating wave" and the Euler system - using high order methods: spectral elements or Fourier expansions. Details on the tuning of the parameters controlling the entropy viscosity are given. © 2011 Springer.

  8. Entropy Viscosity Method for High-Order Approximations of Conservation Laws

    KAUST Repository

    Guermond, J. L.; Pasquetti, R.

    2010-01-01

    A stabilization technique for conservation laws is presented. It introduces in the governing equations a nonlinear dissipation function of the residual of the associated entropy equation and bounded from above by a first order viscous term. Different two-dimensional test cases are simulated - a 2D Burgers problem, the "KPP rotating wave" and the Euler system - using high order methods: spectral elements or Fourier expansions. Details on the tuning of the parameters controlling the entropy viscosity are given. © 2011 Springer.

  9. Heat transfer properties of organic coolants containing high boiling residues

    International Nuclear Information System (INIS)

    Debbage, A.G.; Driver, M.; Waller, P.R.

    1964-01-01

    Heat transfer measurements were made in forced convection with Santowax R, mixtures of Santowax R and pyrolytic high boiling residue, mixtures of Santowax R and CMRE Radiolytic high boiling residue, and OMRE coolant, in the range of Reynolds number 10 4 to 10 5 . The data was correlated with the equation Nu = 0.015 Re b 0.85 Pr b 0.4 with an r.m.s. error of ± 8.5%. The total maximum error arising from the experimental method and inherent errors in the physical property data has been estimated to be less than ± 8.5%. From the correlation and physical property data, the decrease in heat transfer coefficient with increasing high boiling residue concentration has been determined. It has been shown that subcooled boiling in organic coolants containing high boiling residues is a complex phenomenon and the advantages to be gained by operating a reactor in this region may be marginal. Gas bearing pumps used initially in these experiments were found to be unsuitable; a re-designed ball bearing system lubricated with a terphenyl mixture was found to operate successfully. (author)

  10. The economics of soil conservation in developing countries: the case of crop residue mulching

    NARCIS (Netherlands)

    Erenstein, O.C.A.

    1999-01-01

    The study contributes to the search for a methodology to assess soil conservation, particularly in developing countries. The study first assesses the economics of soil conservation in general - with special emphasis on the relationships between technology, economic analysis and policy implications.

  11. NMR WaterLOGSY Reveals Weak Binding of Bisphenol A with Amyloid Fibers of a Conserved 11 Residue Peptide from Androgen Receptor.

    Directory of Open Access Journals (Sweden)

    Julia Asencio-Hernández

    Full Text Available There is growing evidence that bisphenol A (BPA, a molecule largely released in the environment, has detrimental effects on ecosystems and on human health. It acts as an endocrine disruptor targeting steroid hormone receptors, such as the estrogen receptor (ER, estrogen-related receptor (ERR and androgen receptor (AR. BPA-derived molecules have recently been shown to interact with the AR N-terminal domain (AR-NTD, which is known to be largely intrinsically disordered. This N-terminal domain contains an 11 residue conserved domain that forms amyloid fibers upon oxidative dimerisation through its strictly conserved Cys240 residue. We investigate here the interaction of BPA, and other potential endocrine disruptors, with AR-NTD amyloid fibers using the WaterLOGSY NMR experiment. We observed a selective binding of these compounds to the amyloid fibers formed by the AR-NTD conserved region and glutamine homopolymers. This observation suggests that the high potency of endocrine disruptors may result, in part, from their ability to bind amyloid forms of nuclear receptors in addition to their cognate binding sites. This property may be exploited to design future therapeutic strategies targeting AR related diseases such as the spinal bulbar muscular atrophy or prostate cancer. The ability of NMR WaterLOGSY experiments to detect weak interactions between small ligands and amyloid fibers may prove to be of particular interest for identifying promising hit molecules.

  12. Modelling Of Residual Stresses Induced By High Speed Milling Process

    International Nuclear Information System (INIS)

    Desmaison, Olivier; Mocellin, Katia; Jardin, Nicolas

    2011-01-01

    Maintenance processes used in heavy industries often include high speed milling operations. The reliability of the post-process material state has to be studied. Numerical simulation appears to be a very interesting way to supply an efficient residual stresses (RS) distribution prediction.Because the adiabatic shear band and the serrated chip shaping are features of the austenitic stainless steel high speed machining, a 2D high speed orthogonal cutting model is briefly presented. This finite element model, developed on Forge registered software, is based on data taken from Outeiro and al.'s paper [1]. A new behaviour law fully coupling Johnson-Cook's constitutive law and Latham and Cockcroft's damage model is detailed in this paper. It ensures results that fit those found in literature.Then, the numerical tools used on the 2D model are integrated to a 3D high speed milling model. Residual stresses distribution is analysed, on the surface and into the depth of the material. Various revolutions and passes of the two teeth hemispheric mill on the workpiece are simulated. Thus the sensitivity of the residual stresses generation to the cutting conditions can be discussed. In order to validate the 3D model, a comparison of the cutting forces measured by EDF R and D to those given by numerical simulations is achieved.

  13. Using a consensus approach based on the conservation of inter-residue contacts to rank CAPRI models

    KAUST Repository

    Vangone, Anna

    2013-10-17

    Herein we propose the use of a consensus approach, CONSRANK, for ranking CAPRI models. CONSRANK relies on the conservation of inter-residue contacts in the analyzed decoys ensemble. Models are ranked according to their ability to match the most frequently observed contacts. We applied CONSRANK to 19 CAPRI protein-protein targets, covering a wide range of prediction difficulty and involved in a variety of biological functions. CONSRANK results are consistently good, both in terms of native-like (NL) solutions ranked in the top positions and of values of the Area Under the receiver operating characteristic Curve (AUC). For targets having a percentage of NL solutions above 3%, an excellent performance is found, with AUC values approaching 1. For the difficult target T46, having only 3.4% NL solutions, the number of NL solutions in the top 5 and 10 ranked positions is enriched by a factor 30, and the AUC value is as high as 0.997. AUC values below 0.8 are only found for targets featuring a percentage of NL solutions within 1.1%. Remarkably, a false consensus emerges only in one case, T42, which happens to be an artificial protein, whose assembly details remain uncertain, based on controversial experimental data. We also show that CONSRANK still performs very well on a limited number of models, provided that more than 1 NL solution is included in the ensemble, thus extending its applicability to cases where few dozens of models are available.© 2013 Wiley Periodicals, Inc.

  14. Long-term impact of reduced tillage and residue management on soil carbon stabilization: Implications for conservation agriculture on contrasting soil

    NARCIS (Netherlands)

    Chivenge, P.P.; Murwira, H.K.; Giller, K.E.; Mapfumo, P.; Six, J.

    2007-01-01

    Residue retention and reduced tillage are both conservation agricultural management options that may enhance soil organic carbon (SOC) stabilization in tropical soils. Therefore, we evaluated the effects of long-term tillage and residue management on SOC dynamics in a Chromic Luvisol (red clay soil)

  15. Residue management increases fallow water conservation and yield deficit irrigated crops grown in rotation with wheat

    Science.gov (United States)

    No-tillage (NT) residue management provides cover to increase precipitation capture compared with disk tillage (DT) or in the absence of a cover crop. Therefore, NT has the potential to reduce irrigation withdrawals from the declining Ogallala Aquifer. In a 4-year study, we quantified DT and NT effe...

  16. Crop residue is key for sustaining maximum food production and for conservation of our biosphere

    Science.gov (United States)

    Crop residue is key in our efforts to move towards agricultural sustainability. This paper provides a quick overview of some selected references and looks at some of the newest advances related to cover crops. Several authors have described in detail the benefits derived from improving soil quality ...

  17. Computational analysis of perturbations in the post-fusion Dengue virus envelope protein highlights known epitopes and conserved residues in the Zika virus [version 2; referees: 3 approved

    Directory of Open Access Journals (Sweden)

    Sandeep Chakraborty

    2016-09-01

    Full Text Available The dramatic transformation of the Zika virus (ZIKV from a relatively unknown virus to a pathogen generating global-wide panic has exposed the dearth of detailed knowledge about this virus. Decades of research in the related Dengue virus (DENV, finally culminating in a vaccine registered for use in endemic regions (CYD-TDV in three countries, provides key insights in developing strategies for tackling ZIKV, which has caused global panic to microcephaly and Guillain-Barre Syndrome. Dengue virus (DENV, a member of the family Flaviviridae, the causal agent of the self-limiting Dengue fever and the potentially fatal hemorrhagic fever/dengue shock syndrome, has been a scourge in tropical countries for many centuries. The recently solved structure of mature ZIKV (PDB ID:5IRE has provided key insights into the structure of the envelope (E and membrane (M proteins, the primary target of neutralizing antibodies. The previously established MEPP methodology compares two conformations of the same protein and identifies residues with significant spatial and electrostatic perturbations. In the current work, MEPP analyzed the pre-and post-fusion DENV type 2 envelope (E protein, and identified several known epitopes (His317, Tyr299, Glu26, Arg188, etc. (MEPPitope. These residues are overwhelmingly conserved in ZIKV and all DENV serotypes, and also enumerates residue pairs that undergo significant polarity reversal. Characterization of α-helices in E-proteins show that α1 is not conserved in the sequence space of ZIKV and DENV. Furthermore, perturbation of α1 in the post-fusion DENV structure includes a known epitope Asp215, a residue absent in the pre-fusion α1. A cationic β-sheet in the GAG-binding domain that is stereochemically equivalent in ZIKV and all DENV serotypes is also highlighted due to a residue pair (Arg286-Arg288 that has a significant electrostatic polarity reversal upon fusion. Finally, two highly conserved residues (Thr32 and Thr40, with

  18. Tilapia and human CLIC2 structures are highly conserved.

    Science.gov (United States)

    Zeng, Jiao; Li, Zhengjun; Lui, Eei Yin; Lam, Siew Hong; Swaminathan, Kunchithapadam

    2018-01-08

    Chloride intracellular channels (CLICs) exist in soluble and membrane bound forms. We have determined the crystal structure of soluble Clic2 from the euryhaline teleost fish Oreochromis mossambicus. Structural comparison of tilapia and human CLIC2 with other CLICs shows that these proteins are highly conserved. We have also compared the expression levels of clic2 in selected osmoregulatory organs of tilapia, acclimated to freshwater, seawater and hypersaline water. Structural conservation of vertebrate CLICs implies that they might play conserved roles. Also, tissue-specific responsiveness of clic2 suggests that it might be involved in iono-osmoregulation under extreme conditions in tilapia. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation

    DEFF Research Database (Denmark)

    Weinert, Brian T; Wagner, Sebastian A; Horn, Heiko

    2011-01-01

    Posttranslational modification of proteins by acetylation and phosphorylation regulates most cellular processes in living organisms. Surprisingly, the evolutionary conservation of phosphorylated serine and threonine residues is only marginally higher than that of unmodified serines and threonines....... With high-resolution mass spectrometry, we identified 1981 lysine acetylation sites in the proteome of Drosophila melanogaster. We used data sets of experimentally identified acetylation and phosphorylation sites in Drosophila and humans to analyze the evolutionary conservation of these modification sites...... between flies and humans. Site-level conservation analysis revealed that acetylation sites are highly conserved, significantly more so than phosphorylation sites. Furthermore, comparison of lysine conservation in Drosophila and humans with that in nematodes and zebrafish revealed that acetylated lysines...

  20. Conservation

    NARCIS (Netherlands)

    Noteboom, H.P.

    1985-01-01

    The IUCN/WWF Plants Conservation Programme 1984 — 1985. World Wildlife Fund chose plants to be the subject of their fund-raising campaign in the period 1984 — 1985. The objectives were to: 1. Use information techniques to achieve the conservation objectives of the Plants Programme – to save plants;

  1. Conservation.

    Science.gov (United States)

    National Audubon Society, New York, NY.

    This set of teaching aids consists of seven Audubon Nature Bulletins, providing the teacher and student with informational reading on various topics in conservation. The bulletins have these titles: Plants as Makers of Soil, Water Pollution Control, The Ground Water Table, Conservation--To Keep This Earth Habitable, Our Threatened Air Supply,…

  2. [Residual risk: The roles of triglycerides and high density lipoproteins].

    Science.gov (United States)

    Grammer, Tanja; Kleber, Marcus; Silbernagel, Günther; Scharnagl, Hubert; März, Winfried

    2016-06-01

    In clinical trials, the reduction of LDL-cholesterol (LDL-C) with statins reduces the incidence rate of cardiovascular events by approximately one third. This means, that a sizeable "residual risk" remains. Besides high lipoprotein (a), disorders in the metabolism of triglyceride-rich lipoproteins and high density liproteins have been implicated as effectors of the residual risk. Both lipoprotein parameters correlate inversely with each other. Therefore, the etiological contributions of triglycerides and / or of HDL for developing cardiovascular disease can hardly be estimated from either observational studies or from intervention studies. The largely disappointing results of intervention studies with inhibitors of the cholesteryl ester transfer protein and in particular the available set of genetically-epidemiological studies suggest that in the last decade, the importance of HDL cholesterol has been overvalued, while the importance of triglycerides has been underestimated. High triglycerides not always atherogenic, but only if they are associated with the accumulation relatively cholesterol-enriched, incompletely catabolized remnants of chylomicrons and very low density lipoproteins (familial type III hyperlipidemia, metabolic syndrome, diabetes mellitus). The normalization of the concentration of triglycerides and remnants by inhibiting the expression of apolipoprotein C3 is hence a new, promising therapeutic target. © Georg Thieme Verlag KG Stuttgart · New York.

  3. Forensic Analysis of High Explosive Residues from Selected Cloth

    International Nuclear Information System (INIS)

    Mohamad Afiq Mohamed Huri; Umi Kalthom Ahmad

    2014-01-01

    Increased terrorist activities around the Asian region have resulted in the need for improved analytical techniques in forensic analysis. High explosive residues from post-blast clothing are often encountered as physical evidence submitted to a forensic laboratory. Therefore, this study was initiated to detect high explosives residues of cyclotrimethylenetrinitramine (RDX) and pentaerythritol tetranitrate (PETN) on selected cloth in this study. Cotton swabbing technique was employed as a simple and rapid method in recovering analytes from the sample matrix. Analytes were analyzed using Griess spot test, TLC and HPLC. TLC separation employed toluene-ethyl acetate (9:1) as a good solvent system. Reversed phase HPLC separation employed acetonitrile-water (65:35) as the mobile phase and analytes detected using a programmed wavelength. RDX was detected at 235 nm for the first 3.5 min and then switched to 215 nm for PETN. Limits of detection (LODs) of analytes were in the low ppm range (0.05 ppm for RDX and 0.25 ppm for PETN). Analyte recovery studies revealed that the type of cloth has a profound effect on the extraction efficiency. Analytes were recovered better for nylon as compared to cotton cloth. However, no analytes could be recovered from denim cloth. For post-blast samples, only RDX was detected in low concentration for both nylon and cotton cloth. (author)

  4. The conserved Lysine69 residue plays a catalytic role in Mycobacterium tuberculosis shikimate dehydrogenase

    Directory of Open Access Journals (Sweden)

    Rodrigues Valnês

    2009-01-01

    Full Text Available Abstract Background The shikimate pathway is an attractive target for the development of antitubercular agents because it is essential in Mycobacterium tuberculosis, the causative agent of tuberculosis, but absent in humans. M. tuberculosis aroE-encoded shikimate dehydrogenase catalyzes the forth reaction in the shikimate pathway. Structural and functional studies indicate that Lysine69 may be involved in catalysis and/or substrate binding in M. tuberculosis shikimate dehydrogenase. Investigation of the kinetic properties of mutant enzymes can bring important insights about the role of amino acid residues for M. tuberculosis shikimate dehydrogenase. Findings We have performed site-directed mutagenesis, steady-state kinetics, equilibrium binding measurements and molecular modeling for both the wild-type M. tuberculosis shikimate dehydrogenase and the K69A mutant enzymes. The apparent steady-state kinetic parameters for the M. tuberculosis shikimate dehydrogenase were determined; the catalytic constant value for the wild-type enzyme (50 s-1 is 68-fold larger than that for the mutant K69A (0.73 s-1. There was a modest increase in the Michaelis-Menten constant for DHS (K69A = 76 μM; wild-type = 29 μM and NADPH (K69A = 30 μM; wild-type = 11 μM. The equilibrium dissociation constants for wild-type and K69A mutant enzymes are 32 (± 4 μM and 134 (± 21, respectively. Conclusion Our results show that the residue Lysine69 plays a catalytic role and is not involved in substrate binding for the M. tuberculosis shikimate dehydrogenase. These efforts on M. tuberculosis shikimate dehydrogenase catalytic mechanism determination should help the rational design of specific inhibitors, aiming at the development of antitubercular drugs.

  5. A computational tool to predict the evolutionarily conserved protein-protein interaction hot-spot residues from the structure of the unbound protein.

    Science.gov (United States)

    Agrawal, Neeraj J; Helk, Bernhard; Trout, Bernhardt L

    2014-01-21

    Identifying hot-spot residues - residues that are critical to protein-protein binding - can help to elucidate a protein's function and assist in designing therapeutic molecules to target those residues. We present a novel computational tool, termed spatial-interaction-map (SIM), to predict the hot-spot residues of an evolutionarily conserved protein-protein interaction from the structure of an unbound protein alone. SIM can predict the protein hot-spot residues with an accuracy of 36-57%. Thus, the SIM tool can be used to predict the yet unknown hot-spot residues for many proteins for which the structure of the protein-protein complexes are not available, thereby providing a clue to their functions and an opportunity to design therapeutic molecules to target these proteins. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  6. Conductive component after cochlear implantation in patients with residual hearing conservation.

    Science.gov (United States)

    Chole, Richard A; Hullar, Timothy E; Potts, Lisa G

    2014-12-01

    Changes in auditory thresholds following cochlear implantation are generally assumed to be due to damage to neural elements. Theoretical studies have suggested that placement of a cochlear implant can cause a conductive hearing loss. Identification of a conductive component following cochlear implantation could guide improvements in surgical techniques or device designs. The purpose of this study is to characterize new-onset conductive hearing losses after cochlear implantation. In a prospective study, air- and bone-conduction audiometric testing were completed on cochlear implant recipients. An air-bone gap equal to or greater than 15 dB HL at 2 frequencies determined the presence of a conductive component. Of the 32 patients with preoperative bone-conduction hearing, 4 patients had a new-onset conductive component resulting in a mixed hearing loss, with air-conduction thresholds ranging from moderate to profound and an average air-bone gap of 30 dB HL. One had been implanted through the round window, 2 had an extended round window, and 1 had a separate cochleostomy. Loss of residual hearing following cochlear implantation may be due in part to a conductive component. Identifying the mechanism for this conductive component may help minimize hearing loss. Postoperative hearing evaluation should measure both air- and bone-conduction thresholds.

  7. The Effect of Conservation Tillage and Cover Crop Residue on Beneficial Arthropods and Weed Seed Predation in Acorn Squash.

    Science.gov (United States)

    Quinn, N F; Brainard, D C; Szendrei, Z

    2016-12-01

    Conservation tillage combined with cover crops or mulching may enhance natural enemy activity in agroecosystems by reducing soil disturbance and increasing habitat structural complexity. In particular, weed seed predation can increase with vegetation cover and reduced tillage, indicating that mulches may improve the quality of the habitat for weed seed foraging. The purpose of this study was to quantify the effects of tillage and mulching for conservation biological control in cucurbit fields. The effects of mulch and reduced tillage on arthropods and rates of weed seed loss from arenas were examined in field trials on sandy soils in 2014 and 2015. Experimental factors included tillage and cover crop, each with two levels: strip-tillage or full-tillage, and cover crop mulch (rye residue) or no cover crop mulch (unmulched). Arthropod abundance on the crop foliage was not affected by tillage or cover crops. Contrary to expectations, epigeal natural enemies of insects and rates of weed seed removal either did not respond to treatments or were greater in full-tilled plots and plots without mulch. Our study demonstrates the potential importance of weed seed predators in reducing weed seedbanks in vegetable agroecosystems, and suggests that early-season tillage may not be detrimental to epigeal predator assemblages. © The Authors 2016. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  8. Bacillus cereus as indicator in the sterilization of residual water with high energy electrons

    International Nuclear Information System (INIS)

    Mejia Z, E.

    2000-01-01

    One of the main causes of water pollution is the presence of microorganisms that provoke infections, moreover of chemical substances. The processes of residual water treatment finally require of the disinfection for its use or final disposition. The radiation technology for the residual water treatment by mean of electron beams is an innovator process because as well as decomposing the chemical substance or to degrade them, also it provokes a disinfection by which this is proposed as alternative for disinfection of residual water, with the purpose in reusing the water treated in the agriculture, recreation and industry among others secondary activities, solving environmental or health problems. The objective of this work is to evaluate the use of Bacillus cereus as biological indicator in the disinfection by radiation, using High Energy Electrons. To fulfil with this objective, the work was developed in three stages, the first one consisted in the acquisition, propagation and conservation of the Bacillus cereus stumps, considering Escherichia coli and Salmonella typhimurium as pathogenic germs present in residual water. Moreover, the inocule standardization and the conditions of the Electron accelerator Type Pelletron. In the second stage it was performed the irradiation of aqueous samples of the microorganisms simulating biological pollution and the application to problem samples of a treatment plant sited in the Lerma River zone of mixed residual water. And in the third stage was performed a regression analysis to the reported survival for each kind of microorganisms. The results obtained show that with the use of Electron beams was reduced 6 logarithmic units de E. coli at 129 Gy, for S. typhimurium it was reduced 8 logarithmic units at 383 Gy and the B. cereus at 511 Gy was reduced 6.8 logarithmic units. Of the problem samples irradiated at 500 Gy, the concentration of the total account diminished from 8.70 x 10 7 UFC/ml to 550 UFC/ml, the presence of B. Cereus

  9. Generation of monoclonal antibodies against highly conserved antigens.

    Directory of Open Access Journals (Sweden)

    Hongzhe Zhou

    Full Text Available BACKGROUND: Therapeutic antibody development is one of the fastest growing areas of the pharmaceutical industry. Generating high-quality monoclonal antibodies against a given therapeutic target is very crucial for the success of the drug development. However, due to immune tolerance, some proteins that are highly conserved between mice and humans are not very immunogenic in mice, making it difficult to generate antibodies using a conventional approach. METHODOLOGY/PRINCIPAL FINDINGS: In this report, the impaired immune tolerance of NZB/W mice was exploited to generate monoclonal antibodies against highly conserved or self-antigens. Using two highly conserved human antigens (MIF and HMGB1 and one mouse self-antigen (TNF-alpha as examples, we demonstrate here that multiple clones of high affinity, highly specific antibodies with desired biological activities can be generated, using the NZB/W mouse as the immunization host and a T cell-specific tag fused to a recombinant antigen to stimulate the immune system. CONCLUSIONS/SIGNIFICANCE: We developed an efficient and universal method for generating surrogate or therapeutic antibodies against "difficult antigens" to facilitate the development of therapeutic antibodies.

  10. Differential Regulation of Receptor Activation and Agonist Selectivity by Highly Conserved Tryptophans in the Nicotinic Acetylcholine Receptor Binding Site

    OpenAIRE

    Williams, Dustin K.; Stokes, Clare; Horenstein, Nicole A.; Papke, Roger L.

    2009-01-01

    We have shown previously that a highly conserved Tyr in the nicotinic acetylcholine receptor (nAChR) ligand-binding domain (LBD) (α7 Tyr188 or α4 Tyr195) differentially regulates the activity of acetylcholine (ACh) and the α7-selective agonist 3-(4-hydroxy,2-methoxybenzylidene)anabaseine (4OH-GTS-21) in α4β2 and α7 nAChR. In this study, we mutated two highly conserved LBD Trp residues in human α7 and α4β2 and expressed the receptors in Xenopus laevis oocytes. α7 Re...

  11. The role of conserved inulosucrase residues in the reaction and product specificity of Lactobacillus reuteri inulosucrase

    NARCIS (Netherlands)

    Anwar, Munir A.; Leemhuis, Hans; Pijning, Tjaard; Kralj, Slavko; Dijkstra, Bauke W.; Dijkhuizen, Lubbert

    2012-01-01

    The probiotic bacterium Lactobacillus reuteri 121 produces two fructosyltransferase enzymes, a levansucrase and an inulosucrase. Although these two fructosyltransferase enzymes share high sequence similarity, they differ significantly in the type and size distribution of fructooligosaccharide

  12. Residual stress in a thick section high strength T-butt weld

    International Nuclear Information System (INIS)

    Pearce, S.V.; Linton, V.M.; Oliver, E.C.

    2008-01-01

    Residual stresses in a structure are generated as a result of the various fabrication and welding processes used to make the component. Being able to quantify these residual stresses is a key step in determining the continuing integrity of a structure in service. In this work, the residual stresses around a high strength, quenched and tempered steel T-butt web to curved plate weld have been measured using neutron strain scanning. The results show that the residual stresses near the weld were dominated by the welding residual stresses, while the stresses further from the weld were dominated by the bending residual stresses. The results suggest that the combination of welding-induced residual stress and significant pre-welding residual stress, as in the case of a thick bent section of plate can significantly alter the residual stress profile from that in a flat plate

  13. Evolutionary growth process of highly conserved sequences in vertebrate genomes.

    Science.gov (United States)

    Ishibashi, Minaka; Noda, Akiko Ogura; Sakate, Ryuichi; Imanishi, Tadashi

    2012-08-01

    Genome sequence comparison between evolutionarily distant species revealed ultraconserved elements (UCEs) among mammals under strong purifying selection. Most of them were also conserved among vertebrates. Because they tend to be located in the flanking regions of developmental genes, they would have fundamental roles in creating vertebrate body plans. However, the evolutionary origin and selection mechanism of these UCEs remain unclear. Here we report that UCEs arose in primitive vertebrates, and gradually grew in vertebrate evolution. We searched for UCEs in two teleost fishes, Tetraodon nigroviridis and Oryzias latipes, and found 554 UCEs with 100% identity over 100 bps. Comparison of teleost and mammalian UCEs revealed 43 pairs of common, jawed-vertebrate UCEs (jUCE) with high sequence identities, ranging from 83.1% to 99.2%. Ten of them retain lower similarities to the Petromyzon marinus genome, and the substitution rates of four non-exonic jUCEs were reduced after the teleost-mammal divergence, suggesting that robust conservation had been acquired in the jawed vertebrate lineage. Our results indicate that prototypical UCEs originated before the divergence of jawed and jawless vertebrates and have been frozen as perfect conserved sequences in the jawed vertebrate lineage. In addition, our comparative sequence analyses of UCEs and neighboring regions resulted in a discovery of lineage-specific conserved sequences. They were added progressively to prototypical UCEs, suggesting step-wise acquisition of novel regulatory roles. Our results indicate that conserved non-coding elements (CNEs) consist of blocks with distinct evolutionary history, each having been frozen since different evolutionary era along the vertebrate lineage. Copyright © 2012 Elsevier B.V. All rights reserved.

  14. P300/CBP acts as a coactivator to cartilage homeoprotein-1 (Cart1), paired-like homeoprotein, through acetylation of the conserved lysine residue adjacent to the homeodomain.

    Science.gov (United States)

    Iioka, Takashi; Furukawa, Keizo; Yamaguchi, Akira; Shindo, Hiroyuki; Yamashita, Shunichi; Tsukazaki, Tomoo

    2003-08-01

    The paired-like homeoprotein, Cart1, is involved in skeletal development. We describe here that the general coactivator p300/CBP controls the transcription activity of Cart1 through acetylation of a lysine residue that is highly conserved in other homeoproteins. Acetylation of this residue increases the interaction between p300/CBP and Cart1 and enhances its transcriptional activation. Cart1 encodes a paired-like homeoprotein expressed selectively in chondrocyte lineage during embryonic development. Although its target gene remains unknown, gene disruption studies have revealed that Cart1 plays an important role for craniofacial bone formation as well as limb development by cooperating with another homeoprotein, Alx4. In this report, we study the functional involvement of p300/CBP, coactivators with intrinsic histone acetyltransferase (HAT) activity, in the transcriptional control of Cart1. To study the transcription activity of Cart1, a reporter construct containing a putative Cart1 binding site was transiently transfected with the expression vectors of each protein. The interaction between p300/CBP and Cart1 was investigated by glutathione S-transferase (GST) pull-down, yeast two-hybrid, and immunoprecipitation assays. In vitro acetylation assay was performed with the recombinant p300-HAT domain and Cart1 in the presence of acetyl-CoA. p300 and CBP stimulate Cart1-dependent transcription activity, and this transactivation is inhibited by E1A and Tax, oncoproteins that suppress the activity of p300/CBP. Cart1 binds to p300 in vivo and in vitro, and this requires the homeodomain of Cart 1 and N-terminal 139 amino acids of p300. Confocal microscopy analysis shows that Cart1 recruits overexpressed and endogenous p300 to a Cart1-specific subnuclear compartment. Cart1 is acetylated in vivo and sodium butyrate and trichostatin A, histone deacetylase inhibitors, markedly enhance the transcription activity of Cart1. Deletion and mutagenesis analysis identifies the 131st

  15. The Highly Conserved Proline at Position 438 in Pseudorabies Virus gH Is Important for Regulation of Membrane Fusion

    OpenAIRE

    Schröter, Christina; Klupp, Barbara G.; Fuchs, Walter; Gerhard, Marika; Backovic, Marija; Rey, Felix A.; Mettenleiter, Thomas C.

    2014-01-01

    Membrane fusion in herpesviruses requires viral glycoproteins (g) gB and gH/gL. While gB is considered the actual fusion protein but is nonfusogenic per se, the function of gH/gL remains enigmatic. Crystal structures for different gH homologs are strikingly similar despite only moderate amino acid sequence conservation. A highly conserved sequence motif comprises the residues serine-proline-cysteine corresponding to positions 437 to 439 in pseudorabies virus (PrV) gH. The PrV-gH structure sho...

  16. A highly conserved amino acid in VP1 regulates maturation of enterovirus 71.

    Directory of Open Access Journals (Sweden)

    Yong-Xin Zhang

    2017-09-01

    Full Text Available Enterovirus 71 (EV71 is the major causative agent of hand, foot and mouth disease (HFMD in children, causing severe clinical outcomes and even death. Here, we report an important role of the highly conserved alanine residue at position 107 in the capsid protein VP1 (VP1A107 in the efficient replication of EV71. Substitutional mutations of VP1A107 significantly diminish viral growth kinetics without significant effect on viral entry, expression of viral genes and viral production. The results of mechanistic studies reveal that VP1A107 regulates the efficient cleavage of the VP0 precursor during EV71 assembly, which is required, in the next round of infection, for the transformation of the mature virion (160S into an intermediate or A-particle (135S, a key step of virus uncoating. Furthermore, the results of molecular dynamic simulations and hydrogen-bond networks analysis of VP1A107 suggest that flexibility of the VP1 BC loop or the region surrounding the VP1107 residue directly correlates with viral infectivity. It is possible that sufficient flexibility of the region surrounding the VP1107 residue favors VP0 conformational change that is required for the efficient cleavage of VP0 as well as subsequent viral uncoating and viral replication. Taken together, our data reveal the structural role of the highly conserved VP1A107 in regulating EV71 maturation. Characterization of this novel determinant of EV71 virulence would promote the study on pathogenesis of Enteroviruses.

  17. Improving sensitivity of residual current transformers to high frequency earth fault currents

    Directory of Open Access Journals (Sweden)

    Czapp Stanislaw

    2017-09-01

    Full Text Available For protection against electric shock in low voltage systems residual current devices are commonly used. However, their proper operation can be interfered when high frequency earth fault current occurs. Serious hazard of electrocution exists then. In order to detect such a current, it is necessary to modify parameters of residual current devices, especially the operating point of their current transformer. The authors proposed the modification in the structure of residual current devices. This modification improves sensitivity of residual current devices when high frequency earth fault current occurs. The test of the modified residual current device proved that the authors’ proposition is appropriate.

  18. ABCE1 is a highly conserved RNA silencing suppressor.

    Directory of Open Access Journals (Sweden)

    Kairi Kärblane

    Full Text Available ATP-binding cassette sub-family E member 1 (ABCE1 is a highly conserved protein among eukaryotes and archaea. Recent studies have identified ABCE1 as a ribosome-recycling factor important for translation termination in mammalian cells, yeast and also archaea. Here we report another conserved function of ABCE1. We have previously described AtRLI2, the homolog of ABCE1 in the plant Arabidopsis thaliana, as an endogenous suppressor of RNA silencing. In this study we show that this function is conserved: human ABCE1 is able to suppress RNA silencing in Nicotiana benthamiana plants, in mammalian HEK293 cells and in the worm Caenorhabditis elegans. Using co-immunoprecipitation and mass spectrometry, we found a number of potential ABCE1-interacting proteins that might support its function as an endogenous suppressor of RNA interference. The interactor candidates are associated with epigenetic regulation, transcription, RNA processing and mRNA surveillance. In addition, one of the identified proteins is translin, which together with its binding partner TRAX supports RNA interference.

  19. Characterization of conserved arginine residues on Cdt1 that affect licensing activity and interaction with Geminin or Mcm complex.

    Science.gov (United States)

    You, Zhiying; Ode, Koji L; Shindo, Mayumi; Takisawa, Haruhiko; Masai, Hisao

    2016-05-02

    All organisms ensure once and only once replication during S phase through a process called replication licensing. Cdt1 is a key component and crucial loading factor of Mcm complex, which is a central component for the eukaryotic replicative helicase. In higher eukaryotes, timely inhibition of Cdt1 by Geminin is essential to prevent rereplication. Here, we address the mechanism of DNA licensing using purified Cdt1, Mcm and Geminin proteins in combination with replication in Xenopus egg extracts. We mutagenized the 223th arginine of mouse Cdt1 (mCdt1) to cysteine or serine (R-S or R-C, respectively) and 342nd and 346th arginines constituting an arginine finger-like structure to alanine (RR-AA). The RR-AA mutant of Cdt1 could not only rescue the DNA replication activity in Cdt1-depleted extracts but also its specific activity for DNA replication and licensing was significantly increased compared to the wild-type protein. In contrast, the R223 mutants were partially defective in rescue of DNA replication and licensing. Biochemical analyses of these mutant Cdt1 proteins indicated that the RR-AA mutation disabled its functional interaction with Geminin, while R223 mutations resulted in ablation in interaction with the Mcm2∼7 complex. Intriguingly, the R223 mutants are more susceptible to the phosphorylation-induced inactivation or chromatin dissociation. Our results show that conserved arginine residues play critical roles in interaction with Geminin and Mcm that are crucial for proper conformation of the complexes and its licensing activity.

  20. Role of Conserved Disulfide Bridges and Aromatic Residues in Extracellular Loop 2 of Chemokine Receptor CCR8 for Chemokine and Small Molecule Binding

    DEFF Research Database (Denmark)

    Barington, Line; Rummel, Pia C; Lückmann, Michael

    2016-01-01

    and aromatic residues in extracellular loop 2 (ECL2) for ligand binding and activation in the chemokine receptor CCR8. We used IP3 accumulation and radioligand binding experiments to determine the impact of receptor mutagenesis on both chemokine and small molecule agonist and antagonist binding and action...... in CCR8. We find that the 7 transmembrane (7TM) receptor conserved disulfide bridge (7TM bridge) linking transmembrane helix (TM)III and ECL2 is crucial for chemokine and small molecule action, whereas the chemokine receptor conserved disulfide bridge between the N terminus and TMVII is needed only...

  1. High-resolution finite-difference algorithms for conservation laws

    International Nuclear Information System (INIS)

    Towers, J.D.

    1987-01-01

    A new class of Total Variation Decreasing (TVD) schemes for 2-dimensional scalar conservation laws is constructed using either flux-limited or slope-limited numerical fluxes. The schemes are proven to have formal second-order accuracy in regions where neither u/sub x/ nor y/sub y/ vanishes. A new class of high-resolution large-time-step TVD schemes is constructed by adding flux-limited correction terms to the first-order accurate large-time-step version of the Engquist-Osher scheme. The use of the transport-collapse operator in place of the exact solution operator for the construction of difference schemes is studied. The production of spurious extrema by difference schemes is studied. A simple condition guaranteeing the nonproduction of spurious extrema is derived. A sufficient class of entropy inequalities for a conservation law with a flux having a single inflection point is presented. Finite-difference schemes satisfying a discrete version of each entropy inequality are only first-order accurate

  2. Dynamic Epigenetic Control of Highly Conserved Noncoding Elements

    KAUST Repository

    Seridi, Loqmane

    2014-10-07

    Background Many noncoding genomic loci have remained constant over long evolutionary periods, suggesting that they are exposed to strong selective pressures. The molecular functions of these elements have been partially elucidated, but the fundamental reason for their extreme conservation is still unknown. Results To gain new insights into the extreme selection of highly conserved noncoding elements (HCNEs), we used a systematic analysis of multi-omic data to study the epigenetic regulation of such elements during the development of Drosophila melanogaster. At the sequence level, HCNEs are GC-rich and have a characteristic oligomeric composition. They have higher levels of stable nucleosome occupancy than their flanking regions, and lower levels of mononucleosomes and H3.3, suggesting that these regions reside in compact chromatin. Furthermore, these regions showed remarkable modulations in histone modification and the expression levels of adjacent genes during development. Although HCNEs are primarily initiated late in replication, about 10% were related to early replication origins. Finally, HCNEs showed strong enrichment within lamina-associated domains. Conclusion HCNEs have distinct and protective sequence properties, undergo dynamic epigenetic regulation, and appear to be associated with the structural components of the chromatin, replication origins, and nuclear matrix. These observations indicate that such elements are likely to have essential cellular functions, and offer insights into their epigenetic properties.

  3. Dynamic Epigenetic Control of Highly Conserved Noncoding Elements

    KAUST Repository

    Seridi, Loqmane; Ryu, Tae Woo; Ravasi, Timothy

    2014-01-01

    Background Many noncoding genomic loci have remained constant over long evolutionary periods, suggesting that they are exposed to strong selective pressures. The molecular functions of these elements have been partially elucidated, but the fundamental reason for their extreme conservation is still unknown. Results To gain new insights into the extreme selection of highly conserved noncoding elements (HCNEs), we used a systematic analysis of multi-omic data to study the epigenetic regulation of such elements during the development of Drosophila melanogaster. At the sequence level, HCNEs are GC-rich and have a characteristic oligomeric composition. They have higher levels of stable nucleosome occupancy than their flanking regions, and lower levels of mononucleosomes and H3.3, suggesting that these regions reside in compact chromatin. Furthermore, these regions showed remarkable modulations in histone modification and the expression levels of adjacent genes during development. Although HCNEs are primarily initiated late in replication, about 10% were related to early replication origins. Finally, HCNEs showed strong enrichment within lamina-associated domains. Conclusion HCNEs have distinct and protective sequence properties, undergo dynamic epigenetic regulation, and appear to be associated with the structural components of the chromatin, replication origins, and nuclear matrix. These observations indicate that such elements are likely to have essential cellular functions, and offer insights into their epigenetic properties.

  4. High cumulants of conserved charges and their statistical uncertainties

    Science.gov (United States)

    Li-Zhu, Chen; Ye-Yin, Zhao; Xue, Pan; Zhi-Ming, Li; Yuan-Fang, Wu

    2017-10-01

    We study the influence of measured high cumulants of conserved charges on their associated statistical uncertainties in relativistic heavy-ion collisions. With a given number of events, the measured cumulants randomly fluctuate with an approximately normal distribution, while the estimated statistical uncertainties are found to be correlated with corresponding values of the obtained cumulants. Generally, with a given number of events, the larger the cumulants we measure, the larger the statistical uncertainties that are estimated. The error-weighted averaged cumulants are dependent on statistics. Despite this effect, however, it is found that the three sigma rule of thumb is still applicable when the statistics are above one million. Supported by NSFC (11405088, 11521064, 11647093), Major State Basic Research Development Program of China (2014CB845402) and Ministry of Science and Technology (MoST) (2016YFE0104800)

  5. Conserved residues in the coiled-coil pocket of human immunodeficiency virus type 1 gp41 are essential for viral replication and interhelical interaction

    International Nuclear Information System (INIS)

    Mo Hongmei; Konstantinidis, Alex K.; Stewart, Kent D.; Dekhtyar, Tatyana; Ng, Teresa; Swift, Kerry; Matayoshi, Edmund D.; Kati, Warren; Kohlbrenner, William; Molla, Akhteruzzaman

    2004-01-01

    The human immunodeficiency virus type 1 (HIV-1) gp41 plays an important role in mediating the fusion of HIV with host cells. During the fusion process, three N-terminal helices and three C-terminal helices pack in an anti-parallel direction to form a six-helix bundle. X-ray crystallographic analysis of the gp41 core demonstrated that within each coiled-coil interface, there is a deep and large pocket, formed by a cluster of residues in the N-helix coiled-coil. In this report, we systematically analyzed the role of seven conserved residues that are either lining or packing this pocket on the infectivity and interhelical interaction using novel approaches. Our results show that residues L568, V570, W571, and K574 of the N-helix that are lining the side chain and right wall of the pocket are important for establishing a productive infection. Mutations V570A and W571A completely abolished replication, while replication of the L568A and K574A mutants was significantly attenuated relative to wild type. Similarly, residues W628, W631, and I635 of the C-helix that insert into the pocket are essential for infectivity. The impaired infectivity of these seven mutants is in part attributed to the loss in binding affinity of the interhelical interaction. Molecular modeling of the crystal structure of the coiled-coil further shows that alanine substitution of those residues disrupts the hydrophobic interaction between the N- and C-helix. These results suggest that the conserved residues in the coiled-coil domain play a key role in HIV infection and this coiled-coil pocket is a good target for development of inhibitors against HIV. In addition, our data indicate that the novel fluorescence polarization assay described in this study could be valuable in screening for inhibitors that block the interhelical interaction and HIV entry

  6. Evolutionary conservativeness of electric field in the Cu,Zn superoxide dismutase active site. Evidence for co-ordinated mutation of charged amino acid residues.

    Science.gov (United States)

    Desideri, A; Falconi, M; Polticelli, F; Bolognesi, M; Djinovic, K; Rotilio, G

    1992-01-05

    Equipotential lines were calculated, using the Poisson-Boltzmann equation, for six Cu,Zn superoxide dismutases with different protein electric charge and various degrees of sequence homology, namely those from ox, pig, sheep, yeast, and the isoenzymes A and B from the amphibian Xenopus laevis. The three-dimensional structures of the porcine and ovine superoxide dismutases were obtained by molecular modelling reconstruction using the structure of the highly homologous bovine enzyme as a template. The three-dimensional structure of the evolutionary distant yeast Cu,Zn superoxide dismutase was recently resolved by us, while computer-modelled structures are available for X. laevis isoenzymes. The six proteins display large differences in the net protein charge and distribution of electrically charged surface residues but the trend of the equipotential lines in the proximity of the active sites was found to be constant in all cases. These results are in line with the very similar catlytic rate constants experimentally measured for the corresponding enzyme activities. This analysis shows that electrostatic guidance for the enzyme-substrate interaction in Cu,Zn superoxide dismutases is related to a spatial distribution of charges, arranged so as to maintain, in the area surrounding the active sites, an identical electrostatic potential distribution, which is conserved in the evolution of this protein family.

  7. A highly conserved tyrosine of Tim-3 is phosphorylated upon stimulation by its ligand galectin-9

    International Nuclear Information System (INIS)

    Weyer, Philipp S. van de; Muehlfeit, Michael; Klose, Christoph; Bonventre, Joseph V.; Walz, Gerd; Kuehn, E. Wolfgang

    2006-01-01

    Tim-3 is a member of the TIM family of proteins (T-cell immunoglobulin mucin) involved in the regulation of CD4+ T-cells. Tim-3 is a T H 1-specific type 1 membrane protein and regulates T H 1 proliferation and the development of tolerance. Binding of galectin-9 to the extracellular domain of Tim-3 results in apoptosis of T H 1 cells, but the intracellular pathways involved in the regulatory function of Tim-3 are unknown. Unlike Tim-1, which is expressed in renal epithelia and cancer, Tim-3 has not been described in cells other than neuronal or T-cells. Using RT-PCR we demonstrate that Tim-3 is expressed in malignant and non-malignant epithelial tissues. We have cloned Tim-3 from an immortalized liver cell carcinoma line and identified a highly conserved tyrosine in the intracellular tail of Tim-3 (Y265). We demonstrate that Y265 is specifically phosphorylated in vivo by the interleukin inducible T cell kinase (ITK), a kinase which is located in close proximity of the TIM genes on the allergy susceptibility locus 5q33.3. Stimulation of Tim-3 by its ligand galectin-9 results in increased phosphorylation of Y265, suggesting that this tyrosine residue plays an important role in downstream signalling events regulating T-cell fate. Given the role of TIM proteins in autoimmunity and cancer, the conserved SH2 binding domain surrounding Y265 could represent a possible target site for pharmacological intervention

  8. The conserved residue Arg46 in the N-terminal heptad repeat domain of HIV-1 gp41 is critical for viral fusion and entry.

    Directory of Open Access Journals (Sweden)

    Xiaoyi Wang

    Full Text Available During the process of HIV-1 fusion with the target cell, the N-terminal heptad repeat (NHR of gp41 interacts with the C-terminal heptad repeat (CHR to form fusogenic six-helix bundle (6-HB core. We previously identified a crucial residue for 6-HB formation and virus entry--Lys63 (K63 in the C-terminal region of NHR (aa 54-70, which forms a hydrophobic cavity. It can form an important salt bridge with Asp121 (D121 in gp41 CHR. Here, we found another important conserved residue for virus fusion and entry, Arg46 (R46, in the N-terminal region of NHR (aa 35-53, which forms a hydrogen bond with a polar residue, Asn43 (N43, in NHR, as a part of the hydrogen-bond network. R46 can also form a salt bridge with a negatively charged residue, Glu137 (E137, in gp41 CHR. Substitution of R46 with the hydrophobic residue Ala (R46A or the negatively charged residue Glu (R46E resulted in disruption of the hydrogen bond network, breakage of the salt bridge and reduction of 6-HB's stability, leading to impairment of viral fusion and decreased inhibition of N36, an NHR peptide. Similarly, CHR peptide C34 with substitution of E137 for Ala (E137A or Arg (E137R also exhibited reduced inhibitory activity against HIV-1 infection and HIV-1-mediated cell-to-cell fusion. These results suggest that the positively charged residue R46 and its hydrogen bond network, together with the salt bridge between R46 and E137, are important for viral fusion and entry and may therefore serve as a target for designing novel HIV fusion/entry inhibitors.

  9. The conserved basic residues and the charged amino acid residues at the α-helix of the zinc finger motif regulate the nuclear transport activity of triple C2H2 zinc finger proteins

    Science.gov (United States)

    Lin, Chih-Ying

    2018-01-01

    Zinc finger (ZF) motifs on proteins are frequently recognized as a structure for DNA binding. Accumulated reports indicate that ZF motifs contain nuclear localization signal (NLS) to facilitate the transport of ZF proteins into nucleus. We investigated the critical factors that facilitate the nuclear transport of triple C2H2 ZF proteins. Three conserved basic residues (hot spots) were identified among the ZF sequences of triple C2H2 ZF proteins that reportedly have NLS function. Additional basic residues can be found on the α-helix of the ZFs. Using the ZF domain (ZFD) of Egr-1 as a template, various mutants were constructed and expressed in cells. The nuclear transport activity of various mutants was estimated by analyzing the proportion of protein localized in the nucleus. Mutation at any hot spot of the Egr-1 ZFs reduced the nuclear transport activity. Changes of the basic residues at the α-helical region of the second ZF (ZF2) of the Egr-1 ZFD abolished the NLS activity. However, this activity can be restored by substituting the acidic residues at the homologous positions of ZF1 or ZF3 with basic residues. The restored activity dropped again when the hot spots at ZF1 or the basic residues in the α-helix of ZF3 were mutated. The variations in nuclear transport activity are linked directly to the binding activity of the ZF proteins with importins. This study was extended to other triple C2H2 ZF proteins. SP1 and KLF families, similar to Egr-1, have charged amino acid residues at the second (α2) and the third (α3) positions of the α-helix. Replacing the amino acids at α2 and α3 with acidic residues reduced the NLS activity of the SP1 and KLF6 ZFD. The reduced activity can be restored by substituting the α3 with histidine at any SP1 and KLF6 ZFD. The results show again the interchangeable role of ZFs and charge residues in the α-helix in regulating the NLS activity of triple C2H2 ZF proteins. PMID:29381770

  10. pH-induced conformational change of IscU at low pH correlates with protonation/deprotonation of two conserved histidine residues.

    Science.gov (United States)

    Dai, Ziqi; Kim, Jin Hae; Tonelli, Marco; Ali, Ibrahim K; Markley, John L

    2014-08-19

    IscU, the scaffold protein for the major iron-sulfur cluster biosynthesis pathway in microorganisms and mitochondria (ISC pathway), plays important roles in the formation of [2Fe-2S] and [4Fe-4S] clusters and their delivery to acceptor apo-proteins. Our laboratory has shown that IscU populates two distinct, functionally relevant conformational states, a more structured state (S) and a more dynamic state (D), that differ by cis/trans isomerizations about two peptidyl-prolyl peptide bonds [Kim, J. H., Tonelli, M., and Markley, J. L. (2012) Proc. Natl. Acad. Sci. U.S.A., 109, 454-459. Dai Z., Tonelli, M., and Markley, J. L. (2012) Biochemistry, 51, 9595-9602. Cai, K., Frederick, R. O., Kim, J. H., Reinen, N. M., Tonelli, M., and Markley, J. L. (2013) J. Biol. Chem., 288, 28755-28770]. Here, we report our findings on the pH dependence of the D ⇄ S equilibrium for Escherichia coli IscU in which the D-state is stabilized at low and high pH values. We show that the lower limb of the pH dependence curve results from differences in the pKa values of two conserved histidine residues (His10 and His105) in the two states. The net proton affinity of His10 is about 50 times higher and that of His105 is 13 times higher in the D-state than in the S-state. The origin of the high limb of the D ⇄ S pH dependence remains to be determined. These results show that changes in proton inventory need to be taken into account in the steps in iron-sulfur cluster assembly and transfer that involve transitions of IscU between its S- and D-states.

  11. Acute effects of high-dose furosemide on residual renal function in CAPD patients

    NARCIS (Netherlands)

    van Olden, Rudolf W.; Guchelaar, Henk-Jan; Struijk, Dirk G.; Krediet, Raymond T.; Arisz, Lambertus

    2003-01-01

    BACKGROUND: High doses of furosemide can increase urine volume in chronic peritoneal dialysis (CAPD) patients. However, no information is available about effects on urinary solute excretion in relation to residual glomerular filtration rate (GFR), urinary furosemide excretion, and peritoneal solute

  12. Structural basis for new pattern of conserved amino acid residues related to chitin-binding in the antifungal peptide from the coconut rhinoceros beetle Oryctes rhinoceros.

    Science.gov (United States)

    Hemmi, Hikaru; Ishibashi, Jun; Tomie, Tetsuya; Yamakawa, Minoru

    2003-06-20

    Scarabaecin isolated from hemolymph of the coconut rhinoceros beetle Oryctes rhinoceros is a 36-residue polypeptide that has antifungal activity. The solution structure of scarabaecin has been determined from twodimensional 1H NMR spectroscopic data and hybrid distance geometry-simulated annealing protocol calculation. Based on 492 interproton and 10 hydrogen-bonding distance restraints and 36 dihedral angle restraints, we obtained 20 structures. The average backbone root-mean-square deviation for residues 4-35 is 0.728 +/- 0.217 A from the mean structure. The solution structure consists of a two-stranded antiparallel beta-sheet connected by a type-I beta-turn after a short helical turn. All secondary structures and a conserved disulfide bond are located in the C-terminal half of the peptide, residues 18-36. Overall folding is stabilized by a combination of a disulfide bond, seven hydrogen bonds, and numerous hydrophobic interactions. The structural motif of the C-terminal half shares a significant tertiary structural similarity with chitin-binding domains of plant and invertebrate chitin-binding proteins, even though scarabaecin has no overall sequence similarity to other peptide/polypeptides including chitin-binding proteins. The length of its primary structure, the number of disulfide bonds, and the pattern of conserved functional residues binding to chitin in scarabaecin differ from those of chitin-binding proteins in other invertebrates and plants, suggesting that scarabaecin does not share a common ancestor with them. These results are thought to provide further strong experimental evidence to the hypothesis that chitin-binding proteins of invertebrates and plants are correlated by a convergent evolution process.

  13. An evaluation of preservation of residual hearing using the suprameatal approach for cochlear implantation: can this implantation technique be used for preservation of residual hearing?

    NARCIS (Netherlands)

    Postelmans, Job T. F.; van Spronsen, Erik; Grolman, Wilko; Stokroos, Robert J.; Tange, Rinze A.; Maré, Marcel J.; Dreschler, Wouter A.

    2011-01-01

    The preservation of residual hearing has become a high priority in cochlear implant surgery. This study was designed to substantiate whether conservation of residual hearing can be preserved after cochlear implantation using the suprameatal approach. Retrospective chart review. Retrospective chart

  14. Antibody Binding Selectivity: Alternative Sets of Antigen Residues Entail High-Affinity Recognition.

    Directory of Open Access Journals (Sweden)

    Yves Nominé

    Full Text Available Understanding the relationship between protein sequence and molecular recognition selectivity remains a major challenge. The antibody fragment scFv1F4 recognizes with sub nM affinity a decapeptide (sequence 6TAMFQDPQER15 derived from the N-terminal end of human papilloma virus E6 oncoprotein. Using this decapeptide as antigen, we had previously shown that only the wild type amino-acid or conservative replacements were allowed at positions 9 to 12 and 15 of the peptide, indicating a strong binding selectivity. Nevertheless phenylalanine (F was equally well tolerated as the wild type glutamine (Q at position 13, while all other amino acids led to weaker scFv binding. The interfaces of complexes involving either Q or F are expected to diverge, due to the different physico-chemistry of these residues. This would imply that high-affinity binding can be achieved through distinct interfacial geometries. In order to investigate this point, we disrupted the scFv-peptide interface by modifying one or several peptide positions. We then analyzed the effect on binding of amino acid changes at the remaining positions, an altered susceptibility being indicative of an altered role in complex formation. The 23 starting variants analyzed contained replacements whose effects on scFv1F4 binding ranged from minor to drastic. A permutation analysis (effect of replacing each peptide position by all other amino acids except cysteine was carried out on the 23 variants using the PEPperCHIP® Platform technology. A comparison of their permutation patterns with that of the wild type peptide indicated that starting replacements at position 11, 12 or 13 modified the tolerance to amino-acid changes at the other two positions. The interdependence between the three positions was confirmed by SPR (Biacore® technology. Our data demonstrate that binding selectivity does not preclude the existence of alternative high-affinity recognition modes.

  15. Energy conservation and production from solid residues - alternative for two problems: wastes and energy; Conservacao e producao de energia a partir de residuos solidos - alternativa para dois problemas: lixo e energia

    Energy Technology Data Exchange (ETDEWEB)

    Reno, Francisco de Assis Grillo [Universidade Estadual de Campinas, SP (Brazil). Faculdade de Engenharia Mecanica. Planejamento de Sistemas Energeticos]. E-mail: fgrillo@fem.unicamp.br; Streb, Cleci Schalemberger [Universidade Estadual de Campinas, SP (Brazil). Faculdade de Engenharia Mecanica; Piunti, Regina Celia [Universidade Estadual de Campinas, SP (Brazil)]. E-mail: repiunti@ig.com.br

    2002-07-01

    This paper explores possibilities of energy conservation and production through the using domestic solid residues, aiming the disposal impacts and improvement the energy supplying as well. For energy conservation,the recycling, reduction and re utilization will be mentioned. For the energy recovering the burning of organic material in sanitary landfill and incineration of plastics and tires.

  16. Eucaryotic operon genes can define highly conserved syntenies

    Czech Academy of Sciences Publication Activity Database

    Trachtulec, Zdeněk

    2004-01-01

    Roč. 50, - (2004), s. 1-6 ISSN 0015-5500 R&D Projects: GA ČR GA204/01/0997; GA MŠk LN00A079 Institutional research plan: CEZ:AV0Z5052915 Keywords : eukaryotic operon * conserved synteny Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.507, year: 2004

  17. Conserved residues and their role in the structure, function, and stability of acyl-coenzyme A binding protein

    DEFF Research Database (Denmark)

    Kragelund, B B; Poulsen, K; Andersen, K V

    1999-01-01

    In the family of acyl-coenzyme A binding proteins, a subset of 26 sequence sites are identical in all eukaryotes and conserved throughout evolution of the eukaryotic kingdoms. In the context of the bovine protein, the importance of these 26 sequence positions for structure, function, stability...

  18. Residual stress evaluation by Barkhausen signals with a magnetic field sensor for high efficiency electrical motors

    Science.gov (United States)

    Tsuchida, Yuji; Enokizono, Masato

    2018-04-01

    The iron loss of industrial motors increases by residual stress during manufacturing processes. It is very important to make clear the distribution of the residual stress in the motor cores to reduce the iron loss in the motors. Barkhausen signals which occur on electrical steel sheets can be used for the evaluation of the residual stress because they are very sensitive to the material properties. Generally, a B-sensor is used to measure Barkhausen signals, however, we developed a new H-sensor to measure them and applied it into the stress evaluation. It is supposed that the Barkhausen signals by using a H-sensor can be much effective to the residual stress on the electrical steel sheets by referring our results regarding to the stress evaluations. We evaluated the tensile stress of the electrical steel sheets by measuring Barkhausen signals by using our developed H-sensor for high efficiency electrical motors.

  19. Energy conservation and pomeron loops in high energy evolution

    International Nuclear Information System (INIS)

    Gustafson, Goesta

    2007-01-01

    We present a formalism which modifies the Mueller Dipole Model such that it incorporates energy-momentum conservation as well as important colour suppressed effects in the cascade evolution. The formalism is implemented in a Monte Carlo simulation program, and the results are compared to inclusive data from HERA and the Tevatron. We here find a generally very good agreement between our model and the experimental data. (author)

  20. A conserved serine residue regulates the stability of Drosophila Salvador and human WW domain-containing adaptor 45 through proteasomal degradation

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Di, E-mail: DiWu@mail.nankai.edu.cn; Wu, Shian

    2013-04-19

    Highlights: •Ser-17 is key for the stability of Drosophila Sav. •Ala mutation of Ser-17 promotes the proteasomal degradation of Sav. •Ser-17 residue is not the main target of Hpo-induced Sav stabilization. •Hpo-dependent and -independent mechanisms regulate Sav stability. •This mechanism is conserved in the homologue of Sav, human WW45. -- Abstract: The Hippo (Hpo) pathway is a conserved tumor suppressor pathway that controls organ size through the coordinated regulation of apoptosis and proliferation. Drosophila Salvador (Sav), which limits organ size, is a core component of the Hpo pathway. In this study, Ser-17 was shown to be important for the stability of Sav. Alanine mutation of Ser-17 promoted the proteasomal degradation of Sav. Destabilization and stabilization of the Sav protein mediated by alanine mutation of Ser-17 and by Hpo, respectively, were independent of each other. This implies that the stability of Sav is controlled by two mechanisms, one that is Ser-17-dependent and Hpo-independent, and another that is Ser-17-independent and Hpo-dependent. These dual mechanisms also regulated the human counterpart of Drosophila Sav, WW domain-containing adaptor 45 (WW45). The conservation of this regulation adds to its significance in normal physiology and tumorigenesis.

  1. Analysis of Margin Index as a Method for Predicting Residual Disease After Breast-Conserving Surgery in a European Cancer Center.

    LENUS (Irish Health Repository)

    Bolger, Jarlath C

    2011-06-03

    INTRODUCTION: Breast-conserving surgery (BCS), followed by appropriate adjuvant therapies is established as a standard treatment option for women with early-stage invasive breast cancers. A number of factors have been shown to correlate with local and regional disease recurrence. Although margin status is a strong predictor of disease recurrence, consensus is yet to be established on the optimum margin necessary. Margenthaler et al. recently proposed the use of a "margin index," combining tumor size and margin status as a predictor of residual disease after BCS. We applied this new predictive tool to a population of patients with primary breast cancer who presented to a symptomatic breast unit to determine its suitability in predicting those who require reexcision surgery. METHODS: Retrospective analysis of our breast cancer database from January 1, 2000 to June 30, 2010 was performed, including all patients who underwent BCS. Of 531 patients who underwent BCS, 27.1% (144\\/531) required further reexcision procedures, and 55 were eligible for inclusion in the study. Margin index was calculated as: margin index = closest margin (mm)\\/tumor size (mm) × 100, with index >5 considered optimum. RESULTS: Of the 55 patients included, 31% (17\\/55) had residual disease. Fisher\\'s exact test showed margin index not to be a significant predictor of residual disease on reexcision specimen (P = 0.57). Of note, a significantly higher proportion of our patients presented with T2\\/3 tumors (60% vs. 38%). CONCLUSIONS: Although an apparently elegant tool for predicting residual disease after BCS, we have shown that it is not applicable to a symptomatic breast unit in Ireland.

  2. Analysis of margin index as a method for predicting residual disease after breast-conserving surgery in a European cancer center.

    LENUS (Irish Health Repository)

    Bolger, Jarlath C

    2012-02-01

    INTRODUCTION: Breast-conserving surgery (BCS), followed by appropriate adjuvant therapies is established as a standard treatment option for women with early-stage invasive breast cancers. A number of factors have been shown to correlate with local and regional disease recurrence. Although margin status is a strong predictor of disease recurrence, consensus is yet to be established on the optimum margin necessary. Margenthaler et al. recently proposed the use of a "margin index," combining tumor size and margin status as a predictor of residual disease after BCS. We applied this new predictive tool to a population of patients with primary breast cancer who presented to a symptomatic breast unit to determine its suitability in predicting those who require reexcision surgery. METHODS: Retrospective analysis of our breast cancer database from January 1, 2000 to June 30, 2010 was performed, including all patients who underwent BCS. Of 531 patients who underwent BCS, 27.1% (144\\/531) required further reexcision procedures, and 55 were eligible for inclusion in the study. Margin index was calculated as: margin index = closest margin (mm)\\/tumor size (mm) x 100, with index >5 considered optimum. RESULTS: Of the 55 patients included, 31% (17\\/55) had residual disease. Fisher\\'s exact test showed margin index not to be a significant predictor of residual disease on reexcision specimen (P = 0.57). Of note, a significantly higher proportion of our patients presented with T2\\/3 tumors (60% vs. 38%). CONCLUSIONS: Although an apparently elegant tool for predicting residual disease after BCS, we have shown that it is not applicable to a symptomatic breast unit in Ireland.

  3. The Replacement of 10 Non-Conserved Residues in the Core Protein of JFH-1 Hepatitis C Virus Improves Its Assembly and Secretion.

    Directory of Open Access Journals (Sweden)

    Loïc Etienne

    Full Text Available Hepatitis C virus (HCV assembly is still poorly understood. It is thought that trafficking of the HCV core protein to the lipid droplet (LD surface is essential for its multimerization and association with newly synthesized HCV RNA to form the viral nucleocapsid. We carried out a mapping analysis of several complete HCV genomes of all genotypes, and found that the genotype 2 JFH-1 core protein contained 10 residues different from those of other genotypes. The replacement of these 10 residues of the JFH-1 strain sequence with the most conserved residues deduced from sequence alignments greatly increased virus production. Confocal microscopy of the modified JFH-1 strain in cell culture showed that the mutated JFH-1 core protein, C10M, was present mostly at the endoplasmic reticulum (ER membrane, but not at the surface of the LDs, even though its trafficking to these organelles was possible. The non-structural 5A protein of HCV was also redirected to ER membranes and colocalized with the C10M core protein. Using a Semliki forest virus vector to overproduce core protein, we demonstrated that the C10M core protein was able to form HCV-like particles, unlike the native JFH-1 core protein. Thus, the substitution of a few selected residues in the JFH-1 core protein modified the subcellular distribution and assembly properties of the protein. These findings suggest that the early steps of HCV assembly occur at the ER membrane rather than at the LD surface. The C10M-JFH-1 strain will be a valuable tool for further studies of HCV morphogenesis.

  4. Importance of a Conserved Lys/Arg Residue for Ligand/PDZ Domain Interactions as Examined by Protein Semisynthesis

    DEFF Research Database (Denmark)

    Pedersen, Søren W; Moran, Griffin E; Sereikaité, Vita

    2016-01-01

    PDZ domains are ubiquitous small protein domains that are mediators of numerous protein-protein interactions, and play a pivotal role in protein trafficking, synaptic transmission, and the assembly of signaling-transduction complexes. In recent years, PDZ domains have emerged as novel and exciting...... drug targets for diseases (in the brain in particular), so understanding the molecular details of PDZ domain interactions is of fundamental importance. PDZ domains bind to a protein partner at either a C-terminal peptide or internal peptide motifs. Here, we examined the importance of a conserved Lys...

  5. Usherin expression is highly conserved in mouse and human tissues.

    Science.gov (United States)

    Pearsall, Nicole; Bhattacharya, Gautam; Wisecarver, Jim; Adams, Joe; Cosgrove, Dominic; Kimberling, William

    2002-12-01

    Usher syndrome is an autosomal recessive disease that results in varying degrees of hearing loss and retinitis pigmentosa. Three types of Usher syndrome (I, II, and III) have been identified clinically with Usher type II being the most common of the three types. Usher type II has been localized to three different chromosomes 1q41, 3p, and 5q, corresponding to Usher type 2A, 2B, and 2C respectively. Usherin is a basement membrane protein encoded by the USH2A gene. Expression of usherin has been localized in the basement membrane of several tissues, however it is not ubiquitous. Immunohistochemistry detected usherin in the following human tissues: retina, cochlea, small and large intestine, pancreas, bladder, prostate, esophagus, trachea, thymus, salivary glands, placenta, ovary, fallopian tube, uterus, and testis. Usherin was absent in many other tissues such as heart, lung, liver, kidney, and brain. This distribution is consistent with the usherin distribution seen in the mouse. Conservation of usherin is also seen at the nucleotide and amino acid level when comparing the mouse and human gene sequences. Evolutionary conservation of usherin expression at the molecular level and in tissues unaffected by Usher 2a supports the important structural and functional role this protein plays in the human. In addition, we believe that these results could lead to a diagnostic procedure for the detection of Usher syndrome and those who carry an USH2A mutation.

  6. Optimization of Residual Stress of High Temperature Treatment Using Genetic Algorithm and Neural Network

    Directory of Open Access Journals (Sweden)

    M. Susmikanti

    2015-12-01

    Full Text Available In a nuclear industry area, high temperature treatment of materials is a factor which requires special attention. Assessment needs to be conducted on the properties of the materials used, including the strength of the materials. The measurement of material properties under thermal processes may reflect residual stresses. The use of Genetic Algorithm (GA to determine the optimal residual stress is one way to determine the strength of a material. In residual stress modeling with several parameters, it is sometimes difficult to solve for the optimal value through analytical or numerical calculations. Here, GA is an efficient algorithm which can generate the optimal values, both minima and maxima. The purposes of this research are to obtain the optimization of variable in residual stress models using GA and to predict the center of residual stress distribution, using fuzzy neural network (FNN while the artificial neural network (ANN used for modeling. In this work a single-material 316/316L stainless steel bar is modeled. The minimal residual stresses of the material at high temperatures were obtained with GA and analytical calculations. At a temperature of 6500C, the GA optimal residual stress estimation converged at –711.3689 MPa at adistance of 0.002934 mm from center point, whereas the analytical calculation result at that temperature and position is -975.556 MPa . At a temperature of 8500C, the GA result was -969.868 MPa at 0.002757 mm from the center point, while with analytical result was -1061.13 MPa. The difference in residual stress between GA and analytical results at a temperatureof6500C is about 27 %, while at 8500C it is 8.67 %. The distribution of residual stress showed a grouping concentrated around a coordinate of (-76; 76 MPa. The residuals stress model is a degree-two polynomial with coefficients of 50.33, -76.54, and -55.2, respectively, with a standard deviation of 7.874.

  7. High-Order Hyperbolic Residual-Distribution Schemes on Arbitrary Triangular Grids

    Science.gov (United States)

    Mazaheri, Alireza; Nishikawa, Hiroaki

    2015-01-01

    In this paper, we construct high-order hyperbolic residual-distribution schemes for general advection-diffusion problems on arbitrary triangular grids. We demonstrate that the second-order accuracy of the hyperbolic schemes can be greatly improved by requiring the scheme to preserve exact quadratic solutions. We also show that the improved second-order scheme can be easily extended to third-order by further requiring the exactness for cubic solutions. We construct these schemes based on the LDA and the SUPG methodology formulated in the framework of the residual-distribution method. For both second- and third-order-schemes, we construct a fully implicit solver by the exact residual Jacobian of the second-order scheme, and demonstrate rapid convergence of 10-15 iterations to reduce the residuals by 10 orders of magnitude. We demonstrate also that these schemes can be constructed based on a separate treatment of the advective and diffusive terms, which paves the way for the construction of hyperbolic residual-distribution schemes for the compressible Navier-Stokes equations. Numerical results show that these schemes produce exceptionally accurate and smooth solution gradients on highly skewed and anisotropic triangular grids, including curved boundary problems, using linear elements. We also present Fourier analysis performed on the constructed linear system and show that an under-relaxation parameter is needed for stabilization of Gauss-Seidel relaxation.

  8. Mechanistic Basis for Type 2 Long QT Syndrome Caused by KCNH2 Mutations that Disrupt Conserved Arginine Residue in the Voltage Sensor

    Science.gov (United States)

    McBride, Christie M.; Smith, Ashley M.; Smith, Jennifer L.; Reloj, Allison R.; Velasco, Ellyn J.; Powell, Jonathan; Elayi, Claude S.; Bartos, Daniel C.; Burgess, Don E.

    2013-01-01

    KCNH2 encodes the Kv11.1 channel, which conducts the rapidly activating delayed rectifier K+ current (IKr) in the heart. KCNH2 mutations cause type 2 long QT syndrome (LQT2), which increases the risk for life-threatening ventricular arrhythmias. LQT2 mutations are predicted to prolong the cardiac action potential (AP) by reducing IKr during repolarization. Kv11.1 contains several conserved basic amino acids in the fourth transmembrane segment (S4) of the voltage sensor that are important for normal channel trafficking and gating. This study sought to determine the mechanism(s) by which LQT2 mutations at conserved arginine residues in S4 (R531Q, R531W or R534L) alter Kv11.1 function. Western blot analyses of HEK293 cells transiently expressing R531Q, R531W or R534L suggested that only R534L inhibited Kv11.1 trafficking. Voltage-clamping experiments showed that R531Q or R531W dramatically altered Kv11.1 current (IKv11.1) activation, inactivation, recovery from inactivation and deactivation. Coexpression of wild type (to mimic the patients’ genotypes) mostly corrected the changes in IKv11.1 activation and inactivation, but deactivation kinetics were still faster. Computational simulations using a human ventricular AP model showed that accelerating deactivation rates was sufficient to prolong the AP, but these effects were minimal compared to simply reducing IKr. These are the first data to demonstrate that coexpressing wild type can correct activation and inactivation dysfunction caused by mutations at a critical voltage-sensing residue in Kv11.1. We conclude that some Kv11.1 mutations might accelerate deactivation to cause LQT2 but that the ventricular AP duration is much more sensitive to mutations that decrease IKr. This likely explains why most LQT2 mutations are nonsense or trafficking-deficient. PMID:23546015

  9. Mechanistic basis for type 2 long QT syndrome caused by KCNH2 mutations that disrupt conserved arginine residues in the voltage sensor.

    Science.gov (United States)

    McBride, Christie M; Smith, Ashley M; Smith, Jennifer L; Reloj, Allison R; Velasco, Ellyn J; Powell, Jonathan; Elayi, Claude S; Bartos, Daniel C; Burgess, Don E; Delisle, Brian P

    2013-05-01

    KCNH2 encodes the Kv11.1 channel, which conducts the rapidly activating delayed rectifier K+ current (I Kr) in the heart. KCNH2 mutations cause type 2 long QT syndrome (LQT2), which increases the risk for life-threatening ventricular arrhythmias. LQT2 mutations are predicted to prolong the cardiac action potential (AP) by reducing I Kr during repolarization. Kv11.1 contains several conserved basic amino acids in the fourth transmembrane segment (S4) of the voltage sensor that are important for normal channel trafficking and gating. This study sought to determine the mechanism(s) by which LQT2 mutations at conserved arginine residues in S4 (R531Q, R531W or R534L) alter Kv11.1 function. Western blot analyses of HEK293 cells transiently expressing R531Q, R531W or R534L suggested that only R534L inhibited Kv11.1 trafficking. Voltage-clamping experiments showed that R531Q or R531W dramatically altered Kv11.1 current (I Kv11.1) activation, inactivation, recovery from inactivation and deactivation. Coexpression of wild type (to mimic the patients' genotypes) mostly corrected the changes in I Kv11.1 activation and inactivation, but deactivation kinetics were still faster. Computational simulations using a human ventricular AP model showed that accelerating deactivation rates was sufficient to prolong the AP, but these effects were minimal compared to simply reducing I Kr. These are the first data to demonstrate that coexpressing wild type can correct activation and inactivation dysfunction caused by mutations at a critical voltage-sensing residue in Kv11.1. We conclude that some Kv11.1 mutations might accelerate deactivation to cause LQT2 but that the ventricular AP duration is much more sensitive to mutations that decrease I Kr. This likely explains why most LQT2 mutations are nonsense or trafficking-deficient.

  10. Global alteration of the drug-binding pocket of human P-glycoprotein (ABCB1) by substitution of fifteen conserved residues reveals a negative correlation between substrate size and transport efficiency.

    Science.gov (United States)

    Vahedi, Shahrooz; Chufan, Eduardo E; Ambudkar, Suresh V

    2017-11-01

    P-glycoprotein (P-gp), an ATP-dependent efflux pump, is linked to the development of multidrug resistance in cancer cells. However, the drug-binding sites and translocation pathways of this transporter are not yet well-characterized. We recently demonstrated the important role of tyrosine residues in regulating P-gp ATP hydrolysis via hydrogen bond formations with high affinity modulators. Since tyrosine is both a hydrogen bond donor and acceptor, and non-covalent interactions are key in drug transport, in this study we investigated the global effect of enrichment of tyrosine residues in the drug-binding pocket on the drug binding and transport function of P-gp. By employing computational analysis, 15 conserved residues in the drug-binding pocket of human P-gp that interact with substrates were identified and then substituted with tyrosine, including 11 phenylalanine (F72, F303, F314, F336, F732, F759, F770, F938, F942, F983, F994), two leucine (L339, L975), one isoleucine (I306), and one methionine (M949). Characterization of the tyrosine-rich P-gp mutant in HeLa cells demonstrated that this major alteration in the drug-binding pocket by introducing fifteen additional tyrosine residues is well tolerated and has no measurable effect on total or cell surface expression of this mutant. Although the tyrosine-enriched mutant P-gp could transport small to moderate size (transport large (>1000 Daltons) substrates such as NBD-cyclosporine A, Bodipy-paclitaxel and Bodipy-vinblastine was significantly decreased. This was further supported by the physico-chemical characterization of seventeen tested substrates, which revealed a negative correlation between drug transport and molecular size for the tyrosine-enriched P-gp mutant. Published by Elsevier Inc.

  11. Using mutagenesis to explore conserved residues in the RNA-binding groove of influenza A virus nucleoprotein for antiviral drug development

    Science.gov (United States)

    Liu, Chia-Lin; Hung, Hui-Chen; Lo, Shou-Chen; Chiang, Ching-Hui; Chen, I.-Jung; Hsu, John T.-A.; Hou, Ming-Hon

    2016-02-01

    Nucleoprotein (NP) is the most abundant type of RNA-binding viral protein in influenza A virus-infected cells and is necessary for viral RNA transcription and replication. Recent studies demonstrated that influenza NP is a valid target for antiviral drug development. The surface of the groove, covered with numerous conserved residues between the head and body domains of influenza A NP, plays a crucial role in RNA binding. To explore the mechanism by which NP binds RNA, we performed a series of site-directed mutagenesis in the RNA-binding groove, followed by surface plasmon resonance (SPR), to characterize the interactions between RNA and NP. Furthermore, a role of Y148 in NP stability and NP-RNA binding was evaluated. The aromatic residue of Y148 was found to stack with a nucleotide base. By interrupting the stacking interaction between Y148 and an RNA base, we identified an influenza virus NP inhibitor, (E, E)-1,7-bis(4-hydroxy-3-methoxyphenyl) -1,6-heptadiene-3,5-dione; this inhibitor reduced the NP’s RNA-binding affinity and hindered viral replication. Our findings will be useful for the development of new drugs that disrupt the interaction between RNA and viral NP in the influenza virus.

  12. Insights into the smooth-to-rough transitioning in Mycobacterium bolletii unravels a functional Tyr residue conserved in all mycobacterial MmpL family members.

    Science.gov (United States)

    Bernut, Audrey; Viljoen, Albertus; Dupont, Christian; Sapriel, Guillaume; Blaise, Mickaël; Bouchier, Christiane; Brosch, Roland; de Chastellier, Chantal; Herrmann, Jean-Louis; Kremer, Laurent

    2016-03-01

    In mycobacteria, MmpL proteins represent key components that participate in the biosynthesis of the complex cell envelope. Whole genome analysis of a spontaneous rough morphotype variant of Mycobacterium abscessus subsp. bolletii identified a conserved tyrosine that is crucial for the function of MmpL family proteins. Isogenic smooth (S) and rough (R) variants differed by a single mutation linked to a Y842H substitution in MmpL4a. This mutation caused a deficiency in glycopeptidolipid production/transport in the R variant and a gain in the capacity to produce cords in vitro. In zebrafish, increased virulence of the M. bolletii R variant over the parental S strain was found, involving massive production of serpentine cords, abscess formation and rapid larval death. Importantly, this finding allowed us to demonstrate an essential role of Tyr842 in several different MmpL proteins, including Mycobacterium tuberculosis MmpL3. Structural homology models of MmpL4a and MmpL3 identified two additional critical residues located in the transmembrane regions TM10 and TM4 that are facing each other. We propose that these central residues are part of the proton-motive force that supplies the energy for substrate transport. Hence, we provide important insights into mechanistic/structural aspects of MmpL proteins as lipid transporters and virulence determinants in mycobacteria. © 2015 John Wiley & Sons Ltd.

  13. Feedback between residual circulations and sediment distribution in highly turbid estuaries: an analytical model

    NARCIS (Netherlands)

    Talke, S.A.|info:eu-repo/dai/nl/304823554; de Swart, H.E.|info:eu-repo/dai/nl/073449725; Schuttelaars, H.|info:eu-repo/dai/nl/164035656

    2009-01-01

    Motivated by field studies of the Ems estuary which show longitudinal gradients in bottom sediment concentration as high as O(0.01 kg/m4), we develop an analytical model for estuarine residual circulation based on currents from salinity gradients, turbidity gradients, and freshwater discharge.

  14. A glycine residue essential for high ivermectin sensitivity in Cys-loop ion channel receptors

    DEFF Research Database (Denmark)

    Lynagh, Timothy; Lynch, Joseph W.

    2010-01-01

    Ivermectin exerts its anthelmintic effect by activating nematode Cys-loop glutamate-gated receptors. Here we show that a glycine residue at a specific transmembrane domain location is essential for high ivermectin sensitivity in both glycine- and glutamate-gated Cys-loop receptors. We also show...

  15. Role of four conserved aspartic acid residues of EF-loops in the metal ion binding and in the self-assembly of ciliate Euplotes octocarinatus centrin.

    Science.gov (United States)

    Liu, Wen; Duan, Lian; Sun, Tijian; Yang, Binsheng

    2016-12-01

    Ciliate Euplotes octocarinatus centrin (EoCen) is an EF-hand calcium-binding protein closely related to the prototypical calcium sensor protein calmodulin. Four mutants (D37K, D73K, D110K and D146K) were created firstly to elucidate the importance of the first aspartic acid residues (Asp37, Asp73, Asp110 and Asp146) in the beginning of the four EF-loops of EoCen. Aromatic-sensitized Tb 3+ fluorescence indicates that the aspartic acid residues are very important for the metal-binding of EoCen, except for Asp73 (in EF-loop II). Resonance light scattering (RLS) measurements for different metal ions (Ca 2+ and Tb 3+ ) binding proteins suggest that the order of four conserved aspartic acid residues for contributing to the self-assembly of EoCen is Asp37 > Asp146 > Asp110 > Asp73. Cross-linking experiment also exhibits that Asp37 and Asp146 play critical role in the self-assembly of EoCen. Asp37, in site I, which is located in the N-terminal domain, plays the most important role in the metal ion-dependent self-assembly of EoCen, and there is cooperativity between N-terminal and C-terminal domain (especially the site IV). In addition, the dependence of Tb 3+ induced self-assembly of EoCen and the mutants on various factors, including ionic strength and pH, were characterized using RLS. Finally, 2-p-toluidinylnaphthalene-6-sulfonate (TNS) binding, ionic strength and pH control experiments indicate that in the process of EoCen self-assembly, molecular interactions are mediated by both electrostatic and hydrophobic forces, and the hydrophobic interaction has the important status.

  16. Synthesis of high specific active tritiated Leu-enkephalin in the leucine residue

    Energy Technology Data Exchange (ETDEWEB)

    Baba, S.; Hasegawa, H.; Shinohara, Y. (Tokyo Coll. of Pharmacy (Japan))

    1989-12-01

    Leu-enkephalin labelled with tritium in the Leu residue has been prepared. Synthesis of the precursor peptide, (4,5-dehydroLeu{sup 5}-)Leu-enkephalin, was carried out by solid phase synthesis using Fmoc amino acid derivatives. The peptide was tritiated catalytically yielding {sup 3}H-Leu-enkephalin with a specific radioactivity of 4.39 TBq/mmol. The distribution of tritium label was investigated by reversed-phase high performance liquid chromatography with a synchronized accumulating radioisotope detector following acidic and enzymatic hydrolysis, which confirmed that the tritium label was entirely located at the Leu residue. (author).

  17. Evaluation of Some Pesticide Residues in Fruits import by High Performance Liquid Chromatography

    Directory of Open Access Journals (Sweden)

    Lamees Munef Abdul-Latef

    2017-02-01

    Full Text Available Pesticide residues have been found in various fruits and vegetables.  This studycollected 24 samples and reported a method based on High Performance Liquid Chromatography (HPLC. For determination of pesticide residues used in Some fruits which were collected from different markets of Baghdad city to make 24 samples from (peel , core, mixture for each type of fruits markets as:  Oranges( Egypt , Africa, Pomegranate ( Egypt, Mango ( Kenya , Pears (China,  Plum fruits ( Africa , Kiwi (Turkey .That detective of ( 5 different  pesticides (diazinon,  malathion, chlorpyrifos ,parathion  and cypermethrin. The results were detected of multi-residues of  pesticides on the fruit in ( peel , core , mixture may be in the limit of Maximum residue limits(MRL or higher of it   . The pesticides detected that exceeding the limits are: cypermethrin  in Kiwi (peel, core and mixtureat(0.204,0.038, 0.537, in pomegranate detected in (peel and mixture at (0.509,0.189 mg/kg , Diazinondetccted in Egyptian orange in (peel ,core and mixture at (0.031,0.207, 0.099 mg/kg . Malathion and Parathion was not detected at any type of fruits and  that results was compared with codex of FAO/WHO(2013. That data is important to monitor residues in food and to fill gaps in current knowledge would be helpful in assessing human exposure risks from ingestion of contaminated Fruits Imported to our country .

  18. Telomeric expression sites are highly conserved in Trypanosoma brucei.

    Directory of Open Access Journals (Sweden)

    Christiane Hertz-Fowler

    Full Text Available Subtelomeric regions are often under-represented in genome sequences of eukaryotes. One of the best known examples of the use of telomere proximity for adaptive purposes are the bloodstream expression sites (BESs of the African trypanosome Trypanosoma brucei. To enhance our understanding of BES structure and function in host adaptation and immune evasion, the BES repertoire from the Lister 427 strain of T. brucei were independently tagged and sequenced. BESs are polymorphic in size and structure but reveal a surprisingly conserved architecture in the context of extensive recombination. Very small BESs do exist and many functioning BESs do not contain the full complement of expression site associated genes (ESAGs. The consequences of duplicated or missing ESAGs, including ESAG9, a newly named ESAG12, and additional variant surface glycoprotein genes (VSGs were evaluated by functional assays after BESs were tagged with a drug-resistance gene. Phylogenetic analysis of constituent ESAG families suggests that BESs are sequence mosaics and that extensive recombination has shaped the evolution of the BES repertoire. This work opens important perspectives in understanding the molecular mechanisms of antigenic variation, a widely used strategy for immune evasion in pathogens, and telomere biology.

  19. Familial hypofibrinogenaemia associated with heterozygous substitution of a conserved arginine residue; Bbeta255 Arg-->His (Fibrinogen Merivale).

    Science.gov (United States)

    Maghzal, Ghassan J; Brennan, Stephen O; Fellowes, Andrew P; Spearing, Ruth; George, Peter M

    2003-02-21

    Sequencing of all three fibrinogen genes from an individual with hypofibrinogenaemia led to the identification of two new point mutations in the Bbeta gene. Family studies showed the mutations Bbeta255 Arg-->His (Fibrinogen Merivale) and Bbeta148 Lys-->Asn (Fibrinogen Merivale II) were on different alleles and that only the Bbeta255 Arg-->His mutation segregated with hypofibrinogenaemia. Three simple heterozygotes for this mutation had mean fibrinogen concentrations of 1.4 mg/ml, while heterozygotes for the Bbeta148 Lys-->Asn mutation had normal fibrinogen concentrations. ESI MS analysis of endoproteinase Asp-N digests of Bbeta chains showed that the Bbeta255 Arg-->His substitution was not expressed in plasma, confirming it as the cause of the hypofibrinogenaemia. The Bbeta148 Lys-->Asn chains, on the other hand, were equally expressed with wild-type Bbeta chains in simple heterozygotes. Genotype analysis failed to detect either substitution in 182 healthy controls. Arg(255) is located in the first strand of the five-stranded sheet that forms the main feature of the betaD domain and appears to form an essential H bond with Gly(414). Both the Arg and Gly are absolutely conserved, not only in all known Bbeta chains, but also in all homologous alphaE and gamma chains and in all fibrinogen-related proteins. Protein instability from loss of this contact could easily explain the association of this mutation with hypofibrinogenaemia.

  20. High-temperature vitrification of Hanford residual-liquid waste in a continuous melter

    International Nuclear Information System (INIS)

    Barnes, S.M.

    1980-04-01

    Over 270 kg of high-temperature borosilicate glass have been produced in a series of three short-term tests in the High-Temperature Ceramic Melter vitrification system at PNL. The glass produced was formulated to vitrify simulated Hanford residual-liquid waste. The tests were designed to (1) demonstrate the feasibility of utilizing high-temperature, continuous-vitrification technology for the immobilization of the residual-liquid waste, (2) test the airlift draining technique utilized by the high-temperature melter, (3) compare glass produced in this process to residual-liquid glass produced under laboratory conditions, (4) investigate cesium volatility from the melter during waste processing, and (5) determine the maximum residual-liquid glass production rate in the high-temperature melter. The three tests with the residual-liquid composition confirmed the viability of the continuous-melting vitrification technique for the immobilization of this waste. The airlift draining technique was demonstrated in these tests and the glass produced from the melter was shown to be less porous than the laboratory-produced glass. The final glass produced from the second test was compared to a glass of the same composition produced under laboratory conditions. The comparative tests found the glasses to be indistinguishable, as the small differences in the test results fell within the precision range of the characterization testing equipment. The cesium volatility was examined in the final test. This examination showed that 0.44 wt % of the cesium (assumed to be cesium oxide) was volatilized, which translates to a volatilization rate of 115 mg/cm 2 -h

  1. X-Ray Diffraction Techniques and Finite Element Modeling to Control Residual Stress in High-Temperature Pressure Vessels

    National Research Council Canada - National Science Library

    Lee, S

    1999-01-01

    Manufacturing operations, such as swage autofrettage, shot peening, and overload processes, have been used to impart advantageous residual stresses to improve fatigue life in components used in high...

  2. Converting biowaste corncob residue into high value added porous carbon for supercapacitor electrodes.

    Science.gov (United States)

    Qu, Wen-Hui; Xu, Yuan-Yuan; Lu, An-Hui; Zhang, Xiang-Qian; Li, Wen-Cui

    2015-08-01

    In this report, corncob residue, the main by-product in the furfural industry, is used as a precursor to prepare porous carbon by a simple and direct thermal treatment: one-step activation without pre-carbonization. As a consequence, the corncob residue derived porous carbon achieves a high surface area of 1210 m(2) g(-1) after ash-removal. The carbon material has the advantages of low cost and low environmental impact, with a superior electrochemical performance compared to those polymer-based synthetic carbons as electrode material for a supercapacitor. The carbon electrode exhibits a high capacitance of 314 F g(-1) in 6M KOH electrolyte. The corresponding sample also shows a superb cycling stability. Almost no capacitance decay was observed after 100,000 cycles. The excellent electrochemical performance is due to the combination of a high specific surface area with a fraction of mesopores and highly stable structure. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Gains of ubiquitylation sites in highly conserved proteins in the human lineage

    Directory of Open Access Journals (Sweden)

    Kim Dong Seon

    2012-11-01

    Full Text Available Abstract Background Post-translational modification of lysine residues of specific proteins by ubiquitin modulates the degradation, localization, and activity of these target proteins. Here, we identified gains of ubiquitylation sites in highly conserved regions of human proteins that occurred during human evolution. Results We analyzed human ubiquitylation site data and multiple alignments of orthologous mammalian proteins including those from humans, primates, other placental mammals, opossum, and platypus. In our analysis, we identified 281 ubiquitylation sites in 252 proteins that first appeared along the human lineage during primate evolution: one protein had four novel sites; four proteins had three sites each; 18 proteins had two sites each; and the remaining 229 proteins had one site each. PML, which is involved in neurodevelopment and neurodegeneration, acquired three sites, two of which have been reported to be involved in the degradation of PML. Thirteen human proteins, including ERCC2 (also known as XPD and NBR1, gained human-specific ubiquitylated lysines after the human-chimpanzee divergence. ERCC2 has a Lys/Gln polymorphism, the derived (major allele of which confers enhanced DNA repair capacity and reduced cancer risk compared with the ancestral (minor allele. NBR1 and eight other proteins that are involved in the human autophagy protein interaction network gained a novel ubiquitylation site. Conclusions The gain of novel ubiquitylation sites could be involved in the evolution of protein degradation and other regulatory networks. Although gains of ubiquitylation sites do not necessarily equate to adaptive evolution, they are useful candidates for molecular functional analyses to identify novel advantageous genetic modifications and innovative phenotypes acquired during human evolution.

  4. Partial alignment and measurement of residual dipolar couplings of proteins under high hydrostatic pressure

    Energy Technology Data Exchange (ETDEWEB)

    Fu, Yinan; Wand, A. Joshua, E-mail: wand@mail.med.upenn.edu [University of Pennsylvania, Department of Biochemistry and Biophysics, Johnson Research Foundation (United States)

    2013-08-15

    High-pressure NMR spectroscopy has emerged as a complementary approach for investigating various structural and thermodynamic properties of macromolecules. Noticeably absent from the array of experimental restraints that have been employed to characterize protein structures at high hydrostatic pressure is the residual dipolar coupling, which requires the partial alignment of the macromolecule of interest. Here we examine five alignment media that are commonly used at ambient pressure for this purpose. We find that the spontaneous alignment of Pf1 phage, d(GpG) and a C12E5/n-hexnanol mixture in a magnetic field is preserved under high hydrostatic pressure. However, DMPC/DHPC bicelles and collagen gel are found to be unsuitable. Evidence is presented to demonstrate that pressure-induced structural changes can be identified using the residual dipolar coupling.

  5. Homologous high-throughput expression and purification of highly conserved E coli proteins

    Directory of Open Access Journals (Sweden)

    Duchmann Rainer

    2007-06-01

    Full Text Available Abstract Background Genetic factors and a dysregulated immune response towards commensal bacteria contribute to the pathogenesis of Inflammatory Bowel Disease (IBD. Animal models demonstrated that the normal intestinal flora is crucial for the development of intestinal inflammation. However, due to the complexity of the intestinal flora, it has been difficult to design experiments for detection of proinflammatory bacterial antigen(s involved in the pathogenesis of the disease. Several studies indicated a potential association of E. coli with IBD. In addition, T cell clones of IBD patients were shown to cross react towards antigens from different enteric bacterial species and thus likely responded to conserved bacterial antigens. We therefore chose highly conserved E. coli proteins as candidate antigens for abnormal T cell responses in IBD and used high-throughput techniques for cloning, expression and purification under native conditions of a set of 271 conserved E. coli proteins for downstream immunologic studies. Results As a standardized procedure, genes were PCR amplified and cloned into the expression vector pQTEV2 in order to express proteins N-terminally fused to a seven-histidine-tag. Initial small-scale expression and purification under native conditions by metal chelate affinity chromatography indicated that the vast majority of target proteins were purified in high yields. Targets that revealed low yields after purification probably due to weak solubility were shuttled into Gateway (Invitrogen destination vectors in order to enhance solubility by N-terminal fusion of maltose binding protein (MBP, N-utilizing substance A (NusA, or glutathione S-transferase (GST to the target protein. In addition, recombinant proteins were treated with polymyxin B coated magnetic beads in order to remove lipopolysaccharide (LPS. Thus, 73% of the targeted proteins could be expressed and purified in large-scale to give soluble proteins in the range of 500

  6. Visualization of conserved structures by fusing highly variable datasets.

    Science.gov (United States)

    Silverstein, Jonathan C; Chhadia, Ankur; Dech, Fred

    2002-01-01

    Reality (VR) environment. The accuracy of the fusions was determined qualitatively by comparing the transformed atlas overlaid on the appropriate CT. It was examined for where the transformed structure atlas was incorrectly overlaid (false positive) and where it was incorrectly not overlaid (false negative). According to this method, fusions 1 and 2 were correct roughly 50-75% of the time, while fusions 3 and 4 were correct roughly 75-100%. The CT dataset augmented with transformed dataset was viewed arbitrarily in user-centered perspective stereo taking advantage of features such as scaling, windowing and volumetric region of interest selection. This process of auto-coloring conserved structures in variable datasets is a step toward the goal of a broader, standardized automatic structure visualization method for radiological data. If successful it would permit identification, visualization or deletion of structures in radiological data by semi-automatically applying canonical structure information to the radiological data (not just processing and visualization of the data's intrinsic dynamic range). More sophisticated selection of control points and patterns of warping may allow for more accurate transforms, and thus advances in visualization, simulation, education, diagnostics, and treatment planning.

  7. Analytic, high β, flux conserving equilibria for cylindrical tokamaks

    International Nuclear Information System (INIS)

    Sigmar, D.J.; Vahala, G.

    1978-09-01

    Using Grad's theory of generalized differential equations, the temporal evolution from low to high β due to ''adiabatic'' and nonadiabatic (i.e., neutral beam injection) heating of a cylindrical tokamak plasma with circular cross section and peaked current profiles is calculated analytically. The influence of shaping the initial safety factor profile and the beam deposition profile and the effect of minor radius compression on the equilibrium is analyzed

  8. Analytic, high β, flux conserving equilibria for cylindrical tokamaks

    International Nuclear Information System (INIS)

    Sigmar, D.J.; Vahala, G.

    1978-01-01

    Using Grad's theory of generalized differential equations, the temporal evolution from low to high β due to ''adiabatic'' and nonadiabatic (i.e., neutral beam injection) heating of a cylindrical tokamak plasma with circular cross section and peaked current profiles is calculated analytically. The influence of shaping the initial safety factor profile and the beam deposition profile and the effect of minor radius compression on the equilibrium is analyzed

  9. Measurement of residual radioactivity in cooper exposed to high energy heavy ion beam

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Eunjoo; Nakamura, Takashi [Tohoku Univ., Sendai (Japan). Cyclotron and Radioisotope Center; Uwamino, Yoshitomo; Ito, Sachiko; Fukumura, Akifumi

    1999-03-01

    The residual radioactivities produced by high energy heavy ions have been measured using the heavy ion beams of the Heavy Ion Medical Accelerator (HIMAC) at National Institute of Radiological Sciences. The spatial distribution of residual radioactivities in 3.5 cm, 5.5 cm and 10 cm thick copper targets of 10 cm x 10 cm size bombarded by 290 MeV/u, 400 MeV/u-{sup 12}C ion beams and 400 MeV/u-{sup 20}Ne ion beam, respectively, were obtained by measuring the gamma-ray activities of 0.5 mm thick copper foil inserted in the target with a high purity Ge detector after about 1 hour to 6 hours irradiation. (author)

  10. ENTRIA 2014. Memorandum on the disposal of high-level radioactive residuals

    International Nuclear Information System (INIS)

    Roehlig, Klaus-Juergen; Walther, Clemens; Bach, Friedrich-Wilhelm

    2014-01-01

    The memorandum on the disposal of high-level radioactive residuals covers the following issues: description of the problem: a ''wicked problem'', risks and NIMBY, the site selection law, international boundary conditions; disposal strategy and types of facilities: safety and reversibility, long-term surface storage, deep storage; risk and safety; procedural justice and the site selection process; social innovations and the requirement of long-term institutions; conclusion - central stress fields.

  11. High-resolution satellite imagery is an important yet underutilized resource in conservation biology.

    Science.gov (United States)

    Boyle, Sarah A; Kennedy, Christina M; Torres, Julio; Colman, Karen; Pérez-Estigarribia, Pastor E; de la Sancha, Noé U

    2014-01-01

    Technological advances and increasing availability of high-resolution satellite imagery offer the potential for more accurate land cover classifications and pattern analyses, which could greatly improve the detection and quantification of land cover change for conservation. Such remotely-sensed products, however, are often expensive and difficult to acquire, which prohibits or reduces their use. We tested whether imagery of high spatial resolution (≤5 m) differs from lower-resolution imagery (≥30 m) in performance and extent of use for conservation applications. To assess performance, we classified land cover in a heterogeneous region of Interior Atlantic Forest in Paraguay, which has undergone recent and dramatic human-induced habitat loss and fragmentation. We used 4 m multispectral IKONOS and 30 m multispectral Landsat imagery and determined the extent to which resolution influenced the delineation of land cover classes and patch-level metrics. Higher-resolution imagery more accurately delineated cover classes, identified smaller patches, retained patch shape, and detected narrower, linear patches. To assess extent of use, we surveyed three conservation journals (Biological Conservation, Biotropica, Conservation Biology) and found limited application of high-resolution imagery in research, with only 26.8% of land cover studies analyzing satellite imagery, and of these studies only 10.4% used imagery ≤5 m resolution. Our results suggest that high-resolution imagery is warranted yet under-utilized in conservation research, but is needed to adequately monitor and evaluate forest loss and conversion, and to delineate potentially important stepping-stone fragments that may serve as corridors in a human-modified landscape. Greater access to low-cost, multiband, high-resolution satellite imagery would therefore greatly facilitate conservation management and decision-making.

  12. Crystal structure of AFV3-109, a highly conserved protein from crenarchaeal viruses

    Directory of Open Access Journals (Sweden)

    Quevillon-Cheruel Sophie

    2007-01-01

    Full Text Available Abstract The extraordinary morphologies of viruses infecting hyperthermophilic archaea clearly distinguish them from bacterial and eukaryotic viruses. Moreover, their genomes code for proteins that to a large extend have no related sequences in the extent databases. However, a small pool of genes is shared by overlapping subsets of these viruses, and the most conserved gene, exemplified by the ORF109 of the Acidianus Filamentous Virus 3, AFV3, is present on genomes of members of three viral familes, the Lipothrixviridae, Rudiviridae, and "Bicaudaviridae", as well as of the unclassified Sulfolobus Turreted Icosahedral Virus, STIV. We present here the crystal structure of the protein (Mr = 13.1 kD, 109 residues encoded by the AFV3 ORF 109 in two different crystal forms at 1.5 and 1.3 Å resolution. The structure of AFV3-109 is a five stranded β-sheet with loops on one side and three helices on the other. It forms a dimer adopting the shape of a cradle that encompasses the best conserved regions of the sequence. No protein with a related fold could be identified except for the ortholog from STIV1, whose structure was deposited at the Protein Data Bank. We could clearly identify a well bound glycerol inside the cradle, contacting exclusively totally conserved residues. This interaction was confirmed in solution by fluorescence titration. Although the function of AFV3-109 cannot be deduced directly from its structure, structural homology with the STIV1 protein, and the size and charge distribution of the cavity suggested it could interact with nucleic acids. Fluorescence quenching titrations also showed that AFV3-109 interacts with dsDNA. Genomic sequence analysis revealed bacterial homologs of AFV3-109 as a part of a putative previously unidentified prophage sequences in some Firmicutes.

  13. Steam gasification of a thermally pretreated high lignin corn stover simultaneous saccharification and fermentation digester residue

    Energy Technology Data Exchange (ETDEWEB)

    Howe, Daniel T.; Taasevigen, Danny; Garcia-Perez, Manuel; McDonald, Armando G.; Li, Guosheng; Wolcott, Michael

    2017-01-01

    Efficient conversion of all components in lignocellulosic biomass is essential to realizing economic feasibility of biorefineries. However, when utilizing biochemical pathways, lignin cannot be fermented. Furthermore, the high lignin and high ash residue resulting from simultaneous saccharification and fermentation (SSF) reactors is difficult to thermochemically process due to feed line plugging and bed agglomeration. In this study a corn stover SSF digester residue was thermally pretreated at 300°C for 22.5 minutes (min) and then gasified in a bubbling fluidized bed gasifier to study the effect of thermal pretreatment on its processing behavior. Untreated, pelletized SSF residue was gasified at the same conditions to establish the baseline processing behavior. Results indicate that the thermal pretreatment process removes a substantial portion of the polar and non-polar extractives, with a resultant increase in the concentration of lignin, cellulose, and ash. Feed line plugging was not observed, although bed agglomeration was occurring at similar rates for both feedstocks, suggesting that overall ash content is the most important factor affecting bed agglomeration. Benzene, phenol, and polyaromatic hydrocarbons in the tar were present at higher concentrations in the treated material, with higher tar loading in the product gas. Total product gas generation is lower for the treated material, although the overall gas composition does not change.

  14. Determination of tylosin residues in pig tissues using high-performance liquid chromatography.

    Science.gov (United States)

    De Liguoro, M; Anfossi, P; Angeletti, R; Montesissa, C

    1998-06-01

    In accordance with the maximum residue limit of 100 micrograms kg-1 established by EU legislation, a simple and sensitive high-performance liquid chromatographic (HPLC) method was developed for the measurement of tylosin residues in pig tissues (fat, kidney, liver and muscle). Tylosin, a macrolide antibiotic, is extracted with water-methanol and cleaned-up by solid-phase extraction (SPE) on cation-exchange cartridges using methanol elution. Tylosin was determined by reversed-phase HPLC with UV detection at 280 nm and the mean recovery from pig tissues fortified in the range 50-200 micrograms kg-1 was 70-85%, with intra- and inter-day RSDs in the ranges 3.4-9.1 and 3.9-10.1% respectively.

  15. A Development of Advanced Rigorous 2 Step System for the High Resolution Residual Dose Evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Do Hyun; Kim, Jong Woo; Kim, Jea Hyun; Lee, Jae Yong; Shin, Chang Ho [Hanyang Univ., Seoul (Korea, Republic of); Kim, Song Hyun [Kyoto University, Sennan (Japan)

    2016-10-15

    In these days, an activation problem such as residual radiation is one of the important issues. The activated devices and structures can emit the residual radiation. Therefore, the activation should be properly analyzed to make a plan for design, operation, and decontamination of nuclear facilities. For activation calculation, Rigorous 2 Step (R2S) method is introduced as following strategy: (1) the particle transport calculation is performed for an object geometry to get particle spectra and total fluxes; (2) inventories of each cell are calculated by using flux information according to irradiation and decay history; (3) the residual gamma distribution was evaluated by transport code, if needed. This scheme is based on cell calculation of used geometry. In this method, the particle spectra and total fluxes are obtained by mesh tally for activation calculation. It is useful to reduce the effects of gradient flux information. Nevertheless, several limitations are known as follows: Firstly, high relative error of spectra, when lots of meshes were used; secondly, different flux information from spectrum of void in mesh-tally. To calculate high resolution residual dose, several method are developed such as R2Smesh and MCR2S unstructured mesh. The R2Smesh method products better efficiency for obtaining neutron spectra by using fine/coarse mesh. Also, the MCR2S unstructured mesh can effectively separate void spectrum. In this study, the AR2S system was developed to combine the features of those mesh based R2S method. To confirm the AR2S system, the simple activation problem was evaluated and compared with R2S method using same division. Those results have good agreement within 0.83 %. Therefore, it is expected that the AR2S system can properly estimate an activation problem.

  16. Studies on the primary and secondary residues from the dissolution of high-burnup nuclear fuels

    International Nuclear Information System (INIS)

    Schmid, M.

    1986-01-01

    To clarify the composition of residues from the dissolution of high-burnup nuclear fuels a sample with a burnup of 4.5 GWd and a two year cooling period was studied with the help of REM-EDX. In a parallel experiment an inactive simulator of a solution was subjected to a similar chemical treatment. The residues which resulted from this were analysed analogously. As a result of the results the chemistry of the following compounds in HNO 3 were studied: MoO 3 , ZrMo 2 O 5 (OH) 2 x2H 2 O, the oxide of antimony as well as Sb 4 O 4 (OH) 2 (NO 3 ) 2 , PdO.xH 2 O, Ag 2 Se, Ag 2 Te, and CsTcO 4 . Of special interest here were the solubility and precipitation formation of these compounds as well as the influence of a high (ca. 1 mol/l) concentration of uranium on these characteristics. With high radiation doses to the simulated solution a radiolytical reduction of Pd 2+ was established and was studied more closely with pure Pd(NO 3 ) 2 solutions. In primary dissolution residues the presence of the radionuclides Ru-106, Ag-110m, Sb-125, Cs-134, and Cs-137 was γ-spectrometrically proven. The residue was made up primarily of an element combination of Mo and Ru. As other components Rh, Pd and Tc appear in an alloy as the so-called ε phase, which already has to be present in the fuel, because this phase was not exhibited in the similarly handled simulator. Zirconium molybdate was not identified in the real feed slurries, but was definitely present in the precipitation of the simulated feed solution. The analysis of the primary residues also showed pure zirconium particles, presumably from the zirconium alloy of the fuel cans, as well as undissolved fuel particles. The precipitation from the fuel solution was made up of agglomerates of the smallest particles of the ε phase, upon which silver halogenides were crystallized. Radiochemically reduced Pd was also found. (orig./RB) [de

  17. High-throughput sequencing, characterization and detection of new and conserved cucumber miRNAs.

    Directory of Open Access Journals (Sweden)

    Germán Martínez

    Full Text Available Micro RNAS (miRNAs are a class of endogenous small non coding RNAs involved in the post-transcriptional regulation of gene expression. In plants, a great number of conserved and specific miRNAs, mainly arising from model species, have been identified to date. However less is known about the diversity of these regulatory RNAs in vegetal species with agricultural and/or horticultural importance. Here we report a combined approach of bioinformatics prediction, high-throughput sequencing data and molecular methods to analyze miRNAs populations in cucumber (Cucumis sativus plants. A set of 19 conserved and 6 known but non-conserved miRNA families were found in our cucumber small RNA dataset. We also identified 7 (3 with their miRNA* strand not previously described miRNAs, candidates to be cucumber-specific. To validate their description these new C. sativus miRNAs were detected by northern blot hybridization. Additionally, potential targets for most conserved and new miRNAs were identified in cucumber genome.In summary, in this study we have identified, by first time, conserved, known non-conserved and new miRNAs arising from an agronomically important species such as C. sativus. The detection of this complex population of regulatory small RNAs suggests that similarly to that observe in other plant species, cucumber miRNAs may possibly play an important role in diverse biological and metabolic processes.

  18. Effective deleting of residual photoconductivity in high-resistance layers GaAs

    International Nuclear Information System (INIS)

    Sadaev, B.S.; Kadirova, I.T.; Sharipov, E.I.

    2004-01-01

    Full text: The phenomenon of residual photoconductivity as the storage of optical memory (OM) represents practical interest in micro and optoelectronics. The finding - out of the nature OM represents undoubtedly and scientific interest. Now residual photoconductivity (RPC) is explained by potential barriers arising because of non-monocharacteristical of distribution components of the semiconductor or carriers of a current in volume. Depending on a nature non-monocharacteristical the time relaxation RPC changes in a wide limit. The special interest represents RPC created by impurity. In the given work the results of research of a nature RPC created photos by ionization of the filled centres of chrome in compensated epitaxilogic layers arsenide galls are resulted. Epitaxilogic layers were brought up by a vertical method ZFE. Highness was reached (achieved) by special indemnification of the residual donors deep acceptors of chrome. Substrates served n-GoAs. Lassitude of i-layers has made 70-80 microns. Specific resistance of layers has made (1/3) 108 om·sm. (T= 300 K). The structures were photosensitive as at low (T = 77 K) and at room temperatures. The photosensitivity of structures in impurity to a strip of absorption chrome (= 1,4 microns) was comparable (compared) with own. The researches show, that the structures have RPC. Size RPC the greatest ambassador impurity of illumination is carrying out photoionization Cr2 + - of the centres. That is established, RPC impurity of a photocurrent is effectively erased only at certain length of a wave of external illumination

  19. The barley straw residues avoid high erosion rates in persimmon plantations. Eastern Spain

    Science.gov (United States)

    Cerdà, Artemi; González Pelayo, Óscar; Giménez-Morera, Antonio; Jordán, Antonio; Novara, Agata; Pereira, Paulo; Mataix-Solera, Jorge

    2015-04-01

    the bare control plots to 47 gr in the straw covered plots, which resulted in a low erosion rate when the soil is covered with straw (0.23 Mg ha-1 y-1), but extremely high when the soil is not covered (5.07 Mg ha-1 y-1). The results show also a delayed runoff generation due to the effect of the straw. From ponding to surface runoff the bare plots last 198 seconds, but under straw covered soils the time is 506 seconds. Moreover, when runoff is found on the soil surface the time to reach the plot outlet is much delayed under the straw cover, as range from 156 seconds on the bare plots to 406 to the straw covered plots. The management of the agriculture soils in many parts of the Planet is triggering land degradation (Borelli et al., 2013; Haregeweyn et al., 2013; Zhao et al., 2013). The most intense soil erosion rates use to affect agriculture land (Cerdà et al., 2009), and in Eastern Spain it was found that citrus orchards are being seeing as one of the crops with the highest erosion rates due to the managements that avoid the catch crops, weeds or litter, and this is also found in China (Cerdà and Jurgensen, 2008; 2009; Cerdà et al., 2009a; 2009b; Cerdà et al., 2011; 2012) and in China (Wu et al., 1997; Xu et al., 2010; Wang et al., 2011; Wu et al., 2011; Liu et al., 2011; Lü et al., 2011; Xu et al., 2012). The worse land managements found in many of the citrus plantations results in soil degradation too (Lu et al., 1997; Lü et al., 2012; Xu et al., 2012) and we can confirm here that the new Persimmon plantations are triggering the same effect and it is necessary to develop new strategies to reduce the soil losses. The use of cover crops to reduce the soil losses (Lavigne et al., 2012; Le Bellec et al., 2012) and the use of residues such as dried citrus peel has been found successful, but also it is well know the effect of the litter it is a key cover to avoid soil erosion. Meginnis (1935) was one of the pioneers on the research of the cover of litter to avoid

  20. High-Order Entropy Stable Finite Difference Schemes for Nonlinear Conservation Laws: Finite Domains

    Science.gov (United States)

    Fisher, Travis C.; Carpenter, Mark H.

    2013-01-01

    Developing stable and robust high-order finite difference schemes requires mathematical formalism and appropriate methods of analysis. In this work, nonlinear entropy stability is used to derive provably stable high-order finite difference methods with formal boundary closures for conservation laws. Particular emphasis is placed on the entropy stability of the compressible Navier-Stokes equations. A newly derived entropy stable weighted essentially non-oscillatory finite difference method is used to simulate problems with shocks and a conservative, entropy stable, narrow-stencil finite difference approach is used to approximate viscous terms.

  1. Low-energy particle production and residual nuclei production from high-energy hadron-nucleus collisions

    International Nuclear Information System (INIS)

    Alsmiller, F.S.; Alsmiller, R.G. Jr.; Hermann, O.W.

    1987-01-01

    The high-energy hadron-nucleus collision model, EVENTQ, has been modified to include a calculation of the excitation and kinetic energy of the residual compound nucleus. The specific purpose of the modification is to make it possible to use the model in the high-energy radiation transport code, HETC, which, in conjunction with MORSE, is used to transport the low energy particles. It is assumed that the nucleons in the nucleus move in a one-dimensional potential well and have the momentum distribution of a degenerate Fermi gas. The low energy particles produced by the deexcitation of the residual compound nucleus, and the final residual nucleus, are determined from an evaporation model. Comparisons of multiplicities and residual nuclei distributions with experimental data are given. The ''grey'' particles, i.e., charged particles with 0.25 < β < 0.7, are in good agreement with experimental data but the residual nuclei distributions are not. 12 refs., 3 figs

  2. Spatial overlap between environmental policy instruments and areas of high conservation value in forest.

    Science.gov (United States)

    Sverdrup-Thygeson, Anne; Søgaard, Gunnhild; Rusch, Graciela M; Barton, David N

    2014-01-01

    In order to safeguard biodiversity in forest we need to know how forest policy instruments work. Here we use a nationwide network of 9400 plots in productive forest to analyze to what extent large-scale policy instruments, individually and together, target forest of high conservation value in Norway. We studied both instruments working through direct regulation; Strict Protection and Landscape Protection, and instruments working through management planning and voluntary schemes of forest certification; Wilderness Area and Mountain Forest. As forest of high conservation value (HCV-forest) we considered the extent of 12 Biodiversity Habitats and the extent of Old-Age Forest. We found that 22% of productive forest area contained Biodiversity Habitats. More than 70% of this area was not covered by any large-scale instruments. Mountain Forest covered 23%, while Strict Protection and Wilderness both covered 5% of the Biodiversity Habitat area. A total of 9% of productive forest area contained Old-Age Forest, and the relative coverage of the four instruments was similar as for Biodiversity Habitats. For all instruments, except Landscape Protection, the targeted areas contained significantly higher proportions of HCV-forest than areas not targeted by these instruments. Areas targeted by Strict Protection had higher proportions of HCV-forest than areas targeted by other instruments, except for areas targeted by Wilderness Area which showed similar proportions of Biodiversity Habitats. There was a substantial amount of spatial overlap between the policy tools, but no incremental conservation effect of overlapping instruments in terms of contributing to higher percentages of targeted HCV-forest. Our results reveal that although the current policy mix has an above average representation of forest of high conservation value, the targeting efficiency in terms of area overlap is limited. There is a need to improve forest conservation and a potential to cover this need by better

  3. Determination of tylosin residues in different animal tissues by high performance liquid chromatography.

    Science.gov (United States)

    Prats, C; Francesch, R; Arboix, M; Pérez, B

    2002-01-05

    A HPLC method to determine and quantify tylosin residues from calves, pigs and poultry is reported. This procedure permitted tylosin to be separated from muscle, liver, kidney and fat after a simple extraction with chloroform or ethyl acetate under basic conditions. The analytical methodology showed a high specificity and sensitivity and an adequate precision and accuracy with a limit of quantification of 50 microg/kg. Eight calves were administered 20 mg/kg/day of tylosin for 5 days and slaughtered at 7 and 14 days post-administration. Results showed that at the 14th day tylosin levels were lower than the MRL in all target tissues.

  4. Structural and functional studies of the biotin protein ligase from Aquifex aeolicus reveal a critical role for a conserved residue in target specificity.

    Science.gov (United States)

    Tron, Cecile M; McNae, Iain W; Nutley, Margaret; Clarke, David J; Cooper, Alan; Walkinshaw, Malcolm D; Baxter, Robert L; Campopiano, Dominic J

    2009-03-20

    Biotin protein ligase (BPL; EC 6.3.4.15) catalyses the formation of biotinyl-5'-AMP from biotin and ATP, and the succeeding biotinylation of the biotin carboxyl carrier protein. We describe the crystal structures, at 2.4 A resolution, of the class I BPL from the hyperthermophilic bacteria Aquifex aeolicus (AaBPL) in its ligand-free form and in complex with biotin and ATP. The solvent-exposed beta- and gamma-phosphates of ATP are located in the inter-subunit cavity formed by the N- and C-terminal domains. The Arg40 residue from the conserved GXGRXG motif is shown to interact with the carboxyl group of biotin and to stabilise the alpha- and beta-phosphates of the nucleotide. The structure of the mutant AaBPL R40G in both the ligand-free and biotin-bound forms reveals that the mutated loop has collapsed, thus hindering ATP binding. Isothermal titration calorimetry indicated that the presence of biotin is not required for ATP binding to wild-type AaBPL in the absence of Mg(2+), and the binding of biotin and ATP has been determined to occur via a random but cooperative process. The affinity for biotin is relatively unaffected by the R40G mutation. In contrast, the thermodynamic data indicate that binding of ATP to AaBPL R40G is very weak in the absence or in the presence of biotin. The AaBPL R40G mutant remains catalytically active but shows poor substrate specificity; mass spectrometry and Western blot studies revealed that the mutant biotinylates both the target A. aeolicus BCCPDelta67 fragment and BSA, and is subject to self-biotinylation.

  5. The valine and lysine residues in the conserved FxVTxK motif are important for the function of phylogenetically distant plant cellulose synthases

    Energy Technology Data Exchange (ETDEWEB)

    Slabaugh, Erin; Scavuzzo-Duggan, Tess; Chaves, Arielle; Wilson, Liza; Wilson, Carmen; Davis, Jonathan K.; Cosgrove, Daniel J.; Anderson, Charles T.; Roberts, Alison W.; Haigler, Candace H.

    2015-12-08

    Cellulose synthases (CESAs) synthesize the β-1,4-glucan chains that coalesce to form cellulose microfibrils in plant cell walls. In addition to a large cytosolic (catalytic) domain, CESAs have eight predicted transmembrane helices (TMHs). However, analogous to the structure of BcsA, a bacterial CESA, predicted TMH5 in CESA may instead be an interfacial helix. This would place the conserved FxVTxK motif in the plant cell cytosol where it could function as a substrate-gating loop as occurs in BcsA. To define the functional importance of the CESA region containing FxVTxK, we tested five parallel mutations in Arabidopsis thaliana CESA1 and Physcomitrella patens CESA5 in complementation assays of the relevant cesa mutants. In both organisms, the substitution of the valine or lysine residues in FxVTxK severely affected CESA function. In Arabidopsis roots, both changes were correlated with lower cellulose anisotropy, as revealed by Pontamine Fast Scarlet. Analysis of hypocotyl inner cell wall layers by atomic force microscopy showed that two altered versions of Atcesa1 could rescue cell wall phenotypes observed in the mutant background line. Overall, the data show that the FxVTxK motif is functionally important in two phylogenetically distant plant CESAs. The results show that Physcomitrella provides an efficient model for assessing the effects of engineered CESA mutations affecting primary cell wall synthesis and that diverse testing systems can lead to nuanced insights into CESA structure–function relationships. Although CESA membrane topology needs to be experimentally determined, the results support the possibility that the FxVTxK region functions similarly in CESA and BcsA.

  6. Analysis of the Residual Stresses in Helical Cylindrical Springs at High Temperature

    Directory of Open Access Journals (Sweden)

    H. Sun

    2015-01-01

    Full Text Available Creep is one of the basic properties of materials, its speed significantly depends on the temperature. Helical cylindrical springs are widely used in the elements of heating systems. This results in necessity of taking into account the effect of temperature on the stress-strain state of the spring. The object of research is a helical cylindrical spring used at high temperatures. Under this condition the spring state stability should be ensured.The paper studies relaxation of stress state and generation of residual stresses. Calculations are carried out in ABAQUS environment. The purpose of this work is to discuss the law of relaxation and residual stress in the spring.This paper describes the basic creep theories of helical cylindrical spring material. The calculation formulas of shear stress relaxation for a fixed compression ratio are obtained. Distribution and character of stress contour lines in the cross section of spring are presented. The stress relaxation – time relationships are discussed. The approximate formula for calculating relaxation shear stresses in the cross section of helical springs is obtained.The paper investigates creep ratio and law of residual stress variation in the cross-section of spring at 650℃. Computer simulation in ABAQUS environment was used. Research presents a finite element model of the spring creep in the cross-section.The paper conducts analysis of the stress changes for the creep under constant load. Under constant load stresses are quickly decreased in the around area of cross-section and are increased in the centre, i.e. the maximum and minimum stresses come close with time. Research work shows the possibility for using the approximate formula to calculate the relaxation shear stress in the cross section of spring and can provide a theoretical basis for predicting the service life of spring at high temperatures.In research relaxation processes of stress state are studied. Finite element model is cre

  7. Prospects for Parity Non-conservation Experiments with Highly Charged Heavy Ions

    OpenAIRE

    Maul, M.; Schäfer, A.; Greiner, W.; Indelicato, P.

    1996-01-01

    We discuss the prospects for parity non-conservation experiments with highly charged heavy ions. Energy levels and parity mixing for heavy ions with two to five electrons are calculated. We investigate two-photon-transitions and the possibility to observe interference effects between weak-matrix elements and Stark matrix elements for periodic electric field configurations.

  8. A conserved motif in the linker domain of STAT1 transcription factor is required for both recognition and release from high-affinity DNA-binding sites.

    Science.gov (United States)

    Hüntelmann, Bettina; Staab, Julia; Herrmann-Lingen, Christoph; Meyer, Thomas

    2014-01-01

    Binding to specific palindromic sequences termed gamma-activated sites (GAS) is a hallmark of gene activation by members of the STAT (signal transducer and activator of transcription) family of cytokine-inducible transcription factors. However, the precise molecular mechanisms involved in the signal-dependent finding of target genes by STAT dimers have not yet been very well studied. In this study, we have characterized a sequence motif in the STAT1 linker domain which is highly conserved among the seven human STAT proteins and includes surface-exposed residues in close proximity to the bound DNA. Using site-directed mutagenesis, we have demonstrated that a lysine residue in position 567 of the full-length molecule is required for GAS recognition. The substitution of alanine for this residue completely abolished both binding to high-affinity GAS elements and transcriptional activation of endogenous target genes in cells stimulated with interferon-γ (IFNγ), while the time course of transient nuclear accumulation and tyrosine phosphorylation were virtually unchanged. In contrast, two glutamic acid residues (E559 and E563) on each monomer are important for the dissociation of dimeric STAT1 from DNA and, when mutated to alanine, result in elevated levels of tyrosine-phosphorylated STAT1 as well as prolonged IFNγ-stimulated nuclear accumulation. In conclusion, our data indicate that the kinetics of signal-dependent GAS binding is determined by an array of glutamic acid residues located at the interior surface of the STAT1 dimer. These negatively charged residues appear to align the long axis of the STAT1 dimer in a position perpendicular to the DNA, thereby facilitating the interaction between lysine 567 and the phosphodiester backbone of a bound GAS element, which is a prerequisite for transient gene induction.

  9. The procedure for determining the residual life of high-temperature aggregates

    Science.gov (United States)

    Nikiforov, A. S.; Prihodko, E. V.; Kinzhibekova, A. K.; Karmanov, A. E.

    2018-01-01

    One of the main reasons for the withdrawal of high-temperature aggregates for repairs is the destruction of enclosing structures due to the occurrence of temperature stresses. A wide range of refractory materials used, a large number of product names, a difference in the operation of even the same aggregates makes it impossible to apply general principles for determining the residual resource of high-temperature aggregates, which is based, as a rule, on the determination of temperature stresses. In the article there is suggested a technique based on the method of simulation modeling, allowing to estimate the remaining resource and reliability of the operating equipment. There are given data on the calculation of these indicators for a 25-ton steel-casting ladle. The values obtained make it possible to evaluate the rationality of the further operation of the high-temperature unit by the condition of reliability of the enclosing structures.

  10. Balancing forest-regeneration probabilities and maintenance costs in dry grasslands of high conservation priority

    Science.gov (United States)

    Bolliger, Janine; Edwards, Thomas C.; Eggenberg, Stefan; Ismail, Sascha; Seidl, Irmi; Kienast, Felix

    2011-01-01

    Abandonment of agricultural land has resulted in forest regeneration in species-rich dry grasslands across European mountain regions and threatens conservation efforts in this vegetation type. To support national conservation strategies, we used a site-selection algorithm (MARXAN) to find optimum sets of floristic regions (reporting units) that contain grasslands of high conservation priority. We sought optimum sets that would accommodate 136 important dry-grassland species and that would minimize forest regeneration and costs of management needed to forestall predicted forest regeneration. We did not consider other conservation elements of dry grasslands, such as animal species richness, cultural heritage, and changes due to climate change. Optimal sets that included 95–100% of the dry grassland species encompassed an average of 56–59 floristic regions (standard deviation, SD 5). This is about 15% of approximately 400 floristic regions that contain dry-grassland sites and translates to 4800–5300 ha of dry grassland out of a total of approximately 23,000 ha for the entire study area. Projected costs to manage the grasslands in these optimum sets ranged from CHF (Swiss francs) 5.2 to 6.0 million/year. This is only 15–20% of the current total estimated cost of approximately CHF30–45 million/year required if all dry grasslands were to be protected. The grasslands of the optimal sets may be viewed as core sites in a national conservation strategy.

  11. Technical evaluation on high aging, and performance conditions on long-term conservation program

    International Nuclear Information System (INIS)

    Yamashita, Atsushi

    2001-01-01

    In order to secure safety and safe operation of power plants, in every nuclear power plants, conservation actions based on preventive conservation are performed. They contain operative condition monitoring, patrolling inspection, and periodical tests on important systems and apparatus by operators under plant operation and condition monitoring by maintenance workers, and so on, and when finding out their abnormal conditions, their detailed survey is performed to adopt adequate countermeasures such as recovery, exchange, and so on. And, to equipments for nuclear power generation periodical conditions were obliged by legal examinations and by independent inspections. As a result of these conservation actions, even on a plant elapsed about 30 years since beginning of its operation it was thought that the plant was aged with elapsing time even if not recognizing any indication on its aged deterioration at that time. Therefore, for its concrete countermeasure, by supposing long-term operation of a plant with longer operation history, some technical evaluation on aged phenomena were carried out, to investigate on reflection of the obtained results to present conservation actions. Here were described on efforts on the high aging countermeasures, and performing conditions of long-term conservation in the Tsuruga Unit No. 1 Nuclear Power Station. (G.K.)

  12. High qualitative and quantitative conservation of alternative splicing in Caenorhabditis elegans and Caenorhabditis briggsae

    DEFF Research Database (Denmark)

    Rukov, Jakob Lewin; Irimia, Manuel; Mørk, Søren

    2007-01-01

    Alternative splicing (AS) is an important contributor to proteome diversity and is regarded as an explanatory factor for the relatively low number of human genes compared with less complex animals. To assess the evolutionary conservation of AS and its developmental regulation, we have investigated...... the qualitative and quantitative expression of 21 orthologous alternative splice events through the development of 2 nematode species separated by 85-110 Myr of evolutionary time. We demonstrate that most of these alternative splice events present in Caenorhabditis elegans are conserved in Caenorhabditis briggsae....... Moreover, we find that relative isoform expression levels vary significantly during development for 78% of the AS events and that this quantitative variation is highly conserved between the 2 species. Our results suggest that AS is generally tightly regulated through development and that the regulatory...

  13. On residual gas analysis during high temperature baking of graphite tiles

    International Nuclear Information System (INIS)

    Prakash, A A; Chaudhuri, P; Khirwadkar, S; Reddy, D Chenna; Saxena, Y C; Chauhan, N; Raole, P M

    2008-01-01

    Steady-state Super-conducting Tokamak-1 (SST-1) is a medium size tokamak with major radius of 1.1 m and minor radius of 0.20 m. It is designed for plasma discharge duration of 1000 seconds to obtain fully steady-state plasma operation. Plasma Facing Components (PFC), consisting of divertors, passive stabilizers, baffles and poloidal limiters are also designed to be UHV compatible for steady state operation. All PFC are made up of graphite tiles mechanically attached to the copper alloy substrate. Graphite is one of the preferred first wall armour material in present day tokamaks. High thermal shock resistance and low atomic number of carbon are the most important properties of graphite for this application. High temperature vacuum baking of graphite tiles is the standard process to remove the impurities. Residual Gas Analyzer (RGA) has been used for qualitative and quantitative measurements of released gases from graphite tiles during baking. Surface Analysis of graphite tiles has also been done before and after baking. This paper describes the residual gas analysis during baking and surface analysis of graphite tiles

  14. On residual gas analysis during high temperature baking of graphite tiles

    Energy Technology Data Exchange (ETDEWEB)

    Prakash, A A; Chaudhuri, P; Khirwadkar, S; Reddy, D Chenna; Saxena, Y C [Institute for Plasma Research, Bhat, Gandhinagar - 382 428 (India); Chauhan, N; Raole, P M [Facilitation Center for Industrial Plasma Technologies, IPR, Gandhinagar (India)], E-mail: arun@ipr.res.in

    2008-05-01

    Steady-state Super-conducting Tokamak-1 (SST-1) is a medium size tokamak with major radius of 1.1 m and minor radius of 0.20 m. It is designed for plasma discharge duration of 1000 seconds to obtain fully steady-state plasma operation. Plasma Facing Components (PFC), consisting of divertors, passive stabilizers, baffles and poloidal limiters are also designed to be UHV compatible for steady state operation. All PFC are made up of graphite tiles mechanically attached to the copper alloy substrate. Graphite is one of the preferred first wall armour material in present day tokamaks. High thermal shock resistance and low atomic number of carbon are the most important properties of graphite for this application. High temperature vacuum baking of graphite tiles is the standard process to remove the impurities. Residual Gas Analyzer (RGA) has been used for qualitative and quantitative measurements of released gases from graphite tiles during baking. Surface Analysis of graphite tiles has also been done before and after baking. This paper describes the residual gas analysis during baking and surface analysis of graphite tiles.

  15. [Construction of a microbial consortium RXS with high degradation ability for cassava residues and studies on its fermentative characteristics].

    Science.gov (United States)

    He, Jiang; Mao, Zhong-Gui; Zhang, Qing-Hua; Zhang, Jian-Hua; Tang, Lei; Zhang, Hong-Jian

    2012-03-01

    A microbial consortium with high effective and stable cellulosic degradation ability was constructed by successive enrichment and incubation in a peptone cellulose medium using cassava residues and filter paper as carbon sources, where the inoculums were sampled from the environment filled with rotten lignocellulosic materials. The degradation ability to different cellulosic materials and change of main parameters during the degradation process of cassava residues by this consortium was investigated in this study. It was found that, this consortium can efficiently degrade filter paper, absorbent cotton, avicael, wheat-straw and cassava residues. During the degradation process of cassava residues, the key hydrolytic enzymes including cellulase, hemicellulase and pectinase showed a maximum enzyme activity of 34.4, 90.5 and 15.8 U on the second or third day, respectively. After 10 days' fermentation, the degradation ratio of cellulose, hemicellulose and lignin of cassava residues was 79.8%, 85.9% and 19.4% respectively, meanwhile the loss ratio of cassava residues reached 61.5%. Otherwise,it was found that the dominant metabolites are acetic acid, butyric acid, caproic acid and glycerol, and the highest hydrolysis ratio is obtained on the second day by monitoring SCOD, total volatile fatty acids and total sugars. The above results revealed that this consortium can effectively hydrolyze cassava residues (the waste produced during the cassava based bioethanol production) and has great potential to be utilized for the pretreatment of cassava residues for biogas fermentation.

  16. UVB-induced photoperoxidation of lipids of human low and high density lipoproteins. A possible role of tryptophan residues

    International Nuclear Information System (INIS)

    Salmon, S.; Maziere, J.C.; Santus, R.; Bouchemal, N.; Morliere, P.

    1990-01-01

    Ultraviolet radiation of the UVB region readily destroys tryptophan (Trp) residues of low (LDL) and high (HDL) density lipoproteins. The photooxidation of tryptophan residues is accompanied by peroxidation of low and high density lipoproteins unsaturated fatty acids, as measured by thiobarbituric acid assay. Moreover, low and high density lipoproteins are natural carriers of vitamin E and carotenoids. These two antioxidants are also rapidly bleached by UVB. The UVA radiation promotes neither tryptophan residue destruction nor lipid photoperoxidation. The redox cycling Cu 2+ ions considerably increase lipid photoperoxidation. The synergistic action of photo and auto (Cu 2+ -induced) peroxidation induces marked post-irradiation modifications of apolipoproteins as illustrated by degradation of most tryptophan residues after overnight incubation in the dark of pre-irradiated samples. (author)

  17. Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes

    Directory of Open Access Journals (Sweden)

    Kohane Isaac

    2005-11-01

    Full Text Available Abstract Background Recent advances in genome sequencing suggest a remarkable conservation in gene content of mammalian organisms. The similarity in gene repertoire present in different organisms has increased interest in studying regulatory mechanisms of gene expression aimed at elucidating the differences in phenotypes. In particular, a proximal promoter region contains a large number of regulatory elements that control the expression of its downstream gene. Although many studies have focused on identification of these elements, a broader picture on the complexity of transcriptional regulation of different biological processes has not been addressed in mammals. The regulatory complexity may strongly correlate with gene function, as different evolutionary forces must act on the regulatory systems under different biological conditions. We investigate this hypothesis by comparing the conservation of promoters upstream of genes classified in different functional categories. Results By conducting a rank correlation analysis between functional annotation and upstream sequence alignment scores obtained by human-mouse and human-dog comparison, we found a significantly greater conservation of the upstream sequence of genes involved in development, cell communication, neural functions and signaling processes than those involved in more basic processes shared with unicellular organisms such as metabolism and ribosomal function. This observation persists after controlling for G+C content. Considering conservation as a functional signature, we hypothesize a higher density of cis-regulatory elements upstream of genes participating in complex and adaptive processes. Conclusion We identified a class of functions that are associated with either high or low promoter conservation in mammals. We detected a significant tendency that points to complex and adaptive processes were associated with higher promoter conservation, despite the fact that they have emerged

  18. High level compressive residual stresses produced in aluminum alloys by laser shock processing

    International Nuclear Information System (INIS)

    Gomez-Rosas, G.; Rubio-Gonzalez, C.; Ocana, J.L; Molpeceres, C.; Porro, J.A.; Chi-Moreno, W.; Morales, M.

    2005-01-01

    Laser shock processing (LSP) has been proposed as a competitive alternative technology to classical treatments for improving fatigue and wear resistance of metals. We present a configuration and results for metal surface treatments in underwater laser irradiation at 1064 nm. A convergent lens is used to deliver 1.2 J/cm 2 in a 8 ns laser FWHM pulse produced by 10 Hz Q-switched Nd:YAG, two laser spot diameters were used: 0.8 and 1.5 mm. Results using pulse densities of 2500 pulses/cm 2 in 6061-T6 aluminum samples and 5000 pulses/cm 2 in 2024 aluminum samples are presented. High level of compressive residual stresses are produced -1600 MPa for 6061-T6 Al alloy, and -1400 MPa for 2024 Al alloy. It has been shown that surface residual stress level is higher than that achieved by conventional shot peening and with greater depths. This method can be applied to surface treatment of final metal products

  19. High entomological inoculation rate of malaria vectors in area of high coverage of interventions in southwest Ethiopia: Implication for residual malaria transmission

    Directory of Open Access Journals (Sweden)

    Misrak Abraham

    2017-05-01

    Finally, there was an indoor residual malaria transmission in a village of high coverage of bed nets and where the principal malaria vector is susceptibility to propoxur and bendiocarb; insecticides currently in use for indoor residual spraying. The continuing indoor transmission of malaria in such village implies the need for new tools to supplement the existing interventions and to reduce indoor malaria transmission.

  20. Structure of genes for dermaseptins B, antimicrobial peptides from frog skin. Exon 1-encoded prepropeptide is conserved in genes for peptides of highly different structures and activities.

    Science.gov (United States)

    Vouille, V; Amiche, M; Nicolas, P

    1997-09-01

    We cloned the genes of two members of the dermaseptin family, broad-spectrum antimicrobial peptides isolated from the skin of the arboreal frog Phyllomedusa bicolor. The dermaseptin gene Drg2 has a 2-exon coding structure interrupted by a small 137-bp intron, wherein exon 1 encoded a 22-residue hydrophobic signal peptide and the first three amino acids of the acidic propiece; exon 2 contained the 18 additional acidic residues of the propiece plus a typical prohormone processing signal Lys-Arg and a 32-residue dermaseptin progenitor sequence. The dermaseptin genes Drg2 and Drg1g2 have conserved sequences at both untranslated ends and in the first and second coding exons. In contrast, Drg1g2 comprises a third coding exon for a short version of the acidic propiece and a second dermaseptin progenitor sequence. Structural conservation between the two genes suggests that Drg1g2 arose recently from an ancestral Drg2-like gene through amplification of part of the second coding exon and 3'-untranslated region. Analysis of the cDNAs coding precursors for several frog skin peptides of highly different structures and activities demonstrates that the signal peptides and part of the acidic propieces are encoded by conserved nucleotides encompassed by the first coding exon of the dermaseptin genes. The organization of the genes that belong to this family, with the signal peptide and the progenitor sequence on separate exons, permits strikingly different peptides to be directed into the secretory pathway. The recruitment of such a homologous 'secretory' exon by otherwise non-homologous genes may have been an early event in the evolution of amphibian.

  1. Conservative Management for Stable High Ankle Injuries in Professional Football Players.

    Science.gov (United States)

    Knapik, Derrick M; Trem, Anthony; Sheehan, Joseph; Salata, Michael J; Voos, James E

    High ankle "syndesmosis" injuries are common in American football players relative to the general population. At the professional level, syndesmotic sprains represent a challenging and unique injury lacking a standardized rehabilitation protocol during conservative management. PubMed, Biosis Preview, SPORTDiscus, PEDro, and EMBASE databases were searched using the terms syndesmotic injuries, American football, conservative management, and rehabilitation. Clinical review. Level 3. When compared with lateral ankle sprains, syndesmosis injuries result in significantly prolonged recovery times and games lost. For stable syndesmotic injuries, conservative management features a brief period of immobilization and protected weightbearing followed by progressive strengthening exercises and running, and athletes can expect to return to competition in 2 to 6 weeks. Further research investigating the efficacy of dry needling and blood flow restriction therapy is necessary to evaluate the benefit of these techniques in the rehabilitation process. Successful conservative management of stable syndesmotic injuries in professional American football athletes requires a thorough understanding of the anatomy, injury mechanisms, diagnosis, and rehabilitation strategies utilized in elite athletes.

  2. Submillimeter residual losses in high-Tc superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Miller, David [Univ. of California, Berkeley, CA (United States)

    1993-09-01

    Bolometry was used obtain accurate submillimeter residual loss data for epitaxial films of YBa2Cu3O7 (YBCO), Tl2Ca2Ba2Cu3O10, Tl2CaBa2Cu2O8 (TCBCO), and Ba0.6K0.4BiO3 (BKBO). We were able to fit the absorptivity measured for Nb films to an Eliashberg strong coupling calculation; excellent agreement resulted between parameters from best fits and measured Residual Resistivity Ratio. Microwave surface resistance measurements made on the same YBCO and TCBCO films are in excellent agreement with submillimeter measurements. Absorptivities for all YBCO films studied are qualitatively similar, increasing smoothly with frequency, with no gap-like features below the well known absorption edge at 450 cm-1. Losses in YBCO films were fit to a weakly coupled grain model for the a-b plane conductivity. Strong phonon structure was observed in TCBCO films between 60 and 700 cm-1 (2 THz and 23 THz); these losses could not be fitted to the simple weakly coupled grain model, in contrast to the case for other high-Tc superconductors where phonon structure observed in ceramics are is absent in epitaxial oriented films and crystals because of electronic screening due to high conductivity of a-b planes. Absorptivity data for the BKBO films all show a strong absorption onset near the BCS tunneling gap of 3.5 kBTc. Comparison with strong coupling Eliashberg predictions and of a Kramers-Kronig analysis indicate that the absorption onset is consistent with a superconducting energy gap. Effects of magnetic field on residual losses in YBCO films show a resonant absorption feature in vicinity of predicted

  3. ANALISIS RESIDU KLORPIRIFOS DALAM SAYUR-SAYURAN DENGAN TEKNIK HIGH PERFORMANCE LIQUID CHROMATOGRAPHY (HPLC

    Directory of Open Access Journals (Sweden)

    Aman Sentosa Panggabean

    2016-06-01

    Full Text Available The research about analysis of chlorpyrifos residue in vegetables by using High Performance Liquid Chromatography (HPLC technique has been done. To obtain the optimal measurement results, the measurement performed several important parameters in the chromatographic system was composition of mobile phase, volume injection sample, flow rate and pH eluent. Optimum measurement conditions obtained was mobile phase composition (water : methanol with 70 : 30, volume injection sample are 5 mL, flow rate are 0.5mL/menit and pH eluent are 7. The analytical performance that obtained is good showed with the reproducibility value as percentage coefficient variance (% CV was 0.0664%, limit of detection (LOD was 0.44 ppm, with a recovery percentage of > 95%. The results obtained showed the HPLC technique can be used for the routine analysis in the determination of chlorpyrifos for the vegetable samples. Keywords: Chlorpyrifos, Vegetables, HPLC.

  4. Preparation and characterization of high density polyethylene and residual fibre of Attalea funifera Mart (piacava) composites

    International Nuclear Information System (INIS)

    Agrela, Sara P.; Guimaraes, Danilo H.; Jose, Nadia M.; Carvalho, Gleidson G.P.; Carvalho, Ricardo F.

    2009-01-01

    The use of natural fiber reinforcement thermoplastic polymer is continuously increasing. This fact is manly due to its advantages as low cost, availability, recyclability, low energy demand and then environmental appeal if compared to synthetics fibers. The composites were prepared in different fiber volume ratios (5%, 10% and 20%) mixed with high density polyethylene (HDPE) and heated at 190 deg C. Thermogravimetric analysis and differential scanning calorimetry were used to investigate thermal stability. The composites structure was characterized by Fourier Transform Infrared spectroscopy, X-ray diffractometry. Fiber and residue of piassava (Attalea funifera Mart) chemical composition were determined by Van Soest Method. The results indicate that thermo stability of the composites of HDPE prepared with fiber volume ratios up to 20% is only slightly lowered. (author)

  5. Expression and genomic analysis of midasin, a novel and highly conserved AAA protein distantly related to dynein

    Directory of Open Access Journals (Sweden)

    Gibbons I R

    2002-07-01

    Full Text Available Abstract Background The largest open reading frame in the Saccharomyces genome encodes midasin (MDN1p, YLR106p, an AAA ATPase of 560 kDa that is essential for cell viability. Orthologs of midasin have been identified in the genome projects for Drosophila, Arabidopsis, and Schizosaccharomyces pombe. Results Midasin is present as a single-copy gene encoding a well-conserved protein of ~600 kDa in all eukaryotes for which data are available. In humans, the gene maps to 6q15 and encodes a predicted protein of 5596 residues (632 kDa. Sequence alignments of midasin from humans, yeast, Giardia and Encephalitozoon indicate that its domain structure comprises an N-terminal domain (35 kDa, followed by an AAA domain containing six tandem AAA protomers (~30 kDa each, a linker domain (260 kDa, an acidic domain (~70 kDa containing 35–40% aspartate and glutamate, and a carboxy-terminal M-domain (30 kDa that possesses MIDAS sequence motifs and is homologous to the I-domain of integrins. Expression of hemagglutamin-tagged midasin in yeast demonstrates a polypeptide of the anticipated size that is localized principally in the nucleus. Conclusions The highly conserved structure of midasin in eukaryotes, taken in conjunction with its nuclear localization in yeast, suggests that midasin may function as a nuclear chaperone and be involved in the assembly/disassembly of macromolecular complexes in the nucleus. The AAA domain of midasin is evolutionarily related to that of dynein, but it appears to lack a microtubule-binding site.

  6. Constrained dansyl derivatives reveal bacterial specificity of highly conserved thymidylate synthases.

    Science.gov (United States)

    Calò, Sanuele; Tondi, Donatella; Ferrari, Stefania; Venturelli, Alberto; Ghelli, Stefano; Costi, Maria Paola

    2008-03-25

    The elucidation of the structural/functional specificities of highly conserved enzymes remains a challenging area of investigation, and enzymes involved in cellular replication are important targets for functional studies and drug discovery. Thymidylate synthase (TS, ThyA) governs the synthesis of thymidylate for use in DNA synthesis. The present study focused on Lactobacillus casei TS (LcTS) and Escherichia coli TS (EcTS), which exhibit 50 % sequence identity and strong folding similarity. We have successfully designed and validated a chemical model in which linear, but not constrained, dansyl derivatives specifically complement the LcTS active site. Conversely, chemically constrained dansyl derivatives showed up to 1000-fold improved affinity for EcTS relative to the inhibitory activity of linear derivatives. This study demonstrates that the accurate design of small ligands can uncover functional features of highly conserved enzymes.

  7. Enhancing Conservation with High Resolution Productivity Datasets for the Conterminous United States

    Science.gov (United States)

    Robinson, Nathaniel Paul

    Human driven alteration of the earth's terrestrial surface is accelerating through land use changes, intensification of human activity, climate change, and other anthropogenic pressures. These changes occur at broad spatio-temporal scales, challenging our ability to effectively monitor and assess the impacts and subsequent conservation strategies. While satellite remote sensing (SRS) products enable monitoring of the earth's terrestrial surface continuously across space and time, the practical applications for conservation and management of these products are limited. Often the processes driving ecological change occur at fine spatial resolutions and are undetectable given the resolution of available datasets. Additionally, the links between SRS data and ecologically meaningful metrics are weak. Recent advances in cloud computing technology along with the growing record of high resolution SRS data enable the development of SRS products that quantify ecologically meaningful variables at relevant scales applicable for conservation and management. The focus of my dissertation is to improve the applicability of terrestrial gross and net primary productivity (GPP/NPP) datasets for the conterminous United States (CONUS). In chapter one, I develop a framework for creating high resolution datasets of vegetation dynamics. I use the entire archive of Landsat 5, 7, and 8 surface reflectance data and a novel gap filling approach to create spatially continuous 30 m, 16-day composites of the normalized difference vegetation index (NDVI) from 1986 to 2016. In chapter two, I integrate this with other high resolution datasets and the MOD17 algorithm to create the first high resolution GPP and NPP datasets for CONUS. I demonstrate the applicability of these products for conservation and management, showing the improvements beyond currently available products. In chapter three, I utilize this dataset to evaluate the relationships between land ownership and terrestrial production

  8. Residual stress development and relief in high strength aluminium alloys using standard and retrogression thermal treatments

    OpenAIRE

    Robinson, J.S; Tanner, D.A

    2003-01-01

    peer-reviewed Residual stresses develop in the aluminium alloy 7010 when the material is quenched from the solution heat treatment temperature. Residual stress measurements have been made using the X-ray diffraction technique and a longitudinal split sawcut method to determine the magnitude of residual stress that develops in specimens sectioned from large open die forgings as a result of (a) quenching these specimens into water at different temperatures, and (b) cold water quenching from ...

  9. Derivation of residual radionuclide inventory guidelines for implace closure of high-level waste tanks

    International Nuclear Information System (INIS)

    Yuan, L.; Yuan, Y.

    1999-01-01

    Residual radionuclide inventory guidelines were derived for the high-level waste tanks at a vitrification facility. The decommissioning scenario assumed for this derivation was that the tanks were to be stabilized at the present locations and the site is released for unrestricted use following a 100-year institutional control period. It was assumed that loss of institutional control would occur at 100-years following tank closure. The derivation of the residual radionuclide inventory guidelines was based on the requirement that the effective dose equivalent (EDE) to a hypothetical individual who lives in the vicinity of the site should not exceed a dose of 0.15 mSv/yr off-site and 5 mSv/yr on-site following closure of the tanks. The RESRAD computer code, modified for exposure scenarios specific for the site, was used for this evaluation. The results of the derivation indicate that the allowable off-site dose limit will not be exceeded. The estimated potential doses to individuals using water offsite from a creek are negligibly small fractions of the 0.15 mSv/yr allowable dose limit. With an assumed 3% heel remaining in the tanks, the estimated peak dose rate for the future offsite water user is about 0.00025 mSv/yr. The residual radionuclide inventory guidelines derived based on potential doses to the on-site resident farmer indicate that, with the exception of Tc-99 and C-14, a 3% heel remaining in the tanks would not result in doses exceeding the 5 mSv/yr allowable dose limit. For this on-site exposure scenario, the peak dose rates occur at about 2000 years after tank closure. The peak dose rate is calculated to be 25 mSv/yr, with greater than 99% produced by four radionuclides: C-14, Tc-99, Np-237, and Am-241. Ingestion of contaminated vegetation contributes most (90%) of the peak dose. Since the inventories used for the derivation are mostly estimated from fuel depletion calculations. There is a need to determine further the actual inventories of these

  10. Highly conserved non-coding sequences are associated with vertebrate development.

    Directory of Open Access Journals (Sweden)

    Adam Woolfe

    2005-01-01

    Full Text Available In addition to protein coding sequence, the human genome contains a significant amount of regulatory DNA, the identification of which is proving somewhat recalcitrant to both in silico and functional methods. An approach that has been used with some success is comparative sequence analysis, whereby equivalent genomic regions from different organisms are compared in order to identify both similarities and differences. In general, similarities in sequence between highly divergent organisms imply functional constraint. We have used a whole-genome comparison between humans and the pufferfish, Fugu rubripes, to identify nearly 1,400 highly conserved non-coding sequences. Given the evolutionary divergence between these species, it is likely that these sequences are found in, and furthermore are essential to, all vertebrates. Most, and possibly all, of these sequences are located in and around genes that act as developmental regulators. Some of these sequences are over 90% identical across more than 500 bases, being more highly conserved than coding sequence between these two species. Despite this, we cannot find any similar sequences in invertebrate genomes. In order to begin to functionally test this set of sequences, we have used a rapid in vivo assay system using zebrafish embryos that allows tissue-specific enhancer activity to be identified. Functional data is presented for highly conserved non-coding sequences associated with four unrelated developmental regulators (SOX21, PAX6, HLXB9, and SHH, in order to demonstrate the suitability of this screen to a wide range of genes and expression patterns. Of 25 sequence elements tested around these four genes, 23 show significant enhancer activity in one or more tissues. We have identified a set of non-coding sequences that are highly conserved throughout vertebrates. They are found in clusters across the human genome, principally around genes that are implicated in the regulation of development

  11. High-throughput untargeted screening of veterinary drug residues and metabolites in tilapia using high resolution orbitrap mass spectrometry.

    Science.gov (United States)

    Jia, Wei; Chu, Xiaogang; Chang, James; Wang, Perry G; Chen, Ying; Zhang, Feng

    2017-03-08

    An analytical method was developed and validated for simultaneous analysis of one hundred and thirty-seven veterinary drug residues and metabolites from sixteen different classes in tilapia utilizing an improved fully non-targeted way of data acquisition with fragmentation. The automated on-line extraction procedure was achieved in a simple disposable pipet extraction. Ultrahigh-performance liquid chromatography and electrospray ionization quadrupole Orbitrap high-resolution mass spectrometry (UHPLC Q-Orbitrap) was used for the separation and detection of all the analytes. The methodology was validated by taking into consideration the guidelines specified in European SANCO/12571/2013 Guideline 2013 and Commission Decision 2002/657/EC. The extraction recoveries ranged from 81% to 111%. The limits of decision ranged from 0.01 to 2.73 μg kg -1 and the detection capabilities ranged from 0.01 to 4.73 μg kg -1 . The one hundred and thirty-seven compounds behave dynamic 0.1-500 μg kg -1 , with correlation coefficient >0.99. The fully non-targeted data acquisition way improves both sensitivity and selectivity for the fragments, which is beneficial for screening performance and identification capability. This validated method has been successfully applied on screening of veterinary drug residues and metabolites in muscle of tilapia, an important and intensively produced fish in aquaculture. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Long-term impact of reduced tillage and residue management on soil carbon stabilization: Implications for conservation agriculture on contrasting soils

    OpenAIRE

    Chivenge, P.P.; Murwira, H.K.; Giller, K.E.; Mapfumo, P.; Six, J.

    2007-01-01

    Metadata only record The long-term effects of tillage system and residue management on soil organic carbon stabilization are studied in two tropical soils in Zimbabwe, a red clay and a sandy soil. The four tillage systems evaluated were conventional tillage (CT), mulch ripping (MR), clean ripping (CR) and tied ridging (TR). Soil organic carbon (SOC) content was measured for each size fraction as well as total SOC. Based on the findings, the authors conclude that residue management - mainta...

  13. Assessing food allergy risks from residual peanut protein in highly refined vegetable oil

    NARCIS (Netherlands)

    Blom, W.M.; Kruizinga, A.G.; Rubingh, C.M.; Remington, B.C.; Crevel, R.W.R.; Houben, G.F.

    2017-01-01

    Refined vegetable oils including refined peanut oil are widely used in foods. Due to shared production processes, refined non-peanut vegetable oils can contain residual peanut proteins. We estimated the predicted number of allergic reactions to residual peanut proteins using probabilistic risk

  14. Management of high sulfur coal combustion residues, issues and practices: Proceedings

    Energy Technology Data Exchange (ETDEWEB)

    Chugh, Y.P.; Beasley, G.A. [eds.

    1994-10-01

    Papers presented at the following sessions are included in this proceedings: (1) overview topic; (2) characterization of coal combustion residues; (3) environmental impacts of residues management; (4) materials handling and utilization, Part I; and (5) materials handling and utilization, Part II. Selected paper have been processed separately for inclusion in the Energy Science and Technology Database.

  15. Functional Differentiation of Antiporter-Like Polypeptides in Complex I; a Site-Directed Mutagenesis Study of Residues Conserved in MrpA and NuoL but Not in MrpD, NuoM, and NuoN.

    Directory of Open Access Journals (Sweden)

    Eva Sperling

    Full Text Available It has long been known that the three largest subunits in the membrane domain (NuoL, NuoM and NuoN of complex I are homologous to each other, as well as to two subunits (MrpA and MrpD from a Na+/H+ antiporter, Mrp. MrpA and NuoL are more similar to each other and the same is true for MrpD and NuoN. This suggests a functional differentiation which was proven experimentally in a deletion strain model system, where NuoL could restore the loss of MrpA, but not that of MrpD and vice versa. The simplest explanation for these observations was that the MrpA and MrpD proteins are not antiporters, but rather single subunit ion channels that together form an antiporter. In this work our focus was on a set of amino acid residues in helix VIII, which are only conserved in NuoL and MrpA (but not in any of the other antiporter-like subunits. and to compare their effect on the function of these two proteins. By combining complementation studies in B. subtilis and 23Na-NMR, response of mutants to high sodium levels were tested. All of the mutants were able to cope with high salt levels; however, all but one mutation (M258I/M225I showed differences in the efficiency of cell growth and sodium efflux. Our findings showed that, although very similar in sequence, NuoL and MrpA seem to differ on the functional level. Nonetheless the studied mutations gave rise to interesting phenotypes which are of interest in complex I research.

  16. Validation of a Residual Stress Measurement Method by Swept High-Frequency Eddy Currents

    International Nuclear Information System (INIS)

    Lee, C.; Shen, Y.; Lo, C. C. H.; Nakagawa, N.

    2007-01-01

    This paper reports on a swept high-frequency eddy current (SHFEC) measurement method developed for electromagnetic nondestructive characterization of residual stresses in shot peened aerospace materials. In this approach, we regard shot-peened surfaces as modified surface layers of varying conductivity, and determine the conductivity deviation profile by inversion of the SHFEC data. The SHFEC measurement system consists of a pair of closely matched printed-circuit-board coils driven by laboratory instrument under software control. This provides improved sensitivity and high frequency performance compared to conventional coils, so that swept frequency EC measurements up to 50 MHz can be made to achieve the smallest skin depth of 80 μm for nickel-based superalloys. We devised a conductivity profile inversion procedure based on the laterally uniform multi-layer theory of Cheng, Dodd and Deeds. The main contribution of this paper is the methodology validation. Namely, the forward and inverse models were validated against measurements on artificial layer specimens consisting of metal films with different conductivities placed on a metallic substrate. The inversion determined the film conductivities which were found to agree with those measured using the direct current potential drop (DCPD) method

  17. Validation of a Residual Stress Measurement Method by Swept High-Frequency Eddy Currents

    Science.gov (United States)

    Lee, C.; Shen, Y.; Lo, C. C. H.; Nakagawa, N.

    2007-03-01

    This paper reports on a swept high-frequency eddy current (SHFEC) measurement method developed for electromagnetic nondestructive characterization of residual stresses in shot peened aerospace materials. In this approach, we regard shot-peened surfaces as modified surface layers of varying conductivity, and determine the conductivity deviation profile by inversion of the SHFEC data. The SHFEC measurement system consists of a pair of closely matched printed-circuit-board coils driven by laboratory instrument under software control. This provides improved sensitivity and high frequency performance compared to conventional coils, so that swept frequency EC measurements up to 50 MHz can be made to achieve the smallest skin depth of 80 μm for nickel-based superalloys. We devised a conductivity profile inversion procedure based on the laterally uniform multi-layer theory of Cheng, Dodd and Deeds. The main contribution of this paper is the methodology validation. Namely, the forward and inverse models were validated against measurements on artificial layer specimens consisting of metal films with different conductivities placed on a metallic substrate. The inversion determined the film conductivities which were found to agree with those measured using the direct current potential drop (DCPD) method.

  18. High-performance liquid chromatography method validation for determination of tetracycline residues in poultry meat

    Directory of Open Access Journals (Sweden)

    Vikas Gupta

    2014-01-01

    Full Text Available Background: In this study, a method for determination of tetracycline (TC residues in poultry with the help of high-performance liquid chromatography technique was validated. Materials and Methods: The principle step involved in ultrasonic-assisted extraction of TCs from poultry samples by 2 ml of 20% trichloroacetic acid and phosphate buffer (pH 4, which gave a clearer supernatant and high recovery, followed by centrifugation and purification by using 0.22 μm filter paper. Results: Validity study of the method revealed that all obtained calibration curves showed good linearity (r2 > 0.999 over the range of 40-4500 ng. Sensitivity was found to be 1.54 and 1.80 ng for oxytetracycline (OTC and TC. Accuracy was in the range of 87.94-96.20% and 72.40-79.84% for meat. Precision was lower than 10% in all cases indicating that the method can be used as a validated method. Limit of detection was found to be 4.8 and 5.10 ng for OTC and TC, respectively. The corresponding values of limit of quantitation were 11 and 12 ng. Conclusion: The method reliably identifies and quantifies the selected TC and OTC in the reconstituted poultry meat in the low and sub-nanogram range and can be applied in any laboratory.

  19. The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains

    Directory of Open Access Journals (Sweden)

    Wang Yiguo

    2008-10-01

    Full Text Available Abstract Background Many well-represented domains recognize primary sequences usually less than 10 amino acids in length, called Short Linear Motifs (SLiMs. Accurate prediction of SLiMs has been difficult because they are short (often Results Our combined approach revealed that SLiMs are highly conserved in proteins from functional classes that are known to interact with a specific domain, but that they are not conserved in most other protein groups. We found that SLiMs recognized by SH2 domains were highly conserved in receptor kinases/phosphatases, adaptor molecules, and tyrosine kinases/phosphatases, that SLiMs recognized by SH3 domains were highly conserved in cytoskeletal and cytoskeletal-associated proteins, that SLiMs recognized by PDZ domains were highly conserved in membrane proteins such as channels and receptors, and that SLiMs recognized by S/T kinase domains were highly conserved in adaptor molecules, S/T kinases/phosphatases, and proteins involved in transcription or cell cycle control. We studied Tyr-SLiMs recognized by SH2 domains in more detail, and found that SH2-recognized Tyr-SLiMs on the cytoplasmic side of membrane proteins are more highly conserved than those on the extra-cellular side. Also, we found that SH2-recognized Tyr-SLiMs that are associated with SH3 motifs and a tyrosine kinase phosphorylation motif are more highly conserved. Conclusion The interactome of protein domains is reflected by the evolutionary conservation of SLiMs recognized by these domains. Combining scoring matrixes derived from peptide libraries and conservation analysis, we would be able to find those protein groups that are more likely to interact with specific domains.

  20. Behavior of surface residual stress in explosion hardened high manganese austenitic cast steel due to repeated impact loads

    International Nuclear Information System (INIS)

    Oda, Akira; Miyagawa, Hideaki

    1985-01-01

    Explosion hardened high manganese austenitic cast steel is being tried for rail crossing recently. From the previous studies, it became clear that high tensile residual stress was generated in the hardened surface layer by explosion and microcracks were observed. In this study, therefore, the behavior of surface residual stress in explosion hardened steel due to repeated impact loads was examined and compared with those of the original and shot peened steels. The results obtained are summarized as follows: (1) In the initial stage of the repetition of impact, high tensile surface residual stress in explosion hardened steel decreased rapidly with the repetition of impact, while those of the original and shot peened steels increased rapidly. This difference was attributed to the difference in depth of the work hardened layer in three testing materials. (2) Beyond 20 impacts the residual stress of three test specimens decreased gradually, and at more than 2000 impacts the compressive stress of about 500 MPa was produced regardless of the histories of working of testing materials. (3) The linear law in the second stage of residual stress fading was applicable to this case, and the range of the linear relationship was related to the depth of the work hardened layer of testing material. (4) From the changes in half-value breadth and peak intensity of diffraction X-ray, it was supposed that a peculiar microscopic strain exists in explosion hardened steel. (author)

  1. Effects of high-speed homogenization and high-pressure homogenization on structure of tomato residue fibers.

    Science.gov (United States)

    Hua, Xiao; Xu, Shanan; Wang, Mingming; Chen, Ying; Yang, Hui; Yang, Ruijin

    2017-10-01

    Tomato residue fibers obtained after derosination and deproteinization were processed by high-speed homogenization (HSH) and high-pressure homogenization (HPH), and their effects on fiber structure was investigated, respectively. Characterizations including particle size distribution, SEM, TEM and XRD were performed. HSH could break raw fibers to small particles of around 60μm, while HPH could reshape fibers to build network structure. Microfibrils were released and their nanostructure consisting of elementary fibrils was observed by TEM. XRD patterns indicated both HSH and HPH could hardly alter the nanostructure of the fibers. Physicochemical properties including expansibility, WHC and OHC were determined. Both HSH and HPH could increase the soluble fiber content by about 8%, but HSH-HPH combined processing did not show better result. Acid (4mol/L HCl) was used in replacement of water medium and the acidic degradation of fibers could be promoted by high speed shearing or high pressure processing. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Species Richness and Community Structure on a High Latitude Reef: Implications for Conservation and Management

    Directory of Open Access Journals (Sweden)

    Wayne Houston

    2011-07-01

    Full Text Available In spite of the wealth of research on the Great Barrier Reef, few detailed biodiversity assessments of its inshore coral communities have been conducted. Effective conservation and management of marine ecosystems begins with fine-scale biophysical assessments focused on diversity and the architectural species that build the structural framework of the reef. In this study, we investigate key coral diversity and environmental attributes of an inshore reef system surrounding the Keppel Bay Islands near Rockhampton in Central Queensland, Australia, and assess their implications for conservation and management. The Keppels has much higher coral diversity than previously found. The average species richness for the 19 study sites was ~40 with representatives from 68% of the ~244 species previously described for the southern Great Barrier Reef. Using scleractinian coral species richness, taxonomic distinctiveness and coral cover as the main criteria, we found that five out of 19 sites had particularly high conservation value. A further site was also considered to be of relatively high value. Corals at this site were taxonomically distinct from the others (representatives of two families were found here but not at other sites and a wide range of functionally diverse taxa were present. This site was associated with more stressful conditions such as high temperatures and turbidity. Highly diverse coral communities or biodiversity ‘hotspots’ and taxonomically distinct reefs may act as insurance policies for climatic disturbance, much like Noah’s Arks for reefs. While improving water quality and limiting anthropogenic impacts are clearly important management initiatives to improve the long-term outlook for inshore reefs, identifying, mapping and protecting these coastal ‘refugia’ may be the key for ensuring their regeneration against catastrophic climatic disturbance in the meantime.

  3. Identification of an evolutionarily conserved extracellular threonine residue critical for surface expression and its potential coupling of adjacent voltage-sensing and gating domains in voltage-gated potassium channels.

    Science.gov (United States)

    Mckeown, Lynn; Burnham, Matthew P; Hodson, Charlotte; Jones, Owen T

    2008-10-31

    The dynamic expression of voltage-gated potassium channels (Kvs) at the cell surface is a fundamental factor controlling membrane excitability. In exploring possible mechanisms controlling Kv surface expression, we identified a region in the extracellular linker between the first and second of the six (S1-S6) transmembrane-spanning domains of the Kv1.4 channel, which we hypothesized to be critical for its biogenesis. Using immunofluorescence microscopy, flow cytometry, patch clamp electrophysiology, and mutagenesis, we identified a single threonine residue at position 330 within the Kv1.4 S1-S2 linker that is absolutely required for cell surface expression. Mutation of Thr-330 to an alanine, aspartate, or lysine prevented surface expression. However, surface expression occurred upon co-expression of mutant and wild type Kv1.4 subunits or mutation of Thr-330 to a serine. Mutation of the corresponding residue (Thr-211) in Kv3.1 to alanine also caused intracellular retention, suggesting that the conserved threonine plays a generalized role in surface expression. In support of this idea, sequence comparisons showed conservation of the critical threonine in all Kv families and in organisms across the evolutionary spectrum. Based upon the Kv1.2 crystal structure, further mutagenesis, and the partial restoration of surface expression in an electrostatic T330K bridging mutant, we suggest that Thr-330 hydrogen bonds to equally conserved outer pore residues, which may include a glutamate at position 502 that is also critical for surface expression. We propose that Thr-330 serves to interlock the voltage-sensing and gating domains of adjacent monomers, thereby yielding a structure competent for the surface expression of functional tetramers.

  4. Impact of local empowerment on conservation practices in a highly developed country

    OpenAIRE

    Engen, Sigrid; Hausner, Vera Helene

    2017-01-01

    Source at http://dx.doi.org/10.1111/conl.12369 Community-based conservation, where local decision makers are responsible for balancing conservation and development, is often preferred to exclusion- ary conservation that prioritizes use-limitation through strict regulation. Un- raveling the evidence for conservation impact of different governance regimes is challenging. Focusing on conservation practices before and after a reform can provide an early indication of behaviora...

  5. Toward High Carrier Mobility and Low Contact Resistance:Laser Cleaning of PMMA Residues on Graphene Surfaces

    Institute of Scientific and Technical Information of China (English)

    Yuehui Jia; Xin Gong; Pei Peng; Zidong Wang; Zhongzheng Tian; Liming Ren; Yunyi Fu; Han Zhang

    2016-01-01

    Poly(methyl methacrylate)(PMMA) is widely used for graphene transfer and device fabrication.However,it inevitably leaves a thin layer of polymer residues after acetone rinsing and leads to dramatic degradation of device performance.How to eliminate contamination and restore clean surfaces of graphene is still highly demanded.In this paper,we present a reliable and position-controllable method to remove the polymer residues on graphene films by laser exposure.Under proper laser conditions,PMMA residues can be substantially reduced without introducing defects to the underlying graphene.Furthermore,by applying this laser cleaning technique to the channel and contacts of graphene fieldeffect transistors(GFETs),higher carrier mobility as well as lower contact resistance can be realized.This work opens a way for probing intrinsic properties of contaminant-free graphene and fabricating high-performance GFETs with both clean channel and intimate graphene/metal contact.

  6. [Determination of emamectin benzoate residue in vegetables by high performance liquid chromatography with fluorescence detection].

    Science.gov (United States)

    Zhang, Yan; Wu, Yinliang; Hu, Jiye; Wang, Hongwei; Pan, Canping; Liu, Fengmao

    2008-01-01

    A method was developed for the determination of emamectin benzoate residue in cabbage and mushroom using solid-phase extraction (SPE) and high performance liquid chromatography (HPLC) with fluorescence detection. The sample was extracted with ethyl acetate. Further cleanup was performed on a propylsulfonic acid solid phase extraction cartridge, followed by the derivatization with trifluoroacetic anhydride in the presence of N-methylimidazole. The amount of derivatized emamectin benzoate was determined by fluorescence detector after separation by HPLC. The detection limit was 0.10 microg/kg for cabbage and mushroom samples. The recoveries of emamectin benzoate in cabbage and mushroom samples were 78.6%-84.9%. The inter-day relative standard deviation (RSD) and intra-day RSD were 2.7%-6.0% and 3.1%-8.9%, respectively, at the fortified levels of 1.0-20.0 microg/kg. The calibration curve of emamectin benzoate in vegetables at the concentration range of 0.002 mg/L to 0.10 mg/L was linear (r = 0.9999).

  7. Simulation of distortion and residual stress in high pressure die casting – modelling and experiments

    International Nuclear Information System (INIS)

    Hofer, P; Kaschnitz, E; Schumacher, P

    2012-01-01

    Two individual high-pressure die-casting geometries were developed in order to study the influence of process parameters and different alloys on the distortion behaviour of castings. These geometries were a stress lattice and a V-shaped sample tending to form residual stress due to different wall thickness respectively by a deliberate massive gating system. In the experimental castings the influence of the most important process parameters such as die temperature and die opening time and the cooling regime was examined. The time evolution of process temperatures was measured using thermal imaging. The heat transfer coefficients were adapted to the observed temperature distributions. Castings were produced from the two alloys AlSi12 and AlSi10MnMg. The distortion of the castings was measured by means of a tactile measuring device. For the alloy AlSi10MnMg thermo-physical and thermo-mechanical data were obtained using differential scanning calorimetry, laser flash technique, dilatometry and tensile testing at elevated temperatures. These data were used for modelling the material behaviour of the AlSi10MnMg alloy in the numerical model while for the alloy AlSi12(Fe) literature data were used. Process and stress simulation were conducted using the commercial FEM software ANSYS Workbench. A survey on the results of the comparison between simulation and experiment is given for both alloys.

  8. Use of ancient sedimentary DNA as a novel conservation tool for high-altitude tropical biodiversity.

    Science.gov (United States)

    Boessenkool, Sanne; McGlynn, Gayle; Epp, Laura S; Taylor, David; Pimentel, Manuel; Gizaw, Abel; Nemomissa, Sileshi; Brochmann, Christian; Popp, Magnus

    2014-04-01

    Conservation of biodiversity may in the future increasingly depend upon the availability of scientific information to set suitable restoration targets. In traditional paleoecology, sediment-based pollen provides a means to define preanthropogenic impact conditions, but problems in establishing the exact provenance and ecologically meaningful levels of taxonomic resolution of the evidence are limiting. We explored the extent to which the use of sedimentary ancient DNA (sedaDNA) may complement pollen data in reconstructing past alpine environments in the tropics. We constructed a record of afro-alpine plants retrieved from DNA preserved in sediment cores from 2 volcanic crater sites in the Albertine Rift, eastern Africa. The record extended well beyond the onset of substantial anthropogenic effects on tropical mountains. To ensure high-quality taxonomic inference from the sedaDNA sequences, we built an extensive DNA reference library covering the majority of the afro-alpine flora, by sequencing DNA from taxonomically verified specimens. Comparisons with pollen records from the same sediment cores showed that plant diversity recovered with sedaDNA improved vegetation reconstructions based on pollen records by revealing both additional taxa and providing increased taxonomic resolution. Furthermore, combining the 2 measures assisted in distinguishing vegetation change at different geographic scales; sedaDNA almost exclusively reflects local vegetation, whereas pollen can potentially originate from a wide area that in highlands in particular can span several ecozones. Our results suggest that sedaDNA may provide information on restoration targets and the nature and magnitude of human-induced environmental changes, including in high conservation priority, biodiversity hotspots, where understanding of preanthropogenic impact (or reference) conditions is highly limited. © 2013 Society for Conservation Biology.

  9. Low-Intensity Agricultural Landscapes in Transylvania Support High Butterfly Diversity: Implications for Conservation

    Science.gov (United States)

    Loos, Jacqueline; Dorresteijn, Ine; Hanspach, Jan; Fust, Pascal; Rakosy, László; Fischer, Joern

    2014-01-01

    European farmland biodiversity is declining due to land use changes towards agricultural intensification or abandonment. Some Eastern European farming systems have sustained traditional forms of use, resulting in high levels of biodiversity. However, global markets and international policies now imply rapid and major changes to these systems. To effectively protect farmland biodiversity, understanding landscape features which underpin species diversity is crucial. Focusing on butterflies, we addressed this question for a cultural-historic landscape in Southern Transylvania, Romania. Following a natural experiment, we randomly selected 120 survey sites in farmland, 60 each in grassland and arable land. We surveyed butterfly species richness and abundance by walking transects with four repeats in summer 2012. We analysed species composition using Detrended Correspondence Analysis. We modelled species richness, richness of functional groups, and abundance of selected species in response to topography, woody vegetation cover and heterogeneity at three spatial scales, using generalised linear mixed effects models. Species composition widely overlapped in grassland and arable land. Composition changed along gradients of heterogeneity at local and context scales, and of woody vegetation cover at context and landscape scales. The effect of local heterogeneity on species richness was positive in arable land, but negative in grassland. Plant species richness, and structural and topographic conditions at multiple scales explained species richness, richness of functional groups and species abundances. Our study revealed high conservation value of both grassland and arable land in low-intensity Eastern European farmland. Besides grassland, also heterogeneous arable land provides important habitat for butterflies. While butterfly diversity in arable land benefits from heterogeneity by small-scale structures, grasslands should be protected from fragmentation to provide

  10. High-order conservative discretizations for some cases of the rigid body motion

    International Nuclear Information System (INIS)

    Kozlov, Roman

    2008-01-01

    Modified vector fields can be used to construct high-order structure-preserving numerical integrators for ordinary differential equations. In the present Letter we consider high-order integrators based on the implicit midpoint rule, which conserve quadratic first integrals. It is shown that these integrators are particularly suitable for the rigid body motion with an additional quadratic first integral. In this case high-order integrators preserve all four first integrals of motion. The approach is illustrated on the Lagrange top (a rotationally symmetric rigid body with a fixed point on the symmetry axis). The equations of motion are considered in the space fixed frame because in this frame Lagrange top admits a neat description. The Lagrange top motion includes the spherical pendulum and the planar pendulum, which swings in a vertical plane, as particular cases

  11. Probabilistic residual life assessment of high temperature pipings in nuclear power plants against creep fatigue damage: final report

    International Nuclear Information System (INIS)

    Gupta, Sanjay

    2014-02-01

    Residual life assessment of components of nuclear power plants is essential for their operational safety, reliability and financial viability. The high risks involved in the event of failures in nuclear power plants have led to the development of design philosophies that incorporate extreme conservatism in design. The implications of such conservatism in design leads to more frequent maintenance operations than necessary

  12. High-throughput mosquito and fly bioassay system for natural and artificial substrates treated with residual insecticides.

    Science.gov (United States)

    Aldridge, Robert L; Wynn, W Wayne; Britch, Seth C; Allan, Sandra A; Walker, Todd W; Geden, Christopher J; Hogsette, Jerome A; Linthicum, Kenneth J

    2013-03-01

    A high-throughput bioassay system to evaluate the efficacy of residual pesticides against mosquitoes and muscid flies with minimal insect handling was developed. The system consisted of 4 components made of readily available materials: 1) a CO2 anaesthetizing chamber, 2) a specialized aspirator, 3) a cylindrical flat-bottomed glass bioassay chamber assembly, and 4) a customized rack.

  13. Inversion tillage, high residue covers, and different herbicide regimes for palmer amaranth control in liberty link systems

    Science.gov (United States)

    Glyphosate-resistant Palmer amaranth is adversely affecting cotton production in the Southeast US. A field experiment was established in fall 2008 at the E.V. Smith Research Center, Field Crops Unit near Shorter, AL, to investigate the role of inversion tillage, high residue cover crops, and differ...

  14. High energy x-ray synchrotron radiation analysis of residual stress distribution of shot-peened steels

    International Nuclear Information System (INIS)

    Tanaka, Keisuke; Akiniwa, Yoshiaki; Kimachi, Hirohisa; Suzuki, Kenji; Yanase, Etsuya; Nishio, Kouji; Kusumi, Yukihiro

    2001-01-01

    A high energy X-ray beam from synchrotron radiation source SPring-8 was used to determine the residual stress distribution beneath the shot-peened surface of carbon steel plates. By using the monochromatic X-ray beam with an energy of 72 keV, the relation between 2θ and sin 2 ψ was obtained by the side-inclination method upto sin 2 ψ = 0.9. The distribution of the residual stress was determined from the non-linearity of the relation between 2θ and sin 2 ψ. (author)

  15. Simultaneous determination of nitrite and nitrate residues in meat products marketed in Shiraz by high performance liquid chromatography

    Directory of Open Access Journals (Sweden)

    H Golkari

    2012-08-01

    Full Text Available Nitrite and nitrate are the key ingredients and play a multifunctional role in meat curing technology. Despite all of their desirable effects, the addition of nitrite to meat is the major cause of carcinogenic N-nitrosamines formation. In this study, the amount of residual nitrite and nitrate in meat products containing 61% to 80% meat were assessed. The samples were obtained at the fourth day of their production from Shiraz retails and analyzed using high performance liquid chromatography (HPLC. According to the results, the mean concentrations of residual nitrite and nitrate were estimated at 36.96 ± 7.38 and 85.81 ± 5.5 mg/kg in small-diameter (1.5-2 cm sausages. Meanwhile, in large-diameter (5.5-8 cm sausages the residues were estimated at 20.97 ± 3.28 and 124.85±5.3 mg/kg, respectively. In all analyzed samples, the residual nitrite level was found below the permitted level of 120 mg/kg which indicated the application of allowed concentrations of nitrite in such products. The mean values of residual nitrite and nitrate concentrations were statistically different (p

  16. Analysis of Corrosion Residues Collected from the Aluminum Basket Rails of the High-Burnup Demonstration Cask.

    Energy Technology Data Exchange (ETDEWEB)

    Bryan, Charles R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-03-01

    On September, 2015, an inspection was performed on the TN-32B cask that will be used for the high-burnup demonstration project. During the survey, wooden cribbing that had been placed within the cask eleven years earlier to prevent shifting of the basket during transport was removed, revealing two areas of residue on the aluminum basket rails, where they had contacted the cribbing. The residue appeared to be a corrosion product, and concerns were raised that similar attack could exist at more difficult-to-inspect locations in the canister. Accordingly, when the canister was reopened, samples of the residue were collected for analysis. This report presents the results of that assessment, which determined that the corrosion was due to the presence of the cribbing. The corrosion was associated with fungal material, and fungal activity likely contributed to an aggressive chemical environment. Once the cask has been cleaned, there will be no risk of further corrosion.

  17. Traveling waves and conservation laws for highly nonlinear wave equations modeling Hertz chains

    Science.gov (United States)

    Przedborski, Michelle; Anco, Stephen C.

    2017-09-01

    A highly nonlinear, fourth-order wave equation that models the continuum theory of long wavelength pulses in weakly compressed, homogeneous, discrete chains with a general power-law contact interaction is studied. For this wave equation, all solitary wave solutions and all nonlinear periodic wave solutions, along with all conservation laws, are derived. The solutions are explicitly parameterized in terms of the asymptotic value of the wave amplitude in the case of solitary waves and the peak of the wave amplitude in the case of nonlinear periodic waves. All cases in which the solution expressions can be stated in an explicit analytic form using elementary functions are worked out. In these cases, explicit expressions for the total energy and total momentum for all solutions are obtained as well. The derivation of the solutions uses the conservation laws combined with an energy analysis argument to reduce the wave equation directly to a separable first-order differential equation that determines the wave amplitude in terms of the traveling wave variable. This method can be applied more generally to other highly nonlinear wave equations.

  18. Can conservation agriculture improve phosphorus (P) availability in weathered soils? Effects of tillage and residue management on soil P status after 9 years in a Kenyan Oxisol

    NARCIS (Netherlands)

    Margenot, Andrew; Paul, B.K.; Pulleman, M.M.; Parikh, Sanjai; Fonte, Steven J.

    2017-01-01

    The widespread promotion of conservation agriculture (CA) in regions with weathered soils prone to phosphorus (P) deficiency merits explicit consideration of its effect on P availability. A long-term CA field trial located on an acid, weathered soil in western Kenya was evaluated for effects of

  19. Spalling behavior and residual resistance of fibre reinforced Ultra-High performance concrete after exposure to high temperatures

    Directory of Open Access Journals (Sweden)

    Xiong, Ming-Xiang

    2015-12-01

    Full Text Available Experimental results of spalling and residual mechanical properties of ultra-high performance concrete after exposure to high temperatures are presented in this paper. The compressive strength of the ultra-high performance concrete ranged from 160 MPa~185 MPa. This study aimed to discover the effective way to prevent spalling for the ultra-high performance concrete and gauge its mechanical properties after it was subjected to fire. The effects of fiber type, fiber dosage, heating rate and curing condition were investigated. Test results showed that the compressive strength and elastic modulus of the ultra-high performance concrete declined slower than those of normal strength concrete after elevated temperatures. Polypropylene fiber rather than steel fiber was found effective to prevent spalling but affected workability. The effective fiber type and dosage were recommended to prevent spalling and ensure sufficient workability for casting and pumping of the ultra-high performance concrete.En este trabajo se presentan los resultados más relevantes del trabajo experimental realizado para valorar la laminación y las propiedades mecánicas residuales de hormigón de ultra-altas prestaciones tras su exposición a altas temperaturas. La resistencia a la compresión del hormigón de ultra-altas prestaciones osciló entre 160 MPa~185 MPa. El objetivo de este estudio fue descubrir una manera eficaz de prevenir desprendimientos y/o laminaciones en este hormigón y medir sus propiedades mecánicas después de ser sometido al fuego. Las variables estudiadas fueron la presencia y dosificación de fibras, velocidad de calentamiento y condiciones de curado. Los resultados mostraron, tras la exposición a altas temperaturas, que la resistencia a compresión y el módulo de elasticidad del hormigón de ultra-altas prestaciones disminuían más lento que las de un hormigón con resistencia normal. La fibra de polipropileno resultó más eficaz para prevenir

  20. Determining the drivers of population structure in a highly urbanized landscape to inform conservation planning.

    Science.gov (United States)

    Thomassen, Henri A; Harrigan, Ryan J; Semple Delaney, Kathleen; Riley, Seth P D; Serieys, Laurel E K; Pease, Katherine; Wayne, Robert K; Smith, Thomas B

    2018-02-01

    Understanding the environmental contributors to population structure is of paramount importance for conservation in urbanized environments. We used spatially explicit models to determine genetic population structure under current and future environmental conditions across a highly fragmented, human-dominated environment in Southern California to assess the effects of natural ecological variation and urbanization. We focused on 7 common species with diverse habitat requirements, home-range sizes, and dispersal abilities. We quantified the relative roles of potential barriers, including natural environmental characteristics and an anthropogenic barrier created by a major highway, in shaping genetic variation. The ability to predict genetic variation in our models differed among species: 11-81% of intraspecific genetic variation was explained by environmental variables. Although an anthropogenically induced barrier (a major highway) severely restricted gene flow and movement at broad scales for some species, genetic variation seemed to be primarily driven by natural environmental heterogeneity at a local level. Our results show how assessing environmentally associated variation for multiple species under current and future climate conditions can help identify priority regions for maximizing population persistence under environmental change in urbanized regions. © 2017 Society for Conservation Biology.

  1. Solid phase microextraction sampling of high explosive residues in the presence of radionuclides and radionuclide surrogate metals

    International Nuclear Information System (INIS)

    Duff, M.C.; Crump, S.L.; Ray, R.J.; Beals, D.; Cotham, W.E.; Mount, K.; Koons, R.D.; Leggitt, J.

    2008-01-01

    The Federal Bureau of Investigation (FBI) Laboratory currently does not have on site facilities for handling radioactive evidentiary materials and there are no established FBI methods or procedures for decontaminating high explosive (HE) evidence while maintaining evidentiary value. One experimental method for the isolation of HE residue involves using solid phase microextraction (SPME) fibers to remove residue of interest. Due to their high affinity for organics, SPME fibers should have little affinity for most metals. However, no studies have measured the affinity of radionuclides for SPME fibers. The focus of this research was to examine the affinity of dissolved radionuclide ( 239/240 Pu, 238 U, 237 Np, 85 Sr, 133 Ba, 137 Cs, 60 Co and 226 Ra) and stable radionuclide surrogate metals (Sr, Co, Ir, Re, Ni, Ba, Cs, Nb, Ru, and Nd) for SPME fibers at the exposure conditions that favor the uptake of HE residues. Our results from radiochemical and mass spectrometric analyses indicate these metals have little measurable affinity for these SPME fibers during conditions that are conducive to HE residue uptake with subsequent analysis by liquid or gas phase chromatography with mass spectrometric detection. (author)

  2. CT colonography in a Korean population with a high residue diet: Comparison between wet and dry preparations

    International Nuclear Information System (INIS)

    Kim, S.H.; Choi, B.I.; Han, J.K.; Lee, J.M.; Eun, H.W.; Lee, J.Y.; Lee, K.H.; Han, C.J.; Choi, Y.H.; Shin, K.-S.

    2006-01-01

    AIM: To compare wet and dry preparation methods for computed tomography colonography (CTC) in terms of preparation quality, interpretation time, and diagnostic performance for polyp detection in a population with a high residue diet. MATERIALS AND METHODS: Eighty-six patients were divided into two groups. Group 1 (n=24) received a wet preparation of 4 l polyethylene glycol (PEG) solution, and group 2 (n=62) received a dry preparation of phosphor-soda. Abnormal findings, including polyps, and the time required to interpret the CTC images in both groups were documented by a radiologist. CTC findings were compared to those of colonoscopy as a reference standard. Two radiologists evaluated the quality of CTC with regard to residual fluid, faeces, and colonic distension using a four-point scale in consensus. Statistical differences for residual fluid, faeces, distensibility on CTC, and interpretation time between the two groups were analysed. The diagnostic performance of CTC in both groups was also compared. RESULTS: One-hundred and ninety polyps in 70 patients were identified using colonoscopy. Regarding the quality of images produced the wet preparation was significantly better than the dry preparation (p 0.05). CONCLUSION: In a population with a high-residue diet, CTC with wet preparation can be interpreted in a time-efficient manner and is comparable with CTC with dry preparation

  3. An assessment of high carbon stock and high conservation value approaches to sustainable oil palm cultivation in Gabon

    Science.gov (United States)

    Austin, Kemen G.; Lee, Michelle E.; Clark, Connie; Forester, Brenna R.; Urban, Dean L.; White, Lee; Kasibhatla, Prasad S.; Poulsen, John R.

    2017-01-01

    Industrial-scale oil palm cultivation is rapidly expanding in Gabon, where it has the potential to drive economic growth, but also threatens forest, biodiversity and carbon resources. The Gabonese government is promoting an ambitious agricultural expansion strategy, while simultaneously committing to minimize negative environmental impacts of oil palm agriculture. This study estimates the extent and location of suitable land for oil palm cultivation in Gabon, based on an analysis of recent trends in plantation permitting. We use the resulting suitability map to evaluate two proposed approaches to minimizing negative environmental impacts: a High Carbon Stock (HCS) approach, which emphasizes forest protection and climate change mitigation, and a High Conservation Value (HCV) approach, which focuses on safeguarding biodiversity and ecosystems. We quantify the forest area, carbon stock, and biodiversity resources protected under each approach, using newly developed maps of priority species distributions and forest biomass for Gabon. We find 2.7-3.9 Mha of suitable or moderately suitable land that avoid HCS areas, 4.4 million hectares (Mha) that avoid HCV areas, and 1.2-1.7 Mha that avoid both. This suggests that Gabon’s oil palm production target could likely be met without compromising important ecosystem services, if appropriate safeguards are put in place. Our analysis improves understanding of suitability for oil palm in Gabon, determines how conservation strategies align with national targets for oil palm production, and informs national land use planning.

  4. Identification of a highly reactive threonine residue at the active site of γ-glutamyl transpeptidase

    International Nuclear Information System (INIS)

    Stole, E.; Seddon, A.P.; Wellner, D.; Meister, A.

    1990-01-01

    γ-Glutamyl transpeptidase an enzyme of major importance in glutathione metabolism, was inactivated by treating it with L-(αS,5S)-α-amino-3-chloro-4,5-dihydro-5-[3- 14 C]isoxazoleacetic acid. This selective reagent binds stoichiometrically to the enzyme; more than 90% of the label was bound to its light subunit. Enzymatic digestion of the light subunit gave a 14 C-labeled peptide that corresponds to amino acid residues 517-527 of the enzyme and two incomplete digestion products that contain this labeled peptide moiety. The radioactivity associated with this peptide was released with threonine-523 during sequencing by the automated gas-phase Edman method. The light subunit contains 14 other threonine residues and a total of 19 serine residues; these were not labeled. Threonine-523 is situated in the enzyme in an environment that greatly increases its reactivity, indicating that other amino acid residues of the enzyme must also participate in the active-site chemistry of the enzyme

  5. RESIDUAL OPERATIONAL RESOURCE ASSESSMENT OF HIGH TEMPERATURE ELEMENTS OF POWER ENGINEERING EQUIPMENT

    Directory of Open Access Journals (Sweden)

    S. E. Khoroshilov

    2014-01-01

    Full Text Available The paper proposes a specific assessment of heat resistant steel residual resource which  is  based  on  time determination of pore output on grain boundary with due account of an operational temperature, chemical composition and structure of the investigated steel.

  6. Making conservation work for everyone

    Energy Technology Data Exchange (ETDEWEB)

    Wiersma, J. [Veridian Corp., Ajax, ON (Canada)

    2004-07-01

    This presentation discussed the economic value of conservation, the optimal deployment of energy conservation. A sample load profile was presented to demonstrate how much electricity the average residential customer uses on a summer day. The average customer does not have the tools to understand the financial consequences of conservation for different types of equipment at different times of the day. Smart metering technology could help in this regard. Accurate unsubsidized prices are also considered to be the best incentive to conserve because customers will reduce electricity use when the prices are high. It was also suggested that standards for new appliances should be increased effectively to their economic value. The enablers to energy conservation include solid consumer education programs, real time metering in places where it is cost effective, real time pricing in places where it is practical, and power rates that reflect real costs. Barriers to energy conservation include the residual economic advantage that may be insufficient to justify investment; support from local distribution companies and transmission companies if the lost revenue adjustment mechanism (LRAM) is not sufficient to recover lost revenue and if LDCs are not sufficiently involved in the design of the electricity conservation program. 7 figs.

  7. Data on electrical energy conservation using high efficiency motors for the confidence bounds using statistical techniques.

    Science.gov (United States)

    Shaikh, Muhammad Mujtaba; Memon, Abdul Jabbar; Hussain, Manzoor

    2016-09-01

    In this article, we describe details of the data used in the research paper "Confidence bounds for energy conservation in electric motors: An economical solution using statistical techniques" [1]. The data presented in this paper is intended to show benefits of high efficiency electric motors over the standard efficiency motors of similar rating in the industrial sector of Pakistan. We explain how the data was collected and then processed by means of formulas to show cost effectiveness of energy efficient motors in terms of three important parameters: annual energy saving, cost saving and payback periods. This data can be further used to construct confidence bounds for the parameters using statistical techniques as described in [1].

  8. Comparative transcriptome analysis within the Lolium/Festuca species complex reveals high sequence conservation

    DEFF Research Database (Denmark)

    Czaban, Adrian; Sharma, Sapna; Byrne, Stephen

    2015-01-01

    species from the Lolium-Festuca complex, ranging from 52,166 to 72,133 transcripts per assembly. We have also predicted a set of proteins and validated it with a high-confidence protein database from three closely related species (H. vulgare, B. distachyon and O. sativa). We have obtained gene family...... clusters for the four species using OrthoMCL and analyzed their inferred phylogenetic relationships. Our results indicate that VRN2 is a candidate gene for differentiating vernalization and non-vernalization types in the Lolium-Festuca complex. Grouping of the gene families based on their BLAST identity...... enabled us to divide ortholog groups into those that are very conserved and those that are more evolutionarily relaxed. The ratio of the non-synonumous to synonymous substitutions enabled us to pinpoint protein sequences evolving in response to positive selection. These proteins may explain some...

  9. Cortical cytasters: a highly conserved developmental trait of Bilateria with similarities to Ctenophora

    Directory of Open Access Journals (Sweden)

    Salinas-Saavedra Miguel

    2011-12-01

    Full Text Available Abstract Background Cytasters (cytoplasmic asters are centriole-based nucleation centers of microtubule polymerization that are observable in large numbers in the cortical cytoplasm of the egg and zygote of bilaterian organisms. In both protostome and deuterostome taxa, cytasters have been described to develop during oogenesis from vesicles of nuclear membrane that move to the cortical cytoplasm. They become associated with several cytoplasmic components, and participate in the reorganization of cortical cytoplasm after fertilization, patterning the antero-posterior and dorso-ventral body axes. Presentation of the hypothesis The specific resemblances in the development of cytasters in both protostome and deuterostome taxa suggest that an independent evolutionary origin is unlikely. An assessment of published data confirms that cytasters are present in several protostome and deuterostome phyla, but are absent in the non-bilaterian phyla Cnidaria and Ctenophora. We hypothesize that cytasters evolved in the lineage leading to Bilateria and were already present in the most recent common ancestor shared by protostomes and deuterostomes. Thus, cytasters would be an ancient and highly conserved trait that is homologous across the different bilaterian phyla. The alternative possibility is homoplasy, that is cytasters have evolved independently in different lineages of Bilateria. Testing the hypothesis So far, available published information shows that appropriate observations have been made in eight different bilaterian phyla. All of them present cytasters. This is consistent with the hypothesis of homology and conservation. However, there are several important groups for which there are no currently available data. The hypothesis of homology predicts that cytasters should be present in these groups. Increasing the taxonomic sample using modern techniques uniformly will test for evolutionary patterns supporting homology, homoplasy, or secondary loss of

  10. CpG methylation differences between neurons and glia are highly conserved from mouse to human.

    Science.gov (United States)

    Kessler, Noah J; Van Baak, Timothy E; Baker, Maria S; Laritsky, Eleonora; Coarfa, Cristian; Waterland, Robert A

    2016-01-15

    Understanding epigenetic differences that distinguish neurons and glia is of fundamental importance to the nascent field of neuroepigenetics. A recent study used genome-wide bisulfite sequencing to survey differences in DNA methylation between these two cell types, in both humans and mice. That study minimized the importance of cell type-specific differences in CpG methylation, claiming these are restricted to localized genomic regions, and instead emphasized that widespread and highly conserved differences in non-CpG methylation distinguish neurons and glia. We reanalyzed the data from that study and came to markedly different conclusions. In particular, we found widespread cell type-specific differences in CpG methylation, with a genome-wide tendency for neuronal CpG-hypermethylation punctuated by regions of glia-specific hypermethylation. Alarmingly, our analysis indicated that the majority of genes identified by the primary study as exhibiting cell type-specific CpG methylation differences were misclassified. To verify the accuracy of our analysis, we isolated neuronal and glial DNA from mouse cortex and performed quantitative bisulfite pyrosequencing at nine loci. The pyrosequencing results corroborated our analysis, without exception. Most interestingly, we found that gene-associated neuron vs. glia CpG methylation differences are highly conserved across human and mouse, and are very likely to be functional. In addition to underscoring the importance of independent verification to confirm the conclusions of genome-wide epigenetic analyses, our data indicate that CpG methylation plays a major role in neuroepigenetics, and that the mouse is likely an excellent model in which to study the role of DNA methylation in human neurodevelopment and disease. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  11. Evolutionary conservation of essential and highly expressed genes in Pseudomonas aeruginosa

    Directory of Open Access Journals (Sweden)

    Scharfe Maren

    2010-04-01

    Full Text Available Abstract Background The constant increase in development and spread of bacterial resistance to antibiotics poses a serious threat to human health. New sequencing technologies are now on the horizon that will yield massive increases in our capacity for DNA sequencing and will revolutionize the drug discovery process. Since essential genes are promising novel antibiotic targets, the prediction of gene essentiality based on genomic information has become a major focus. Results In this study we demonstrate that pooled sequencing is applicable for the analysis of sequence variations of strain collections with more than 10 individual isolates. Pooled sequencing of 36 clinical Pseudomonas aeruginosa isolates revealed that essential and highly expressed proteins evolve at lower rates, whereas extracellular proteins evolve at higher rates. We furthermore refined the list of experimentally essential P. aeruginosa genes, and identified 980 genes that show no sequence variation at all. Among the conserved nonessential genes we found several that are involved in regulation, motility and virulence, indicating that they represent factors of evolutionary importance for the lifestyle of a successful environmental bacterium and opportunistic pathogen. Conclusion The detailed analysis of a comprehensive set of P. aeruginosa genomes in this study clearly disclosed detailed information of the genomic makeup and revealed a large set of highly conserved genes that play an important role for the lifestyle of this microorganism. Sequencing strain collections enables for a detailed and extensive identification of sequence variations as potential bacterial adaptation processes, e.g., during the development of antibiotic resistance in the clinical setting and thus may be the basis to uncover putative targets for novel treatment strategies.

  12. A guide to calculating habitat-quality metrics to inform conservation of highly mobile species

    Science.gov (United States)

    Bieri, Joanna A.; Sample, Christine; Thogmartin, Wayne E.; Diffendorfer, James E.; Earl, Julia E.; Erickson, Richard A.; Federico, Paula; Flockhart, D. T. Tyler; Nicol, Sam; Semmens, Darius J.; Skraber, T.; Wiederholt, Ruscena; Mattsson, Brady J.

    2018-01-01

    Many metrics exist for quantifying the relative value of habitats and pathways used by highly mobile species. Properly selecting and applying such metrics requires substantial background in mathematics and understanding the relevant management arena. To address this multidimensional challenge, we demonstrate and compare three measurements of habitat quality: graph-, occupancy-, and demographic-based metrics. Each metric provides insights into system dynamics, at the expense of increasing amounts and complexity of data and models. Our descriptions and comparisons of diverse habitat-quality metrics provide means for practitioners to overcome the modeling challenges associated with management or conservation of such highly mobile species. Whereas previous guidance for applying habitat-quality metrics has been scattered in diversified tracks of literature, we have brought this information together into an approachable format including accessible descriptions and a modeling case study for a typical example that conservation professionals can adapt for their own decision contexts and focal populations.Considerations for Resource ManagersManagement objectives, proposed actions, data availability and quality, and model assumptions are all relevant considerations when applying and interpreting habitat-quality metrics.Graph-based metrics answer questions related to habitat centrality and connectivity, are suitable for populations with any movement pattern, quantify basic spatial and temporal patterns of occupancy and movement, and require the least data.Occupancy-based metrics answer questions about likelihood of persistence or colonization, are suitable for populations that undergo localized extinctions, quantify spatial and temporal patterns of occupancy and movement, and require a moderate amount of data.Demographic-based metrics answer questions about relative or absolute population size, are suitable for populations with any movement pattern, quantify demographic

  13. Habitat Re-Creation (Ecological Restoration) as a Strategy for Conserving Insect Communities in Highly Fragmented Landscapes.

    Science.gov (United States)

    Shuey, John A

    2013-12-05

    Because of their vast diversity, measured by both numbers of species as well as life history traits, insects defy comprehensive conservation planning. Thus, almost all insect conservation efforts target individual species. However, serious insect conservation requires goals that are set at the faunal level and conservation success requires strategies that conserve intact communities. This task is complicated in agricultural landscapes by high levels of habitat fragmentation and isolation. In many regions, once widespread insect communities are now functionally trapped on islands of ecosystem remnants and subject to a variety of stressors associated with isolation, small population sizes and artificial population fragmentation. In fragmented landscapes ecological restoration can be an effective strategy for reducing localized insect extinction rates, but insects are seldom included in restoration design criteria. It is possible to incorporate a few simple conservation criteria into restoration designs that enhance impacts to entire insect communities. Restoration can be used as a strategy to address fragmentation threats to isolated insect communities if insect communities are incorporated at the onset of restoration planning. Fully incorporating insect communities into restoration designs may increase the cost of restoration two- to three-fold, but the benefits to biodiversity conservation and the ecological services provided by intact insect communities justify the cost.

  14. Butterflies of the high altitude Atacama Desert: habitat use and conservation

    Directory of Open Access Journals (Sweden)

    Emma eDespland

    2014-09-01

    Full Text Available The butterfly fauna of the high-altitude desert of Northern Chile, though depauperate, shows high endemism, is poorly known and is of considerable conservation concern. This study surveys butterflies along the Andean slope between 2400 and 500 m asl (prepuna, puna and Andean steppe habitats as well as in high and low altitude wetlands and in the neoriparian vegetation of agricultural sites. We also include historical sightings from museum records. We compare abundances between altitudes, between natural and impacted sites, as well as between two sampling years with different precipitation regimes. The results confirm high altitudinal turnover and show greatest similarity between wetland and slope faunas at similar altitudes. Results also underscore vulnerability to weather fluctuations, particularly in the more arid low-altitude sites, where abundances were much lower in the low precipitation sampling season and several species were not observed at all. Finally, we show that some species have shifted to the neoriparian vegetation of the agricultural landscape, whereas others were only observed in less impacted habitats dominated by native plants. These results suggest that acclimation to novel habitats depends on larval host plant use. The traditional agricultural environment can provide habitat for many, but not all, native butterfly species, but an estimation of the value of these habitats requires better understanding of butterfly life-history strategies and relationships with host plants.

  15. Development of residual gas ionization profile monitor for high intensity proton beams

    CERN Document Server

    Sato, Y; Hirose, E; Ieiri, M; Igarashi, Y; Inaba, S; Katoh, Y; Minakawa, M; Noumi, H; Saitó, M; Suzuki, Y; Takahashi, H; Takasaki, M; Tanaka, K; Toyoda, A; Yamada, Y; Yamanoi, Y; Watanabe, H

    2006-01-01

    Nondestructive beam profile monitor utilizing ionizations of residual gas has been developed for continuous monitoring of 3?0(J-PARC). Knock-on electrons produced in the ionizations of residual gas vacuumed to 1 Pa are collected with a uniform electric field applied between electrodes. Applying a uniform electric field parallel to the electric field is essential to reduce diffusion of electrons crossing over magnetic flux. A prototype monitor has been constructed and installed in EP2-C beam line at KEK 12 GeV proton synchrotron (12 Ge V-PS). The profiles measured with the present monitor agree with the ones measured with the existing destructive profile monitor. The present monitor shows sufficient performances as a candidate of the profile monitor at J-PARC. In the present article, the working principle of the present monitor, the results of test experiments, and further developments are described in detail.

  16. A study for high accuracy measurement of residual stress by deep hole drilling technique

    Science.gov (United States)

    Kitano, Houichi; Okano, Shigetaka; Mochizuki, Masahito

    2012-08-01

    The deep hole drilling technique (DHD) received much attention in recent years as a method for measuring through-thickness residual stresses. However, some accuracy problems occur when residual stress evaluation is performed by the DHD technique. One of the reasons is that the traditional DHD evaluation formula applies to the plane stress condition. The second is that the effects of the plastic deformation produced in the drilling process and the deformation produced in the trepanning process are ignored. In this study, a modified evaluation formula, which is applied to the plane strain condition, is proposed. In addition, a new procedure is proposed which can consider the effects of the deformation produced in the DHD process by investigating the effects in detail by finite element (FE) analysis. Then, the evaluation results obtained by the new procedure are compared with that obtained by traditional DHD procedure by FE analysis. As a result, the new procedure evaluates the residual stress fields better than the traditional DHD procedure when the measuring object is thick enough that the stress condition can be assumed as the plane strain condition as in the model used in this study.

  17. Highly sensitive and selective colorimetric detection of cartap residue in agricultural products.

    Science.gov (United States)

    Liu, Wei; Zhang, Daohong; Tang, Yafan; Wang, Yashan; Yan, Fei; Li, Zhonghong; Wang, Jianlong; Zhou, H Susan

    2012-11-15

    The residue of pesticide has posed a serious threat to human health. Fast, broad-spectrum detection methods are necessary for on-site screening of various types of pesticides. With citrate-coated Au nanoparticles (Au NPs) as colorimetric probes, a visual and spectrophotometric method for rapid assay of cartap, which is one of the most important pesticides in agriculture, is reported for the first time. Based on the color change of Au colloid solution from wine-red to blue resulting from the aggregation of Au NPs, cartap could be detected in the concentration range of 0.05-0.6 mg/kg with a low detection limit of 0.04 mg/kg, which is much lower than the strictest cartap safety requirement of 0.1 mg/kg. Due to the limited research on the rapid detection of cartap based on Au NPs, the performance of the present method was evaluated through aggregation kinetics, interference influence, and sample pretreatment. To further demonstrate the selectivity and applicability of the method, cartap detection is realized in cabbage and tea with excellent analyte concentration recovery. These results demonstrate that the present method provides an easy and effective way to analyze pesticide residue in common products, which is of benefit for the rapid risk evaluation and on-site screening of pesticide residue. Copyright © 2012 Elsevier B.V. All rights reserved.

  18. ENTRIA 2014. Memorandum on the disposal of high-level radioactive residuals; ENTRIA 2014. Memorandum zur Entsorgung hochradioaktiver Reststoffe

    Energy Technology Data Exchange (ETDEWEB)

    Roehlig, Klaus-Juergen; Walther, Clemens; Bach, Friedrich-Wilhelm [Niedersaechsische Technische Hochschule, Braunschweig, Clausthal-Zellerfeld, Hannover (Germany); and others

    2014-04-30

    The memorandum on the disposal of high-level radioactive residuals covers the following issues: description of the problem: a ''wicked problem'', risks and NIMBY, the site selection law, international boundary conditions; disposal strategy and types of facilities: safety and reversibility, long-term surface storage, deep storage; risk and safety; procedural justice and the site selection process; social innovations and the requirement of long-term institutions; conclusion - central stress fields.

  19. Revealing Pesticide Residues Under High Pesticide Stress in Taiwan's Agricultural Environment Probed by Fresh Honey Bee (Hymenoptera: Apidae) Pollen.

    Science.gov (United States)

    Nai, Yu-Shin; Chen, Tsui-Yao; Chen, Yi-Cheng; Chen, Chun-Ting; Chen, Bor-Yann; Chen, Yue-Wen

    2017-10-01

    Significant pesticide residues are among the most serious problems for sustainable agriculture. In the beekeeping environment, pesticides not only impact a honey bee's survival, but they also contaminate bee products. Taiwan's agricultural environment has suffered from pesticide stress that was higher than that found in Europe and America. This study deciphered problems of pesticide residues in fresh honey bee pollen samples collected from 14 monitoring apiaries in Taiwan, which reflected significant contaminations within the honey bee population. In total, 155 pollen samples were screened for 232 pesticides, and 56 pesticides were detected. Among the residues, fluvalinate and chlorpyrifos showed the highest concentrations, followed by carbendazim, carbaryl, chlorfenapyr, imidacloprid, ethion, and flufenoxuron. The average frequency of pesticide residues detected in pollen samples was ca. 74.8%. The amounts and types of pesticides were higher in winter and in southwestern Taiwan. Moreover, five of these pollen samples were contaminated with 11-15 pesticides, with average levels between 1,560 and 6,390 μg/kg. Compared with the literature, this study emphasized that pollen gathered by honey bee was highly contaminated with more pesticides in Taiwan than in the America, France, and Spain. The ubiquity of pesticides in the pollen samples was likely due to the field applications of common pesticides. Recently, the Taiwanese government began to improve the pesticide policy. According to the resurvey data in 2016, there were reductions in several pesticide contamination parameters in pollen samples from west to southwest Taiwan. A long-term investigation of pollen pesticide residues should be conducted to inspect pesticides usage in Taiwan's agriculture. © The Author 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  20. The numerical high cycle fatigue damage model of fillet weld joint under weld-induced residual stresses

    Science.gov (United States)

    Nguyen Van Do, Vuong

    2018-04-01

    In this study, a development of nonlinear continuum damage mechanics (CDM) model for multiaxial high cycle fatigue is proposed in which the cyclic plasticity constitutive model has been incorporated in the finite element (FE) framework. T-joint FE simulation of fillet welding is implemented to characterize sequentially coupled three-dimensional (3-D) of thermo-mechanical FE formulation and simulate the welding residual stresses. The high cycle fatigue damage model is then taken account into the fillet weld joints under the various cyclic fatigue load types to calculate the fatigue life considering the residual stresses. The fatigue crack initiation and the propagation in the present model estimated for the total fatigue is compared with the experimental results. The FE results illustrated that the proposed high cycle fatigue damage model in this study could become a powerful tool to effectively predict the fatigue life of the welds. Parametric studies in this work are also demonstrated that the welding residual stresses cannot be ignored in the computation of the fatigue life of welded structures.

  1. Cosmetic results in early stage breast cancer patients with high-dose brachytherapy after conservative surgery

    International Nuclear Information System (INIS)

    Torres, Felipe; Pineda, Beatriz E

    2004-01-01

    Purpose: to reveal cosmetic results in patients at early stages of low risk breast cancer treated with partial accelerated radiotherapy using high dose rate brachytherapy. Methods and materials: from March 2001 to July 2003,14 stages l and ll breast cancer patients were treated at the Colombian national cancer institute in Bogota with conservative surgery and radiotherapy upon the tumor bed (partial accelerated radiotherapy), using interstitial implants with iridium 192 (high dose rate brachytherapy) with a dose of 32 Gys, over 4 days, at 8 fractions twice a day. Results: with an average follow up of 17.7 months, good cosmetic results were found among 71.4 % of patients and excellent results among 14.3% of patients, furthermore none of the patients neither local nor regional or distant relapses. Conclusion: among patients who suffer from breast cancer at early stages, it showed is possible to apply partial accelerated radiotherapy upon the tumor bed with high doses over 4 days with good to excellent cosmetic results

  2. Evaluation of gas chromatography – electron ionization – full scan high resolution Orbitrap mass spectrometry for pesticide residue analysis

    Energy Technology Data Exchange (ETDEWEB)

    Mol, Hans G.J., E-mail: hans.mol@wur.nl; Tienstra, Marc; Zomer, Paul

    2016-09-07

    Gas chromatography with electron ionization and full scan high resolution mass spectrometry with an Orbitrap mass analyzer (GC-EI-full scan Orbitrap HRMS) was evaluated for residue analysis. Pesticides in fruit and vegetables were taken as an example application. The relevant aspects for GC-MS based residue analysis, including the resolving power (15,000 to 120,000 FWHM at m/z 200), scan rate, dynamic range, selectivity, sensitivity, analyte identification, and utility of existing EI-libraries, are assessed and discussed in detail. The optimum acquisition conditions in full scan mode (m/z 50–500) were a resolving power of 60,000 and an automatic-gain-control target value of 3E6. These conditions provided (i) an optimum mass accuracy: within 2 ppm over a wide concentration range, with/without matrix, enabling the use of ±5 ppm mass extraction windows (ii) adequate scan speed: minimum 12 scans/peak, (iii) an intra-scan dynamic range sufficient to achieve LOD/LOQs ≤0.5 pg in fruit/vegetable matrices (corresponding to ≤0.5 μg kg{sup −1}) for most pesticides. EI-Orbitrap spectra were consistent over a very wide concentration range (5 orders) with good match values against NIST (EI-quadrupole) spectra. The applicability for quantitative residue analysis was verified by validation of 54 pesticides in three matrices (tomato, leek, orange) at 10 and 50 μg/kg. The method involved a QuEChERS-based extraction with a solvent switch into iso-octane, and 1 μL hot splitless injection into the GC-HRMS system. A recovery between 70 and 120% and a repeatability RSD <10% was obtained in most cases. Linearity was demonstrated for the range ≤5–250 μg kg{sup −1}. The pesticides could be identified according to the applicable EU criteria for GC-HRMS (SANTE/11945/2015). GC-EI-full scan Orbitrap HRMS was found to be highly suited for quantitative pesticide residue analysis. The potential of qualitative screening to extend the scope makes it an attractive

  3. Evaluation of gas chromatography – electron ionization – full scan high resolution Orbitrap mass spectrometry for pesticide residue analysis

    International Nuclear Information System (INIS)

    Mol, Hans G.J.; Tienstra, Marc; Zomer, Paul

    2016-01-01

    Gas chromatography with electron ionization and full scan high resolution mass spectrometry with an Orbitrap mass analyzer (GC-EI-full scan Orbitrap HRMS) was evaluated for residue analysis. Pesticides in fruit and vegetables were taken as an example application. The relevant aspects for GC-MS based residue analysis, including the resolving power (15,000 to 120,000 FWHM at m/z 200), scan rate, dynamic range, selectivity, sensitivity, analyte identification, and utility of existing EI-libraries, are assessed and discussed in detail. The optimum acquisition conditions in full scan mode (m/z 50–500) were a resolving power of 60,000 and an automatic-gain-control target value of 3E6. These conditions provided (i) an optimum mass accuracy: within 2 ppm over a wide concentration range, with/without matrix, enabling the use of ±5 ppm mass extraction windows (ii) adequate scan speed: minimum 12 scans/peak, (iii) an intra-scan dynamic range sufficient to achieve LOD/LOQs ≤0.5 pg in fruit/vegetable matrices (corresponding to ≤0.5 μg kg"−"1) for most pesticides. EI-Orbitrap spectra were consistent over a very wide concentration range (5 orders) with good match values against NIST (EI-quadrupole) spectra. The applicability for quantitative residue analysis was verified by validation of 54 pesticides in three matrices (tomato, leek, orange) at 10 and 50 μg/kg. The method involved a QuEChERS-based extraction with a solvent switch into iso-octane, and 1 μL hot splitless injection into the GC-HRMS system. A recovery between 70 and 120% and a repeatability RSD <10% was obtained in most cases. Linearity was demonstrated for the range ≤5–250 μg kg"−"1. The pesticides could be identified according to the applicable EU criteria for GC-HRMS (SANTE/11945/2015). GC-EI-full scan Orbitrap HRMS was found to be highly suited for quantitative pesticide residue analysis. The potential of qualitative screening to extend the scope makes it an attractive alternative to

  4. NOA36 Protein Contains a Highly Conserved Nucleolar Localization Signal Capable of Directing Functional Proteins to the Nucleolus, in Mammalian Cells

    Science.gov (United States)

    de Melo, Ivan S.; Jimenez-Nuñez, Maria D.; Iglesias, Concepción; Campos-Caro, Antonio; Moreno-Sanchez, David; Ruiz, Felix A.; Bolívar, Jorge

    2013-01-01

    NOA36/ZNF330 is an evolutionarily well-preserved protein present in the nucleolus and mitochondria of mammalian cells. We have previously reported that the pro-apoptotic activity of this protein is mediated by a characteristic cysteine-rich domain. We now demonstrate that the nucleolar localization of NOA36 is due to a highly-conserved nucleolar localization signal (NoLS) present in residues 1–33. This NoLS is a sequence containing three clusters of two or three basic amino acids. We fused the amino terminal of NOA36 to eGFP in order to characterize this putative NoLS. We show that a cluster of three lysine residues at positions 3 to 5 within this sequence is critical for the nucleolar localization. We also demonstrate that the sequence as found in human is capable of directing eGFP to the nucleolus in several mammal, fish and insect cells. Moreover, this NoLS is capable of specifically directing the cytosolic yeast enzyme polyphosphatase to the target of the nucleolus of HeLa cells, wherein its enzymatic activity was detected. This NoLS could therefore serve as a very useful tool as a nucleolar marker and for directing particular proteins to the nucleolus in distant animal species. PMID:23516598

  5. Basic numerical study on gap influence of residual stress and distortion during high-brightness laser butt welding

    International Nuclear Information System (INIS)

    Serizawa, Hisashi; Mori, Daiki; Murakawa, Hidekazu

    2013-01-01

    High-brightness laser such as fiber laser or disk laser is expected to minimize the total heat input energy in welding due to its high beam quality, and the welding residual stress and distortion also seem to be reduced as a result. However, the diameter of high-brightness laser beam is less than 0.6 mm and it is difficult to set the beam position to contact face between two parts because in general there would be a gap due to quality of parts. In this study, in order to reveal the effect of gap on the residual stress and the welding distortion during fiber laser welding, the butt welding of two plates were examined through the thermal elastic-plastic analysis with a new gap element. From the result of thermal analyses, it was found that the homogeneous ellipsoid body could be applicable to model the shape of heat source for the fiber laser and the gap width would not influence the penetration shape when the gap width was changed from 0.1 to 0.25 mm. In addition, the elastic-plastic analyses indicated that the transverse shrinkage slightly increased with increasing the gap width, while this shrinkage without gap was much smaller than that with gap. Also, it was revealed that the welding speed largely affects both the welding residual stress and distortion. Moreover, it was found that the residual stress was almost independent of the jig position, while the position of fixtures slightly affected the transverse shrinkage. (author)

  6. Alternatives to crop residues for soil amendment

    OpenAIRE

    Powell, J.M.; Unger, P.W.

    1997-01-01

    Metadata only record In semiarid agroecosystems, crop residues can provide important benefits of soil and water conservation, nutrient cycling, and improved subsequent crop yields. However, there are frequently multiple competing uses for residues, including animal forage, fuel, and construction material. This chapter discusses the various uses of crop residues and examines alternative soil amendments when crop residues cannot be left on the soil.

  7. Determination of Beta-Lactam residues in milk by high performance liquid chromatography

    Directory of Open Access Journals (Sweden)

    Roseane Brandão de Brito

    2006-01-01

    Full Text Available A high performance liquid chromatographic method to assay beta-lactam residues in milk was developed and validated. Milk samples were spiked with standard solutions and deproteinated. The extract was cleaned-up on C18 SPE cartridge, the antibiotics eluted with acetonitrile:water (50:50 v/v and derivatized with acetic anhydride and 1-methyl-imidazole solution containing HgCl2. The chromatographic analysis was performed on C18 column using mobile phase consisting of acetonitrile and phosphate buffer (pH 6.5 in the presence of Na2S2O3 gradient and detection at 325 nm. The method was selective for ampicillin, penicillin G and penicillin V, the latter used as internal standard. Average recoveries for ampicillin and penicillin G ranged, respectively, from 60.0% to 104.9% and from 82.7% to 109.2%, with coefficients of variation from 11.1% to 24.6%, and from 2.1% to 25.2%, indicating accuracy and precision. Detection limit of 4.0 µg/L for ampicillin and 3.0 µg/L for penicillin G, and quantification limits of 4.0 µg/L for both were estimated.Um método para determinar resíduos de antibióticos beta-lactâmicos em leite por cromatografia líquida de alta eficiência (CLAE foi desenvolvido e validado. Amostras brancas foram adicionadas de padrão e desproteinizadas. O extrato foi purificado por extração em fase sólida C18, os antibióticos eluídos com acetonitrila:água (50:50 v/v e posteriormente derivatizados com anidrido acético e solução de 1-metil-imidazol contendo HgCl2. A análise cromatográfica foi realizada utilizando coluna C18, fase móvel composta por acetonitrila e tampão fosfato pH 6,5, na presença de Na2S2O3 em gradiente e detecção a 325 nm. O método foi seletivo para ampicilina, penicilina G e penicilina V, sendo este último utilizado como padrão interno. As médias de recuperação para ampicilina e penicilina G situaram-se, respectivamente, na faixa de 60,0% a 104,9% e de 82,7% a 109,2%, com coeficientes de varia

  8. A novel, highly conserved metallothionein family in basidiomycete fungi and characterization of two representative SlMTa and SlMTb genes in the ectomycorrhizal fungus Suillus luteus.

    Science.gov (United States)

    Nguyen, Hoai; Rineau, François; Vangronsveld, Jaco; Cuypers, Ann; Colpaert, Jan V; Ruytinx, Joske

    2017-07-01

    The basidiomycete Suillus luteus is an important member of the ectomycorrhizal community that thrives in heavy metal polluted soils covered with pioneer pine forests. This study aimed to identify potential heavy metal chelators in S. luteus. Two metallothionein (MT) coding genes, SlMTa and SlMTb, were identified. When heterologously expressed in yeast, both SlMTa and SlMTb can rescue the Cu sensitive mutant from Cu toxicity. In S. luteus, transcription of both SlMTa and SlMTb is induced by Cu but not Cd or Zn. Several putative Cu-sensing and metal-response elements are present in the promoter sequences. These results indicate that SlMTa and SlMTb function as Cu-thioneins. Homologs of the S. luteus MTs are present in 49 species belonging to 10 different orders of the subphylum Agaricomycotina and are remarkably conserved. The length of the proteins, number and distribution of cysteine residues indicate a novel family of fungal MTs. The ubiquitous and highly conserved features of these MTs suggest that they are important for basic cellular functions in species in the subphylum Agaricomycotina. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

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

    Science.gov (United States)

    Sabin, Charles; Corti, Davide; Buzon, Victor; Seaman, Mike S; Lutje Hulsik, David; Hinz, Andreas; Vanzetta, Fabrizia; Agatic, Gloria; Silacci, Chiara; Mainetti, Lara; Scarlatti, Gabriella; Sallusto, Federica; Weiss, Robin; Lanzavecchia, Antonio; Weissenhorn, Winfried

    2010-11-18

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

  10. Swertia chirayta, a Threatened High-Value Medicinal Herb: Microhabitats and Conservation Challenges in Sikkim Himalaya, India

    Directory of Open Access Journals (Sweden)

    Bharat Kumar Pradhan

    2015-11-01

    Full Text Available Assessing the impact of threats, identifying favorable growing conditions, and predicting future population scenarios are vital for the conservation and management of threatened species. This study investigated the availability, microhabitat characteristics, threat status, and community associations of Swertia chirayta, a highly threatened Himalayan medicinal herb, in 22 populations in Sikkim, India, using the vertical belt transect method. Of the 14 microhabitats identified, open grassy slope emerged as the most favorable and wet grassy slope as the least favorable for S. chirayta. The species was dominant in 8 of the 10 major plant communities identified. Among 9 major types of disturbance identified, human movement and collection of non-timber forest products appeared as the biggest threats to S. chirayta. Disturbances significantly affected the availability of the species. S. chirayta, though under high anthropogenic threat, maintains high microhabitat pliability, which is vital for its conservation and management, provided immediate conservation measures are taken.

  11. Highly sensitive rapid fluorescence detection of protein residues on surgical instruments

    International Nuclear Information System (INIS)

    Kovalev, Valeri I; Bartona, James S; Richardson, Patricia R; Jones, Anita C

    2006-01-01

    There is a risk of contamination of surgical instruments by infectious protein residues, in particular, prions which are the agents for Creutzfeldt-Jakob Disease in humans. They are exceptionally resistant to conventional sterilization, therefore it is important to detect their presence as contaminants so that alternative cleaning procedures can be applied. We describe the development of an optimized detection system for fluorescently labelled protein, suitable for in-hospital use. We show that under optimum conditions the technique can detect ∼10 attomole/cm 2 with a scan speed of ∼3-10 cm 2 /s of the test instrument's surface. A theoretical analysis and experimental measurements will be discussed

  12. Evaluation of highly conserved hsp65-specific nested PCR primers for diagnosing Mycobacterium tuberculosis.

    Science.gov (United States)

    Priyadarshini, P; Tiwari, K; Das, A; Kumar, D; Mishra, M N; Desikan, P; Nath, G

    2017-02-01

    To evaluate the sensitivity and specificity of a new nested set of primers designed for the detection of Mycobacterium tuberculosis complex targeting a highly conserved heat shock protein gene (hsp65). The nested primers were designed using multiple sequence alignment assuming the nucleotide sequence of the M. tuberculosis H37Rv hsp65 genome as base. Multidrug-resistant Mycobacterium species along with other non-mycobacterial and fungal species were included to evaluate the specificity of M. tuberculosis hsp65 gene-specific primers. The sensitivity of the primers was determined using serial 10-fold dilutions, and was 100% as shown by the bands in the case of M. tuberculosis complex. None of the other non M. tuberculosis complex bacterial and fungal species yielded any band on nested polymerase chain reaction (PCR). The first round of amplification could amplify 0.3 ng of the template DNA, while nested PCR could detect 0.3 pg. The present hsp65-specific primers have been observed to be sensitive, specific and cost-effective, without requiring interpretation of biochemical tests, real-time PCR, sequencing or high-performance liquid chromatography. These primer sets do not have the drawbacks associated with those protocols that target insertion sequence 6110, 16S rDNA, rpoB, recA and MPT 64.

  13. Extraction of high added value biological compounds from sardine, sardine-type fish and mackerel canning residues--a review.

    Science.gov (United States)

    Ferraro, Vincenza; Carvalho, Ana P; Piccirillo, Clara; Santos, Manuela M; Castro, Paula M L; Pintado, Manuela E

    2013-08-01

    Different valuable compounds, which can be employed in medicine or in other industries (i.e. food, agrochemical, pharmaceutical) can be recovered from by-products and waste from the fish canning industries. They include lipids, proteins, bio-polymers, minerals, amino acids and enzymes; they can be extracted from wastewaters and/or from solid residues (head, viscera, skin, tails and flesh) generated along the canning process, through the filleting, cooking, salting or smoking stages. In this review, the opportunities for the extraction and the valorisation of bioactive compounds from sardine, sardine-type fish and mackerel canning residues are examined and discussed. These are amongst the most consumed fishes in the Mediterranean area; moreover, canning is one of the most important and common methods of preservation. The large quantities of by-products generated have great potentials for the extraction of biologically desirable high added value compounds. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. Novel cross-strand three-purine stack of the highly conserved 5'-GA/AAG-5' internal loop at the 3'-end termini of Parvovirus Genomes

    International Nuclear Information System (INIS)

    Chou, S.-H.; Chin, K.-H.

    2001-01-01

    We have used two-dimensional nuclear magnetic resonance (2D-NMR), distance geometry (DG) and molecular dynamics / energy minimization (MD/EM) methods to study a 2x3 asymmetric internal loop structure of the highly conserved '5'-(GA)/(AAG)-5' bubble' present at the 3'-end hairpin of the single-stranded DNA genome of parvoviruses. This motif contains an unpaired adenosine stacked between two bracketed sheared G·A pairs. However, the phenomenal cross-strand G-G and A-A stacking in the tandem sheared G·A pairs has undergone considerable change. A novel three-purine stacking pattern is observed instead; the inserted A18 base is completely un-stacked from its neighboring G17 and A19 bases, but well stacked with the cross-strand A4 and G3 bases to form a novel A4/A18/G3 stack that is different from the double G/G, A/A or quadruple G/G/G/G stack present in the 5'-(GA)/(AG)-5' or 5'-(GGA)/(AGG)-5' motifs. Unlike the bulged purine residue that usually causes about 20 degree kink in the helical axis of the parent helix when bracketed by canonical G·C or A·T base pairs, no significant kink is observed in the present helix containing a bulged-adenine that is bracketed by sheared G ·A pairs. The phosphodiesters connecting G3-A4 and G17-A18 residues adopt unusual ζ torsional angles close to the trans domain, yet that connecting A18-A19 residues resumes the normal ζ(g - ) value. The well structured '5'-(GAA)/(AG)-5'' internal loop in the parvovirus genomes explains its resistance to single-strand specific endonuclease susceptibility

  15. Active disease and residual damage in treated Wegener's granulomatosis: an observational study using pulmonary high-resolution computed tomography

    International Nuclear Information System (INIS)

    Komocsi, Andras; Reuter, Michael; Heller, Martin; Murakoezi, Henriette; Gross, Wolfgang L.; Schnabel, Armin

    2003-01-01

    The purpose of this study was to determine to what extent high-resolution computed tomography (HRCT) of the lungs can distinguish active inflammatory disease from inactive cicatricial disease in patients treated for Wegener's granulomatosis (WG). Twenty-eight WG patients with active pulmonary disease underwent a first HRCT examination immediately before standard immunosuppressive treatment and a second examination after clinical remission had been achieved. Lesions remaining after treatment were categorized as residual damage and were compared with findings during active disease to see by what features active and cicatricial disease can be distinguished. During active disease 17 patients had nodules/masses, 12 had ground-glass opacities, 6 had septal lines and 6 had non-septal lines. After treatment, ground-glass opacities had resolved completely. Nodules/masses had resolved in 8 patients and had diminished in 7 patients. Residual nodules were distinguished from nodules/masses in active disease by lack of cavitation and a diameter of mostly <15 mm. In one-third of patients lines resolved, but in 8 instances new lines evolved during immunosuppression. During a follow-up period of a median 26.5 months (range 20.0-33.8), patients with residual nodules or lines had no more relapses than patients with completely cleared lungs. Treated pulmonary WG leaves substantial residual damage. High-resolution CT does assist in the distinction between active and inactive lesions. Ground-glass opacities, cavitating nodules/masses and masses measuring more than 3 cm represent active disease ordinarily. Non-cavitary small nodules and septal or non-septal lines can be either active or cicatricial lesions. The nature of these lesions needs to be clarified by longitudinal observation. (orig.)

  16. A highly conserved basidiomycete peptide synthetase produces a trimeric hydroxamate siderophore.

    Science.gov (United States)

    Brandenburger, Eileen; Gressler, Markus; Leonhardt, Robin; Lackner, Gerald; Habel, Andreas; Hertweck, Christian; Brock, Matthias; Hoffmeister, Dirk

    2017-08-25

    The model white-rot basidiomycete Ceriporiopsis ( Gelatoporia ) subvermispora B encodes putative natural product biosynthesis genes. Among them is the gene for the seven-domain nonribosomal peptide synthetase CsNPS2. It is a member of the as-yet uncharacterized fungal type VI siderophore synthetase family which is highly conserved and widely distributed among the basidiomycetes. These enzymes include only one adenylation (A) domain, i.e., one complete peptide synthetase module and two thiolation/condensation (T-C) di-domain partial modules which, together, constitute an AT 1 C 1 T 2 C 2 T 3 C 3 domain setup. The full-length CsNPS2 enzyme (274.5 kDa) was heterologously produced as polyhistidine fusion in Aspergillus niger as soluble and active protein. N 5 -acetyl- N 5 -hydroxy-l-ornithine (l-AHO) and N 5 - cis -anhydromevalonyl- N 5 -hydroxy-l-ornithine (l-AMHO) were accepted as substrates, as assessed in vitro using the substrate-dependent [ 32 P]ATP-pyrophosphate radioisotope exchange assay. Full-length holo -CsNPS2 catalyzed amide bond formation between three l-AHO molecules to release the linear l-AHO trimer, called basidioferrin, as product in vitro , which was verified by LC-HRESIMS. Phylogenetic analyses suggest that type VI family siderophore synthetases are widespread in mushrooms and have evolved in a common ancestor of basidiomycetes. Importance : The basidiomycete nonribosomal peptide synthetase CsNPS2 represents a member of a widely distributed but previously uninvestigated class (type VI) of fungal siderophore synthetases. Genes orthologous to CsNPS2 are highly conserved across various phylogenetic clades of the basidiomycetes. Hence, our work serves as a broadly applicable model for siderophore biosynthesis and iron metabolism in higher fungi. Also, our results on the amino acid substrate preference of CsNPS2 supports further understanding of the substrate selectivity of fungal adenylation domains. Methodologically, this report highlights the

  17. The RING 2.0 web server for high quality residue interaction networks.

    Science.gov (United States)

    Piovesan, Damiano; Minervini, Giovanni; Tosatto, Silvio C E

    2016-07-08

    Residue interaction networks (RINs) are an alternative way of representing protein structures where nodes are residues and arcs physico-chemical interactions. RINs have been extensively and successfully used for analysing mutation effects, protein folding, domain-domain communication and catalytic activity. Here we present RING 2.0, a new version of the RING software for the identification of covalent and non-covalent bonds in protein structures, including π-π stacking and π-cation interactions. RING 2.0 is extremely fast and generates both intra and inter-chain interactions including solvent and ligand atoms. The generated networks are very accurate and reliable thanks to a complex empirical re-parameterization of distance thresholds performed on the entire Protein Data Bank. By default, RING output is generated with optimal parameters but the web server provides an exhaustive interface to customize the calculation. The network can be visualized directly in the browser or in Cytoscape. Alternatively, the RING-Viz script for Pymol allows visualizing the interactions at atomic level in the structure. The web server and RING-Viz, together with an extensive help and tutorial, are available from URL: http://protein.bio.unipd.it/ring. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. High energy X-ray diffraction analysis of strain and residual stress in silicon nitride ceramic diffusion bonds

    International Nuclear Information System (INIS)

    Vila, M.; Prieto, C.; Miranzo, P.; Osendi, M.I.; Terry, A.E.; Vaughan, G.B.M.

    2005-01-01

    High resolution X-ray scanning diffractometry is used to study the residual stress in binary metal/ceramic (Ni/Si 3 N 4 ) diffusion bonds fabricated by simultaneous high temperature heating and uniaxial pressing. In order to diminish the experimental error on the stress determination, the method consists of three steps: (i) to measure the axial and radial strains following some selected lines at the inner volume of the ceramic; (ii) to fit the strain data using finite element method (FEM) analysis and (iii) to determinate stresses by using the results obtained from the FEM method in the strain calculation

  19. Identification of Key Residues for Enzymatic Carboxylate Reduction

    Directory of Open Access Journals (Sweden)

    Holly Stolterfoht

    2018-02-01

    Full Text Available Carboxylate reductases (CARs, E.C. 1.2.1.30 generate aldehydes from their corresponding carboxylic acid with high selectivity. Little is known about the structure of CARs and their catalytically important amino acid residues. The identification of key residues for carboxylate reduction provides a starting point to gain deeper understanding of enzymatic carboxylate reduction. A multiple sequence alignment of CARs with confirmed activity recently identified in our lab and from the literature revealed a fingerprint of conserved amino acids. We studied the function of conserved residues by multiple sequence alignments and mutational replacements of these residues. In this study, single-site alanine variants of Neurospora crassa CAR were investigated to determine the contribution of conserved residues to the function, expressability or stability of the enzyme. The effect of amino acid replacements was investigated by analyzing enzymatic activity of the variants in vivo and in vitro. Supported by molecular modeling, we interpreted that five of these residues are essential for catalytic activity, or substrate and co-substrate binding. We identified amino acid residues having significant impact on CAR activity. Replacement of His 237, Glu 433, Ser 595, Tyr 844, and Lys 848 by Ala abolish CAR activity, indicating their key role in acid reduction. These results may assist in the functional annotation of CAR coding genes in genomic databases. While some other conserved residues decreased activity or had no significant impact, four residues increased the specific activity of NcCAR variants when replaced by alanine. Finally, we showed that NcCAR wild-type and mutants efficiently reduce aliphatic acids.

  20. Acacia shrubs respond positively to high severity wildfire: Implications for conservation and fuel hazard management.

    Science.gov (United States)

    Gordon, Christopher E; Price, Owen F; Tasker, Elizabeth M; Denham, Andrew J

    2017-01-01

    High severity wildfires pose threats to human assets, but are also perceived to impact vegetation communities because a small number of species may become dominant immediately after fire. However there are considerable gaps in our knowledge about species-specific responses of plants to different fire severities, and how this influences fuel hazard in the short and long-term. Here we conduct a floristic survey at sites before and two years after a wildfire of unprecedented size and severity in the Warrumbungle National Park (Australia) to explore relationships between post-fire growth of a fire responsive shrub genera (Acacia), total mid-story vegetation cover, fire severity and fuel hazard. We then survey 129 plots surrounding the park to assess relationships between mid-story vegetation cover and time-since-fire. Acacia species richness and cover were 2.3 and 4.3 times greater at plots after than before the fire. However the same common dominant species were present throughout the study. Mid-story vegetation cover was 1.5 times greater after than before the wildfire, and Acacia species contribution to mid-story cover increased from 10 to 40%. Acacia species richness was not affected by fire severity, however strong positive associations were observed between Acacia and total mid-story vegetation cover and severity. Our analysis of mid-story vegetation recovery showed that cover was similarly high between 2 and 30years post-fire, then decreased until 52years. Collectively, our results suggest that Acacia species are extremely resilient to high severity wildfire and drive short to mid-term increases in fuel hazard. Our results are discussed in relation to fire regime management from the twin perspectives of conserving biodiversity and mitigating human losses due to wildfire. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Residue analysis of sixty pesticides in red swamp crayfish using QuEChERS with high-performance liquid chromatography-tandem mass spectrometry

    Science.gov (United States)

    In this study, a multi-residue analytical method using QuEChERS extraction and dispersive solid-phase extraction (d-SPE) cleanup followed by high-performance liquid chromatography–tandem mass spectrometry (HPLC-MS/MS) was developed for rapid determination of 60 pesticide residues in whole crayfish a...

  2. Recurrence and mortality according to Estrogen Receptor status for breast cancer patients undergoing conservative surgery. Ipsilateral breast tumour recurrence dynamics provides clues for tumour biology within the residual breast

    International Nuclear Information System (INIS)

    Demicheli, Romano; Ardoino, Ilaria; Boracchi, Patrizia; Coradini, Danila; Agresti, Roberto; Ferraris, Cristina; Gennaro, Massimiliano; Hrushesky, William JM; Biganzoli, Elia

    2010-01-01

    the study was designed to determine how tumour hormone receptor status affects the subsequent pattern over time (dynamics) of breast cancer recurrence and death following conservative primary breast cancer resection. Time span from primary resection until both first recurrence and death were considered among 2825 patients undergoing conservative surgery with or without breast radiotherapy. The hazard rates for ipsilateral breast tumour recurrence (IBTR), distant metastasis (DM) and mortality throughout 10 years of follow-up were assessed. DM dynamics displays the same bimodal pattern (first early peak at about 24 months, second late peak at the sixth-seventh year) for both estrogen receptor (ER) positive (P) and negative (N) tumours and for all local treatments and metastatic sites. The hazard rates for IBTR maintain the bimodal pattern for ERP and ERN tumours; however, each IBTR recurrence peak for ERP tumours is delayed in comparison to the corresponding timing of recurrence peaks for ERN tumours. Mortality dynamics is markedly different for ERP and ERN tumours with more early deaths among patients with ERN than among patients with ERP primary tumours. DM dynamics is not influenced by the extent of conservative primary tumour resection and is similar for both ER phenotypes across different metastatic sites, suggesting similar mechanisms for tumour development at distant sites despite apparently different microenvironments. The IBTR risk peak delay observed in ERP tumours is an exception to the common recurrence risk rhythm. This suggests that the microenvironment within the residual breast tissue may enforce more stringent constraints upon ERP breast tumour cell growth than other tissues, prolonging the latency of IBTR. This local environment is, however, apparently less constraining to ERN cells, as IBTR dynamics is similar to the corresponding recurrence dynamics among other distant tissues

  3. Development of an improved high resolution mass spectrometry based multi-residue method for veterinary drugs in various food matrices.

    Science.gov (United States)

    Kaufmann, A; Butcher, P; Maden, K; Walker, S; Widmer, M

    2011-08-26

    Multi-residue methods for veterinary drugs or pesticides in food are increasingly often based on ultra performance liquid chromatography (UPLC) coupled to high resolution mass spectrometry (HRMS). Previous available time of flight (TOF) technologies, showing resolutions up to 15,000 full width at half maximum (FWHM), were not sufficiently selective for monitoring low residue concentrations in difficult matrices (e.g. hormones in tissue or antibiotics in honey). The approach proposed in this paper is based on a single stage Orbitrap mass spectrometer operated at 50,000 FWHM. Extracts (liver and kidney) which were produced according to a validated multi-residue method (time of flight detection based) could not be analyzed by Orbitrap because of extensive signal suppression. This required the improvement of established extraction and clean-up procedures. The introduced, more extensive deproteinzation steps and dedicated instrumental settings successfully eliminated these detrimental suppression effects. The reported method, covering more than 100 different veterinary dugs, was validated according to the EU Commission Decision 2002/657/EEC. Validated matrices include muscle, kidney, liver, fish and honey. Significantly better performance parameters (e.g. linearity, reproducibility and detection limits) were obtained when comparing the new method with the older, TOF based method. These improvements are attributed to the higher resolution (50,000 versus 12,000 FWHM) and the superior mass stability of the of the Orbitrap over the previously utilized TOF instrument. Copyright © 2010 Elsevier B.V. All rights reserved.

  4. A dominant EV71-specific CD4+ T cell epitope is highly conserved among human enteroviruses.

    Directory of Open Access Journals (Sweden)

    Ruicheng Wei

    Full Text Available CD4+ T cell-mediated immunity plays a central role in determining the immunopathogenesis of viral infections. However, the role of CD4+ T cells in EV71 infection, which causes hand, foot and mouth disease (HFMD, has yet to be elucidated. We applied a sophisticated method to identify promiscuous CD4+ T cell epitopes contained within the sequence of the EV71 polyprotein. Fifteen epitopes were identified, and three of them are dominant ones. The most dominant epitope is highly conserved among enterovirus species, including HFMD-related coxsackieviruses, HFMD-unrelated echoviruses and polioviruses. Furthermore, the CD4+ T cells specific to the epitope indeed cross-reacted with the homolog of poliovirus 3 Sabin. Our findings imply that CD4+ T cell responses to poliovirus following vaccination, or to other enteroviruses to which individuals may be exposed in early childhood, may have a modulating effect on subsequent CD4+ T cell response to EV71 infection or vaccine.

  5. Comparative analyses reveal high levels of conserved colinearity between the finger millet and rice genomes.

    Science.gov (United States)

    Srinivasachary; Dida, Mathews M; Gale, Mike D; Devos, Katrien M

    2007-08-01

    Finger millet is an allotetraploid (2n = 4x = 36) grass that belongs to the Chloridoideae subfamily. A comparative analysis has been carried out to determine the relationship of the finger millet genome with that of rice. Six of the nine finger millet homoeologous groups corresponded to a single rice chromosome each. Each of the remaining three finger millet groups were orthologous to two rice chromosomes, and in all the three cases one rice chromosome was inserted into the centromeric region of a second rice chromosome to give the finger millet chromosomal configuration. All observed rearrangements were, among the grasses, unique to finger millet and, possibly, the Chloridoideae subfamily. Gene orders between rice and finger millet were highly conserved, with rearrangements being limited largely to single marker transpositions and small putative inversions encompassing at most three markers. Only some 10% of markers mapped to non-syntenic positions in rice and finger millet and the majority of these were located in the distal 14% of chromosome arms, supporting a possible correlation between recombination and sequence evolution as has previously been observed in wheat. A comparison of the organization of finger millet, Panicoideae and Pooideae genomes relative to rice allowed us to infer putative ancestral chromosome configurations in the grasses.

  6. A highly conserved metalloprotease effector enhances virulence in the maize anthracnose fungus Colletotrichum graminicola.

    Science.gov (United States)

    Sanz-Martín, José M; Pacheco-Arjona, José Ramón; Bello-Rico, Víctor; Vargas, Walter A; Monod, Michel; Díaz-Mínguez, José M; Thon, Michael R; Sukno, Serenella A

    2016-09-01

    Colletotrichum graminicola causes maize anthracnose, an agronomically important disease with a worldwide distribution. We have identified a fungalysin metalloprotease (Cgfl) with a role in virulence. Transcriptional profiling experiments and live cell imaging show that Cgfl is specifically expressed during the biotrophic stage of infection. To determine whether Cgfl has a role in virulence, we obtained null mutants lacking Cgfl and performed pathogenicity and live microscopy assays. The appressorium morphology of the null mutants is normal, but they exhibit delayed development during the infection process on maize leaves and roots, showing that Cgfl has a role in virulence. In vitro chitinase activity assays of leaves infected with wild-type and null mutant strains show that, in the absence of Cgfl, maize leaves exhibit increased chitinase activity. Phylogenetic analyses show that Cgfl is highly conserved in fungi. Similarity searches, phylogenetic analysis and transcriptional profiling show that C. graminicola encodes two LysM domain-containing homologues of Ecp6, suggesting that this fungus employs both Cgfl-mediated and LysM protein-mediated strategies to control chitin signalling. © 2015 BSPP and John Wiley & Sons Ltd.

  7. Pig epidermal growth factor precursor contains segments that are highly conserved among species

    DEFF Research Database (Denmark)

    Jørgensen, P E; Jensen, L.G.; Sørensen, B S

    1998-01-01

    segment with that of the human, the rat and the mouse EGF precursors, in order to identify highly conserved domains. The examined part of the precursor contains EGF itself and six so-called EGF-like modules. The overall amino acid identity among the four species is 64%. However, the amino acid identity...... differed from around 30% in some segments to around 70% in others. The highest amino acid identity, 71%, was observed for a 345-aa segment that contains three EGF-like modules and which is homologous to a part of the low-density lipoprotein receptor (LDL receptor). The amino acid identities are 64% for EGF...... itself, and 50-67% for the remaining three EGF-like modules. The segment of the LDL receptor that is homologous to a part of the EGF precursor is important for the function of the LDL receptor, and EGF-like modules seem to be involved in protein-protein interactions in a number of proteins. In conclusion...

  8. Current situation of energy conservation in high energy-consuming industries in Taiwan

    International Nuclear Information System (INIS)

    Chan, D.Y.-L.; Yang, K.-H.; Hsu, C.-H.; Chien, M.-H.; Hong, G.-B.

    2007-01-01

    Growing concern in Taiwan has arisen about energy consumption and its adverse environmental impact. The current situation of energy conservation in high energy-consuming industries in Taiwan, including the iron and steel, chemical, cement, pulp and paper, textiles and electric/electrical industries has been presented. Since the energy consumption of the top 100 energy users (T100) comprised over 50% of total industry energy consumption, focusing energy consumption reduction efforts on T100 energy users can achieve significant results. This study conducted on-site energy audits of 314 firms in Taiwan during 2000-2004, and identified potential electricity savings of 1,022,656 MWH, fuel oil savings of 174,643 kiloliters (KL), steam coal savings of 98,620 ton, and natural gas (NG) savings of 10,430 kilo cubic meters. The total potential energy saving thus was 489,505 KL of crude oil equivalent (KLOE), representing a reduction of 1,447,841 ton in the carbon dioxide emissions, equivalent to the annual carbon dioxide absorption capacity of a 39,131-ha plantation forest

  9. Consideration of microstructure evolution and residual stress measurement near severe worked surface using high energy x-ray

    International Nuclear Information System (INIS)

    Hashimoto, Tadafumi; Mochizuki, Masahito; Shobu, Takahisa

    2012-01-01

    It is necessary to establish a measurement method that can evaluate accurate stress on the surface. However, the microstructure evolution takes place near the surface due to severe plastic deformation, since structural members have been superpositioned a lot of working processes to complete. As well known, a plane stress can't be assumed on the severe worked surface. Therefore we have been proposed the measurement method that can be measured the in-depth distribution of residual stress components by using high energy X-ray from a synchrotron radiation source. There is the combination of the constant penetration depth method and tri-axial stress analysis. Measurements were performed by diffraction planes for the orientation parameter Γ=0.25 of which elastic constants are nearly equal to the mechanical one. The stress components obtained must be converted to the stress components in real space by using optimization technique, since it corresponds to the weighted average stress components associated with the attenuation of X-ray in materials. The predicted stress components distribution agrees very well with the corrected one which was measured by the conventional removal method. To verify the availability of the proposed method, thermal aging variation of residual stress components on the severe worked surface under elevated temperature was investigated using specimen superpositioned working processes (i.e., welding, machining, peening). It is clarified that the residual stress components increase with thermal aging, using the diffraction planes in hard elastic constants to the bulk. This result suggests that the thermal stability of residual stress has the dependence of the diffraction plane. (author)

  10. Conditioning of high activity solid waste: fuel claddings and dissolution residues

    International Nuclear Information System (INIS)

    Anon.

    1982-01-01

    This chapter reports on experimental studies of embedding into matrix material, the melting and conversion of zircaloy, and waste properties and characterization. Methods are developed for embedding the waste scrap into a solid and resistant matrix material in order to confine the radioactivity and to prevent it from dispersion. The matrix materials investigated are lead alloys, ceramics and compacted graphite or aluminium powder. The treatment of fuel hulls by melting or chemical conversion is described. Cemented hulls are characterized and the pyrophoricity of zircaloy fines is investigated. Topics considered include the embedding of hulls into graphite and aluminium, the embedding of hulls and dissolution residues into alumino-ceramics, the solidification of alpha-bearing wastes into a ceramic matrix, and the conditioning of cladding waste by eutectoidic melting and by embedding in glass

  11. Highly sensitive rapid fluorescence detection of protein residues on surgical instruments

    Energy Technology Data Exchange (ETDEWEB)

    Kovalev, Valeri I [School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS (United Kingdom); Bartona, James S [School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS (United Kingdom); Richardson, Patricia R [School of Chemistry, University of Edinburgh, Edinburgh, EH9 3JJ (United Kingdom); Jones, Anita C [School of Chemistry, University of Edinburgh, Edinburgh, EH9 3JJ (United Kingdom)

    2006-07-15

    There is a risk of contamination of surgical instruments by infectious protein residues, in particular, prions which are the agents for Creutzfeldt-Jakob Disease in humans. They are exceptionally resistant to conventional sterilization, therefore it is important to detect their presence as contaminants so that alternative cleaning procedures can be applied. We describe the development of an optimized detection system for fluorescently labelled protein, suitable for in-hospital use. We show that under optimum conditions the technique can detect {approx}10 attomole/cm{sup 2} with a scan speed of {approx}3-10 cm{sup 2}/s of the test instrument's surface. A theoretical analysis and experimental measurements will be discussed.

  12. Tumor residual pós-quimioterapia neoadjuvante para câncer de mama: impacto sobre o tratamento cirúrgico conservador Residual tumor after neoadjuvant chemotherapy for breast cancer: impact on conservative surgical treatment

    Directory of Open Access Journals (Sweden)

    Edison Mantovani Barbosa

    1999-05-01

    regression occurred irregularly, several refractory tumor cells remaining at the primary tumor site. Resistant tumor cells, independent of the primary tumor, were found in mammary tissue. Other histopathological findings, resulting from chemotherapy in tumoral and mammary tissues, such as calcifications and fibrosis, and in axillary homolateral lymph nodes were obtained. Conclusion: the effect of neoadjuvant chemotherapy is not uniform, refratory tumor cells remaining not only at primary tumor site, but also in distant regions. Furthermore, we found no correlation between the regression of the tumor and the axillary metastatic lymph nodes. Thus, a conservative surgery after neoadjuvant chemotherapy (FEC should be avoided.

  13. High precision conformal radiotherapy employing conservative margins in childhood benign and low-grade brain tumours

    International Nuclear Information System (INIS)

    Jalali, Rakesh; Budrukkar, Ashwini; Sarin, Rajiv; Sharma, Dayananda S.

    2005-01-01

    Background and purpose: To report local control and follow up outcome data of high precision conformal radiotherapy in childhood brain tumours. Materials and methods: Between December 1999 and December 2002, 26 children (17 boys and 9 girls, median age 11.5 years) with incompletely excised or recurrent benign and low-grade brain tumours [13 craniopharyngiomas, 11 low-grade gliomas (LGG) and 2 others] were treated with three-dimensional (3D) conformal radiotherapy (CRT) (12 patients) and stereotactic conformal radiotherapy (SCRT) (14 patients). Gross tumour volume (GTV) included neuro-imaging based visible tumour and/or resected tumour bed. Clinical target volume (CTV) consisted of GTV + 5 mm margin and planning target volume (PTV) consisted of additional 5 mm margin for CRT and 2 mm for SCRT. Treatment was delivered with 3-9 conformal fixed fields to a median dose of 54 Gy/30 fractions. Results: The actuarial 2 and 3 year disease free and overall survival was 96 and 100%, respectively (median follow up: 25 months, range 12-47 months). Radiological follow up available in 25 patients revealed complete response in 1, partial regression in 10, stable disease in 13 and progression in 1 patient (within the CTV). One patient with craniopharyngioma on a routine imaging revealed a mild asymptomatic cyst enlargement, which resolved with conservative management. A patient with chiasmatic glioma developed cystic degeneration and hydrocephalus 9 months after SCRT requiring cyst drainage and placement of a ventriculoperitoneal shunt. Conclusion: High-precision conformal techniques delivering irradiation to a computer generated target volume employing 7-10 mm 3D margins beyond the visible tumour and/or resected tumour bed appear to be safe in children with incompletely resected or recurrent benign and low-grade brain tumours, based on these data

  14. Accuracy of high-field intraoperative MRI in the detectability of residual tumor in glioma grade IV resections

    Energy Technology Data Exchange (ETDEWEB)

    Hesselmann, Volker; Mager, Ann-Kathrin [Asklepios-Klinik Nord, Hamburg (Germany). Radiology/Neurologie; Goetz, Claudia; Kremer, Paul [Asklepios-Klinik Nord, Hamburg (Germany). Dept. of Neurosurgery; Detsch, Oliver [Asklepios-Klinik Nord, Hamburg (Germany). Dept. of Anaesthesiology and Intensive Care Medicine; Theisgen, Hannah-Katharina [Universitaetsklinikum Schleswig-Holstein, Kiel (Germany). Dept. of Neurosurgery; Friese, Michael; Gottschalk, Joachim [Asklepios-Klinik Nord, Hamburg (Germany). Dept. of Pathology and Neuropathology; Schwindt, Wolfram [Univ. Hospital Muenster (Germany). Dept. of Clinical Radiology

    2017-06-15

    To assess the sensitivity/specificity of tumor detection by T1 contrast enhancement in intraoperative MRI (ioMRI) in comparison to histopathological assessment as the gold standard in patients receiving surgical resection of grade IV glioblastoma. 68 patients with a primary or a recurrent glioblastoma scheduled for surgery including fluorescence guidance and neuronavigation were included (mean age: 59 years, 26 female, 42 male patients). The ioMRI after the first resection included transverse FLAIR, DWI, T2-FFE and T1 - 3 d FFE ± GD-DPTA. The second resection was performed whenever residual contrast-enhancing tissue was detected on ioMRI. Resected tissue samples were histopathologically evaluated (gold standard). Additionally, we evaluated the early postoperative MRI scan acquired within 48 h post-OP for remaining enhancing tissue and compared them with the ioMRI scan. In 43 patients ioMRI indicated residual tumorous tissue, which could be confirmed in the histological specimens of the second resection. In 16 (4 with recurrent, 12 with primary glioblastoma) cases, ioMRI revealed truly negative results without residual tumor and follow-up MRI confirmed complete resection. In 7 cases (3 with recurrent, 4 with primary glioblastoma) ioMRI revealed a suspicious result without tumorous tissue in the histopathological workup. In 2 (1 for each group) patients, residual tumorous tissue was detected in spite of negative ioMRI. IoMRI had a sensitivity of 95 % (94 % recurrent and 96 % for primary glioblastoma) and a specificity of 69.5 % (57 % and 75 %, respectively). The positive predictive value was 86 % (84 % for recurrent and 87 % for primary glioblastoma), and the negative predictive value was 88 % (80 % and 92 %, respectively). ioMRI is effective for detecting remaining tumorous tissue after glioma resection. However, scars and leakage of contrast agent can be misleading and limit specificity. Intraoperative MRI (ioMRI) presents with a high sensitivity for residual

  15. Accuracy of high-field intraoperative MRI in the detectability of residual tumor in glioma grade IV resections

    International Nuclear Information System (INIS)

    Hesselmann, Volker; Mager, Ann-Kathrin; Goetz, Claudia; Kremer, Paul; Detsch, Oliver; Theisgen, Hannah-Katharina; Friese, Michael; Gottschalk, Joachim; Schwindt, Wolfram

    2017-01-01

    To assess the sensitivity/specificity of tumor detection by T1 contrast enhancement in intraoperative MRI (ioMRI) in comparison to histopathological assessment as the gold standard in patients receiving surgical resection of grade IV glioblastoma. 68 patients with a primary or a recurrent glioblastoma scheduled for surgery including fluorescence guidance and neuronavigation were included (mean age: 59 years, 26 female, 42 male patients). The ioMRI after the first resection included transverse FLAIR, DWI, T2-FFE and T1 - 3 d FFE ± GD-DPTA. The second resection was performed whenever residual contrast-enhancing tissue was detected on ioMRI. Resected tissue samples were histopathologically evaluated (gold standard). Additionally, we evaluated the early postoperative MRI scan acquired within 48 h post-OP for remaining enhancing tissue and compared them with the ioMRI scan. In 43 patients ioMRI indicated residual tumorous tissue, which could be confirmed in the histological specimens of the second resection. In 16 (4 with recurrent, 12 with primary glioblastoma) cases, ioMRI revealed truly negative results without residual tumor and follow-up MRI confirmed complete resection. In 7 cases (3 with recurrent, 4 with primary glioblastoma) ioMRI revealed a suspicious result without tumorous tissue in the histopathological workup. In 2 (1 for each group) patients, residual tumorous tissue was detected in spite of negative ioMRI. IoMRI had a sensitivity of 95 % (94 % recurrent and 96 % for primary glioblastoma) and a specificity of 69.5 % (57 % and 75 %, respectively). The positive predictive value was 86 % (84 % for recurrent and 87 % for primary glioblastoma), and the negative predictive value was 88 % (80 % and 92 %, respectively). ioMRI is effective for detecting remaining tumorous tissue after glioma resection. However, scars and leakage of contrast agent can be misleading and limit specificity. Intraoperative MRI (ioMRI) presents with a high sensitivity for residual

  16. A highly conserved glycine within linker I and the extreme C terminus of G protein alpha subunits interact cooperatively in switching G protein-coupled receptor-to-effector specificity

    DEFF Research Database (Denmark)

    Kostenis, Evi; Martini, Lene; Ellis, James

    2004-01-01

    Numerous studies have attested to the importance of the extreme C terminus of G protein alpha subunits in determining their selectivity of receptor recognition. We have previously reported that a highly conserved glycine residue within linker I is important for constraining the fidelity of receptor...... recognition by Galpha(q) proteins. Herein, we explored whether both modules (linker I and extreme C terminus) interact cooperatively in switching G protein-coupled receptor (GPCR)-to-effector specificity and created as models mutant Galpha(q) proteins in which glycine was replaced with various amino acids...... and the C-terminal five Galpha(q) residues with the corresponding Galpha(i) or Galpha(s) sequence. Coupling properties of the mutated Galpha(q) proteins were determined after coexpression with a panel of 13 G(i)-and G(s) -selective receptors and compared with those of Galpha proteins modified in only one...

  17. Silicone Wristband Passive Samplers Yield Highly Individualized Pesticide Residue Exposure Profiles.

    Science.gov (United States)

    Aerts, Raf; Joly, Laure; Szternfeld, Philippe; Tsilikas, Khariklia; De Cremer, Koen; Castelain, Philippe; Aerts, Jean-Marie; Van Orshoven, Jos; Somers, Ben; Hendrickx, Marijke; Andjelkovic, Mirjana; Van Nieuwenhuyse, An

    2018-01-02

    Monitoring human exposure to pesticides and pesticide residues (PRs) remains crucial for informing public health policies, despite strict regulation of plant protection product and biocide use. We used 72 low-cost silicone wristbands as noninvasive passive samplers to assess cumulative 5-day exposure of 30 individuals to polar PRs. Ethyl acetate extraction and LC-MS/MS analysis were used for the identification of PRs. Thirty-one PRs were detected of which 15 PRs (48%) were detected only in worn wristbands, not in environmental controls. The PRs included 16 fungicides (52%), 8 insecticides (26%), 2 herbicides (6%), 3 pesticide derivatives (10%), 1 insect repellent (3%), and 1 pesticide synergist (3%). Five detected pesticides were not approved for plant protection use in the EU. Smoking and dietary habits that favor vegetable consumption were associated with higher numbers and higher cumulative concentrations of PRs in wristbands. Wristbands featured unique PR combinations. Our results suggest both environment and diet contributed to PR exposure in our study group. Silicone wristbands could serve as sensitive passive samplers to screen population-wide cumulative dietary and environmental exposure to authorized, unauthorized and banned pesticides.

  18. RNA expression in a cartilaginous fish cell line reveals ancient 3′ noncoding regions highly conserved in vertebrates

    Science.gov (United States)

    Forest, David; Nishikawa, Ryuhei; Kobayashi, Hiroshi; Parton, Angela; Bayne, Christopher J.; Barnes, David W.

    2007-01-01

    We have established a cartilaginous fish cell line [Squalus acanthias embryo cell line (SAE)], a mesenchymal stem cell line derived from the embryo of an elasmobranch, the spiny dogfish shark S. acanthias. Elasmobranchs (sharks and rays) first appeared >400 million years ago, and existing species provide useful models for comparative vertebrate cell biology, physiology, and genomics. Comparative vertebrate genomics among evolutionarily distant organisms can provide sequence conservation information that facilitates identification of critical coding and noncoding regions. Although these genomic analyses are informative, experimental verification of functions of genomic sequences depends heavily on cell culture approaches. Using ESTs defining mRNAs derived from the SAE cell line, we identified lengthy and highly conserved gene-specific nucleotide sequences in the noncoding 3′ UTRs of eight genes involved in the regulation of cell growth and proliferation. Conserved noncoding 3′ mRNA regions detected by using the shark nucleotide sequences as a starting point were found in a range of other vertebrate orders, including bony fish, birds, amphibians, and mammals. Nucleotide identity of shark and human in these regions was remarkably well conserved. Our results indicate that highly conserved gene sequences dating from the appearance of jawed vertebrates and representing potential cis-regulatory elements can be identified through the use of cartilaginous fish as a baseline. Because the expression of genes in the SAE cell line was prerequisite for their identification, this cartilaginous fish culture system also provides a physiologically valid tool to test functional hypotheses on the role of these ancient conserved sequences in comparative cell biology. PMID:17227856

  19. High risks of losing genetic diversity in an endemic Mauritian gecko: implications for conservation.

    Directory of Open Access Journals (Sweden)

    Steeves Buckland

    Full Text Available Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko, is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA markers in 13 subpopulations to: (i assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii estimate effective population sizes and migration rates of subpopulations; and (iii examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable

  20. The existence of High Conservation Value Forest (HCVF in Perum Perhutani KPH Kendal to support Implementation of FSC Certification

    Directory of Open Access Journals (Sweden)

    Sulistyowati Sri

    2018-01-01

    Full Text Available High Conservation Value Forest (HCVF is the identification of High Conservation Values that are important and need to be protected. Under FSC certification mechanism, HCVF becomes one of Principles and Criteria to attain certification. In this study, we identify the existence of HCVF in Perum Perhutani KPH Kendal to support implementation process of FSC certification. Qualitative method was conducted through observation and secondary data from Perum Perhutani KPH Kendal. Data analysis showed through ecolabel certification, Perum Perhutani KPH Kendal has been identified HCVF area covering 2,715.5 hectares consists of HCV 1 until 6. Secondary Natural Forest (HAS Subah and Kaliwungu for Ulolanang and Pagerwunung Nature Reserve buffer zone include as HCV 1.1, conservation area of leopard (Panthera pardus melas and Pangolin (Manis javanica.for HCV 1.2, conservation area of lutung (Trachypiyhecus auratus as endemic species for CITES App I and Critically Endangered species include as HCV 1.3, Goa kiskendo for bats species habitat include as HCV 1.4, regions of interest species for Deer (Cervus timorensis and Kepodang (Oriolus chinensis as HCV 2.3, Germplasm Protection Region/ KPPN area with high biodiversity include as HCV 3, river border area and water springs for HCV 4. While, utilization of firewood, grass for cattle fodder include as HCV 5 and 14 cultural sites include as HCV 6. From monitoring and evaluation of HCVF data, showed that in 2011-2015 the level of diversity for flora and fauna were increased.

  1. The existence of High Conservation Value Forest (HCVF) in Perum Perhutani KPH Kendal to support Implementation of FSC Certification

    Science.gov (United States)

    Sulistyowati, Sri; Hadi, Sudharto P.

    2018-02-01

    High Conservation Value Forest (HCVF) is the identification of High Conservation Values that are important and need to be protected. Under FSC certification mechanism, HCVF becomes one of Principles and Criteria to attain certification. In this study, we identify the existence of HCVF in Perum Perhutani KPH Kendal to support implementation process of FSC certification. Qualitative method was conducted through observation and secondary data from Perum Perhutani KPH Kendal. Data analysis showed through ecolabel certification, Perum Perhutani KPH Kendal has been identified HCVF area covering 2,715.5 hectares consists of HCV 1 until 6. Secondary Natural Forest (HAS) Subah and Kaliwungu for Ulolanang and Pagerwunung Nature Reserve buffer zone include as HCV 1.1, conservation area of leopard (Panthera pardus melas) and Pangolin (Manis javanica).for HCV 1.2, conservation area of lutung (Trachypiyhecus auratus) as endemic species for CITES App I and Critically Endangered species include as HCV 1.3, Goa kiskendo for bats species habitat include as HCV 1.4, regions of interest species for Deer (Cervus timorensis) and Kepodang (Oriolus chinensis) as HCV 2.3, Germplasm Protection Region/ KPPN area with high biodiversity include as HCV 3, river border area and water springs for HCV 4. While, utilization of firewood, grass for cattle fodder include as HCV 5 and 14 cultural sites include as HCV 6. From monitoring and evaluation of HCVF data, showed that in 2011-2015 the level of diversity for flora and fauna were increased.

  2. Tsetse salivary gland proteins 1 and 2 are high affinity nucleic acid binding proteins with residual nuclease activity.

    Directory of Open Access Journals (Sweden)

    Guy Caljon

    Full Text Available Analysis of the tsetse fly salivary gland EST database revealed the presence of a highly enriched cluster of putative endonuclease genes, including tsal1 and tsal2. Tsal proteins are the major components of tsetse fly (G. morsitans morsitans saliva where they are present as monomers as well as high molecular weight complexes with other saliva proteins. We demonstrate that the recombinant tsetse salivary gland proteins 1&2 (Tsal1&2 display DNA/RNA non-specific, high affinity nucleic acid binding with K(D values in the low nanomolar range and a non-exclusive preference for duplex. These Tsal proteins exert only a residual nuclease activity with a preference for dsDNA in a broad pH range. Knockdown of Tsal expression by in vivo RNA interference in the tsetse fly revealed a partially impaired blood digestion phenotype as evidenced by higher gut nucleic acid, hematin and protein contents.

  3. High quality residues from cover crops favor changes in microbial community and enhance C and N sequestration

    Directory of Open Access Journals (Sweden)

    Ileana Frasier

    2016-04-01

    Full Text Available The objective of the study was to evaluate the effect of a change in management on the soil microbial community and C sequestration. We conducted a 3-year field study in La Pampa (Argentina with rotation of sorghum (Sorghum bicolor in zero tillage alternating with rye (Secale cereale and vetch (Vicia villosa ssp. dasycarpa. Soil was sampled once a year at two depths. Soil organic matter fractions, dissolved organic matter, microbial biomass (MBC and community composition (DNA extraction, qPCR, and phospholipid FAME profiles were determined. Litter, aerial- and root biomass were collected and all material was analyzed for C and N. Results showed a rapid response of microbial biomass to a bacterial dominance independent of residue quality. Vetch had the highest diversity index, while the fertilized treatment had the lowest one. Vetch–sorghum rotation with high N mineralization rates and diverse microbial community sequestered more C and N in stable soil organic matter fractions than no-till sorghum alone or with rye, which had lower N turnover rates. These results reaffirm the importance of enhanced soil biodiversity for maintaining soil ecosystem functioning and services. The supply of high amounts of N-rich residues as provided by grass–legume cover crops could fulfill this objective.

  4. High hole mobility p-type GaN with low residual hydrogen concentration prepared by pulsed sputtering

    Science.gov (United States)

    Arakawa, Yasuaki; Ueno, Kohei; Kobayashi, Atsushi; Ohta, Jitsuo; Fujioka, Hiroshi

    2016-08-01

    We have grown Mg-doped GaN films with low residual hydrogen concentration using a low-temperature pulsed sputtering deposition (PSD) process. The growth system is inherently hydrogen-free, allowing us to obtain high-purity Mg-doped GaN films with residual hydrogen concentrations below 5 × 1016 cm-3, which is the detection limit of secondary ion mass spectroscopy. In the Mg profile, no memory effect or serious dopant diffusion was detected. The as-deposited Mg-doped GaN films showed clear p-type conductivity at room temperature (RT) without thermal activation. The GaN film doped with a low concentration of Mg (7.9 × 1017 cm-3) deposited by PSD showed hole mobilities of 34 and 62 cm2 V-1 s-1 at RT and 175 K, respectively, which are as high as those of films grown by a state-of-the-art metal-organic chemical vapor deposition apparatus. These results indicate that PSD is a powerful tool for the fabrication of GaN-based vertical power devices.

  5. PCA determination of the radiometric noise of high spectral resolution infrared observations from spectral residuals: Application to IASI

    Science.gov (United States)

    Serio, C.; Masiello, G.; Camy-Peyret, C.; Jacquette, E.; Vandermarcq, O.; Bermudo, F.; Coppens, D.; Tobin, D.

    2018-02-01

    The problem of characterizing and estimating the instrumental or radiometric noise of satellite high spectral resolution infrared spectrometers directly from Earth observations is addressed in this paper. An approach has been developed, which relies on the Principal Component Analysis (PCA) with a suitable criterion to select the optimal number of PC scores. Different selection criteria have been set up and analysed, which is based on the estimation theory of Least Squares and/or Maximum Likelihood Principle. The approach is independent of any forward model and/or radiative transfer calculations. The PCA is used to define an orthogonal basis, which, in turn, is used to derive an optimal linear reconstruction of the observations. The residual vector that is the observation vector minus the calculated or reconstructed one is then used to estimate the instrumental noise. It will be shown that the use of the spectral residuals to assess the radiometric instrumental noise leads to efficient estimators, which are largely independent of possible departures of the true noise from that assumed a priori to model the observational covariance matrix. Application to the Infrared Atmospheric Sounder Interferometer (IASI) has been considered. A series of case studies has been set up, which make use of IASI observations. As a major result, the analysis confirms the high stability and radiometric performance of IASI. The approach also proved to be efficient in characterizing noise features due to mechanical micro-vibrations of the beam splitter of the IASI instrument.

  6. Technique for the residual life assessment of high temperature components based on creep-rupture testing on welded miniature specimens

    Energy Technology Data Exchange (ETDEWEB)

    Garzillo, A.; Guardamagna, C.; Moscotti, L.; Ranzani, L. [Ente Nazionale per l`Energia Elettrica, Milan (Italy)

    1995-06-01

    Following the present trend in the development of advanced methodologies for residual life assessment of high temperature components operating in power plants, particularly in non destructive methods, a testing technique has been set up at ENEL-CRAM based on creep-rupture testa in an argon on welded miniature specimens. Five experimental systems for creep-rupture tests in an argon atmosphere have been set up which include high accuracy systems, vacuum chambers and exrwnsometer devices. With the aim of establishing and validating the suitability of the experimental methodology, creep-rupture and interrupted creep testing programmes have been performed on miniature specimens (2 mm diameter and 10 mm gauge lenght). On the basis of experience gathered by various European research laboratories, a miniature specimen construction procedure has been developed using a laser welding technique for joining threaded heads to sample material. Low alloy ferritic steels, such as virgin 2.25CrlMo, 0.5Cr 0.5Mo 0.25V, and IN 738 superalloy miniature specimens have been investigated and the results, compared with those from standard specimens, show a regular trend in deformation vs time. Additional efforts to provide guidelines for material sampling from each plant component will be required in order to reduce uncertainties in residual life prediction.

  7. Utilization of HSC-ROSE residue as coking aid for the production of high quality coke from brown coal

    Energy Technology Data Exchange (ETDEWEB)

    Bohlmann, D.; Limmer, H.; Naundorf, W.; Hood, R.L.; Washimi, K. (VEB Petrolchemisches Kombinat, Schwedt (German Democratic Republic))

    1989-04-01

    Evaluates suitability of HSC-ROSE petroleum pitch as binder for production of brown coal coke. This pitch has been available in the GDR since installation in 1988 of a 750 kt/a HSC (high conversion soaker cracking) plant, which processes 360 C visbreaker residue from Soviet crude oil, and the building of a ROSE (residue oil supercritical reaction) plant. Laboratory as well as semi-industrial experiments were carried out at the Freiberg Academy, GDR on pulverizing, briquetting and coking various brown coal types with HSC-ROSE pitch. Briquetting and coking results are shown in tables. Experiments showed that the resulting coke has 124% higher compression strength and 100% higher abrasion strength than regular brown coal coke without HSC-ROSE binder. The high quality coke is adequate for use as metallurgical blast furnace coke. An economic assessment of modifying an existing brown coal coking plant to process 2 Mt/a brown coal with 10% pitch binder is made. Required investment amounts to 54 million US dollars, estimated annual profits based on 1987 prices are 19.5 million US dollars. 4 refs.

  8. High-frequency ultrasound for intraoperative margin assessments in breast conservation surgery: a feasibility study

    International Nuclear Information System (INIS)

    Doyle, Timothy E; Neumayer, Leigh A; Factor, Rachel E; Ellefson, Christina L; Sorensen, Kristina M; Ambrose, Brady J; Goodrich, Jeffrey B; Hart, Vern P; Jensen, Scott C; Patel, Hemang

    2011-01-01

    In addition to breast imaging, ultrasound offers the potential for characterizing and distinguishing between benign and malignant breast tissues due to their different microstructures and material properties. The aim of this study was to determine if high-frequency ultrasound (20-80 MHz) can provide pathology sensitive measurements for the ex vivo detection of cancer in margins during breast conservation surgery. Ultrasonic tests were performed on resected margins and other tissues obtained from 17 patients, resulting in 34 specimens that were classified into 15 pathology categories. Pulse-echo and through-transmission measurements were acquired from a total of 57 sites on the specimens using two single-element 50-MHz transducers. Ultrasonic attenuation and sound speed were obtained from time-domain waveforms. The waveforms were further processed with fast Fourier transforms to provide ultrasonic spectra and cepstra. The ultrasonic measurements and pathology types were analyzed for correlations. The specimens were additionally re-classified into five pathology types to determine specificity and sensitivity values. The density of peaks in the ultrasonic spectra, a measure of spectral structure, showed significantly higher values for carcinomas and precancerous pathologies such as atypical ductal hyperplasia than for normal tissue. The slopes of the cepstra for non-malignant pathologies displayed significantly greater values that differentiated them from the normal and malignant tissues. The attenuation coefficients were sensitive to fat necrosis, fibroadenoma, and invasive lobular carcinoma. Specificities and sensitivities for differentiating pathologies from normal tissue were 100% and 86% for lobular carcinomas, 100% and 74% for ductal carcinomas, 80% and 82% for benign pathologies, and 80% and 100% for fat necrosis and adenomas. Specificities and sensitivities were also determined for differentiating each pathology type from the other four using a multivariate

  9. High-frequency ultrasound for intraoperative margin assessments in breast conservation surgery: a feasibility study

    Directory of Open Access Journals (Sweden)

    Hart Vern P

    2011-10-01

    Full Text Available Abstract Background In addition to breast imaging, ultrasound offers the potential for characterizing and distinguishing between benign and malignant breast tissues due to their different microstructures and material properties. The aim of this study was to determine if high-frequency ultrasound (20-80 MHz can provide pathology sensitive measurements for the ex vivo detection of cancer in margins during breast conservation surgery. Methods Ultrasonic tests were performed on resected margins and other tissues obtained from 17 patients, resulting in 34 specimens that were classified into 15 pathology categories. Pulse-echo and through-transmission measurements were acquired from a total of 57 sites on the specimens using two single-element 50-MHz transducers. Ultrasonic attenuation and sound speed were obtained from time-domain waveforms. The waveforms were further processed with fast Fourier transforms to provide ultrasonic spectra and cepstra. The ultrasonic measurements and pathology types were analyzed for correlations. The specimens were additionally re-classified into five pathology types to determine specificity and sensitivity values. Results The density of peaks in the ultrasonic spectra, a measure of spectral structure, showed significantly higher values for carcinomas and precancerous pathologies such as atypical ductal hyperplasia than for normal tissue. The slopes of the cepstra for non-malignant pathologies displayed significantly greater values that differentiated them from the normal and malignant tissues. The attenuation coefficients were sensitive to fat necrosis, fibroadenoma, and invasive lobular carcinoma. Specificities and sensitivities for differentiating pathologies from normal tissue were 100% and 86% for lobular carcinomas, 100% and 74% for ductal carcinomas, 80% and 82% for benign pathologies, and 80% and 100% for fat necrosis and adenomas. Specificities and sensitivities were also determined for differentiating each

  10. Impacts of weld residual stresses and fatigue crack growth threshold on crack arrest under high-cycle thermal fluctuations

    International Nuclear Information System (INIS)

    Taheri, Said; Julan, Emricka; Tran, Xuan-Van; Robert, Nicolas

    2017-01-01

    Highlights: • For crack growth analysis, weld residual stress field must be considered through its SIF in presence of a crack. • Presence of cracks of same depth proves their arrest, where equal depth is because mean stress acts only on crack opening. • Not considering amplitudes under a fatigue crack growth threshold (FCGT) does not compensate the lack of FGCT in Paris law. • Propagation rates are close for axisymmetric and circumferential semi-elliptical cracks. - Abstract: High cycle thermal crazing has been observed in some residual heat removal (RHR) systems made of 304 stainless steel in PWR nuclear plants. This paper deals with two types of analyses including logical argumentation and simulation. Crack arrest in networks is demonstrated due to the presence of two cracks of the same depth in the network. This identical depth may be proved assuming that mean stress acts only on crack opening and that cracks are fully open during the load cycle before arrest. Weld residual stresses (WRS) are obtained by an axisymmetric simulation of welding on a tube with a chamfer. Axisymmetric and 3D parametric studies of crack growth on: representative sequences for variable amplitude thermal loading, fatigue crack growth threshold (FCGT), permanent mean stress, cyclic counting methods and WRS, are performed with Code-Aster software using XFEM methodology. The following results are obtained on crack depth versus time: the effect of WRS on crack growth cannot be determined by the initial WRS field in absence of crack, but by the associated stress intensity factor. Moreover the relation between crack arrest depth and WRS is analyzed. In the absence of FCGT Paris’s law may give a significant over-estimation of crack depth even if amplitudes of loading smaller than FCGT have not been considered. Appropriate depth versus time may be obtained using different values of FCGT, but axisymmetric simulations do not really show a possibility of arrest for shallow cracks in

  11. Impacts of weld residual stresses and fatigue crack growth threshold on crack arrest under high-cycle thermal fluctuations

    Energy Technology Data Exchange (ETDEWEB)

    Taheri, Said, E-mail: Said.taheri@edf.fr [EDF-LAB, IMSIA, 7 Boulevard Gaspard Monge, 91120 Palaiseau Cedex (France); Julan, Emricka [EDF-LAB, AMA, 7 Boulevard Gaspard Monge, 91120 Palaiseau Cedex (France); Tran, Xuan-Van [EDF Energy R& D UK Centre/School of Mechanical, Aerospace and Civil Engineering, The University of Manchester, Manchester M13 9PL (United Kingdom); Robert, Nicolas [EDF-DPN, UNIE, Strategic Center, Saint Denis (France)

    2017-01-15

    Highlights: • For crack growth analysis, weld residual stress field must be considered through its SIF in presence of a crack. • Presence of cracks of same depth proves their arrest, where equal depth is because mean stress acts only on crack opening. • Not considering amplitudes under a fatigue crack growth threshold (FCGT) does not compensate the lack of FGCT in Paris law. • Propagation rates are close for axisymmetric and circumferential semi-elliptical cracks. - Abstract: High cycle thermal crazing has been observed in some residual heat removal (RHR) systems made of 304 stainless steel in PWR nuclear plants. This paper deals with two types of analyses including logical argumentation and simulation. Crack arrest in networks is demonstrated due to the presence of two cracks of the same depth in the network. This identical depth may be proved assuming that mean stress acts only on crack opening and that cracks are fully open during the load cycle before arrest. Weld residual stresses (WRS) are obtained by an axisymmetric simulation of welding on a tube with a chamfer. Axisymmetric and 3D parametric studies of crack growth on: representative sequences for variable amplitude thermal loading, fatigue crack growth threshold (FCGT), permanent mean stress, cyclic counting methods and WRS, are performed with Code-Aster software using XFEM methodology. The following results are obtained on crack depth versus time: the effect of WRS on crack growth cannot be determined by the initial WRS field in absence of crack, but by the associated stress intensity factor. Moreover the relation between crack arrest depth and WRS is analyzed. In the absence of FCGT Paris’s law may give a significant over-estimation of crack depth even if amplitudes of loading smaller than FCGT have not been considered. Appropriate depth versus time may be obtained using different values of FCGT, but axisymmetric simulations do not really show a possibility of arrest for shallow cracks in

  12. Fracture and Residual Characterization of Tungsten Carbide Cobalt Coatings on High Strength Steel

    National Research Council Canada - National Science Library

    Parker, Donald S

    2003-01-01

    Tungsten carbide cobalt coatings applied via high velocity oxygen fuel thermal spray deposition are essentially anisotropic composite structures with aggregates of tungsten carbide particles bonded...

  13. Geometrid moth assemblages reflect high conservation value of naturally regenerated secondary forests in temperate China

    NARCIS (Netherlands)

    Zou, Yi; Sang, Weiguo; Warren-Thomas, Eleanor; Axmacher, Jan Christoph

    2016-01-01

    The widespread destruction of mature forests in China has led to massive ecological degradation, counteracted in recent decades by substantial efforts to promote forest plantations and protect secondary forest ecosystems. The value of the resulting forests for biodiversity conservation is widely

  14. Liberals, Conservatives and Romantic Nationalists in Interwar Education Policy in Greece: "The High Mountains" Episode

    Science.gov (United States)

    Athanasiades, Harris

    2015-01-01

    Greek historiography of interwar education policy unproblematically accepts the assumption that the bone of contention between the "Liberal demoticists" and the "Conservative purists" was the language issue; particularly whether "demotic" or "katharevousa" should be the language of instruction in schooling.…

  15. Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes.

    NARCIS (Netherlands)

    Snel, B.; Noort, V. van; Huynen, M.A.

    2004-01-01

    Differences between species have been suggested to largely reside in the network of connections among the genes. Nevertheless, the rate at which these connections evolve has not been properly quantified. Here, we measure the extent to which co-regulation between pairs of genes is conserved over

  16. Analyses of residual iron in carbon nanotubes produced by camphor/ferrocene pyrolysis and purified by high temperature annealing

    Energy Technology Data Exchange (ETDEWEB)

    Antunes, E.F., E-mail: ericafa@las.inpe.br [Instituto Tecnologico de Aeronautica (ITA), Praca Marechal Eduardo Gomes, 50, CEP 12.228-900, Sao Jose dos Campos, SP (Brazil); Instituto Nacional de Pesquisas Espaciais (INPE), Av. dos Astronautas, 1758, CEP 12.227-010, Sao Jose dos Campos, SP (Brazil); Resende, V.G. de; Mengui, U.A. [Instituto Nacional de Pesquisas Espaciais (INPE), Av. dos Astronautas, 1758, CEP 12.227-010, Sao Jose dos Campos, SP (Brazil); Cunha, J.B.M. [Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Goncalves, 9500, CEP 91.501-970, Porto Alegre, RS (Brazil); Corat, E.J.; Massi, M. [Instituto Nacional de Pesquisas Espaciais (INPE), Av. dos Astronautas, 1758, CEP 12.227-010, Sao Jose dos Campos, SP (Brazil)

    2011-07-01

    A detailed analysis of iron-containing phases in multiwall carbon nanotube (MWCNT) powder was carried out. The MWCNTs were produced by camphor/ferrocene and purified by high temperature annealing in an oxygen-free atmosphere (N{sub 2} or VC). Thermogravimetric analysis, Moessbauer spectroscopy, X-ray diffraction and X-ray photoelectron spectroscopy enabled the evaluation of the residual iron in MWCNTs after purification. The VC treatments provided MWCNTs with a purity degree higher than 99%. Moreover, Raman spectroscopy revealed a significant improvement in graphitic ordering after thermal annealing. A brief description of the mechanism of iron removal was included. We highlight the mobility of iron atoms through graphitic sheets and the large contact angle of iron clusters formed on MWCNT surfaces at high temperatures.

  17. Androgen receptor status is highly conserved during tumor progression of breast cancer.

    Science.gov (United States)

    Grogg, André; Trippel, Mafalda; Pfaltz, Katrin; Lädrach, Claudia; Droeser, Raoul A; Cihoric, Nikola; Salhia, Bodour; Zweifel, Martin; Tapia, Coya

    2015-11-09

    highly conserved during tumor progression and a change only occurs in a small fraction (4.1 %). Our study supports the notion that targeting AR could be effective for many BC patients and that re-testing of AR status in formerly negative or mixed type BC's is recommended.

  18. Androgen receptor status is highly conserved during tumor progression of breast cancer

    International Nuclear Information System (INIS)

    Grogg, André; Trippel, Mafalda; Pfaltz, Katrin; Lädrach, Claudia; Droeser, Raoul A.; Cihoric, Nikola; Salhia, Bodour; Zweifel, Martin; Tapia, Coya

    2015-01-01

    With the advent of new and more efficient anti-androgen drugs targeting androgen receptor (AR) in breast cancer (BC) is becoming an increasingly important area of investigation. This would potentially be most useful in triple negative BC (TNBC), where better therapies are still needed. The assessment of AR status is generally performed on the primary tumor even if the tumor has already metastasized. Very little is known regarding discrepancies of AR status during tumor progression. To determine the prevalence of AR positivity, with emphasis on TNBCs, and to investigate AR status during tumor progression, we evaluated a large series of primary BCs and matching metastases and recurrences. AR status was performed on 356 primary BCs, 135 matching metastases, and 12 recurrences using a next-generation Tissue Microarray (ngTMA). A commercially available AR antibody was used to determine AR-status by immunohistochemistry. AR positivity was defined as any nuclear staining in tumor cells ≥1 %. AR expression was correlated with pathological tumor features of the primary tumor. Additionally, the concordance rate of AR expression between the different tumor sites was determined. AR status was positive in: 87 % (307/353) of primary tumors, 86.1 % (105/122) of metastases, and in 66.7 % (8/12) of recurrences. TNBC tested positive in 11.4 %, (4/35) of BCs. A discrepant result was seen in 4.3 % (5/117) of primary BC and matching lymph node (LN) metastases. Three AR negative primary BCs were positive in the matching LN metastasis, representing 17.6 % of all negative BCs with lymph node metastases (3/17). Two AR positive primary BCs were negative in the matching LN metastasis, representing 2.0 % of all AR positive BCs with LN metastases (2/100). No discrepancies were seen between primary BC and distant metastases or recurrence (n = 17). Most primary (87 %) and metastasized (86.1 %) BCs are AR positive including a significant fraction of TNBCs (11.4 %). Further, AR status is highly

  19. Conservation hotspots for the turtles on the high seas of the Atlantic Ocean.

    Directory of Open Access Journals (Sweden)

    Hsiang-Wen Huang

    Full Text Available Understanding the distribution of bycaught sea turtles could inform conservation strategies and priorities. This research analyses the distribution of turtles caught as longline fisheries bycatch on the high seas of the Atlantic Ocean. This research collected 18,142 bycatch observations and 47.1 million hooks from large-scale Taiwanese longline vessels in the Atlantic Ocean from June 2002 to December 2013. The coverage rates were ranged from 0.48% to 17.54% by year. Seven hundred and sixty-seven turtles were caught, and the major species were leatherback (59.8%, olive ridley (27.1% and loggerhead turtles (8.7%. Most olive ridley (81.7% and loggerhead (82.1% turtles were hooked, while the leatherbacks were both hooked (44.0% and entangled (31.8%. Depending on the species, 21.4% to 57.7% were dead when brought onboard. Most of the turtles were caught in tropical areas, especially in the Gulf of Guinea (15°N-10°S, 30°W-10°E, but loggerheads were caught in the south Atlantic Ocean (25°S-35°S, 40°W-10°E and 30°S-40°S, 55°W-45°W. The bycatch rate was the highest at 0.030 per 1000 hooks for leatherbacks in the tropical area. The bycatch rates of olive ridley ranged from 0 to 0.010 per thousand hooks. The loggerhead bycatch rates were higher in the northern and southern Atlantic Ocean and ranged from 0.0128 to 0.0239 per thousand hooks. Due to the characteristics of the Taiwanese deep-set longline fleet, bycatch rates were lower than those of coastal longline fisheries, but mortality rates were higher because of the long hours of operation. Gear and bait modification should be considered to reduce sea turtle bycatch and increase survival rates while reducing the use of shallow hooks would also be helpful.

  20. Conservation hotspots for the turtles on the high seas of the Atlantic Ocean.

    Science.gov (United States)

    Huang, Hsiang-Wen

    2015-01-01

    Understanding the distribution of bycaught sea turtles could inform conservation strategies and priorities. This research analyses the distribution of turtles caught as longline fisheries bycatch on the high seas of the Atlantic Ocean. This research collected 18,142 bycatch observations and 47.1 million hooks from large-scale Taiwanese longline vessels in the Atlantic Ocean from June 2002 to December 2013. The coverage rates were ranged from 0.48% to 17.54% by year. Seven hundred and sixty-seven turtles were caught, and the major species were leatherback (59.8%), olive ridley (27.1%) and loggerhead turtles (8.7%). Most olive ridley (81.7%) and loggerhead (82.1%) turtles were hooked, while the leatherbacks were both hooked (44.0%) and entangled (31.8%). Depending on the species, 21.4% to 57.7% were dead when brought onboard. Most of the turtles were caught in tropical areas, especially in the Gulf of Guinea (15°N-10°S, 30°W-10°E), but loggerheads were caught in the south Atlantic Ocean (25°S-35°S, 40°W-10°E and 30°S-40°S, 55°W-45°W). The bycatch rate was the highest at 0.030 per 1000 hooks for leatherbacks in the tropical area. The bycatch rates of olive ridley ranged from 0 to 0.010 per thousand hooks. The loggerhead bycatch rates were higher in the northern and southern Atlantic Ocean and ranged from 0.0128 to 0.0239 per thousand hooks. Due to the characteristics of the Taiwanese deep-set longline fleet, bycatch rates were lower than those of coastal longline fisheries, but mortality rates were higher because of the long hours of operation. Gear and bait modification should be considered to reduce sea turtle bycatch and increase survival rates while reducing the use of shallow hooks would also be helpful.

  1. Long-term prognosis of acute lateral ankle ligamentous sprains: high incidence of recurrences and residual symptoms.

    Science.gov (United States)

    Kemler, Ellen; Thijs, Karin M; Badenbroek, Ilse; van de Port, Ingrid G L; Hoes, Arno W; Backx, Frank J G

    2016-12-01

    Acute lateral ankle ligamentous sprains (ALALS) are common injuries. This injury does not always have a favourable long-term outcome. Studies reporting the prognosis of ALALS after functional treatment are scarce. To determine the prognosis of functionally treated ALALS, in terms of recurrent ALALS and residual symptoms. Retrospective cohort study. Patients were recruited from 20 family practices, nine physical therapy practices, the emergency departments of a regional hospital and a university hospital. Adult patients with an ALALS caused by an inversion trauma were invited to participate in this study 2.5-5 years after their initial injury. Functional treatment of the initial ALALS. Acute lateral ankle ligamentous sprain recurrences and residual symptoms. A total of 44 patients were included, with an average follow-up period after the initial ankle sprain of 204 weeks (range 150-274 weeks). Eight patients (18.1%) had reinjured their ankle. Explicit pain around the ankle joint at physical examination was experienced by 45.5%. Clinical symptoms of anterior ankle impingement were present in 25% (all athletes), with radiologically confirmed tibiotalar osteophyte bone formation in 82% of them. A large proportion of patients with ALALS experience recurrences and persistent symptoms after their initial ankle injury. The high percentage of patients with anterior ankle impingement syndromes illustrates the need for early assessment of this impairment in patients with persistent complaints. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. Estimation of residual stress in cold rolled iron-disks from strain measurements on the high resolution Fourier diffractometer

    International Nuclear Information System (INIS)

    Aksenov, V.L.; Balagurov, A.M.; Taran, Yu.V.

    1995-01-01

    The results of estimating residual stresses in cold rolled iron disks by measurements with the high resolution Fourier diffractometer (HRFD) at the IBR-2 pulsed reactor are presented. These measurements were made for calibration of magnetic and ultrasonic measurements carried out at the Fraunhofer-Institute for Nondestructive Testing in Saarbrucken (Germany). The tested objects were cold rolled steel disks of 2.5 mm thickness and diameter of about 500 mm used for forming small, gas pressure tanks. Neutron diffraction experiments were carried out at the scattering angle 2θ=+152 d eg with resolution Δd/d=1.5·10 -3 . The gauge volume was chosen according to the magnetic measurements lateral resolution 20x20 mm 2 . In the nearest future the neutron diffraction measurements with cold rolled iron disks at the scattering angle 2θ=±90 0 are planned. Also the texture analysis will be included in the Rietveld refinement procedure for more correct calculation of residual stress fields in the cold rolled materials. 8 refs., 10 figs., 1 tab

  3. High Temperature Exposure of HPC – Experimental Analysis of Residual Properties and Thermal Response

    Directory of Open Access Journals (Sweden)

    Pavlík Zbyšek

    2016-01-01

    Full Text Available The effect of high temperature exposure on properties of a newly designed High Performance Concrete (HPC is studied in the paper. The HPC samples are exposed to the temperatures of 200, 400, 600, 800, and 1000°C respectively. Among the basic physical properties, bulk density, matrix density and total open porosity are measured. The mechanical resistivity against disruptive temperature action is characterised by compressive strength, flexural strength and dynamic modulus of elasticity. To study the chemical and physical processes in HPC during its high-temperature exposure, Simultaneous Thermal Analysis (STA is performed. Linear thermal expansion coefficient is determined as function of temperature using thermodilatometry (TDA. In order to describe the changes in microstructure of HPC induced by high temperature loading, MIP measurement of pore size distribution is done. Increase of the total open porosity and connected decrease of the mechanical parameters for temperatures higher than 200 °C were identified.

  4. Filtrates & Residues: Experimental Work with Tin (II) Chloride in a High School.

    Science.gov (United States)

    Sanchez, Manuela Martin

    1988-01-01

    Presents a high school chemistry lab experiment using tin (II) chloride to explore the concepts of hydrolysis, Le Chatelier's principle, and electrolysis. Presents methodology and the chemistry involved. Offers questions for the students. (MVL)

  5. Molecular evolution of vertebrate neurotrophins: co-option of the highly conserved nerve growth factor gene into the advanced snake venom arsenalf.

    Science.gov (United States)

    Sunagar, Kartik; Fry, Bryan Grieg; Jackson, Timothy N W; Casewell, Nicholas R; Undheim, Eivind A B; Vidal, Nicolas; Ali, Syed A; King, Glenn F; Vasudevan, Karthikeyan; Vasconcelos, Vitor; Antunes, Agostinho

    2013-01-01

    Neurotrophins are a diverse class of structurally related proteins, essential for neuronal development, survival, plasticity and regeneration. They are characterized by major family members, such as the nerve growth factors (NGF), brain-derived neurotrophic factors (BDNF) and neurotrophin-3 (NT-3), which have been demonstrated here to lack coding sequence variations and follow the regime of negative selection, highlighting their extremely important conserved role in vertebrate homeostasis. However, in stark contrast, venom NGF secreted as part of the chemical arsenal of the venomous advanced snake family Elapidae (and to a lesser extent Viperidae) have characteristics consistent with the typical accelerated molecular evolution of venom components. This includes a rapid rate of diversification under the significant influence of positive-selection, with the majority of positively-selected sites found in the secreted β-polypeptide chain (74%) and on the molecular surface of the protein (92%), while the core structural and functional residues remain highly constrained. Such focal mutagenesis generates active residues on the toxin molecular surface, which are capable of interacting with novel biological targets in prey to induce a myriad of pharmacological effects. We propose that caenophidian NGFs could participate in prey-envenoming by causing a massive release of chemical mediators from mast cells to mount inflammatory reactions and increase vascular permeability, thereby aiding the spread of other toxins and/or by acting as proapoptotic factors. Despite their presence in reptilian venom having been known for over 60 years, this is the first evidence that venom-secreted NGF follows the molecular evolutionary pattern of other venom components, and thus likely participates in prey-envenomation.

  6. Molecular Evolution of Vertebrate Neurotrophins: Co-Option of the Highly Conserved Nerve Growth Factor Gene into the Advanced Snake Venom Arsenalf

    Science.gov (United States)

    Sunagar, Kartik; Fry, Bryan Grieg; Jackson, Timothy N. W.; Casewell, Nicholas R.; Undheim, Eivind A. B.; Vidal, Nicolas; Ali, Syed A.; King, Glenn F.; Vasudevan, Karthikeyan; Vasconcelos, Vitor; Antunes, Agostinho

    2013-01-01

    Neurotrophins are a diverse class of structurally related proteins, essential for neuronal development, survival, plasticity and regeneration. They are characterized by major family members, such as the nerve growth factors (NGF), brain-derived neurotrophic factors (BDNF) and neurotrophin-3 (NT-3), which have been demonstrated here to lack coding sequence variations and follow the regime of negative selection, highlighting their extremely important conserved role in vertebrate homeostasis. However, in stark contrast, venom NGF secreted as part of the chemical arsenal of the venomous advanced snake family Elapidae (and to a lesser extent Viperidae) have characteristics consistent with the typical accelerated molecular evolution of venom components. This includes a rapid rate of diversification under the significant influence of positive-selection, with the majority of positively-selected sites found in the secreted β-polypeptide chain (74%) and on the molecular surface of the protein (92%), while the core structural and functional residues remain highly constrained. Such focal mutagenesis generates active residues on the toxin molecular surface, which are capable of interacting with novel biological targets in prey to induce a myriad of pharmacological effects. We propose that caenophidian NGFs could participate in prey-envenoming by causing a massive release of chemical mediators from mast cells to mount inflammatory reactions and increase vascular permeability, thereby aiding the spread of other toxins and/or by acting as proapoptotic factors. Despite their presence in reptilian venom having been known for over 60 years, this is the first evidence that venom-secreted NGF follows the molecular evolutionary pattern of other venom components, and thus likely participates in prey-envenomation. PMID:24312363

  7. Molecular evolution of vertebrate neurotrophins: co-option of the highly conserved nerve growth factor gene into the advanced snake venom arsenalf.

    Directory of Open Access Journals (Sweden)

    Kartik Sunagar

    Full Text Available Neurotrophins are a diverse class of structurally related proteins, essential for neuronal development, survival, plasticity and regeneration. They are characterized by major family members, such as the nerve growth factors (NGF, brain-derived neurotrophic factors (BDNF and neurotrophin-3 (NT-3, which have been demonstrated here to lack coding sequence variations and follow the regime of negative selection, highlighting their extremely important conserved role in vertebrate homeostasis. However, in stark contrast, venom NGF secreted as part of the chemical arsenal of the venomous advanced snake family Elapidae (and to a lesser extent Viperidae have characteristics consistent with the typical accelerated molecular evolution of venom components. This includes a rapid rate of diversification under the significant influence of positive-selection, with the majority of positively-selected sites found in the secreted β-polypeptide chain (74% and on the molecular surface of the protein (92%, while the core structural and functional residues remain highly constrained. Such focal mutagenesis generates active residues on the toxin molecular surface, which are capable of interacting with novel biological targets in prey to induce a myriad of pharmacological effects. We propose that caenophidian NGFs could participate in prey-envenoming by causing a massive release of chemical mediators from mast cells to mount inflammatory reactions and increase vascular permeability, thereby aiding the spread of other toxins and/or by acting as proapoptotic factors. Despite their presence in reptilian venom having been known for over 60 years, this is the first evidence that venom-secreted NGF follows the molecular evolutionary pattern of other venom components, and thus likely participates in prey-envenomation.

  8. Variability of residual stresses and superposition effect in multipass grinding of high-carbon high-chromium steel

    Science.gov (United States)

    Karabelchtchikova, Olga; Rivero, Iris V.

    2005-02-01

    The distribution of residual stresses (RS) and surface integrity generated in heat treatment and subsequent multipass grinding was investigated in this experimental study to examine the source of variability and the nature of the interactions of the experimental factors. A nested experimental design was implemented to (a) compare the sources of the RS variability, (b) to examine RS distribution and tensile peak location due to experimental factors, and (c) to analyze the superposition relationship in the RS distribution due to multipass grinding technique. To characterize the material responses, several techniques were used, including microstructural analysis, hardness-toughness and roughness examinations, and retained austenite and RS measurements using x-ray diffraction. The causality of the RS was explained through the strong correlation of the surface integrity characteristics and RS patterns. The main sources of variation were the depth of the RS distribution and the multipass grinding technique. The grinding effect on the RS was statistically significant; however, it was mostly predetermined by the preexisting RS induced in heat treatment. Regardless of the preceding treatments, the effect of the multipass grinding technique exhibited similar RS patterns, which suggests the existence of the superposition relationship and orthogonal memory between the passes of the grinding operation.

  9. Activation of the oxidative stress regulator PpYap1 through conserved cysteine residues during methanol metabolism in the yeast Pichia pastoris.

    Science.gov (United States)

    Yano, Taisuke; Yurimoto, Hiroya; Sakai, Yasuyoshi

    2009-06-01

    The methylotrophic yeast Pichia pastoris can grow on methanol as sole source of carbon and energy. The first reaction in yeast methanol metabolism, catalyzed by an abundant peroxisomal enzyme, alcohol oxidase, generates high levels of H(2)O(2), but the oxidative stress response during methanol metabolism has not been elucidated. In this study, we isolated the Yap1 homolog of P. pastoris (PpYap1) and analyzed the properties of a PpYAP1-disruption strain. The PpYap1 transcription factor is activated after exposure to various reactive agents, and therefore functions as a regulator of the redox system in P. pastoris. We have also identified PpGPX1, the unique glutathione peroxidase-encoding gene in P. pastoris whose expression is induced by PpYap1. PpGpx1, but not the ScTsa1 or SpTpx1 homolog PpTsa1, functions as a H(2)O(2) sensor and activates PpYap1. This study is the first demonstration of a yeast Yap1 family protein activated during conventional metabolism.

  10. Evolving transpeptidase and hydrolytic variants of γ-glutamyl transpeptidase from Bacillus licheniformis by targeted mutations of conserved residue Arg109 and their biotechnological relevance.

    Science.gov (United States)

    Bindal, Shruti; Sharma, Sujata; Singh, Tej P; Gupta, Rani

    2017-05-10

    γ-Glutamyl transpeptidase (GGT) catalyzes the transfer of the γ-glutamyl moiety from donor compounds such as l-glutamine (Gln) and glutathione (GSH) to an acceptor. During the biosynthesis of various γ-glutamyl-containing compounds using GGT enzyme, auto-transpeptidation reaction leads to the formation of unwanted byproducts. Therefore, in order to alter the auto-transpeptidase activity of the GGT enzyme, the binding affinity of Gln should be modified. Structural studies of the Bacillus licheniformis GGT (BlGT) complexed with the glutamic acid has shown that glutamic acid has strong ionic interactions through its α-carboxlic group with the guanidine moiety of Arg109. This interaction appears to be an important contributor for the binding affinity of Gln. In view of this, six mutants of Bacillus licheniformis ER15 GGT (BlGGT) viz. Arg109Lys, Arg109Ser, Arg109Met, Arg109Leu, Arg109Glu and Arg109Phe were prepared. As seen from the structure of BlGT, the mutation of Arg109 to Lys109 may reduce the affinity for Gln to some extent, whereas the other mutations are expected to lower the affinity much more. Biophysical characterization and functional studies revealed that Arg109Lys mutant has increased transpeptidation activity and catalytic efficiency than the other mutants. The Arg109Lys mutant showed high conversion rates for l-theanine synthesis as well. Moreover, the Arg109Met mutant showed increased hydrolytic activity as it completely altered the binding of Gln at the active site. Also, the salt stability of the enzyme was significantly improved on replacing Arg109 by Met109 which is required for hydrolytic applications of GGTs in food industries. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Charles Sabin

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

  12. Bacillus cereus as indicator in the sterilization of residual water with high energy electrons; Bacillus cereus como indicador en la desinfeccion de aguas residuales con electrones de alta energia

    Energy Technology Data Exchange (ETDEWEB)

    Mejia Z, E

    2000-07-01

    One of the main causes of water pollution is the presence of microorganisms that provoke infections, moreover of chemical substances. The processes of residual water treatment finally require of the disinfection for its use or final disposition. The radiation technology for the residual water treatment by mean of electron beams is an innovator process because as well as decomposing the chemical substance or to degrade them, also it provokes a disinfection by which this is proposed as alternative for disinfection of residual water, with the purpose in reusing the water treated in the agriculture, recreation and industry among others secondary activities, solving environmental or health problems. The objective of this work is to evaluate the use of Bacillus cereus as biological indicator in the disinfection by radiation, using High Energy Electrons. To fulfil with this objective, the work was developed in three stages, the first one consisted in the acquisition, propagation and conservation of the Bacillus cereus stumps, considering Escherichia coli and Salmonella typhimurium as pathogenic germs present in residual water. Moreover, the inocule standardization and the conditions of the Electron accelerator Type Pelletron. In the second stage it was performed the irradiation of aqueous samples of the microorganisms simulating biological pollution and the application to problem samples of a treatment plant sited in the Lerma River zone of mixed residual water. And in the third stage was performed a regression analysis to the reported survival for each kind of microorganisms. The results obtained show that with the use of Electron beams was reduced 6 logarithmic units de E. coli at 129 Gy, for S. typhimurium it was reduced 8 logarithmic units at 383 Gy and the B. cereus at 511 Gy was reduced 6.8 logarithmic units. Of the problem samples irradiated at 500 Gy, the concentration of the total account diminished from 8.70 x 10{sup 7} UFC/ml to 550 UFC/ml, the presence of B

  13. High Resolution Mapping of Soils and Landforms for the Desert Renewable Energy Conservation Plan (DRECP)

    Science.gov (United States)

    Potter, Christopher S.; Li, Shuang

    2014-01-01

    The Desert Renewable Energy Conservation Plan (DRECP), a major component of California's renewable energy planning efforts, is intended to provide effective protection and conservation of desert ecosystems, while allowing for the sensible development of renewable energy projects. This NASA mapping report was developed to support the DRECP and the Bureau of Land Management (BLM). We outline in this document remote sensing image processing methods to deliver new maps of biological soils crusts, sand dune movements, desert pavements, and sub-surface water sources across the DRECP area. We focused data processing first on the largely unmapped areas most likely to be used for energy developments, such as those within Renewable Energy Study Areas (RESA) and Solar Energy Zones (SEZs). We used imagery (multispectral and radar) mainly from the years 2009-2011.

  14. High-Quality 3d Models and Their Use in a Cultural Heritage Conservation Project

    Science.gov (United States)

    Tucci, G.; Bonora, V.; Conti, A.; Fiorini, L.

    2017-08-01

    Cultural heritage digitization and 3D modelling processes are mainly based on laser scanning and digital photogrammetry techniques to produce complete, detailed and photorealistic three-dimensional surveys: geometric as well as chromatic aspects, in turn testimony of materials, work techniques, state of preservation, etc., are documented using digitization processes. The paper explores the topic of 3D documentation for conservation purposes; it analyses how geomatics contributes in different steps of a restoration process and it presents an overview of different uses of 3D models for the conservation and enhancement of the cultural heritage. The paper reports on the project to digitize the earthenware frieze of the Ospedale del Ceppo in Pistoia (Italy) for 3D documentation, restoration work support, and digital and physical reconstruction and integration purposes. The intent to design an exhibition area suggests new ways to take advantage of 3D data originally acquired for documentation and scientific purposes.

  15. A High-Accuracy Linear Conservative Difference Scheme for Rosenau-RLW Equation

    Directory of Open Access Journals (Sweden)

    Jinsong Hu

    2013-01-01

    Full Text Available We study the initial-boundary value problem for Rosenau-RLW equation. We propose a three-level linear finite difference scheme, which has the theoretical accuracy of Oτ2+h4. The scheme simulates two conservative properties of original problem well. The existence, uniqueness of difference solution, and a priori estimates in infinite norm are obtained. Furthermore, we analyze the convergence and stability of the scheme by energy method. At last, numerical experiments demonstrate the theoretical results.

  16. Hearing sensitivity in context: Conservation implications for a highly vocal endangered species

    OpenAIRE

    Owen, Megan A.; Keating, Jennifer L.; Denes, Samuel K.; Hawk, Kathy; Fiore, Angela; Thatcher, Julie; Becerra, Jennifer; Hall, Suzanne; Swaisgood, Ronald R.

    2016-01-01

    Hearing sensitivity is a fundamental determinant of a species’ vulnerability to anthropogenic noise, however little is known about the hearing capacities of most conservation dependent species. When audiometric data are integrated with other aspects of species’ acoustic ecology, life history, and characteristic habitat topography and soundscape, predictions can be made regarding probable vulnerability to the negative impacts of different types of anthropogenic noise. Here we used an adaptive ...

  17. Innovative Surgical Management of the Synovial Chondromatosis of Temporo-Mandibular Joints: Highly Conservative Surgical Technique.

    Science.gov (United States)

    Ionna, Franco; Amantea, Massimiliano; Mastrangelo, Filiberto; Ballini, Andrea; Maglione, Maria Grazia; Aversa, Corrado; De Cecio, Rossella; Russo, Daniela; Marrelli, Massimo; Tatullo, Marco

    2016-07-01

    Synovial chondromatosis (SC) is an uncommon disease characterized by a benign nodular cartilaginous proliferation arising from the joint synovium, bursae, or tendon sheaths. Although the temporomandibular joint is rarely affected by neoplastic lesions, SC is the most common neoplastic lesion of this joint. The treatment of this disease consists in the extraoral surgery with a wide removal of the lesion; in this study, the authors described a more conservative intraoral surgical approach. Patient with SC of temporomandibular joint typically refer a limitation in the mouth opening, together with a persistent not physiological mandibular protrusion and an appearance of a neoformation located at the right preauricular region: the authors reported 1 scholar patient. After biopsy of the neoformation, confirming the synovial chondromatosis, the patient underwent thus to the surgical excision of the tumor, via authors' conservative transoral approach, to facilitate the enucleation of the neoformation. The mass fully involved the pterygo-maxillary fossa with involvement of the parotid lodge and of the right TMJ: this multifocal extension suggested for a trans-oral surgical procedure, in the light of the suspicion of a possible malignant nature of the neoplasm. Our intraoral conservative approach to surgery is aimed to reduce the presence of unaesthetic scars in preauricular and facial regions, with surgical results undoubtedly comparable to the traditional surgical techniques much more aggressive. Our technique could be a valid, alternative, and safe approach to treat this rare and complex kind of oncological disease.

  18. Residual gas entering high density hydrogen plasma: rarefaction due to rapid heating

    NARCIS (Netherlands)

    N. den Harder,; D.C. Schram,; W. J. Goedheer,; de Blank, H. J.; M. C. M. van de Sanden,; van Rooij, G. J.

    2015-01-01

    The interaction of background molecular hydrogen with magnetized (0.4 T) high density (1–5 × 10 20  m −3 ) low temperature (∼3 eV) hydrogen plasma was inferred from the Fulcher band emission in the linear plasma generator Pilot-PSI. In the plasma center,

  19. Residual stress in a M3:2 PM high speed steel; effect of mechanical loading

    DEFF Research Database (Denmark)

    Højerslev, Christian; Odén, Magnus; Carstensen, Jesper V.

    2001-01-01

    X-ray lattice strains were investigated in an AISI M3:2 PM high-speed steel in the as heat treated condition and after exposure to alternating mechanical load. The volume changes during heat treatment were monitored with dilatometry. Hardened and tempered AISI M3:2 steel consists of tempered lath...

  20. Analysis of Metal Flow Behavior and Residual Stress Formation of Complex Functional Profiles under High-Speed Cold Roll-Beating

    Directory of Open Access Journals (Sweden)

    Fengkui Cui

    2018-01-01

    Full Text Available To obtain a good surface layer performance of the complex functional profile during the high-speed cold roll-beating forming process, this paper analyzed the metal plastic flow and residual stress-formed mechanism by using a theoretical model of the metal flow and residual stress generation. By using simulation software, the cold roll-beating forming process of a spline shaft was simulated and analyzed. The metal flow and residual stress formation law in the motion were researched. In a practical experiment, the changes in the grains in the spline tooth profile section and the residual stress distribution on the tooth profile were studied. A microcorrespondence relationship was established between the metal plastic flow and the residual stress generation. The conclusions indicate that the rate at which the metal flow decreases changes gradually at different metal layers. The residual stress value is directly related to the plastic flow difference. As the roll-beating speed increases, the uneven degree of plastic deformation at the workpiece surface increases, and the residual stress in the tooth profile is generally greater. At the same roll-beating speed, the rate change trend of the metal flow decreases gradually from the surface to the inner layer and from the dedendum to the addendum. The residual stress distribution on the surface of the tooth profile decreases from the dedendum to the addendum. These findings provide a basis and guidance for the controlled use of residual stress, obtaining better surface layer quality in the high-speed cold roll-beating process of the complex functional profile.

  1. Cycling of grain legume residue nitrogen

    DEFF Research Database (Denmark)

    Jensen, E.S.

    1995-01-01

    Symbiotic nitrogen fixation by legumes is the main input of nitrogen in ecological agriculture. The cycling of N-15-labelled mature pea (Pisum sativum L.) residues was studied during three years in small field plots and lysimeters. The residual organic labelled N declined rapidly during the initial...... management methods in order to conserve grain legume residue N sources within the soil-plant system....

  2. Limits to evaporation residue cross sections from fission and particle decay at high angular momentum

    International Nuclear Information System (INIS)

    Newton, J.O.

    1980-06-01

    In recent years there has been great interest in nuclear properties at very high angular momentum. The heavy-ion (HI),xnγ reaction and to a lesser extent the (HI,xn,ypγ) reactions, have so far offered the most powerful experimental technique for their study. Measurements on the resolved discrete γ-rays from the decay of yrast or near-yrast states has lead to considerable understanding of states with angular momenta up to a little over 20h and in a few special cases as high as 37 h. To investigate nuclei at still higher angular angular momenta one can study the so called 'continuum γ-rays', which cannot be resolved by present techniques because so many pathways are involved. The author considers the factors which determine the upper limits of the angular momenta for which continuum γ-ray studies can be usefully employed and how one may gain information beyond these limits

  3. Nonoperative options for management of residual stones after cholecystostomy in high-risk patients

    Science.gov (United States)

    Reed, David M.; Daye, S. S.; Lincer, R. M.

    1993-05-01

    Cholecystostomy is frequently performed to obtain control of sepsis in high risk patients with acute cholecystitis. Retained stones in the gallbladder may cause future clinical problems. We present two patients with cholecystostomy tubes managed non-operatively. A review of other reported methods for stone extraction or destruction is also presented. Knowledge of safe and effective techniques for removal of these stones, using minimally invasive techniques is useful to the general surgeon.

  4. High-Order Hyperbolic Residual-Distribution Schemes on Arbitrary Triangular Grids

    Science.gov (United States)

    2015-06-22

    for efficient CFD calculations in high-order methods,3 because the grid adaptation almost necessarily introduces irregularity in the grid. In fact...problems. References 1P.A. Gnoffo. Multi-dimensional, inviscid flux reconstruction for simulation of hypersonic heating on tetrahedral grids. In Proc. of...Kitamura, E. Shima, Y. Nakamura, and P.L. Roe. Evaluation of euler fluxes for hypersonic heating computations. AIAA J., 48(4):763–776, 2010. 3Z.J. Wang, K

  5. High-resolution phylogenetic analysis of residual bacterial species of fouled membranes after NaOCl cleaning.

    Science.gov (United States)

    Navarro, Ronald R; Hori, Tomoyuki; Inaba, Tomohiro; Matsuo, Kazuyuki; Habe, Hiroshi; Ogata, Atsushi

    2016-05-01

    Biofouling is one of the major problems during wastewater treatment using membrane bioreactors (MBRs). In this regard, sodium hypochlorite (NaOCl) has been widely used to wash fouled membranes for maintenance and recovery purposes. Advanced chemical and biological characterization was conducted in this work to evaluate the performance of aqueous NaOCl solutions during washing of polyacrylonitrile membranes. Fouled membranes from MBR operations supplemented with artificial wastewater were washed with 0.1% and 0.5% aqueous NaOCl solutions for 5, 10 and 30 min. The changes in organics composition on the membrane surface were directly monitored by an attenuated total reflection Fourier transform infrared (ATR-FT-IR) spectrometer. In addition, high-throughput Illumina sequencing of 16S rRNA genes was applied to detect any residual microorganisms. Results from ATR-FT-IR analysis indicated the complete disappearance of functional groups representing different fouling compounds after at least 30 min of treatment with 0.1% NaOCl. However, the biomolecular survey revealed the presence of residual bacteria even after 30 min of treatment with 0.5% NaOCl solution. Evaluation of microbial diversity of treated samples using Chao1, Shannon and Simpson reciprocal indices showed an increase in evenness while no significant decline in richness was observed. These implied that only the population of dominant species was mainly affected. The high-resolution phylogenetic analysis revealed the presence of numerous operational taxonomic units (OTUs) whose close relatives exhibit halotolerance. Some OTUs related to thermophilic and acid-resistant strains were also identified. Finally, the taxonomic analysis of recycled membranes that were previously washed with NaOCl also showed the presence of numerous halotolerant-related OTUs in the early stage of fouling. This further suggested the possible contribution of such chemical tolerance on their survival against NaOCl washing, which in turn

  6. PERSPECTIVES OF PHYTOSTABILIZATION BY JATROPHA CURCAS OF MINING RESIDUES FROM ABANDONED ZAIDA MINE (HIGH MOULOUYA, MOROCCO)

    International Nuclear Information System (INIS)

    El himer, S.; Bouabdli, A.; Baghdad, B.; Saidi, N; Zouahri, A.

    2012-01-01

    Full text: Mine of Zaida (High Moulouya, Morocco) has been object of multiple research works (Saidi et al. 2002, Saidi 2004, Bouabdli et al. 2004, Bouabdli et al. 2005, El Hachimi 2005, El Hachimi 2006, Baghdad et al. 2006, Baghdad 2008, 2011, Berrah El Kheir et al. 2008, Berrah El Kheir et al. 2010, El Himer et al. 2012) which demonstrated the impact of a large volume of materials issued of the mining activities on the different compartments of the ecosystem. In fact, these materials are a potential source of trace metals, which induces a major risk for living beings because of their mobility and bioavailability. Among the techniques that minimize this problem the phytostabilization can be cited ; this method appears to be safe, alternative and usable regardless the level of pollution. It consists in revegetation of soils polluted by species tolerant to trace elements. In this context, the use of shrubs is particularly interesting because their root systems are well developed and dense, limiting the runoff and leaching of trace metals to different compartments of ecosystem. In our study we were interested in the culture of Jatropha curcas ; it is a perennial shrub belonging to the Euphorbiaceae family, this plant has been the subject of several research projects on the one hand due to its economic interest and low operating cost (biofuel, fertilizer, traditional medicine, fight against erosion, insecticides, soap production, ...), on the other hand due to its low requirements (easy to cultivate, rapid growth, drought resistance) and tolerance to marginal lands. This travel proposes to study the growth and ability of Jatropha curcas to extract trace metals in various substrates from Zaida mine (High Moulouya, Morocco) in order to evaluate its potential of phytostabilization. The results indicate that Jatropha curcas shows proper installation despite the high levels of trace metals in experimental substrates. This plant is characterized by the ability to adapt and

  7. Method Development for Pesticide Residue Analysis in Farmland Soil using High Perfomance Liquid Chromatography

    Science.gov (United States)

    Theresia Djue Tea, Marselina; Sabarudin, Akhmad; Sulistyarti, Hermin

    2018-01-01

    A method for the determination of diazinon and chlorantraniliprole in soil samples has been developed. The analyte was extracted with acetonitrile from farmland soil sample. Determination and quantification of diazinon and chlorantraniliprole were perfomed by high perfomance liquid chromatography (HPLC) with an UV detector. Several parameters of HPLC method were optimized with respect to sensitivity, high resolution of separation, and accurate determination of diazinon and chlorantraniliprole. Optimum conditions for the separation of two pesticides were eluent composition of acetonitrile:water ratio of 60:40, 0.4 mL/min of flow rate, and 220 nm of wavelength. Under the optimum conditions, diazinon linearity was in the range from 1-25 ppm with R2 of 0.9976, 1.19 mgL-1 LOD, and 3.98 mgL-1 LOQ; while the linearity of chlorantraniliprole was in the range from 0.2-5 mgL-1 with R2 of 0.9972, 0.39 mgL-1 LOD, and 1.29 mgL-1 LOQ. When the method was applied to the soil sample, both pesticides showed acceptable recoveries for real sample of more than 85%: thus, the developed method meets the validation requirement. Under this developed method, the concentrations of both pesticides in the soil samples were below the LOD and LOQ (0.577 mgL-1 for diazinon and 0.007 mgL-1 for chlorantraniliprole). Therefore, it can be concluded that the soil samples used in this study have neither diazinon nor chlorantraniliprole.

  8. The importance of incorporating functional habitats into conservation planning for highly mobile species in dynamic systems.

    Science.gov (United States)

    Webb, Matthew H; Terauds, Aleks; Tulloch, Ayesha; Bell, Phil; Stojanovic, Dejan; Heinsohn, Robert

    2017-10-01

    The distribution of mobile species in dynamic systems can vary greatly over time and space. Estimating their population size and geographic range can be problematic and affect the accuracy of conservation assessments. Scarce data on mobile species and the resources they need can also limit the type of analytical approaches available to derive such estimates. We quantified change in availability and use of key ecological resources required for breeding for a critically endangered nomadic habitat specialist, the Swift Parrot (Lathamus discolor). We compared estimates of occupied habitat derived from dynamic presence-background (i.e., presence-only data) climatic models with estimates derived from dynamic occupancy models that included a direct measure of food availability. We then compared estimates that incorporate fine-resolution spatial data on the availability of key ecological resources (i.e., functional habitats) with more common approaches that focus on broader climatic suitability or vegetation cover (due to the absence of fine-resolution data). The occupancy models produced significantly (P increase or decrease in the area of one functional habitat (foraging or nesting) did not necessarily correspond to an increase or decrease in the other. Thus, an increase in the extent of occupied area may not equate to improved habitat quality or function. We argue these patterns are typical for mobile resource specialists but often go unnoticed because of limited data over relevant spatial and temporal scales and lack of spatial data on the availability of key resources. Understanding changes in the relative availability of functional habitats is crucial to informing conservation planning and accurately assessing extinction risk for mobile resource specialists. © 2017 Society for Conservation Biology.

  9. Visceral organ weights, digestion and carcass characteristics of beef bulls differing in residual feed intake offered a high concentrate diet.

    Science.gov (United States)

    Fitzsimons, C; Kenny, D A; McGee, M

    2014-06-01

    This study examined the relationship of residual feed intake (RFI) with digestion, body composition, carcass traits and visceral organ weights in beef bulls offered a high concentrate diet. Individual dry matter (DM) intake (DMI) and growth were measured in a total of 67 Simmental bulls (mean initial BW 431 kg (s.d.=63.7)) over 3 years. Bulls were offered concentrates (860 g/kg rolled barley, 60 g/kg soya bean meal, 60 g/kg molasses and 20 g/kg minerals per vitamins) ad libitum plus 0.8 kg grass silage DM daily for 105 days pre-slaughter. Ultrasonic muscle and fat depth, body condition score (BCS), muscularity score, skeletal measurements, blood metabolites, rumen fermentation and total tract digestibility (indigestible marker) were determined. After slaughter, carcasses and perinephric and retroperitoneal fat were weighed, carcasses were graded for conformation and fat score and weight of non-carcass organs, liver, heart, kidneys, lungs, gall bladder, spleen, reticulo-rumen full and empty and intestines full, were determined. The residuals of the regression of DMI on average daily gain (ADG), mid-test metabolic BW (BW0.75) and the fixed effect of year, using all animals, were used to compute individual RFI coefficients. Animals were ranked on RFI and assigned to high (inefficient), medium or low groupings. Overall mean ADG and daily DMI were 1.6 kg (s.d.=0.36) and 9.4 kg (s.d.=1.16), respectively. High RFI bulls consumed 7 and 14% more DM than medium and low RFI bulls, respectively (P0.05) for ADG, BW, BCS, skeletal measurements, muscularity scores, ultrasonic measurements, carcass weight, perinephric and retroperitoneal fat weight, kill-out proportion and carcass conformation and fat score. However, regression analysis indicated that a 1 kg DM/day increase in RFI was associated with a decrease in kill-out proportion of 20 g/kg (Pcarcass conformation of 0.74 units (Pcarcass organs did not differ (P>0.05) between RFI groups except for the empty weight of reticulo

  10. Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts

    Directory of Open Access Journals (Sweden)

    Ouyang Shu

    2005-09-01

    Full Text Available Abstract Background The Solanaceae is a family of closely related species with diverse phenotypes that have been exploited for agronomic purposes. Previous studies involving a small number of genes suggested sequence conservation across the Solanaceae. The availability of large collections of Expressed Sequence Tags (ESTs for the Solanaceae now provides the opportunity to assess sequence conservation and divergence on a genomic scale. Results All available ESTs and Expressed Transcripts (ETs, 449,224 sequences for six Solanaceae species (potato, tomato, pepper, petunia, tobacco and Nicotiana benthamiana, were clustered and assembled into gene indices. Examination of gene ontologies revealed that the transcripts within the gene indices encode a similar suite of biological processes. Although the ESTs and ETs were derived from a variety of tissues, 55–81% of the sequences had significant similarity at the nucleotide level with sequences among the six species. Putative orthologs could be identified for 28–58% of the sequences. This high degree of sequence conservation was supported by expression profiling using heterologous hybridizations to potato cDNA arrays that showed similar expression patterns in mature leaves for all six solanaceous species. 16–19% of the transcripts within the six Solanaceae gene indices did not have matches among Solanaceae, Arabidopsis, rice or 21 other plant gene indices. Conclusion Results from this genome scale analysis confirmed a high level of sequence conservation at the nucleotide level of the coding sequence among Solanaceae. Additionally, the results indicated that part of the Solanaceae transcriptome is likely to be unique for each species.

  11. Reducing the impurity incorporation from residual gas by ion bombardment during high vacuum magnetron sputtering

    International Nuclear Information System (INIS)

    Rosen, Johanna; Widenkvist, Erika; Larsson, Karin; Kreissig, Ulrich; Mraz, Stanislav; Martinez, Carlos; Music, Denis; Schneider, J. M.

    2006-01-01

    The influence of ion energy on the hydrogen incorporation has been investigated for alumina thin films, deposited by reactive magnetron sputtering in an Ar/O 2 /H 2 O environment. Ar + with an average kinetic energy of ∼5 eV was determined to be the dominating species in the plasma. The films were analyzed with x-ray diffraction, x-ray photoelectron spectroscopy, and elastic recoil detection analysis, demonstrating evidence for amorphous films with stoichiometric O/Al ratio. As the substrate bias potential was increased from -15 V (floating potential) to -100 V, the hydrogen content decreased by ∼70%, from 9.1 to 2.8 at. %. Based on ab initio calculations, these results may be understood by thermodynamic principles, where a supply of energy enables surface diffusion, H 2 formation, and desorption [Rosen et al., J. Phys.: Condens. Matter 17, L137 (2005)]. These findings are of importance for the understanding of the correlation between ion energy and film composition and also show a pathway to reduce impurity incorporation during film growth in a high vacuum ambient

  12. High throughput mutagenesis for identification of residues regulating human prostacyclin (hIP receptor expression and function.

    Directory of Open Access Journals (Sweden)

    Anke Bill

    Full Text Available The human prostacyclin receptor (hIP receptor is a seven-transmembrane G protein-coupled receptor (GPCR that plays a critical role in vascular smooth muscle relaxation and platelet aggregation. hIP receptor dysfunction has been implicated in numerous cardiovascular abnormalities, including myocardial infarction, hypertension, thrombosis and atherosclerosis. Genomic sequencing has discovered several genetic variations in the PTGIR gene coding for hIP receptor, however, its structure-function relationship has not been sufficiently explored. Here we set out to investigate the applicability of high throughput random mutagenesis to study the structure-function relationship of hIP receptor. While chemical mutagenesis was not suitable to generate a mutagenesis library with sufficient coverage, our data demonstrate error-prone PCR (epPCR mediated mutagenesis as a valuable method for the unbiased screening of residues regulating hIP receptor function and expression. Here we describe the generation and functional characterization of an epPCR derived mutagenesis library compromising >4000 mutants of the hIP receptor. We introduce next generation sequencing as a useful tool to validate the quality of mutagenesis libraries by providing information about the coverage, mutation rate and mutational bias. We identified 18 mutants of the hIP receptor that were expressed at the cell surface, but demonstrated impaired receptor function. A total of 38 non-synonymous mutations were identified within the coding region of the hIP receptor, mapping to 36 distinct residues, including several mutations previously reported to affect the signaling of the hIP receptor. Thus, our data demonstrates epPCR mediated random mutagenesis as a valuable and practical method to study the structure-function relationship of GPCRs.

  13. High throughput mutagenesis for identification of residues regulating human prostacyclin (hIP) receptor expression and function.

    Science.gov (United States)

    Bill, Anke; Rosethorne, Elizabeth M; Kent, Toby C; Fawcett, Lindsay; Burchell, Lynn; van Diepen, Michiel T; Marelli, Anthony; Batalov, Sergey; Miraglia, Loren; Orth, Anthony P; Renaud, Nicole A; Charlton, Steven J; Gosling, Martin; Gaither, L Alex; Groot-Kormelink, Paul J

    2014-01-01

    The human prostacyclin receptor (hIP receptor) is a seven-transmembrane G protein-coupled receptor (GPCR) that plays a critical role in vascular smooth muscle relaxation and platelet aggregation. hIP receptor dysfunction has been implicated in numerous cardiovascular abnormalities, including myocardial infarction, hypertension, thrombosis and atherosclerosis. Genomic sequencing has discovered several genetic variations in the PTGIR gene coding for hIP receptor, however, its structure-function relationship has not been sufficiently explored. Here we set out to investigate the applicability of high throughput random mutagenesis to study the structure-function relationship of hIP receptor. While chemical mutagenesis was not suitable to generate a mutagenesis library with sufficient coverage, our data demonstrate error-prone PCR (epPCR) mediated mutagenesis as a valuable method for the unbiased screening of residues regulating hIP receptor function and expression. Here we describe the generation and functional characterization of an epPCR derived mutagenesis library compromising >4000 mutants of the hIP receptor. We introduce next generation sequencing as a useful tool to validate the quality of mutagenesis libraries by providing information about the coverage, mutation rate and mutational bias. We identified 18 mutants of the hIP receptor that were expressed at the cell surface, but demonstrated impaired receptor function. A total of 38 non-synonymous mutations were identified within the coding region of the hIP receptor, mapping to 36 distinct residues, including several mutations previously reported to affect the signaling of the hIP receptor. Thus, our data demonstrates epPCR mediated random mutagenesis as a valuable and practical method to study the structure-function relationship of GPCRs.

  14. Controlling residual dipolar couplings in high-resolution NMR of proteins by strain induced alignment in a gel

    International Nuclear Information System (INIS)

    Ishii, Yoshitaka; Markus, Michelle A.; Tycko, Robert

    2001-01-01

    Water-soluble biological macromolecules can be weakly aligned by dissolution in a strained, hydrated gel such as cross-linked polyacrylamide, an effect termed 'strain-induced alignment in a gel' (SAG). SAG induces nonzero nuclear magnetic dipole-dipole couplings that can be measured in high-resolution NMR spectra and used as structural constraints. The dependence of experimental 15 N- 1 H dipolar couplings extracted from two-dimensional heteronuclear single quantum coherence (HSQC) spectra on several properties of compressed polyacrylamide, including the extent of compression, the polyacrylamide concentration, and the cross-link density, is reported for the B1 immunoglobulin binding domain of streptococcal protein G (protein G/B1, 57 residues). It is shown that the magnitude of macromolecular alignment can be widely varied by adjusting these properties, although the orientation and asymmetry of the alignment tensor are not affected significantly. The dependence of the 15 N relaxation times T 1 and T 2 of protein G/B1 on polyacrylamide concentration are also reported. In addition, the results of 15 N relaxation and HSQC experiments on the RNA binding domain of prokaryotic protein S4 from Bacillus stearothermophilus (S4 Δ41, residues 43-200) in a compressed polyacrylamide gel are presented. These results demonstrate the applicability of SAG to proteins of higher molecular weight and greater complexity. A modified in-phase/anti-phase (IPAP) HSQC technique is described that suppresses natural-abundance 15 N background signals from amide groups in polyacrylamide, resulting in cleaner HSQC spectra in SAG experiments. The mechanism of protein alignment in strained polyacrylamide gels is contrasted with that in liquid crystalline media

  15. Residual stresses

    International Nuclear Information System (INIS)

    Sahotra, I.M.

    2006-01-01

    The principal effect of unloading a material strained into the plastic range is to create a permanent set (plastic deformation), which if restricted somehow, gives rise to a system of self-balancing within the same member or reaction balanced by other members of the structure., known as residual stresses. These stresses stay there as locked-in stresses, in the body or a part of it in the absence of any external loading. Residual stresses are induced during hot-rolling and welding differential cooling, cold-forming and extruding: cold straightening and spot heating, fabrication and forced fitting of components constraining the structure to a particular geometry. The areas which cool more quickly develop residual compressive stresses, while the slower cooling areas develop residual tensile stresses, and a self-balancing or reaction balanced system of residual stresses is formed. The phenomenon of residual stresses is the most challenging in its application in surface modification techniques determining endurance mechanism against fracture and fatigue failures. This paper discusses the mechanism of residual stresses, that how the residual stresses are fanned and what their behavior is under the action of external forces. Such as in the case of a circular bar under limit torque, rectangular beam under limt moment, reclaiming of shafts welds and peening etc. (author)

  16. NFAT5 regulates HIV-1 in primary monocytes via a highly conserved long terminal repeat site.

    Directory of Open Access Journals (Sweden)

    Shahin Ranjbar

    2006-12-01

    Full Text Available To replicate, HIV-1 capitalizes on endogenous cellular activation pathways resulting in recruitment of key host transcription factors to its viral enhancer. RNA interference has been a powerful tool for blocking key checkpoints in HIV-1 entry into cells. Here we apply RNA interference to HIV-1 transcription in primary macrophages, a major reservoir of the virus, and specifically target the transcription factor NFAT5 (nuclear factor of activated T cells 5, which is the most evolutionarily divergent NFAT protein. By molecularly cloning and sequencing isolates from multiple viral subtypes, and performing DNase I footprinting, electrophoretic mobility shift, and promoter mutagenesis transfection assays, we demonstrate that NFAT5 functionally interacts with a specific enhancer binding site conserved in HIV-1, HIV-2, and multiple simian immunodeficiency viruses. Using small interfering RNA to ablate expression of endogenous NFAT5 protein, we show that the replication of three major HIV-1 viral subtypes (B, C, and E is dependent upon NFAT5 in human primary differentiated macrophages. Our results define a novel host factor-viral enhancer interaction that reveals a new regulatory role for NFAT5 and defines a functional DNA motif conserved across HIV-1 subtypes and representative simian immunodeficiency viruses. Inhibition of the NFAT5-LTR interaction may thus present a novel therapeutic target to suppress HIV-1 replication and progression of AIDS.

  17. Proteomic Analysis of Pathogenic Fungi Reveals Highly Expressed Conserved Cell Wall Proteins

    Directory of Open Access Journals (Sweden)

    Jackson Champer

    2016-01-01

    Full Text Available We are presenting a quantitative proteomics tally of the most commonly expressed conserved fungal proteins of the cytosol, the cell wall, and the secretome. It was our goal to identify fungi-typical proteins that do not share significant homology with human proteins. Such fungal proteins are of interest to the development of vaccines or drug targets. Protein samples were derived from 13 fungal species, cultured in rich or in minimal media; these included clinical isolates of Aspergillus, Candida, Mucor, Cryptococcus, and Coccidioides species. Proteomes were analyzed by quantitative MSE (Mass Spectrometry—Elevated Collision Energy. Several thousand proteins were identified and quantified in total across all fractions and culture conditions. The 42 most abundant proteins identified in fungal cell walls or supernatants shared no to very little homology with human proteins. In contrast, all but five of the 50 most abundant cytosolic proteins had human homologs with sequence identity averaging 59%. Proteomic comparisons of the secreted or surface localized fungal proteins highlighted conserved homologs of the Aspergillus fumigatus proteins 1,3-β-glucanosyltransferases (Bgt1, Gel1-4, Crf1, Ecm33, EglC, and others. The fact that Crf1 and Gel1 were previously shown to be promising vaccine candidates, underlines the value of the proteomics data presented here.

  18. The conservation value of South East Asia's highly degraded forests: evidence from leaf-litter ants

    Science.gov (United States)

    Woodcock, Paul; Edwards, David P.; Fayle, Tom M.; Newton, Rob J.; Khen, Chey Vun; Bottrell, Simon H.; Hamer, Keith C.

    2011-01-01

    South East Asia is widely regarded as a centre of threatened biodiversity owing to extensive logging and forest conversion to agriculture. In particular, forests degraded by repeated rounds of intensive logging are viewed as having little conservation value and are afforded meagre protection from conversion to oil palm. Here, we determine the biological value of such heavily degraded forests by comparing leaf-litter ant communities in unlogged (natural) and twice-logged forests in Sabah, Borneo. We accounted for impacts of logging on habitat heterogeneity by comparing species richness and composition at four nested spatial scales, and examining how species richness was partitioned across the landscape in each habitat. We found that twice-logged forest had fewer species occurrences, lower species richness at small spatial scales and altered species composition compared with natural forests. However, over 80 per cent of species found in unlogged forest were detected within twice-logged forest. Moreover, greater species turnover among sites in twice-logged forest resulted in identical species richness between habitats at the largest spatial scale. While two intensive logging cycles have negative impacts on ant communities, these degraded forests clearly provide important habitat for numerous species and preventing their conversion to oil palm and other crops should be a conservation priority. PMID:22006966

  19. Wet high-intensity magnetic separation for the concentration of Witwatersrand gold-uranium ores and residues

    International Nuclear Information System (INIS)

    Corrans, I.J.; Levin, J.

    1979-01-01

    Wet high-intensity magnetic separation (WHIMS) for the concentration of gold and uranium was tested on many Witwatersrand cyanidation residues, and on some ores and flotation tailings. The results varied, but many indicated recoveries of over 60 per cent of the gold and uranium. The main source of loss is the inefficiency of WHIMS for material of smaller particle size than 20μm. The recoveries in the continuous tests were lower than those in the batch tests. The continuous tests indicated an operational difficulty that could be experienced in practice, namely the tendency for wood chips and ferromagnetic particles to block the matrix of the separator. It was decided that a solution to the problem lies in the modification of the separator to allow continuous removal of the matrix for cleaning. A system has been developed for this purpose and is being demonstrated on a pilot-plant scale. Promising results were obtained in tests on a process that combines a coarse grind, gravity concentration, and WHIMS. In the gravity-concentration step, considerable recoveries, generally over 50 per cent, of high-grade pyrite were obtained, together with high recoveries of gold and moderate, but possibly important, recoveries of uranium. A simple model describing the operation of the WHIMS machine in terms of the operating parameters is described. This should reduce the amount of empirical testwork required for the optimization of operating conditions and should provide a basis for scale-up calculations. The economics of the WHIMS process is discussed [af

  20. Early detection of tumor relapse/regrowth by consecutive minimal residual disease monitoring in high-risk neuroblastoma patients

    Science.gov (United States)

    Hirase, Satoshi; Saitoh, Atsuro; Hartomo, Tri Budi; Kozaki, Aiko; Yanai, Tomoko; Hasegawa, Daiichiro; Kawasaki, Keiichiro; Kosaka, Yoshiyuki; Matsuo, Masafumi; Yamamoto, Nobuyuki; Mori, Takeshi; Hayakawa, Akira; Iijima, Kazumoto; Nishio, Hisahide; Nishimura, Noriyuki

    2016-01-01

    Neuroblastoma is an aggressive pediatric tumor accounting for ~15% of cancer-associated mortalities in children. Despite the current intensive therapy, >50% of high-risk patients experience tumor relapse or regrowth caused by the activation of minimal residual disease (MRD). Although several MRD detection protocols using various reverse transcription-quantitative polymerase chain reaction (RT-qPCR) markers have been reported to evaluate the therapeutic response and disease status of neuroblastoma patients, their clinical significance remains elusive. The present study reports two high-risk neuroblastoma patients, whose MRD was consecutively monitored using 11 RT-qPCR markers (CHRNA3, CRMP1, DBH, DCX, DDC, GABRB3, GAP43, ISL1, KIF1A, PHOX2B and TH) during their course of treatment. The two patients initially responded to the induction therapy and reached MRD-negative status. The patients' MRD subsequently became positive with no elevation of their urinary homovanillic acid, urinary vanillylmandelic acid and serum neuron-specific enolase levels at 13 or 19 weeks prior to the clinical diagnosis of tumor relapse or regrowth. The present cases highlight the possibility of consecutive MRD monitoring using 11 markers to enable an early detection of tumor relapse or regrowth in high-risk neuroblastoma patients. PMID:27446404

  1. Relationship between residual feed intake and digestibility for lactating Holstein cows fed high and low starch diets.

    Science.gov (United States)

    Potts, S B; Boerman, J P; Lock, A L; Allen, M S; VandeHaar, M J

    2017-01-01

    We determined if differences in digestibility among cows explained variation in residual feed intake (RFI) in 4 crossover design experiments. Lactating Holstein cows (n=109; 120±30d in milk; mean ± SD) were fed diets high (HS) or low (LS) in starch. The HS diets were 30% (±1.8%) starch and 27% (±1.2%) neutral detergent fiber (NDF); LS diets were 14% (±2.2%) starch and 40% (±5.3%) NDF. Each experiment consisted of two 28-d treatment periods, with apparent total-tract digestibility measured using indigestible NDF as an internal marker during the last 5d of each period. Individual cow dry matter (DM) intake and milk yield were recorded daily, body weight was measured 3 to 5 times per week, and milk components were analyzed 2 d/wk. Individual DM intake was regressed on milk energy output, metabolic body weight, body energy gain, and fixed effects of parity, experiment, cohort (a group of cows that received treatments in the same sequence) nested within experiment, and diet nested within cohort and experiment, with the residual being RFI. High RFI cows ate more than expected and were deemed less efficient. Residual feed intake correlated negatively with digestibility of starch for both HS (r=-0.31) and LS (r=-0.23) diets, and with digestibilities of DM (r=-0.30) and NDF (r=-0.23) for LS diets but was not correlated with DM or NDF digestibility for HS diets. For each cohort within an experiment, cows were classified as high RFI (HRFI; >0.5 SD), medium RFI (MRFI; ±0.5 SD), and low RFI (LRFI; Digestibility of DM was similar (~66%) among HRFI and LRFI for HS diets but greater for LRFI when fed LS diets (64 vs. 62%). For LS diets, digestibility of DM could account for up to 31% of the differences among HRFI and LRFI for apparent diet energy density, as determined from individual cow performance, indicating that digestibility explains some of the between-animal differences for the ability to convert gross energy into net energy. Some of the differences in digestibility

  2. Impacts of Tropical Forest Disturbance Upon Avifauna on a Small Island with High Endemism: Implications for Conservation

    Directory of Open Access Journals (Sweden)

    Martin Thomas

    2010-01-01

    Full Text Available Tropical forests are rapidly being lost across Southeast Asia and this is predicted to have severe implications for many of the region′s bird species. However, relationships between forest disturbance and avifaunal assemblages remain poorly understood, particularly on small island ecosystems such as those found in the biodiversity ′hotspot′ of Wallacea. This study examines how avifaunal richness varies across a disturbance gradient in a forest reserve on Buton Island, southeast Sulawesi. Particular emphasis is placed upon examining responses in endemic and red-listed species with high conservation importance. Results indicate that overall avian richness increases between primary and 30-year-old regenerating secondary forest and then decreases through disturbed secondary forest, but is highest in cleared farmland. However, high species richness in farmland does not signify high species distinctiveness; bird community composition here differs significantly from that found in forest sites, and is poor in supporting forest specialists and endemic species. Certain large-bodied endemics such as the Knobbed Hornbill (Rhyticeros cassidix appear to be sensitive to moderate disturbance, with populations occurring at greatest density within primary forest. However, overall endemic species richness, as well as that of endemic frugivores and insectivores, is similar in primary and secondary forest types. Results indicate that well-established secondary forest in particular has an important role in supporting species with high conservational importance, possessing community composition similar to that found in primary forest and supporting an equally high richness of endemic species.

  3. Noise exposure and hearing conservation practices in an industry with high incidence of workers' compensation claims for hearing loss.

    Science.gov (United States)

    Daniell, William E; Swan, Susan S; McDaniel, Mary M; Stebbins, John G; Seixas, Noah S; Morgan, Michael S

    2002-10-01

    Washington State has experienced a striking increase in workers' compensation claims for hearing loss. This cross-sectional study examined noise exposures and hearing conservation practices in one industry with a high rate of hearing loss claims. We evaluated 10 representative foundries with personal noise dosimetry, management interviews, employee interviews, and existing audiometry. Noise levels routinely exceeded 85 dBA. All companies were out of compliance with hearing conservation regulations. Most employees with important findings on audiograms were not aware of their findings. There was a significant positive correlation between management-interview scores and worksite-average employee-interview scores (r = 0.70, P = 0.02). Companies where more effort is put into hearing conservation program activities can achieve a greater positive impact on employee awareness. However, there were broad deficiencies even in the better programs in this sample, suggesting that workers in this industry probably face a continuing substantial risk of occupational hearing loss. Copyright 2002 Wiley-Liss, Inc.

  4. Universal antibodies against the highly conserved influenza fusion peptide cross-neutralize several subtypes of influenza A virus

    Energy Technology Data Exchange (ETDEWEB)

    Hashem, Anwar M. [Centre for Vaccine Evaluation, Biologics and Genetic Therapies Directorate, HPFB, Health Canada, Ottawa, ON (Canada); Department of Microbiology, Faculty of Medicine, King Abdulaziz University, Jeddah (Saudi Arabia); Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON (Canada); Van Domselaar, Gary [National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB (Canada); Li, Changgui; Wang, Junzhi [National Institute for the Control of Pharmaceutical and Biological Products, Beijing (China); She, Yi-Min; Cyr, Terry D. [Centre for Vaccine Evaluation, Biologics and Genetic Therapies Directorate, HPFB, Health Canada, Ottawa, ON (Canada); Sui, Jianhua [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, 44 Binney Street, Boston, MA 02115 (United States); He, Runtao [National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB (Canada); Marasco, Wayne A. [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, 44 Binney Street, Boston, MA 02115 (United States); Li, Xuguang, E-mail: Sean.Li@hc-sc.gc.ca [Centre for Vaccine Evaluation, Biologics and Genetic Therapies Directorate, HPFB, Health Canada, Ottawa, ON (Canada); Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON (Canada)

    2010-12-10

    Research highlights: {yields} The fusion peptide is the only universally conserved epitope in all influenza viral hemagglutinins. {yields} Anti-fusion peptide antibodies are universal antibodies that cross-react with all influenza HA subtypes. {yields} The universal antibodies cross-neutralize different influenza A subtypes. {yields} The universal antibodies inhibit the fusion process between the viruses and the target cells. -- Abstract: The fusion peptide of influenza viral hemagglutinin plays a critical role in virus entry by facilitating membrane fusion between the virus and target cells. As the fusion peptide is the only universally conserved epitope in all influenza A and B viruses, it could be an attractive target for vaccine-induced immune responses. We previously reported that antibodies targeting the first 14 amino acids of the N-terminus of the fusion peptide could bind to virtually all influenza virus strains and quantify hemagglutinins in vaccines produced in embryonated eggs. Here we demonstrate that these universal antibodies bind to the viral hemagglutinins in native conformation presented in infected mammalian cell cultures and neutralize multiple subtypes of virus by inhibiting the pH-dependant fusion of viral and cellular membranes. These results suggest that this unique, highly-conserved linear sequence in viral hemagglutinin is exposed sufficiently to be attacked by the antibodies during the course of infection and merits further investigation because of potential importance in the protection against diverse strains of influenza viruses.

  5. Universal antibodies against the highly conserved influenza fusion peptide cross-neutralize several subtypes of influenza A virus

    International Nuclear Information System (INIS)

    Hashem, Anwar M.; Van Domselaar, Gary; Li, Changgui; Wang, Junzhi; She, Yi-Min; Cyr, Terry D.; Sui, Jianhua; He, Runtao; Marasco, Wayne A.; Li, Xuguang

    2010-01-01

    Research highlights: → The fusion peptide is the only universally conserved epitope in all influenza viral hemagglutinins. → Anti-fusion peptide antibodies are universal antibodies that cross-react with all influenza HA subtypes. → The universal antibodies cross-neutralize different influenza A subtypes. → The universal antibodies inhibit the fusion process between the viruses and the target cells. -- Abstract: The fusion peptide of influenza viral hemagglutinin plays a critical role in virus entry by facilitating membrane fusion between the virus and target cells. As the fusion peptide is the only universally conserved epitope in all influenza A and B viruses, it could be an attractive target for vaccine-induced immune responses. We previously reported that antibodies targeting the first 14 amino acids of the N-terminus of the fusion peptide could bind to virtually all influenza virus strains and quantify hemagglutinins in vaccines produced in embryonated eggs. Here we demonstrate that these universal antibodies bind to the viral hemagglutinins in native conformation presented in infected mammalian cell cultures and neutralize multiple subtypes of virus by inhibiting the pH-dependant fusion of viral and cellular membranes. These results suggest that this unique, highly-conserved linear sequence in viral hemagglutinin is exposed sufficiently to be attacked by the antibodies during the course of infection and merits further investigation because of potential importance in the protection against diverse strains of influenza viruses.

  6. A high-order relaxation method with projective integration for solving nonlinear systems of hyperbolic conservation laws

    Science.gov (United States)

    Lafitte, Pauline; Melis, Ward; Samaey, Giovanni

    2017-07-01

    We present a general, high-order, fully explicit relaxation scheme which can be applied to any system of nonlinear hyperbolic conservation laws in multiple dimensions. The scheme consists of two steps. In a first (relaxation) step, the nonlinear hyperbolic conservation law is approximated by a kinetic equation with stiff BGK source term. Then, this kinetic equation is integrated in time using a projective integration method. After taking a few small (inner) steps with a simple, explicit method (such as direct forward Euler) to damp out the stiff components of the solution, the time derivative is estimated and used in an (outer) Runge-Kutta method of arbitrary order. We show that, with an appropriate choice of inner step size, the time step restriction on the outer time step is similar to the CFL condition for the hyperbolic conservation law. Moreover, the number of inner time steps is also independent of the stiffness of the BGK source term. We discuss stability and consistency, and illustrate with numerical results (linear advection, Burgers' equation and the shallow water and Euler equations) in one and two spatial dimensions.

  7. On-treatment non-high-density lipoprotein cholesterol, apolipoprotein B, triglycerides, and lipid ratios in relation to residual vascular risk after treatment with potent statin therapy

    DEFF Research Database (Denmark)

    Mora, Samia; Glynn, Robert J; Boekholdt, S Matthijs

    2012-01-01

    The goal of this study was to determine whether residual risk after high-dose statin therapy for primary prevention individuals with reduced levels of low-density lipoprotein cholesterol (LDL-C) is related to on-treatment apolipoprotein B, non-high-density lipoprotein cholesterol (non-HDL-C), tri...

  8. Using sulfite chemistry for robust bioconversion of Douglas-fir forest residue to bioethanol at high titer and lignosulfonate: A pilot-scale evaluation

    Science.gov (United States)

    J.Y. Zhu; M. Subhosh Chandra; Feng Gu; Roland Gleisner; J.Y. Zhu; John Sessions; Gevan Marrs; Johnway Gao; Dwight Anderson

    2015-01-01

    This study demonstrated at the pilot-scale (50 kg) use of Douglas-fir forest harvest residue, an underutilized forest biomass, for the production of high titer and high yield bioethanol using sulfite chemistry without solid–liquor separation and detoxification. Sulfite Pretreatment to Overcome the Recalcitrance of Lignocelluloses (SPORL) was directly applied to the...

  9. A new world monkey microsatellite (ap74) highly conserved in primates

    International Nuclear Information System (INIS)

    Oklander, Luciana Ines; Steinberg, Eliana Ruth; Dolores Mudry, Marta

    2012-01-01

    Given their great variability, microsatellites or STRS became the most commonly used genetic markers over the last 15 years. The analysis of these markers requires minimum quantities of DNA, allowing the use of noninvasive samples, such as feces or hair. We amplified the microsatellite ap74 in blood and hair samples in order to analyze the levels of genomic conservation among a wide range of primates including: lemur catta, alouatta caraya, ateles belzebuth, ateles chamek, pan troglodytes, papio sp., and Homo sapiens. in all cases we obtained amplification products that exhibited similar size both in monkeys and human (oscillating between 126 and 176 bp), except in the lemur where the detected fragment presented a size of approximately 1000 bp. the analysis of the nucleotide sequences permitted the evaluation of the molecular modifications experienced during the evolutionary process in primates.

  10. Residual stresses

    International Nuclear Information System (INIS)

    Macherauch, E.

    1978-01-01

    Residual stresses are stresses which exist in a material without the influence of external powers and moments. They come into existence when the volume of a material constantly changes its form as a consequence of mechanical, thermal, and/or chemical processes and is hindered by neighbouring volumes. Bodies with residual stress are in mechanical balance. These residual stresses can be manifested by means of all mechanical interventions disturbing this balance. Acoustical, optical, radiological, and magnetical methods involving material changes caused by residual stress can also serve for determining residual stress. Residual stresses have an ambivalent character. In technical practice, they are feared and liked at the same time. They cause trouble because they can be the cause for unexpected behaviour of construction elements. They are feared since they can cause failure, in the worst case with catastrophical consequences. They are appreciated, on the other hand, because, in many cases, they can contribute to improvements of the material behaviour under certain circumstances. But they are especially liked for their giving convenient and (this is most important) mostly uncontrollable explanations. For only in very few cases we have enough knowledge and possibilities for the objective evaluation of residual stresses. (orig.) [de

  11. Energy production from agricultural residues: High methane yields in pilot-scale two-stage anaerobic digestion

    International Nuclear Information System (INIS)

    Parawira, W.; Read, J.S.; Mattiasson, B.; Bjoernsson, L.

    2008-01-01

    There is a large, unutilised energy potential in agricultural waste fractions. In this pilot-scale study, the efficiency of a simple two-stage anaerobic digestion process was investigated for stabilisation and biomethanation of solid potato waste and sugar beet leaves, both separately and in co-digestion. A good phase separation between hydrolysis/acidification and methanogenesis was achieved, as indicated by the high carbon dioxide production, high volatile fatty acid concentration and low pH in the acidogenic reactors. Digestion of the individual substrates gave gross energy yields of 2.1-3.4 kWh/kg VS in the form of methane. Co-digestion, however, gave up to 60% higher methane yield, indicating that co-digestion resulted in improved methane production due to the positive synergism established in the digestion liquor. The integrity of the methane filters (MFs) was maintained throughout the period of operation, producing biogas with 60-78% methane content. A stable effluent pH showed that the methanogenic reactors had good ability to withstand the variations in load and volatile fatty acid concentrations that occurred in the two-stage process. The results of this pilot-scale study show that the two-stage anaerobic digestion system is suitable for effective conversion of semi-solid agricultural residues as potato waste and sugar beet leaves

  12. Practical application of in silico fragmentation based residue screening with ion mobility high-resolution mass spectrometry.

    Science.gov (United States)

    Kaufmann, Anton; Butcher, Patrick; Maden, Kathry; Walker, Stephan; Widmer, Mirjam

    2017-07-15

    A screening concept for residues in complex matrices based on liquid chromatography coupled to ion mobility high-resolution mass spectrometry LC/IMS-HRMS is presented. The comprehensive four-dimensional data (chromatographic retention time, drift time, mass-to-charge and ion abundance) obtained in data-independent acquisition (DIA) mode was used for data mining. An in silico fragmenter utilizing a molecular structure database was used for suspect screening, instead of targeted screening with reference substances. The utilized data-independent acquisition mode relies on the MS E concept; where two constantly alternating HRMS scans (low and high fragmentation energy) are acquired. Peak deconvolution and drift time alignment of ions from the low (precursor ion) and high (product ion) energy scan result in relatively clean product ion spectra. A bond dissociation in silico fragmenter (MassFragment) supplied with mol files of compounds of interest was used to explain the observed product ions of each extracted candidate component (chromatographic peak). Two complex matrices (fish and bovine liver extract) were fortified with 98 veterinary drugs. Out of 98 screened compounds 94 could be detected with the in silico based screening approach. The high correlation among drift time and m/z value of equally charged ions was utilized for an orthogonal filtration (ranking). Such an orthogonal ion mobility based filter removes multiply charged ions (e.g. peptides and proteins from the matrix) as well as noise and artefacts. Most significantly, this filtration dramatically reduces false positive findings but hardly increases false negative findings. The proposed screening approach may offer new possibilities for applications where reference compounds are hardly or not at all commercially available. Such areas may be the analysis of metabolites of drugs, pyrrolizidine alkaloids, marine toxins, derivatives of sildenafil or novel designer drugs (new psychoactive substances

  13. Intestinal microbiota profiles associated with low and high residual feed intake in chickens across two geographical locations.

    Directory of Open Access Journals (Sweden)

    Sina-Catherine Siegerstetter

    Full Text Available Intestinal microbe-host interactions can affect the feed efficiency (FE of chickens. As inconsistent findings for FE-associated bacterial taxa were reported across studies, the present objective was to identify whether bacterial profiles and predicted metabolic functions that were associated with residual feed intake (RFI and performance traits in female and male chickens were consistent across two different geographical locations. At six weeks of life, the microbiota in ileal, cecal and fecal samples of low (n = 34 and high (n = 35 RFI chickens were investigated by sequencing the V3-5 region of the 16S rRNA gene. Location-associated differences in α-diversity and relative abundances of several phyla and genera were detected. RFI-associated bacterial abundances were found at the phylum and genus level, but differed among the three intestinal sites and between males and females. Correlation analysis confirmed that, of the taxonomically classifiable bacteria, Lactobacillus (5% relative abundance and two Lactobacillus crispatus-OTUs in feces were indicative for high RFI in females (P < 0.05. In males, Ruminococcus in cecal digesta (3.1% relative abundance and Dorea in feces (<0.1% relative abundance were best indicative for low RFI, whereas Acinetobacter in feces (<1.5% relative abundance related to high RFI (P < 0.05. Predicted metabolic functions in feces of males confirmed compositional relationships as functions related to amino acid, fatty acid and vitamin metabolism correlated with low RFI, whereas an increasing abundance of bacterial signaling and interaction (i.e. cellular antigens genes correlated with high RFI (P < 0.05. In conclusion, RFI-associated bacterial profiles could be identified across different geographical locations. Results indicated that consortia of low-abundance taxa in the ileum, ceca and feces may play a role for FE in chickens, whereby only bacterial FE-associations found in ileal and cecal digesta may serve as useful

  14. Identification of a highly conserved domain in the EcoRII methyltransferase which can be photolabeled with S-adenosyl-L-[methyl-3H]methionine. Evidence for UV-induced transmethylation of cysteine 186

    International Nuclear Information System (INIS)

    Som, S.; Friedman, S.

    1991-01-01

    DNA methyltransferases can be photolabeled with S-adenosyl-L-methionine (AdoMet). Specific incorporation of radioactivity has been demonstrated after photolabeling with either [methyl-3H]AdoMet or [35S]AdoMet. The labeling is believed to occur at the AdoMet binding site. With the purpose of localizing the site responsible for [methyl-3H]AdoMet photolabeling, we cleaved the labeled EcoRII methyltransferase by chemical and enzymatic reactions and isolated the radiolabeled peptides by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and high pressure liquid chromatography. The labeled peptides were identified by amino-terminal sequencing. A common region was localized which accounted for 65-70% of the total label. This region includes a highly conserved core sequence present in all DNA (cytosine 5)-methyltransferases. One such fragment was digested further with chymotrypsin, and amino acid analysis of the resulting 3H-labeled peptide was consistent with the sequence Ala-Gly-Phe-Pro-(Cys)-Gln-Pro-Phe-Ser-Leu. However, the cysteine residue was not recovered as carboxymethylcysteine. The Pro-Cys bond was found to be protected from cleavage at cysteine residues after cyanylation. These results suggest that the cysteine residue is modified by the labeling reaction. The chymotryptic fragment was hydrolyzed enzymatically to single amino acids, and the labeled amino acid was identified as S-methylcysteine by thin layer chromatography. These results indicate that the cysteine residue is located at or close to the AdoMet binding site of EcoRII methyltransferase

  15. Advanced technique for ultra-thin residue inspection with sub-10nm thickness using high-energy back-scattered electrons

    Science.gov (United States)

    Han, Jin-Hee

    2018-03-01

    Recently the aspect ratio of capacitor and via hole of memory semiconductor device has been dramatically increasing in order to store more information in a limited area. A small amount of remained residues after etch process on the bottom of the high aspect ratio structure can make a critical failure in device operation. Back-scattered electrons (BSE) are mainly used for inspecting the defect located at the bottom of the high aspect ratio structure or analyzing the overlay of the multi-layer structure because these electrons have a high linearity with the direction of emission and a high kinetic energy above 50eV. However, there is a limitation on that it cannot detect ultra-thin residue material having a thickness of several nanometers because the surface sensitivity is extremely low. We studied the characteristics of BSE spectra using Monte Carlo simulations for several cases which the high aspect ratio structures have extreme microscopic residues. Based on the assumption that most of the electrons emitted without energy loss are localized on the surface, we selected the detection energy window which has a range of 20eV below the maximum energy of the BSE. This window section is named as the high-energy BSE region. As a result of comparing the detection sensitivity of the conventional and the high-energy BSE detection mode, we found that the detection sensitivity for the residuals which have 2nm thickness is improved by more than 10 times in the high-energy BSE mode. This BSE technology is a new inspection method that can greatly be improved the inspection sensitivity for the ultra-thin residual material presented in the high aspect ratio structure, and its application will be expanded.

  16. Determination of diacylhydrazines-type insect growth regulator JS-118 residues in cabbage and soil by high performance liquid chromatography with DAD detection.

    Science.gov (United States)

    Hu, J-Y; Deng, Z-B; Qin, D-M

    2009-12-01

    JS-118 is a diacylhydrazines-type insect growth regulator used extensively in China now. An analytical method for residues determination of JS-118 in cabbage and soil samples by high performance liquid chromatography with DAD detection was established and optimized. Primary secondary amine solid phase extraction cartridge was used for sample preparation. Mean recoveries for the analyte ranged from 96.6% to 107.0% with CV value less than 4.7%. The limit of quantification is 0.01 mg/kg. Direct confirmation of JS-118 residues in samples was realized by high performance liquid chromatography-mass spectrometry. The proposed method is simple, rapid and reliable to perform and could be utilized for monitoring of pesticides residues.

  17. Highly uniform residual layers for arrays of 3D nanoimprinted cavities in Fabry-Pérot-filter-array-based nanospectrometers

    Science.gov (United States)

    Memon, Imran; Shen, Yannan; Khan, Abdullah; Woidt, Carsten; Hillmer, Hartmut

    2016-04-01

    Miniaturized optical spectrometers can be implemented by an array of Fabry-Pérot (FP) filters. FP filters are composed of two highly reflecting parallel mirrors and a resonance cavity. Each filter transmits a small spectral band (filter line) depending on its individual cavity height. The optical nanospectrometer, a miniaturized FP-based spectrometer, implements 3D NanoImprint technology for the fabrication of multiple FP filter cavities in a single process step. However, it is challenging to avoid the dependency of residual layer (RL) thickness on the shape of the printed patterns in NanoImprint. Since in a nanospectrometer the filter cavities vary in height between neighboring FP filters and, thus, the volume of each cavity varies causing that the RL varies slightly or noticeably between different filters. This is one of the few disadvantages of NanoImprint using soft templates such as substrate conformal imprint lithography which is used in this paper. The advantages of large area soft templates can be revealed substantially if the problem of laterally inhomogeneous RLs can be avoided or reduced considerably. In the case of the nanospectrometer, non-uniform RLs lead to random variations in the designed cavity heights resulting in the shift of desired filter lines. To achieve highly uniform RLs, we report a volume-equalized template design with the lateral distribution of 64 different cavity heights into several units with each unit comprising four cavity heights. The average volume of each unit is kept constant to obtain uniform filling of imprint material per unit area. The imprint results, based on the volume-equalized template, demonstrate highly uniform RLs of 110 nm thickness.

  18. Hearing sensitivity in context: Conservation implications for a highly vocal endangered species

    Directory of Open Access Journals (Sweden)

    Megan A. Owen

    2016-04-01

    Full Text Available Hearing sensitivity is a fundamental determinant of a species’ vulnerability to anthropogenic noise, however little is known about the hearing capacities of most conservation dependent species. When audiometric data are integrated with other aspects of species’ acoustic ecology, life history, and characteristic habitat topography and soundscape, predictions can be made regarding probable vulnerability to the negative impacts of different types of anthropogenic noise. Here we used an adaptive psychoacoustic technique to measure hearing thresholds in the endangered giant panda; a species that uses acoustic communication to coordinate reproduction. Our results suggest that giant pandas have functional hearing into the ultrasonic range, with good sensitivity between 10.0 and 16.0 kHz, and best sensitivity measured at 12.5–14.0 kHz. We estimated the lower and upper limits of functional hearing as 0.10 and 70.0 kHz respectively. While these results suggest that panda hearing is similar to that of some other terrestrial carnivores, panda hearing thresholds above 14.0 kHz were significantly lower (i.e., more sensitive than those of the polar bear, the only other bear species for which data are available. We discuss the implications of this divergence, as well as the relationship between hearing sensitivity and the spectral parameters of panda vocalizations. We suggest that these data, placed in context, can be used towards the development of a sensory-based model of noise disturbance for the species.

  19. Increased Butyrate Production During Long-Term Fermentation of In Vitro-Digested High Amylose Cornstarch Residues with Human Feces.

    Science.gov (United States)

    Li, Li; Jiang, Hongxin; Kim, Hyun-Jung; Yum, Man-Yu; Campbell, Mark R; Jane, Jay-Lin; White, Pamela J; Hendrich, Suzanne

    2015-09-01

    An in vitro semi-continuous long-term (3 wk) anaerobic incubation system simulating lower gut fermentation was used to determine variability in gut microbial metabolism between 4 predigested high amylose-resistant starch residues (SR): SRV, SRVI, SRVII, and SRGEMS in human fecal samples. Subjects participated twice, 5 mo apart: 30 in Phase I (15 lean, 9 overweight and 6 obese), 29 in Phase II (15 lean, 9 overweight, 5 obese); 13 of 15 lean subjects participated in both phases. Of the 4 SRs, SRV displayed the highest gelatinization temperature, peak temperature, enthalpy changes, and the least digestibility compared with the other SRs. In both phases, compared with blank controls, all SRs increased butyrate ∼2-fold which stabilized at week 2 and only SRV caused greater propionate concentration (∼30%) after 3 wk which might have been partly mediated by its lesser digestibility. Fecal samples from lean and overweight/obese subjects incubated with SRs showed similar short-chain fatty acid production across both time points, which suggests that resistant starch may benefit individuals across BMIs. © 2015 Institute of Food Technologists®

  20. Evidence in Latin America of recurrence of V388M, a phenylketonuria mutation with high in vitro residual activity

    Energy Technology Data Exchange (ETDEWEB)

    Desviat, L.R.; Perez, B.; De Lucca, M. [Universidad Autonoma de Madrid, (Spain)] [and others

    1995-08-01

    Phenylketonuria mutation V388M is frequent in the Iberian Peninsula. In vitro, the V388M mutant enzyme has similar immunoreactive protein and phenylalanine hydroxylase mRNA and had 43% residual activity, which correlates well with the mild phenotype exhibited by the homozygous patients. In Spain it has been detected in 5.7% of the mutant alleles and is always associated with haplotype 1.7. This mutation is also present in high frequency in some Latin American countries (Brazil, 9% Chile, 13%). It is interesting that in Chile most of the alleles bearing this mutation carry haplotype 4.3, although in Brazil it is found only on the background of haplotype 1.7. The origin of V388M in Spain on haplotype 1.7 and in Chile on haplotype 4.3 is clearly different. Recurrence is the most plausible explanation, because the mutation involves a CpG dinucleotide, and a recombination event transferring the mutation from haplotype 1 to 4 is unlikely. 29 refs., 2 figs., 3 tabs.

  1. Multi-residue determination of 210 drugs in pork by ultra-high-performance liquid chromatography-tandem mass spectrometry.

    Science.gov (United States)

    Yin, Zhiqiang; Chai, Tingting; Mu, Pengqian; Xu, Nana; Song, Yue; Wang, Xinlu; Jia, Qi; Qiu, Jing

    2016-09-09

    This paper presents a multi-residue analytical method for 210 drugs in pork using ultra-high-performance liquid chromatography-Q-Trap tandem mass spectrometry (UPLC-MS/MS) within 20min via positive ESI in scheduled multi-reaction monitoring (MRM) mode. The 210 drugs, belonging to 21 different chemical classes, included macrolides, sulfonamides, tetracyclines, β-lactams, β-agonists, aminoglycosides, antiviral drugs, glycosides, phenothiazine, protein anabolic hormones, non-steroidal anti-inflammatory drugs (NSAIDs), quinolones, antifungal drugs, corticosteroids, imidazoles, piperidines, piperazidines, insecticides, amides, alkaloids and others. A rapid and simple preparation method was applied to process the animal tissues, including solvent extraction with an acetonitrile/water mixture (80/20, v/v), defatting and clean-up processes. The recoveries ranged from 52% to 130% with relative standard deviations (RSDs)<20% for spiked concentrations of 10, 50 and 250μg/kg. More than 90% of the analytes achieved low limits of quantification (LOQs)<10μg/kg. The decision limit (CCα), detection capability (CCβ) values were in the range of 2-502μg/kg and 4-505μg/kg, respectively. This method is significant for food safety monitoring and controlling veterinary drug use. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. High glucose recovery from direct enzymatic hydrolysis of bisulfite-pretreatment on non-detoxified furfural residues.

    Science.gov (United States)

    Xing, Yang; Bu, Lingxi; Sun, Dafeng; Liu, Zhiping; Liu, Shijie; Jiang, Jianxin

    2015-10-01

    This study reports four schemes to pretreat wet furfural residues (FRs) with sodium bisulfite for production of fermentable sugar. The results showed that non-detoxified FRs (pH 2-3) had great potential to lower the cost of bioconversion. The optimal process was that unwashed FRs were first pretreated with bisulfite, and the whole slurry was then directly used for enzymatic hydrolysis. A maximum glucose yield of 99.4% was achieved from substrates pretreated with 0.1 g NaHSO3/g dry substrate (DS), at a relatively low temperature of 100 °C for 3 h. Compared with raw material, enzymatic hydrolysis at a high-solid of 16.5% (w/w) specifically showed more excellent performance with bisulfite treated FRs. Direct bisulfite pretreatment improved the accessibility of substrates and the total glucose recovery. Lignosulfonate in the non-detoxified slurry decreased the non-productive adsorption of cellulase on the substrate, thus improving enzymatic hydrolysis. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Determination of benzimidazole residues and their metabolites in raw milk using high performance liquid chromatography-diode array detection

    Directory of Open Access Journals (Sweden)

    Marija Denžić Lugomer

    2017-01-01

    Full Text Available A new analytical method using high performance liquid chromatography-diode array detector (HPLC-DAD was developed for the analysis of 18 benzimidazoles and their metabolites in milk. Samples were extracted with acetonitrile and n-hexane and purified by polymer cation exchange (PCX solid phase extraction cartridges. LC separation was performed on Xbridge C18 with gradient elution using acetonitrile and ammonium acetate buffer. The DAD detection was set at 298, 312, 254 and 290 nm. The method was validated according to the criteria of Commission Decision 2002/657/EC. The following validation parameters were set: accuracy (expressed as recovery 31.7-137.6 %, limit of decision (CCα 6.0-120.6 μg kg-1, detection capability (CCβ 6.1-120.8 μg kg-1, limit of detection (LOD 1-4 μg kg-1, limit of quantification (LOQ 4-18 μg kg-1, precision as CV 7.0-22.5 %, withinlaboratory reproducibility expressed as CV 8.8-30.6 %. Finally, the developed method was applied to the analysis of collected milk samples. A total of 50 milk samples was analysed for benzimidazole residues. All obtained concentrations for all compounds were below the LOQ values.

  4. Similarity of multi-fragmentation of residual nucleus created in nucleus-nucleus interactions at high energies

    International Nuclear Information System (INIS)

    Abdel-Hafiez, A.; Chernyavski, M.M.; Orlova, G.I.; Gulamov, K.G.; Navotny, V.SH.; Uzhinskii, V.V.

    2000-01-01

    Experimental data on multi-fragmentation of residual krypton nuclei created in the interactions of the krypton nuclei with photoemulsion nuclei ut energy of 0.9 GeV per nucleon are presented in a comparison with the analogous data on fragmentation of gold residual nuclei at the energy of 10.7 GeV/nucleon. It is shown for the first time that there are two regimes of nuclear multifragmentation: the former is when less than one-half of nucleons of projectile nucleus are knocked out, the later is when more than one-half of nucleons are knocked out. Residual nuclei with closed masses created at different reactions are fragmenting practically simultaneously when more than one-half of nucleons of original nuclei are knocked out. The evidence of existence of a radial flow of the spectator fragment at the decay of residual krypton nuclei is found

  5. 77 FR 11785 - Energy Conservation Program: Public Meeting and Availability of the Framework Document for High...

    Science.gov (United States)

    2012-02-28

    ... standards for high-intensity discharge (HID) lamps. Accordingly, DOE will hold a public meeting to discuss..._standards/commercial/high_intensity_discharge_lamps.html . DATES: The Department will hold a public meeting... Technologies Program, Mailstop EE-2J, Framework Document for High-Intensity Discharge Lamps, EERE-2010-BT-STD...

  6. Surgical versus conservative treatment for high-risk stress fractures of the lower leg (anterior tibial cortex, navicular and fifth metatarsal base): a systematic review

    NARCIS (Netherlands)

    Mallee, Wouter H.; Weel, Hanneke; van Dijk, C. Niek; van Tulder, Maurits W.; Kerkhoffs, Gino M.; Lin, Chung-Wei Christine

    2015-01-01

    To compare surgical and conservative treatment for high-risk stress fractures of the anterior tibial cortex, navicular and proximal fifth metatarsal. Systematic searches of CENTRAL, MEDLINE, EMBASE, CINAHL, SPORTDiscus and PEDro were performed to identify relevant prospective and retrospective

  7. High-Level Systemic Expression of Conserved Influenza Epitope in Plants on the Surface of Rod-Shaped Chimeric Particles

    Directory of Open Access Journals (Sweden)

    Natalia V. Petukhova

    2014-04-01

    Full Text Available Recombinant viruses based on the cDNA copy of the tobacco mosaic virus (TMV genome carrying different versions of the conserved M2e epitope from influenza virus A cloned into the coat protein (CP gene were obtained and partially characterized by our group previously; cysteines in the human consensus M2e sequence were changed to serine residues. This work intends to show some biological properties of these viruses following plant infections. Agroinfiltration experiments on Nicotiana benthamiana confirmed the efficient systemic expression of M2e peptides, and two point amino acid substitutions in recombinant CPs significantly influenced the symptoms and development of viral infections. Joint expression of RNA interference suppressor protein p19 from tomato bushy stunt virus (TBSV did not affect the accumulation of CP-M2e-ser recombinant protein in non-inoculated leaves. RT-PCR analysis of RNA isolated from either infected leaves or purified TMV-M2e particles proved the genetic stability of TMV‑based viral vectors. Immunoelectron microscopy of crude plant extracts demonstrated that foreign epitopes are located on the surface of chimeric virions. The rod‑shaped geometry of plant-produced M2e epitopes is different from the icosahedral or helical filamentous arrangement of M2e antigens on the carrier virus-like particles (VLP described earlier. Thereby, we created a simple and efficient system that employs agrobacteria and plant viral vectors in order to produce a candidate broad-spectrum flu vaccine.

  8. Curli Fibers Are Highly Conserved between Salmonella typhimurium and Escherichia coli with Respect to Operon Structure and Regulation

    Science.gov (United States)

    Römling, Ute; Bian, Zhao; Hammar, Mårten; Sierralta, Walter D.; Normark, Staffan

    1998-01-01

    Mouse-virulent Salmonella typhimurium strains SR-11 and ATCC 14028-1s express curli fibers, thin aggregative fibers, at ambient temperature on plates as judged by Western blot analysis and electron microscopy. Concomitantly with curli expression, cells develop a rough and dry colony morphology and bind the dye Congo red (called the rdar morphotype). Cloning and characterization of the two divergently transcribed operons required for curli biogenesis, csgBA(C) and csgDEFG, from S. typhimurium SR-11 revealed the same gene order and flanking genes as in Escherichia coli. The divergence of the curli region between S. typhimurium and E. coli at the nucleotide level is above average (22.4%). However, a high level of conservation at the protein level, which ranged from 86% amino acid homology for the fiber subunit CsgA to 99% homology for the lipoprotein CsgG, implies functional constraints on the gene products. Consequently, S. typhimurium genes on low-copy-number plasmids were able to complement respective E. coli mutants, although not always to wild-type levels. rpoS and ompR are required for transcriptional activation of (at least) the csgD promoter. The high degree of conservation at the protein level and the identical regulation patterns in E. coli and S. typhimurium suggest similar roles of curli fibers in the same ecological niche in the two species. PMID:9457880

  9. Conserved host response to highly pathogenic avian influenza virus infection in human cell culture, mouse and macaque model systems

    Directory of Open Access Journals (Sweden)

    McDermott Jason E

    2011-11-01

    Full Text Available Abstract Background Understanding host response to influenza virus infection will facilitate development of better diagnoses and therapeutic interventions. Several different experimental models have been used as a proxy for human infection, including cell cultures derived from human cells, mice, and non-human primates. Each of these systems has been studied extensively in isolation, but little effort has been directed toward systematically characterizing the conservation of host response on a global level beyond known immune signaling cascades. Results In the present study, we employed a multivariate modeling approach to characterize and compare the transcriptional regulatory networks between these three model systems after infection with a highly pathogenic avian influenza virus of the H5N1 subtype. Using this approach we identified functions and pathways that display similar behavior and/or regulation including the well-studied impact on the interferon response and the inflammasome. Our results also suggest a primary response role for airway epithelial cells in initiating hypercytokinemia, which is thought to contribute to the pathogenesis of H5N1 viruses. We further demonstrate that we can use a transcriptional regulatory model from the human cell culture data to make highly accurate predictions about the behavior of important components of the innate immune system in tissues from whole organisms. Conclusions This is the first demonstration of a global regulatory network modeling conserved host response between in vitro and in vivo models.

  10. Liquid paraffin as new dilution medium for the analysis of high boiling point residual solvents with static headspace-gas chromatography.

    Science.gov (United States)

    D'Autry, Ward; Zheng, Chao; Bugalama, John; Wolfs, Kris; Hoogmartens, Jos; Adams, Erwin; Wang, Bochu; Van Schepdael, Ann

    2011-07-15

    Residual solvents are volatile organic compounds which can be present in pharmaceutical substances. A generic static headspace-gas chromatography analysis method for the identification and control of residual solvents is described in the European Pharmacopoeia. Although this method is proved to be suitable for the majority of samples and residual solvents, the method may lack sensitivity for high boiling point residual solvents such as N,N-dimethylformamide, N,N-dimethylacetamide, dimethyl sulfoxide and benzyl alcohol. In this study, liquid paraffin was investigated as new dilution medium for the analysis of these residual solvents. The headspace-gas chromatography method was developed and optimized taking the official Pharmacopoeia method as a starting point. The optimized method was validated according to ICH criteria. It was found that the detection limits were below 1μg/vial for each compound, indicating a drastically increased sensitivity compared to the Pharmacopoeia method, which failed to detect the compounds at their respective limit concentrations. Linearity was evaluated based on the R(2) values, which were above 0.997 for all compounds, and inspection of residual plots. Instrument and method precision were examined by calculating the relative standard deviations (RSD) of repeated analyses within the linearity and accuracy experiments, respectively. It was found that all RSD values were below 10%. Accuracy was checked by a recovery experiment at three different levels. Mean recovery values were all in the range 95-105%. Finally, the optimized method was applied to residual DMSO analysis in four different Kollicoat(®) sample batches. Copyright © 2011 Elsevier B.V. All rights reserved.

  11. Bed Agglomeration During the Steam Gasification of a High Lignin Corn Stover Simultaneous Saccharification and Fermentation (SSF) Digester Residue

    Energy Technology Data Exchange (ETDEWEB)

    Howe, Daniel T.; Taasevigen, Danny J.; Gerber, Mark A.; Gray, Michel J.; Fernandez, Carlos A.; Saraf, Laxmikant; Garcia-Perez, Manuel; Wolcott, Michael P.

    2015-11-13

    This research investigates the bed agglomeration phenomena during the steam gasification of a high lignin residue produced from the simultaneous saccharification and fermentation (SSF) of corn stover in a bubbling fluidized bed. The studies were conducted at 895°C using alumina as bed material. Biomass was fed at 1.5 kg/hr, while steam was fed to give a velocity equal to 2.5 times the minimum fluidization velocity, with a steam/carbon ratio of 0.9. The pelletized feedstock was co-fed with a cooling nitrogen stream to mitigate feed line plugging issues. Tar production was high at 50.3 g/Nm3, and the fraction of C10+ compounds was greater than that seen in the gasification of traditional lignocellulosic feedstocks. Carbon closures over 94 % were achieved for all experiments. Bed agglomeration was found to be problematic, indicated by pressure drop increases observed below the bed and upstream of the feed line. Two size categories of solids were recovered from the reactor, +60 mesh and -60 mesh. After a 2.75-hour experiment, 61.7 wt % was recovered as -60 mesh particles and 38.2 wt% of the recovered reactor solids were +60 mesh. A sizeable percentage, 31.8 wt%, was +20 mesh. The -60 mesh particles were mainly formed by the initial bed material (Al2O3). Almost 50 wt. % of the + 20 mesh particles was found to be formed by organics. The unreacted carbon remaining in the reactor resulted in a low conversion rate to product gas. ICP-AES, SEM, SEM-EDS, and XRD confirmed that the large agglomerates (+ 20 mesh) were not encapsulated bed material but rather un-gasified feedstock pellets with sand particles attached to it.

  12. Poor results of 5-aminolevulinic acid-photodynamic therapy for residual high-grade dysplasia and early cancer in barrett esophagus after endoscopic resection

    NARCIS (Netherlands)

    Peters, F.; Kara, M.; Rosmolen, W.; Aalders, M.; ten Kate, F.; Krishnadath, K.; van Lanschot, J.; Fockens, P.; Bergman, J.

    2005-01-01

    BACKGROUND AND STUDY AIMS: The aim of the study was to evaluate the efficacy of photodynamic therapy (PDT) in the treatment of residual high-grade dysplasia or early cancer (HGD/EC) after endoscopic resection in Barrett esophagus. PATIENTS AND METHODS: Study patients were separated into group A,

  13. The Roles of Several Residues of Escherichia coli DNA Photolyase in the Highly Efficient Photo-Repair of Cyclobutane Pyrimidine Dimers

    Directory of Open Access Journals (Sweden)

    Lei Xu

    2010-01-01

    Full Text Available Escherichia coli DNA photolyase is an enzyme that repairs the major kind of UV-induced lesions, cyclobutane pyrimidine dimer (CPD in DNA utilizing 350–450 nm light as energy source. The enzyme has very high photo-repair efficiency (the quantum yield of the reaction is ~0.85, which is significantly greater than many model compounds that mimic photolyase. This suggests that some residues of the protein play important roles in the photo-repair of CPD. In this paper, we have focused on several residues discussed their roles in catalysis by reviewing the existing literature and some hypotheses.

  14. Loss of second and sixth conserved cysteine residues from trypsin inhibitor-like cysteine-rich domain-type protease inhibitors in Bombyx mori may induce activity against microbial proteases.

    Science.gov (United States)

    Li, Youshan; Liu, Huawei; Zhu, Rui; Xia, Qingyou; Zhao, Ping

    2016-12-01

    Previous studies have indicated that most trypsin inhibitor-like cysteine-rich domain (TIL)-type protease inhibitors, which contain a single TIL domain with ten conserved cysteines, inhibit cathepsin, trypsin, chymotrypsin, or elastase. Our recent findings suggest that Cys 2nd and Cys 6th were lost from the TIL domain of the fungal-resistance factors in Bombyx mori, BmSPI38 and BmSPI39, which inhibit microbial proteases and the germination of Beauveria bassiana conidia. To reveal the significance of these two missing cysteines in relation to the structure and function of TIL-type protease inhibitors in B. mori, cysteines were introduced at these two positions (D36 and L56 in BmSPI38, D38 and L58 in BmSPI39) by site-directed mutagenesis. The homology structure model of TIL domain of the wild-type and mutated form of BmSPI39 showed that two cysteine mutations may cause incorrect disulfide bond formation of B. mori TIL-type protease inhibitors. The results of Far-UV circular dichroism (CD) spectra indicated that both the wild-type and mutated form of BmSPI39 harbored predominantly random coil structures, and had slightly different secondary structure compositions. SDS-PAGE and Western blotting analysis showed that cysteine mutations affected the multimerization states and electrophoretic mobility of BmSPI38 and BmSPI39. Activity staining and protease inhibition assays showed that the introduction of cysteine mutations dramaticly reduced the activity of inhibitors against microbial proteases, such as subtilisin A from Bacillus licheniformis, protease K from Engyodontium album, protease from Aspergillus melleus. We also systematically analyzed the key residue sites, which may greatly influence the specificity and potency of TIL-type protease inhibitors. We found that the two missing cysteines in B. mori TIL-type protease inhibitors might be crucial for their inhibitory activities against microbial proteases. The genetic engineering of TIL-type protease inhibitors may be

  15. Solid residues

    International Nuclear Information System (INIS)

    Mulder, E.; Duin, P.J. van; Grootenboer, G.J.

    1995-01-01

    A summary is presented of the many investigations that have been done on solid residues of atmospheric fluid bed combustion (AFBC). These residues are bed ash, cyclone ash and bag filter ash. Physical and chemical properties are discussed and then the various uses of residues (in fillers, bricks, gravel, and for recovery of aluminium) are summarised. Toxicological properties of fly ash and stack ash are discussed as are risks of pneumoconiosis for workers handling fly ash, and contamination of water by ashes. On the basis of present information it is concluded that risks to public health from exposure to emissions of coal fly ash from AFBC appear small or negligible as are health risk to workers in the coal fly ash processing industry. 35 refs., 5 figs., 12 tabs

  16. Catchment-scale conservation units identified for the threatened Yarra pygmy perch (Nannoperca obscura) in highly modified river systems.

    Science.gov (United States)

    Brauer, Chris J; Unmack, Peter J; Hammer, Michael P; Adams, Mark; Beheregaray, Luciano B

    2013-01-01

    Habitat fragmentation caused by human activities alters metapopulation dynamics and decreases biological connectivity through reduced migration and gene flow, leading to lowered levels of population genetic diversity and to local extinctions. The threatened Yarra pygmy perch, Nannoperca obscura, is a poor disperser found in small, isolated populations in wetlands and streams of southeastern Australia. Modifications to natural flow regimes in anthropogenically-impacted river systems have recently reduced the amount of habitat for this species and likely further limited its opportunity to disperse. We employed highly resolving microsatellite DNA markers to assess genetic variation, population structure and the spatial scale that dispersal takes place across the distribution of this freshwater fish and used this information to identify conservation units for management. The levels of genetic variation found for N. obscura are amongst the lowest reported for a fish species (mean heterozygosity of 0.318 and mean allelic richness of 1.92). We identified very strong population genetic structure, nil to little evidence of recent migration among demes and a minimum of 11 units for conservation management, hierarchically nested within four major genetic lineages. A combination of spatial analytical methods revealed hierarchical genetic structure corresponding with catchment boundaries and also demonstrated significant isolation by riverine distance. Our findings have implications for the national recovery plan of this species by demonstrating that N. obscura populations should be managed at a catchment level and highlighting the need to restore habitat and avoid further alteration of the natural hydrology.

  17. High Elevation Refugia for Bombus terricola (Hymenoptera: Apidae) Conservation and Wild Bees of the White Mountain National Forest.

    Science.gov (United States)

    Tucker, Erika M; Rehan, Sandra M

    2017-01-01

    Many wild bee species are in global decline, yet much is still unknown about their diversity and contemporary distributions. National parks and forests offer unique areas of refuge important for the conservation of rare and declining species populations. Here we present the results of the first biodiversity survey of the bee fauna in the White Mountain National Forest (WMNF). More than a thousand specimens were collected from pan and sweep samples representing 137 species. Three species were recorded for the first time in New England and an additional seven species were documented for the first time in the state of New Hampshire. Four introduced species were also observed in the specimens collected. A checklist of the species found in the WMNF, as well as those found previously in Strafford County, NH, is included with new state records and introduced species noted as well as a map of collecting locations. Of particular interest was the relatively high abundance of Bombus terricola Kirby 1837 found in many of the higher elevation collection sites and the single specimen documented of Bombus fervidus (Fabricius 1798). Both of these bumble bee species are known to have declining populations in the northeast and are categorized as vulnerable on the International Union for Conservation of Nature's Red List. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America.

  18. Characterization of STIP, a multi-domain nuclear protein, highly conserved in metazoans, and essential for embryogenesis in Caenorhabditis elegans

    International Nuclear Information System (INIS)

    Ji Qiongmei; Huang, C.-H.; Peng Jianbin; Hashmi, Sarwar; Ye Tianzhang; Chen Ying

    2007-01-01

    We report here the identification and characterization of STIP, a multi-domain nuclear protein that contains a G-patch, a coiled-coil, and several short tryptophan-tryptophan repeats highly conserved in metazoan species. To analyze their functional role in vivo, we cloned nematode stip-1 genes and determined the spatiotemporal pattern of Caenorhabditis elegans STIP-1 protein. RNA analyses and Western blots revealed that stip-1 mRNA was produced via trans-splicing and translated as a 95-kDa protein. Using reporter constructs, we found STIP-1 to be expressed at all developmental stages and in many tissue/cell types including worm oocyte nuclei. We found that STIP-1 is targeted to the nucleus and forms large polymers with a rod-like shape when expressed in mammalian cells. Using deletion mutants, we mapped the regions of STIP-1 involved in nuclear import and polymer assembly. We further showed that knockdown of C. elegans stip-1 by RNA interference arrested development and resulted in morphologic abnormalities around the 16-cell stage followed by 100% lethality, suggesting its essential role in worm embryogenesis. Importantly, the embryonic lethal phenotype could be faithfully rescued with Drosophila and human genes via transgenic expression. Our data provide the first direct evidence that STIP have a conserved essential nuclear function across metazoans from worms to humans

  19. Formation of toroidal pre-heat plasma without residual magnetic field for high-beta pinch experiments

    International Nuclear Information System (INIS)

    Ikeda, Nagayasu; Tamaru, Ken; Nagata, Akiyoshi.

    1979-01-01

    Formation of toroidal pre-heat plasma was studied. The pre-heat plasma without residual magnetic field was made by chopping the current for pre-heat, A small toroidal-pinch system was used for the experiment. The magnetic field was measured with a magnetic probe. One turn loop was used for the measurement of the toroidal one-turn electric field. A pair of Rogoski coil was used for the measurement of plasma current. The dependence of residual magnetic field on chopping time was measured. By fast chopping of the primary current in the pre-heating circuit, the poloidal magnetic field was reduced to several percent within 5 microsecond. After chopping, no instability was observed in the principal discharge plasma produced within several microsecond. As the conclusion, it can be said that the control of residual field can be made by current chopping. (Kato, T.)

  20. Determinations of total residue, total oxide and density of high-level liquid waste (HLLW) by gravimetric method

    International Nuclear Information System (INIS)

    Li Yun; Gao Yueying; Yang Ming; Jin Liyun

    1992-01-01

    Gravimetric method for determination of total residue, total oxide and density of HLLW is developed. An aliquot of the original HLLW solution is piped on to the small quartz disc and put into the mini muffle furnace carefully. It is first heated to below 100 degree C (for 1.5 hours to remove the free water, and then heated to 180 degree C for 2 hours to remove the crystal water in a furnace. The total residue is weighed at room temperature. The precision is better than 3% for the determination of total residue and total oxide. An aliquot of the original HLLW solution is piped into the weighing bottle and weighed. The precision is better than 1%

  1. High Re-Operation Rates Using Conserve Metal-On-Metal Total Hip Articulations

    DEFF Research Database (Denmark)

    Mogensen, S L; Jakobsen, Thomas; Christoffersen, Hardy

    2016-01-01

    INTRODUCTION: Metal-on-metal hip articulations have been intensely debated after reports of adverse reactions and high failure rates. The aim of this study was to retrospectively evaluate the implant of a metal-on.metal total hip articulation (MOM THA) from a single manufacture in a two-center st......INTRODUCTION: Metal-on-metal hip articulations have been intensely debated after reports of adverse reactions and high failure rates. The aim of this study was to retrospectively evaluate the implant of a metal-on.metal total hip articulation (MOM THA) from a single manufacture in a two...

  2. High spatial resolution mapping of land cover types in a priority area for conservation in the Brazilian savanna

    Science.gov (United States)

    Ribeiro, F.; Roberts, D. A.; Hess, L. L.; Davis, F. W.; Caylor, K. K.; Nackoney, J.; Antunes Daldegan, G.

    2017-12-01

    Savannas are heterogeneous landscapes consisting of highly mixed land cover types that lack clear distinct boundaries. The Brazilian Cerrado is a Neotropical savanna considered a biodiversity hotspot for conservation due to its biodiversity richness and rapid transformation of its landscape by crop and pasture activities. The Cerrado is one of the most threatened Brazilian biomes and only 2.2% of its original extent is strictly protected. Accurate mapping and monitoring of its ecosystems and adjacent land use are important to select areas for conservation and to improve our understanding of the dynamics in this biome. Land cover mapping of savannas is difficult due to spectral similarity between land cover types resulting from similar vegetation structure, floristically similar components, generalization of land cover classes, and heterogeneity usually expressed as small patch sizes within the natural landscape. These factors are the major contributor to misclassification and low map accuracies among remote sensing studies in savannas. Specific challenges to map the Cerrado's land cover types are related to the spectral similarity between classes of land use and natural vegetation, such as natural grassland vs. cultivated pasture, and forest ecosystem vs. crops. This study seeks to classify and evaluate the land cover patterns across an area ranked as having extremely high priority for future conservation in the Cerrado. The main objective of this study is to identify the representativeness of each vegetation type across the landscape using high to moderate spatial resolution imagery using an automated scheme. A combination of pixel-based and object-based approaches were tested using RapidEye 3A imagery (5m spatial resolution) to classify the Cerrado's major land cover types. The random forest classifier was used to map the major ecosystems present across the area, and demonstrated to have an effective result with 68% of overall accuracy. Post

  3. Identification of a highly conserved valine-glycine-phenylalanine amino acid triplet required for HIV-1 Nef function

    Directory of Open Access Journals (Sweden)

    Meuwissen Pieter J

    2012-04-01

    Full Text Available Abstract Background The Nef protein of HIV facilitates virus replication and disease progression in infected patients. This role as pathogenesis factor depends on several genetically separable Nef functions that are mediated by interactions of highly conserved protein-protein interaction motifs with different host cell proteins. By studying the functionality of a series of nef alleles from clinical isolates, we identified a dysfunctional HIV group O Nef in which a highly conserved valine-glycine-phenylalanine (VGF region, which links a preceding acidic cluster with the following proline-rich motif into an amphipathic surface was deleted. In this study, we aimed to study the functional importance of this VGF region. Results The dysfunctional HIV group O8 nef allele was restored to the consensus sequence, and mutants of canonical (NL4.3, NA-7, SF2 and non-canonical (B2 and C1422 HIV-1 group M nef alleles were generated in which the amino acids of the VGF region were changed into alanines (VGF→AAA and tested for their capacity to interfere with surface receptor trafficking, signal transduction and enhancement of viral replication and infectivity. We found the VGF motif, and each individual amino acid of this motif, to be critical for downregulation of MHC-I and CXCR4. Moreover, Nef’s association with the cellular p21-activated kinase 2 (PAK2, the resulting deregulation of cofilin and inhibition of host cell actin remodeling, and targeting of Lck kinase to the trans-golgi-network (TGN were affected as well. Of particular interest, VGF integrity was essential for Nef-mediated enhancement of HIV virion infectivity and HIV replication in peripheral blood lymphocytes. For targeting of Lck kinase to the TGN and viral infectivity, especially the phenylalanine of the triplet was essential. At the molecular level, the VGF motif was required for the physical interaction of the adjacent proline-rich motif with Hck. Conclusion Based on these findings, we

  4. Bioethanol production: an integrated process of low substrate loading hydrolysis-high sugars liquid fermentation and solid state fermentation of enzymatic hydrolysis residue.

    Science.gov (United States)

    Chu, Qiulu; Li, Xin; Ma, Bin; Xu, Yong; Ouyang, Jia; Zhu, Junjun; Yu, Shiyuan; Yong, Qiang

    2012-11-01

    An integrated process of enzymatic hydrolysis and fermentation was investigated for high ethanol production. The combination of enzymatic hydrolysis at low substrate loading, liquid fermentation of high sugars concentration and solid state fermentation of enzymatic hydrolysis residue was beneficial for conversion of steam explosion pretreated corn stover to ethanol. The results suggested that low substrate loading hydrolysis caused a high enzymatic hydrolysis yield; the liquid fermentation of about 200g/L glucose by Saccharomyces cerevisiae provided a high ethanol concentration which could significantly decrease cost of the subsequent ethanol distillation. A solid state fermentation of enzymatic hydrolysis residue was combined, which was available to enhance ethanol production and cellulose-to-ethanol conversion. The results of solid state fermentation demonstrated that the solid state fermentation process accompanied by simultaneous saccharification and fermentation. Copyright © 2012 Elsevier Ltd. All rights reserved.

  5. Ancient Exaptation of a CORE-SINE Retroposon into a Highly Conserved Mammalian Neuronal Enhancer of the Proopiomelanocortin Gene

    Science.gov (United States)

    Bumaschny, Viviana F; Low, Malcolm J; Rubinstein, Marcelo

    2007-01-01

    The proopiomelanocortin gene (POMC) is expressed in the pituitary gland and the ventral hypothalamus of all jawed vertebrates, producing several bioactive peptides that function as peripheral hormones or central neuropeptides, respectively. We have recently determined that mouse and human POMC expression in the hypothalamus is conferred by the action of two 5′ distal and unrelated enhancers, nPE1 and nPE2. To investigate the evolutionary origin of the neuronal enhancer nPE2, we searched available vertebrate genome databases and determined that nPE2 is a highly conserved element in placentals, marsupials, and monotremes, whereas it is absent in nonmammalian vertebrates. Following an in silico paleogenomic strategy based on genome-wide searches for paralog sequences, we discovered that opossum and wallaby nPE2 sequences are highly similar to members of the superfamily of CORE-short interspersed nucleotide element (SINE) retroposons, in particular to MAR1 retroposons that are widely present in marsupial genomes. Thus, the neuronal enhancer nPE2 originated from the exaptation of a CORE-SINE retroposon in the lineage leading to mammals and remained under purifying selection in all mammalian orders for the last 170 million years. Expression studies performed in transgenic mice showed that two nonadjacent nPE2 subregions are essential to drive reporter gene expression into POMC hypothalamic neurons, providing the first functional example of an exapted enhancer derived from an ancient CORE-SINE retroposon. In addition, we found that this CORE-SINE family of retroposons is likely to still be active in American and Australian marsupial genomes and that several highly conserved exonic, intronic and intergenic sequences in the human genome originated from the exaptation of CORE-SINE retroposons. Together, our results provide clear evidence of the functional novelties that transposed elements contributed to their host genomes throughout evolution. PMID:17922573

  6. Ancient exaptation of a CORE-SINE retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene.

    Directory of Open Access Journals (Sweden)

    Andrea M Santangelo

    2007-10-01

    Full Text Available The proopiomelanocortin gene (POMC is expressed in the pituitary gland and the ventral hypothalamus of all jawed vertebrates, producing several bioactive peptides that function as peripheral hormones or central neuropeptides, respectively. We have recently determined that mouse and human POMC expression in the hypothalamus is conferred by the action of two 5' distal and unrelated enhancers, nPE1 and nPE2. To investigate the evolutionary origin of the neuronal enhancer nPE2, we searched available vertebrate genome databases and determined that nPE2 is a highly conserved element in placentals, marsupials, and monotremes, whereas it is absent in nonmammalian vertebrates. Following an in silico paleogenomic strategy based on genome-wide searches for paralog sequences, we discovered that opossum and wallaby nPE2 sequences are highly similar to members of the superfamily of CORE-short interspersed nucleotide element (SINE retroposons, in particular to MAR1 retroposons that are widely present in marsupial genomes. Thus, the neuronal enhancer nPE2 originated from the exaptation of a CORE-SINE retroposon in the lineage leading to mammals and remained under purifying selection in all mammalian orders for the last 170 million years. Expression studies performed in transgenic mice showed that two nonadjacent nPE2 subregions are essential to drive reporter gene expression into POMC hypothalamic neurons, providing the first functional example of an exapted enhancer derived from an ancient CORE-SINE retroposon. In addition, we found that this CORE-SINE family of retroposons is likely to still be active in American and Australian marsupial genomes and that several highly conserved exonic, intronic and intergenic sequences in the human genome originated from the exaptation of CORE-SINE retroposons. Together, our results provide clear evidence of the functional novelties that transposed elements contributed to their host genomes throughout evolution.

  7. Identification of immunogenic HLA-B7 "Achilles' heel" epitopes within highly conserved regions of HIV

    DEFF Research Database (Denmark)

    De Groot, Anne S; Rivera, Daniel S; McMurry, Julie A

    2008-01-01

    Genetic polymorphisms in class I human leukocyte antigen molecules (HLA) have been shown to determine susceptibility to HIV infection as well as the rate of progression to AIDS. In particular, the HLA-B7 supertype has been shown to be associated with high viral loads and rapid progression to dise...

  8. Energy Partitioning and Thyroid Hormone Levels During Salmonella enteritidis Infections in Pullets with High or Low Residual Feed Intake

    NARCIS (Netherlands)

    Eerden, van E.; Brand, van den H.; Heetkamp, M.J.W.; Decuypere, M.P.; Kemp, B.

    2006-01-01

    This experiment was conducted to investigate whether feed efficiency, as measured by residual feed intake as a phenotypic trait, affects energy partitioning in pullets that have received Salmonella inoculation as an immune challenge. In each of 8 trials, energy partitioning was measured during 5 wk

  9. Numerical Analysis of Joule Heating Behavior and Residual Compressive Stress around Crack Tip under High Electric Load

    Directory of Open Access Journals (Sweden)

    Thomas Jin-Chee Liu

    2017-01-01

    Full Text Available This paper discusses the Joule heating effect and residual compressive stress near the crack tip under the electro-thermo-structural coupling state. For the crack tip field, the compressive condition is important for retarding or stopping the crack growth.

  10. A highly conserved Poc1 protein characterized in embryos of the hydrozoan Clytia hemisphaerica: localization and functional studies.

    Directory of Open Access Journals (Sweden)

    Cécile Fourrage

    Full Text Available Poc1 (Protein of Centriole 1 proteins are highly conserved WD40 domain-containing centriole components, well characterized in the alga Chlamydomonas, the ciliated protazoan Tetrahymena, the insect Drosophila and in vertebrate cells including Xenopus and zebrafish embryos. Functions and localizations related to the centriole and ciliary axoneme have been demonstrated for Poc1 in a range of species. The vertebrate Poc1 protein has also been reported to show an additional association with mitochondria, including enrichment in the specialized "germ plasm" region of Xenopus oocytes. We have identified and characterized a highly conserved Poc1 protein in the cnidarian Clytia hemisphaerica. Clytia Poc1 mRNA was found to be strongly expressed in eggs and early embryos, showing a punctate perinuclear localization in young oocytes. Fluorescence-tagged Poc1 proteins expressed in developing embryos showed strong localization to centrioles, including basal bodies. Anti-human Poc1 antibodies decorated mitochondria in Clytia, as reported in human cells, but failed to recognise endogenous or fluorescent-tagged Clytia Poc1. Injection of specific morpholino oligonucleotides into Clytia eggs prior to fertilization to repress Poc1 mRNA translation interfered with cell division from the blastula stage, likely corresponding to when neosynthesis normally takes over from maternally supplied protein. Cell cycle lengthening and arrest were observed, phenotypes consistent with an impaired centriolar biogenesis or function. The specificity of the defects could be demonstrated by injection of synthetic Poc1 mRNA, which restored normal development. We conclude that in Clytia embryos, Poc1 has an essentially centriolar localization and function.

  11. Computation and Analysis of High Rocky Slope Safety in a Water Conservancy Project

    Directory of Open Access Journals (Sweden)

    Meng Yang

    2015-01-01

    Full Text Available An integrated method, covering the actual monitoring analysis, practical geological model, and theoretical mathematical simulation model, is systematically proposed and successfully applied. Deformation characteristic of a unique high rocky slope was firstly analyzed from multiple angles and multiple layers by changeable elevations and distances. Arrangements of monitoring points were listed and monitoring equipment was designed to comprise a complete monitoring system. Present larger displacement was concluded for bottom larger displacement caused by water erosion and middle larger displacement formed by seepage. Temporal and spatial displacements rule study of multiple-points linkage effects with water factor proved this conclusion. To better excavate useful message and analyze the deep rule from the practical monitoring data, the slope geological model was conducted and rock mechanic parameters were researched. Finally, a unique three-dimensional finite element model was applied to approach the structure character using numerical simulations. The corresponding strength criterion was used to determine the safety coefficient by selecting a typical section. Subsequently, an integrated three-dimensional finite element model of the slope and dam was developed and more detailed deformation evolution mechanism was revealed. This study is expected to provide a powerful and systematic method to analyze very high, important, and dangerous slopes.

  12. Constrained instanton and baryon number non-conservation at high energies

    International Nuclear Information System (INIS)

    Sil'vestrov, P.G.

    1992-01-01

    The main subject of this paper is the calculation of corrections to instanton action ΔS∼(mρ) 4 log(mρ)/g 2 (ρ is the intanton radius) in the SU(2) Yang-Mills theory. The total cross section for baryon number violating processes at high energies is usually parametrized as σ tat ∝exp(4π/αF(ε)), where α=g 2 /4π, ε=√s/E 0 , E 0 =√6πm w /α. In the present paper the third nontrivial term of the F(ε) expansion is obtained. The unknown correction to F(ε) are expected to be of the order of ε 8/3 . The total cross section is extremely sensitive to the value of single instanton action. For sufficiently heavy Higgs boson the ρ-dependent part of the instanton action is changed drastically. 21 refs.; 1 fig

  13. Residual basins

    International Nuclear Information System (INIS)

    D'Elboux, C.V.; Paiva, I.B.

    1980-01-01

    Exploration for uranium carried out over a major portion of the Rio Grande do Sul Shield has revealed a number of small residual basins developed along glacially eroded channels of pre-Permian age. Mineralization of uranium occurs in two distinct sedimentary units. The lower unit consists of rhythmites overlain by a sequence of black shales, siltstones and coal seams, while the upper one is dominated by sandstones of probable fluvial origin. (Author) [pt

  14. Numerical calculation and analysis of natural convection removal of the spent fuel residual heat of 10 MW high temperature gas cooled reactor

    International Nuclear Information System (INIS)

    Wang Jinhua; Huang Yifan; Wu Bin

    2013-01-01

    The spent fuel of 10 MW High Temperature Gas Cooled Reactor (HTR-10) could be stored in the shielded tank, and the tank is stored in the concrete shielded canister in spent fuel storage room, the residual heat of the spent fuel could be removed by the air. The ability of residual heat removal is analyzed in the paper, and the temperature field is numerically calculated through FEA program ANSYS, the analysis and the calculation are used to validate the safety of the spent fuel and the tank, the ultimate temperature of the spent fuel and the tank should below the safety limit. The calculation shows that the maximum temperature locates in the middle of the fuel pebble bed in the spent fuel tank, and the temperature decreases gradually with radial distance, the temperature in the tank body is evenly distributed, and the temperature in the concrete shielded canister decreases gradually with radial distance. It is feasible to remove the residual heat of the spent fuel storage tank by natural ventilation, in natural ventilation condition, the temperature of the spent fuel and the tank is lower than the temperature limit, which provides theoretical evidence for the choice of the residual heat removal method. (authors)

  15. Rapid trace level determination of sulfonamide residues in honey with online extraction using short C-18 column by high-performance liquid chromatography with fluorescence detection.

    Science.gov (United States)

    Sajid, Muhammad; Na, Na; Safdar, Muhammad; Lu, Xin; Ma, Lin; He, Lan; Ouyang, Jin

    2013-11-01

    A sensitive and inexpensive quantification method with online extraction using a short C-18 column for sulfonamide residues in honey by high performance liquid chromatography with fluorescence detector was developed and validated. In sample preparation, acid hydrolysis was used to break the N-glycoside bond between the honey sugar and sulfonamide drugs and derivatization of sulfonamide residues with fluorescamine was conducted at pH 3.5 using a citrate buffer (0.5M) in the honey matrix. The chromatography was carried out on Zorbax Extended C-18 (250mm×4.6mm; 5μm) column, using a mixture of acetonitrile and an acetate buffer (pH 4.50, 20mM) as a mobile phase. A Zorbax Extended C-18 (12mm×4.6mm; 5μm) column was used for online extraction of fifteen sulfonamide residues from honey sample with the help of a two position valve. The limit of quantification of sulfonamide residues in honey was less than 3ngg(-1), and the percentage recovery of study compounds in spiked honey sample was from 80% for sulfacetamide to 100% of sulfachloropyridazine. The developed method has excellent linearity for all studied sulfonamides with a correlation coefficient 0.993. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. Mice selectively bred for high voluntary wheel-running behavior conserve more fat despite increased exercise.

    Science.gov (United States)

    Hiramatsu, Layla; Garland, Theodore

    2018-04-20

    Physical activity is an important component of energy expenditure, and acute changes in activity can lead to energy imbalances that affect body composition, even under ad libitum food availability. One example of acute increases in physical activity is four replicate, selectively-bred High Runner (HR) lines of mice that voluntarily run ~3-fold more wheel revolutions per day over 6-day trials and are leaner, as compared with four non-selected control (C) lines. We expected that voluntary exercise would increase food consumption, build lean mass, and reduce fat mass, but that these effects would likely differ between HR and C lines or between the sexes. We compared wheel running, cage activity, food consumption, and body composition between HR and C lines for young adults of both sexes, and examined interrelationships of those traits across 6 days of wheel access. Before wheel testing, HR mice weighed less than C, primarily due to reduced lean mass, and females were lighter than males, entirely due to lower lean mass. Over 6 days of wheel access, all groups tended to gain small amounts of lean mass, but lose fat mass. HR mice lost less fat than C mice, in spite of much higher activity levels, resulting in convergence to a fat mass of ~1.7 g for all 4 groups. HR mice consumed more food than C mice (with body mass as a covariate), even accounting for their higher activity levels. No significant sex-by-linetype interactions were observed for any of the foregoing traits. Structural equation models showed that the four sex-by-linetype groups differed considerably in the complex phenotypic architecture of these traits. Interrelationships among traits differed by genetic background and sex, lending support to the idea that recommendations regarding weight management, diet, and exercise may need to be tailored to the individual level. Copyright © 2018 Elsevier Inc. All rights reserved.

  17. Toxicity and cosmetic result of partial breast high-dose-rate interstitial brachytherapy for conservatively operated early breast cancer

    International Nuclear Information System (INIS)

    Xiu Xia; Tripuraneni Prabhakar; Giap Huan; Lin Ray; Chu Colin

    2007-01-01

    Objective: Objective To study the method, side effects and cosmetic outcome of high- dose-rate (HDR) accelerated partial breast interstitial irradiation (APBI) alone in early stage breast cancer' after conservative surgery. Methods: From February 2002 to June 2003,47 breast cancer lesions from 46 patients suffering from stage I/II breast cancer were treated with HDR 192 Ir APBI after conservative surgery. All patients were over 40 year-old, with T1-2N0-1 (≤3 lymph nodes positive), surgical margin > 1-2 mm, but those having lobular or inflammatory breast cancer were excluded. HDR brachytherapy with 34 Gy, 10 fractions/5 days was used after surgery, toxic reaction and cosmetic outcome were observed in one month, 6 and 12 months respectively. Results: Follow up of 1846 months, 34 months was carried out for the whole group. During the treatment, acute reactions including: erythema, edema, tenderness and infection, all under I-II grade, none of III-IV grade were observed in 21 patients(46%); late toxicity reactions: skin fibrosis, breast tenderness, fat necrosis, and telangiectasia, totally 20 patients (43%) were observed: 2 patients in III grade but one patient received 6 cycle chemotherapy. The result of cosmetic outcome evaluation was excellent or good, at 6 months 95% and 12 months 98%, respectively, but there was no recurfence. Conclusions: Excellent and favorable cosmetic results are noted after APBI by interstitial alone. Acute and late reactions are few. Long term observation is necessary for the rate of' local control. (authors)

  18. Atomic Level Cleaning of Poly Methyl Methacrylate Residues from the Graphene Surface Using Radiolized Water at High Temperatures (Postprint)

    Science.gov (United States)

    2017-09-05

    arbitrary substrates like oxides, semiconductors , or even on other 2-D materials in order to make 2-D heterostructures.11–19 Poly-methyl...Following approaches utilized in semiconductor manufacturing, where PMMA is cleaned from the surface of semiconductors after lithographic patterning, wet...of these suggest the presence of significant amount of PMMA residue and inorganic particles made of SiOx and carbon in different places of the chip

  19. Comments on the note by L.S. Nelson: ''unusually high (oxidizer/Pu) ratios in the macro-residues from plutonium droplet combustion''

    International Nuclear Information System (INIS)

    Allen, M.D.; Morgan, L.G.

    1982-01-01

    An alternative explanation for unusually high ratios of oxidizers/plutonium in the residues from plutonium droplet combustion is offered in response to a note by L.S. Nelson. Two additional experiments are suggested that would be helpful in clarifying the high oxidizer/Pu ratios. The first would be to measure the true surface area for a spherule after its explosion. The second is an experiment analogous to a gas analysis experiment. The conclusion is put forth that adsorbed gases are the most likely cause of the high O/M ratios described by Nelson

  20. Metabolomic study of plasma from female mink (Neovison vison) with low and high residual feed intake during restrictive and ad libitum feeding

    DEFF Research Database (Denmark)

    Hedemann, Mette Skou; Damgaard, Birthe Marie

    2012-01-01

    was high during restrictive feeding, e.g. betaine, carnitine, and creatine. During ad libitum feeding the plasma level of metabolites that can be characterized as biomarkers of meat intake (creatinine, carnosine, 1- and 3 methylhistidine) was high. The plasma level of lysophosphatidylcholine species......Metabolite profiling may elucidate changes in metabolic pathways under various physiological or nutritional conditions. In the present study two groups of female mink characterized as having a high (16 mink) or low (14 mink) residual feed intake were investigated during restrictive and ad libitum...

  1. Distinct activation phenotype of a highly conserved novel HLA-B57-restricted epitope during dengue virus infection.

    Science.gov (United States)

    Townsley, Elizabeth; Woda, Marcia; Thomas, Stephen J; Kalayanarooj, Siripen; Gibbons, Robert V; Nisalak, Ananda; Srikiatkhachorn, Anon; Green, Sharone; Stephens, Henry A F; Rothman, Alan L; Mathew, Anuja

    2014-01-01

    Variation in the sequence of T-cell epitopes between dengue virus (DENV) serotypes is believed to alter memory T-cell responses during second heterologous infections. We identified a highly conserved, novel, HLA-B57-restricted epitope on the DENV NS1 protein. We predicted higher frequencies of B57-NS1(26-34) -specific CD8(+) T cells in peripheral blood mononuclear cells from individuals undergoing secondary rather than primary DENV infection. However, high tetramer-positive T-cell frequencies during acute infection were seen in only one of nine subjects with secondary infection. B57-NS1(26-34) -specific and other DENV epitope-specific CD8(+) T cells, as well as total CD8(+) T cells, expressed an activated phenotype (CD69(+) and/or CD38(+)) during acute infection. In contrast, expression of CD71 was largely limited to DENV epitope-specific CD8(+) T cells. In vitro stimulation of cell lines indicated that CD71 expression was differentially sensitive to stimulation by homologous and heterologous variant peptides. CD71 may represent a useful marker of antigen-specific T-cell activation. © 2013 John Wiley & Sons Ltd.

  2. A Web-Based GIS for Reporting Water Usage in the High Plains Underground Water Conservation District

    Science.gov (United States)

    Jia, M.; Deeds, N.; Winckler, M.

    2012-12-01

    The High Plains Underground Water Conservation District (HPWD) is the largest and oldest of the Texas water conservation districts, and oversees approximately 1.7 million irrigated acres. Recent rule changes have motivated HPWD to develop a more automated system to allow owners and operators to report well locations, meter locations, meter readings, the association between meters and wells, and contiguous acres. INTERA, Inc. has developed a web-based interactive system for HPWD water users to report water usage and for the district to better manage its water resources. The HPWD web management system utilizes state-of-the-art GIS techniques, including cloud-based Amazon EC2 virtual machine, ArcGIS Server, ArcSDE and ArcGIS Viewer for Flex, to support web-based water use management. The system enables users to navigate to their area of interest using a well-established base-map and perform a variety of operations and inquiries against their spatial features. The application currently has six components: user privilege management, property management, water meter registration, area registration, meter-well association and water use report. The system is composed of two main databases: spatial database and non-spatial database. With the help of Adobe Flex application at the front end and ArcGIS Server as the middle-ware, the spatial feature geometry and attributes update will be reflected immediately in the back end. As a result, property owners, along with the HPWD staff, collaborate together to weave the fabric of the spatial database. Interactions between the spatial and non-spatial databases are established by Windows Communication Foundation (WCF) services to record water-use report, user-property associations, owner-area associations, as well as meter-well associations. Mobile capabilities will be enabled in the near future for field workers to collect data and synchronize them to the spatial database. The entire solution is built on a highly scalable cloud

  3. Conservation Value

    OpenAIRE

    Tisdell, Clement A.

    2010-01-01

    This paper outlines the significance of the concept of conservation value and discusses ways in which it is determined paying attention to views stemming from utilitarian ethics and from deontological ethics. The importance of user costs in relation to economic decisions about the conservation and use of natural resources is emphasised. Particular attention is given to competing views about the importance of conserving natural resources in order to achieve economic sustainability. This then l...

  4. Wide-Scope Screening Method for Multiclass Veterinary Drug Residues in Fish, Shrimp, and Eel Using Liquid Chromatography-Quadrupole High-Resolution Mass Spectrometry.

    Science.gov (United States)

    Turnipseed, Sherri B; Storey, Joseph M; Lohne, Jack J; Andersen, Wendy C; Burger, Robert; Johnson, Aaron S; Madson, Mark R

    2017-08-30

    A screening method for veterinary drug residues in fish, shrimp, and eel using LC with a high-resolution MS instrument has been developed and validated. The method was optimized for over 70 test compounds representing a variety of veterinary drug classes. Tissues were extracted by vortex mixing with acetonitrile acidified with 2% acetic acid and 0.2% p-toluenesulfonic acid. A centrifuged portion of the extract was passed through a novel solid phase extraction cartridge designed to remove interfering matrix components from tissue extracts. The eluent was then evaporated and reconstituted for analysis. Data were collected with a quadrupole-Orbitrap high-resolution mass spectrometer using both nontargeted and targeted acquisition methods. Residues were detected on the basis of the exact mass of the precursor and a product ion along with isotope pattern and retention time matching. Semiquantitative data analysis compared MS 1 signal to a one-point extracted matrix standard at a target testing level. The test compounds were detected and identified in salmon, tilapia, catfish, shrimp, and eel extracts fortified at the target testing levels. Fish dosed with selected analytes and aquaculture samples previously found to contain residues were also analyzed. The screening method can be expanded to monitor for an additional >260 veterinary drugs on the basis of exact mass measurements and retention times.

  5. Matrix effect in analysis of pesticide residues in fruits and vegetables by high performance liquid chromatography with quadrupole-time of flight mass spectrometry

    Directory of Open Access Journals (Sweden)

    Andoralov A.M.

    2017-03-01

    Full Text Available For modern food safety control are using techniques that allow to determinate a large number of components. So for determination of pesticide residues in fruits and vegetables commonly used methods of gas and liquid chromatography with time-of-flight mass-spectrometric detection. This system allows to carry out quantitative determination several hundreds of pesticides and their identification by the characteristic fragments of the mass spectrum. The main problem when using mass spectrometric detection is a matrix effect, which is caused by the influence of matrix components extracted with pesticides from the sample. In this work, attempts have been made to reduce the influence of the matrix in the analysis of pesticide residues by high performance liquid chromatography with time of flight mass spectrometry (HPLC / TOFMS.

  6. Conservation and Role of Electrostatics in Thymidylate Synthase.

    Science.gov (United States)

    Garg, Divita; Skouloubris, Stephane; Briffotaux, Julien; Myllykallio, Hannu; Wade, Rebecca C

    2015-11-27

    Conservation of function across families of orthologous enzymes is generally accompanied by conservation of their active site electrostatic potentials. To study the electrostatic conservation in the highly conserved essential enzyme, thymidylate synthase (TS), we conducted a systematic species-based comparison of the electrostatic potential in the vicinity of its active site. Whereas the electrostatics of the active site of TS are generally well conserved, the TSs from minimal organisms do not conform to the overall trend. Since the genomes of minimal organisms have a high thymidine content compared to other organisms, the observation of non-conserved electrostatics was surprising. Analysis of the symbiotic relationship between minimal organisms and their hosts, and the genetic completeness of the thymidine synthesis pathway suggested that TS from the minimal organism Wigglesworthia glossinidia (W.g.b.) must be active. Four residues in the vicinity of the active site of Escherichia coli TS were mutated individually and simultaneously to mimic the electrostatics of W.g.b TS. The measured activities of the E. coli TS mutants imply that conservation of electrostatics in the region of the active site is important for the activity of TS, and suggest that the W.g.b. TS has the minimal activity necessary to support replication of its reduced genome.

  7. Loss of a highly conserved sterile alpha motif domain gene (WEEP) results in pendulous branch growth in peach trees.

    Science.gov (United States)

    Hollender, Courtney A; Pascal, Thierry; Tabb, Amy; Hadiarto, Toto; Srinivasan, Chinnathambi; Wang, Wanpeng; Liu, Zhongchi; Scorza, Ralph; Dardick, Chris

    2018-05-15

    Plant shoots typically grow upward in opposition to the pull of gravity. However, exceptions exist throughout the plant kingdom. Most conspicuous are trees with weeping or pendulous branches. While such trees have long been cultivated and appreciated for their ornamental value, the molecular basis behind the weeping habit is not known. Here, we characterized a weeping tree phenotype in Prunus persica (peach) and identified the underlying genetic mutation using a genomic sequencing approach. Weeping peach tree shoots exhibited a downward elliptical growth pattern and did not exhibit an upward bending in response to 90° reorientation. The causative allele was found to be an uncharacterized gene, Ppa013325 , having a 1.8-Kb deletion spanning the 5' end. This gene, dubbed WEEP , was predominantly expressed in phloem tissues and encodes a highly conserved 129-amino acid protein containing a sterile alpha motif (SAM) domain. Silencing WEEP in the related tree species Prunus domestica (plum) resulted in more outward, downward, and wandering shoot orientations compared to standard trees, supporting a role for WEEP in directing lateral shoot growth in trees. This previously unknown regulator of branch orientation, which may also be a regulator of gravity perception or response, provides insights into our understanding of how tree branches grow in opposition to gravity and could serve as a critical target for manipulating tree architecture for improved tree shape in agricultural and horticulture applications. Copyright © 2018 the Author(s). Published by PNAS.

  8. Neuronal patterning of the tubular collar cord is highly conserved among enteropneusts but dissimilar to the chordate neural tube.

    Science.gov (United States)

    Kaul-Strehlow, Sabrina; Urata, Makoto; Praher, Daniela; Wanninger, Andreas

    2017-08-01

    A tubular nervous system is present in the deuterostome groups Chordata (cephalochordates, tunicates, vertebrates) and in the non-chordate Enteropneusta. However, the worm-shaped enteropneusts possess a less complex nervous system featuring only a short hollow neural tube, whereby homology to its chordate counterpart remains elusive. Since the majority of data on enteropneusts stem from the harrimaniid Saccoglossus kowalevskii, putative interspecific variations remain undetected resulting in an unreliable ground pattern that impedes homology assessments. In order to complement the missing data from another enteropneust family, we investigated expression of key neuronal patterning genes in the ptychoderid Balanoglossus misakiensis. The collar cord of B. misakiensis shows anterior Six3/6 and posterior Otx + Engrailed expression, in a region corresponding to the chordate brain. Neuronal Nk2.1/Nk2.2 expression is absent. Interestingly, we found median Dlx and lateral Pax6 expression domains, i.e., a condition that is reversed compared to chordates. Comparative analyses reveal that adult nervous system patterning is highly conserved among the enteropneust families Harrimaniidae, Spengelidae and Ptychoderidae. BmiDlx and BmiPax6 have no corresponding expression domains in the chordate brain, which may be indicative of independent acquisition of a tubular nervous system in Enteropneusta and Chordata.

  9. Assessment of some high-order finite difference schemes on the scalar conservation law with periodical conditions

    Directory of Open Access Journals (Sweden)

    Alina BOGOI

    2016-12-01

    Full Text Available Supersonic/hypersonic flows with strong shocks need special treatment in Computational Fluid Dynamics (CFD in order to accurately capture the discontinuity location and his magnitude. To avoid numerical instabilities in the presence of discontinuities, the numerical schemes must generate low dissipation and low dispersion error. Consequently, the algorithms used to calculate the time and space-derivatives, should exhibit a low amplitude and phase error. This paper focuses on the comparison of the numerical results obtained by simulations with some high resolution numerical schemes applied on linear and non-linear one-dimensional conservation low. The analytical solutions are provided for all benchmark tests considering smooth periodical conditions. All the schemes converge to the proper weak solution for linear flux and smooth initial conditions. However, when the flux is non-linear, the discontinuities may develop from smooth initial conditions and the shock must be correctly captured. All the schemes accurately identify the shock position, with the price of the numerical oscillation in the vicinity of the sudden variation. We believe that the identification of this pure numerical behavior, without physical relevance, in 1D case is extremely useful to avoid problems related to the stability and convergence of the solution in the general 3D case.

  10. The highly conserved codon following the slippery sequence supports -1 frameshift efficiency at the HIV-1 frameshift site.

    Directory of Open Access Journals (Sweden)

    Suneeth F Mathew

    Full Text Available HIV-1 utilises -1 programmed ribosomal frameshifting to translate structural and enzymatic domains in a defined proportion required for replication. A slippery sequence, U UUU UUA, and a stem-loop are well-defined RNA features modulating -1 frameshifting in HIV-1. The GGG glycine codon immediately following the slippery sequence (the 'intercodon' contributes structurally to the start of the stem-loop but has no defined role in current models of the frameshift mechanism, as slippage is inferred to occur before the intercodon has reached the ribosomal decoding site. This GGG codon is highly conserved in natural isolates of HIV. When the natural intercodon was replaced with a stop codon two different decoding molecules-eRF1 protein or a cognate suppressor tRNA-were able to access and decode the intercodon prior to -1 frameshifting. This implies significant slippage occurs when the intercodon is in the (perhaps distorted ribosomal A site. We accommodate the influence of the intercodon in a model of frame maintenance versus frameshifting in HIV-1.

  11. The implications of RCRA [Resource Conservation and Recovery Act] regulation for the disposal of transuranic and high-level waste

    International Nuclear Information System (INIS)

    Sigmon, C.F.; Sharples, F.E.; Smith, E.D.

    1988-01-01

    In May of 1987 the Department of Energy (DOE) published a rule interpreting the definition of ''byproduct'' under the Atomic Energy Act. This byproduct rule clarified the role of the Resource Conservation and Recovery Act (RCRA) in the regulation of DOE's radioactive waste management activities. According to the rule, only the radioactive portion of DOE's mixed radioactive and hazardous waste (mixed waste), including mixed transuranic (TRU) and high-level waste (HLW), is exempt from RCRA under the byproduct exemption. The portion of a waste that is hazardous as defined by RCRA is subject to full regulation under RCRA. Because the radioactive and hazardous portions of m any, if not most, DOE wastes are likely to be inseparable, the rule in effect makes most mixed wastes subject to dual regulation. The potential application of RCRA to facilities such as the Waste Isolation Pilot Plant (WIPP) and the HLW repository creates unique challenges for both the DOE and regulatory authorities. Strategies must be developed to assure compliance with RCRA without either causing excessive administrative burdens or abandoning the goal of minimizing radiation exposure. This paper will explore some of the potential regulatory options for and recent trends in the regulation of TRU and HLW under RCRA

  12. Influence of lubricant oil residual fraction on recycled high density polyethylene properties and plastic packaging reverse logistics proposal

    Directory of Open Access Journals (Sweden)

    Harley Moraes Martins

    2015-10-01

    Full Text Available Abstract To recycle post-consumer HDPE contaminated with waste lubricating oils, companies include prior washing and drying in the process. This consumes large amounts of water and energy, generates significant effluent requiring treatment. This study assesses lubricating oil influence on HDPE properties to evaluate the feasibility of its direct mechanical recycling without washing. The current lubricating oil packaging reverse logistics in Rio de Janeiro municipality is also analyzed. HDPE bottle samples were processed with seven oil contents ranging from 1.6-29.4 (wt%. The results indicated the possibility to reprocess the polymer with oily residue not exceeding 3.2%. At higher levels, the external oil lubricating action affects the plastic matrix processing in the extruder and injection, and the recycled material has a burnt oil odor and free oil on the surface. Small residual oil amounts retain the plastic properties comparable to the washed recycled polymer and exhibited benefits associated with the oil plasticizer action. However, oil presence above 7.7% significantly changes the properties and reduces the elasticity and flexural modulus and the plastic matrix crystallinity.

  13. EN AW-4032 T6 Piston Alloy After High-Temperature Exposure: Residual Strength and Microstructural Features

    Science.gov (United States)

    Balducci, Eleonora; Ceschini, Lorella; Morri, Alessandro; Morri, Andrea

    2017-08-01

    This study aims to evaluate the effects of prolonged thermal exposure on both microstructural evolution and mechanical properties of the EN AW-4032 T6 piston alloy. For the purpose, the experimental activities have been carried out on samples machined from forged and heat-treated automotive pistons. The effects of overaging have been investigated in the temperature range of 140-290 °C, firstly by evaluating the time-temperature-hardness curves and then by carrying out room-temperature tensile tests on overaged samples. The material softening was substantial and extremely rapid when the soaking temperature exceeded 250 °C. During overaging, both the tensile strength and the residual hardness considerably decreased, and a relationship between these parameters has been established. The alloy behavior in the plastic field has been modeled according to the Hollomon's equation, showing that both the strain hardening exponent and the strength coefficient are a function of the residual hardness. The results were finally related to the corresponding microstructural changes: OM and FEG-SEM metallographic and fractographic analyses on overaged samples gave evidence of coarsened precipitates along the grain boundaries.

  14. The high pressure liquid chromatography and its application to the separation of polynuclear aromatic hydrocarbons in atmospheric dust and burning residues

    International Nuclear Information System (INIS)

    Lopez, M.-C.

    1975-09-01

    A new technique of analysis is described: the high speed liquid chromatography or more exactly the high performance liquid chromatography because of the progress achieved on the new packings of the columns. The main types of chromatography, according to the phenomena involved are described: adsorption, partition, ion-exchange and exclusion chromatography. A brief outline is given of the theory for determination of stationary and mobile phases in order to obtain the optimum conditions of separation. Some exemples of possible applications are given, particularly the use of this technique for the separation of polycyclic aromatic hydrocarbons in atmospheric pollution and burning residues [fr

  15. Origin of high carrier mobility and low residual stress in RF superimposed DC sputtered Al doped ZnO thin film for next generation flexible devices

    Science.gov (United States)

    Kumar, Naveen; Dubey, Ashish; Bahrami, Behzad; Venkatesan, S.; Qiao, Qiquan; Kumar, Mukesh

    2018-04-01

    In this work, the energy and flux of high energetic ions were controlled by RF superimposed DC sputtering process to increase the grain size and suppress grain boundary potential with minimum residual stress in Al doped ZnO (AZO) thin film. AZO thin films were deposited at different RF/(RF + DC) ratios by keeping total power same and were investigated for their electrical, optical, structural and nanoscale grain boundaries potential. All AZO thin film showed high crystallinity and orientation along (002) with peak shift as RF/(RF + DC) ratio increased from 0.0, pure DC, to 1.0, pure RF. This peak shift was correlated with high residual stress in as-grown thin film. AZO thin film grown at mixed RF/(RF + DC) of 0.75 showed high electron mobility, low residual stress and large crystallite size in comparison to other AZO thin films. The nanoscale grain boundary potential was mapped using Kelvin Probe Force Microscopy in all AZO thin film and it was observed that carrier mobility is controlled not only by grains size but also by grain boundary potential. The XPS analysis confirms the variation in oxygen vacancies and zinc interstitials which explain the origin of low grain boundaries potential and high carrier mobility in AZO thin film deposited at 0.75 RF/(RF + DC) ratio. This study proposes a new way to control the grain size and grain boundary potential to further tune the optoelectronic-mechanical properties of AZO thin films for next generation flexible and optoelectronic devices.

  16. High conservation level of CD8(+) T cell immunogenic regions within an unusual H1N2 human influenza variant.

    Science.gov (United States)

    Komadina, Naomi; Quiñones-Parra, Sergio M; Kedzierska, Katherine; McCaw, James M; Kelso, Anne; Leder, Karin; McVernon, Jodie

    2016-10-01

    Current seasonal influenza vaccines require regular updates due to antigenic drift causing loss of effectiveness and therefore providing little or no protection against novel influenza A subtypes. Next generation vaccines capable of eliciting CD8(+) T cell (CTL) mediated cross-protective immunity may offer a long-term alternative strategy. However, measuring pre- and existing levels of CTL cross-protection in humans is confounded by differences in infection histories across individuals. During 2000-2003, H1N2 viruses circulated persistently in the human population for the first time and we hypothesized that the viral nucleoprotein (NP) contained novel CTL epitopes that may have contributed to the survival of the viruses. This study describes the immunogenic NP peptides of H1N1, H2N2, and H3N2 influenza viruses isolated from humans over the past century, 1918-2003, by comparing this historical dataset to reference NP peptides from H1N2 that circulated in humans during 2000-2003. Observed peptides sequences ranged from highly conserved (15%) to highly variable (12%), with variation unrelated to reported immunodominance. No unique NP peptides which were exclusive to the H1N2 viruses were noted. However, the virus had inherited the NP from a recently emerged H3N2 variant containing novel peptides, which may have assisted its persistence. Any advantage due to this novelty was subsequently lost with emergence of a newer H3N2 variant in 2003. Our approach has potential to provide insight into the population context in which influenza viruses emerge, and may help to inform immunogenic peptide selection for CTL-inducing influenza vaccines. J. Med. Virol. 88:1725-1732, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  17. Evaluation of a new modified QuEChERS method for the monitoring of carbamate residues in high-fat cheeses by using UHPLC-MS/MS.

    Science.gov (United States)

    Hamed, Ahmed M; Moreno-González, David; Gámiz-Gracia, Laura; García-Campaña, Ana M

    2017-01-01

    A simple and efficient method for the determination of 28 carbamates in high-fat cheeses is proposed. The methodology is based on a modified quick, easy, cheap, effective, rugged, and safe procedure as sample treatment using a new sorbent (Z-Sep + ) followed by ultra-high performance liquid chromatography with tandem mass spectrometry determination. The method has been validated in different kinds of cheese (Gorgonzola, Roquefort, and Camembert), achieving recoveries of 70-115%, relative standard deviations lower than 13% and limits of quantification lower than 5.4 μg/kg, below the maximum residue levels tolerated for these compounds by the European legislation. The matrix effect was lower than ±30% for all the studied pesticides. The combination of ultra-high performance liquid chromatography and tandem mass spectrometry with this modified quick, easy, cheap, effective, rugged, and safe procedure using Z-Sep + allowed a high sample throughput and an efficient cleaning of extracts for the control of these residues in cheeses with a high fat content. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Validation of a high-performance liquid chromatographic method with UV detection for the determination of ethopabate residues in poultry liver.

    Science.gov (United States)

    Granja, Rodrigo H M M; Niño, Alfredo M Montes; Zucchetti, Roberto A M; Niño, Rosario E Montes; Salerno, Alessandro G

    2008-01-01

    Ethopabate is frequently used in the prophylaxis and treatment of coccidiosis in poultry. Residues of this drug in food present a potential risk to consumers. A simple, rapid, and sensitive column high-performance liquid chromatographic (HPLC) method with UV detection for determination of ethopabate in poultry liver is presented. The drug is extracted with acetonitrile. After evaporation, the residue is dissolved with an acetone-hexane mixture and cleaned up by solid-phase extraction using Florisil columns. The analyte is then eluted with methanol. LC analysis is carried out on a C18 5 microm Gemini column, 15 cm x 4.6 mm. Ethopabate is quantified by means of UV detection at 270 nm. Parameters such as decision limit, detection capability, precision, recovery, ruggedness, and measurement uncertainty were calculated according to method validation guidelines provided in 2002/657/EC and ISO/IEC 17025:2005. Decision limit and detection capability were determined to be 2 and 3 microg/kg, respectively. Average recoveries from poultry samples fortified with 10, 15, and 20 microg/kg levels of ethopabate were 100-105%. A complete statistical analysis was performed on the results obtained, including an estimation of the method uncertainty. The method is to be implemented into Brazil's residue monitoring and control program for ethopabate.

  19. [High throuput analysis of organophosphorus pesticide residues and their metabolites in animal original foods by dual gas chromatography-dual pulse flame photometric detection].

    Science.gov (United States)

    Yang, Lixin; Li, Heli; Miao, Hong; Zeng, Fangang; Li, Ruifeng; Chen, Huijing; Zhao, Yunfeng; Wu, Yongning

    2011-10-01

    A method was established for the quantitative determination of 54 organophosphorus pesticide residues and their metabolites in foods of animal origin by dual gas chromatography-dual pulse flame photometric detection. Homogenized samples were extracted with acetone and methylene chloride, and cleaned-up by gel permeation chromatography (GPC). The response of each analyte showed a good linearity with a correlation coefficient not less than 0. 99. The recovery experiments were performed by a blank sample spiked at low, medium and high fortification levels. The recoveries for beef, mutton, pork, chicken were in the range of 50. 5% -128. 1% with the relative standard deviations (n = 6) of 1. 1% -25. 5%, which demonstrated the good precision and accuracy of the present method. The limits of detection for the analytes were in the range of 0. 001 -0. 170 mg/kg, and the limits of quantification were in the range of 0. 002 -0. 455 mg/kg. Animal food samples collected from markets such as meat, liver and kidney were analyzed, and the residues of dichlorovos and disulfoton-sulfoxide were found in the some samples. The established method is sensitive and selective enough to detect organophosphorus pesticide residues in animal foods.

  20. Surgical versus conservative treatment for high-risk stress fractures of the lower leg (anterior tibial cortex, navicular and fifth metatarsal base): a systematic review

    NARCIS (Netherlands)

    Mallee, W.H.; Weel, H.; van Dijk, C.N.; van Tulder, M.W.; Kerkhoffs, G.M.; Lin, C.W.C.

    2015-01-01

    Aim To compare surgical and conservative treatment for high-risk stress fractures of the anterior tibial cortex, navicular and proximal fifth metatarsal. Methods Systematic searches of CENTRAL, MEDLINE, EMBASE, CINAHL, SPORTDiscus and PEDro were performed to identify relevant prospective and

  1. Comparing the cost-effectiveness of water conservation policies in a depleting aquifer:A dynamic analysis of the Kansas High Plains

    Science.gov (United States)

    This research analyzes two groundwater conservation policies in the Kansas High Plains located within the Ogallala aquifer: 1) cost-share assistance to increase irrigation efficiency; and 2) incentive payments to convert irrigated crop production to dryland crop production. To compare the cost-effec...

  2. Spatially conserved regulatory elements identified within human and mouse Cd247 gene using high-throughput sequencing data from the ENCODE project

    DEFF Research Database (Denmark)

    Pundhir, Sachin; Hannibal, Tine Dahlbæk; Bang-Berthelsen, Claus Heiner

    2014-01-01

    . In this study, we have utilized the wealth of high-throughput sequencing data produced during the Encyclopedia of DNA Elements (ENCODE) project to identify spatially conserved regulatory elements within the Cd247 gene from human and mouse. We show the presence of two transcription factor binding sites...

  3. Residual Convolutional Neural Network for the Determination of IDH Status in Low- and High-Grade Gliomas from MR Imaging.

    Science.gov (United States)

    Chang, Ken; Bai, Harrison X; Zhou, Hao; Su, Chang; Bi, Wenya Linda; Agbodza, Ena; Kavouridis, Vasileios K; Senders, Joeky T; Boaro, Alessandro; Beers, Andrew; Zhang, Biqi; Capellini, Alexandra; Liao, Weihua; Shen, Qin; Li, Xuejun; Xiao, Bo; Cryan, Jane; Ramkissoon, Shakti; Ramkissoon, Lori; Ligon, Keith; Wen, Patrick Y; Bindra, Ranjit S; Woo, John; Arnaout, Omar; Gerstner, Elizabeth R; Zhang, Paul J; Rosen, Bruce R; Yang, Li; Huang, Raymond Y; Kalpathy-Cramer, Jayashree

    2018-03-01

    Purpose: Isocitrate dehydrogenase ( IDH ) mutations in glioma patients confer longer survival and may guide treatment decision making. We aimed to predict the IDH status of gliomas from MR imaging by applying a residual convolutional neural network to preoperative radiographic data. Experimental Design: Preoperative imaging was acquired for 201 patients from the Hospital of University of Pennsylvania (HUP), 157 patients from Brigham and Women's Hospital (BWH), and 138 patients from The Cancer Imaging Archive (TCIA) and divided into training, validation, and testing sets. We trained a residual convolutional neural network for each MR sequence (FLAIR, T2, T1 precontrast, and T1 postcontrast) and built a predictive model from the outputs. To increase the size of the training set and prevent overfitting, we augmented the training set images by introducing random rotations, translations, flips, shearing, and zooming. Results: With our neural network model, we achieved IDH prediction accuracies of 82.8% (AUC = 0.90), 83.0% (AUC = 0.93), and 85.7% (AUC = 0.94) within training, validation, and testing sets, respectively. When age at diagnosis was incorporated into the model, the training, validation, and testing accuracies increased to 87.3% (AUC = 0.93), 87.6% (AUC = 0.95), and 89.1% (AUC = 0.95), respectively. Conclusions: We developed a deep learning technique to noninvasively predict IDH genotype in grade II-IV glioma using conventional MR imaging using a multi-institutional data set. Clin Cancer Res; 24(5); 1073-81. ©2017 AACR . ©2017 American Association for Cancer Research.

  4. Residual nilpotence and residual solubility of groups

    International Nuclear Information System (INIS)

    Mikhailov, R V

    2005-01-01

    The properties of the residual nilpotence and the residual solubility of groups are studied. The main objects under investigation are the class of residually nilpotent groups such that each central extension of these groups is also residually nilpotent and the class of residually soluble groups such that each Abelian extension of these groups is residually soluble. Various examples of groups not belonging to these classes are constructed by homological methods and methods of the theory of modules over group rings. Several applications of the theory under consideration are presented and problems concerning the residual nilpotence of one-relator groups are considered.

  5. Extreme sequence divergence but conserved ligand-binding specificity in Streptococcus pyogenes M protein.

    Directory of Open Access Journals (Sweden)

    2006-05-01

    Full Text Available Many pathogenic microorganisms evade host immunity through extensive sequence variability in a protein region targeted by protective antibodies. In spite of the sequence variability, a variable region commonly retains an important ligand-binding function, reflected in the presence of a highly conserved sequence motif. Here, we analyze the limits of sequence divergence in a ligand-binding region by characterizing the hypervariable region (HVR of Streptococcus pyogenes M protein. Our studies were focused on HVRs that bind the human complement regulator C4b-binding protein (C4BP, a ligand that confers phagocytosis resistance. A previous comparison of C4BP-binding HVRs identified residue identities that could be part of a binding motif, but the extended analysis reported here shows that no residue identities remain when additional C4BP-binding HVRs are included. Characterization of the HVR in the M22 protein indicated that two relatively conserved Leu residues are essential for C4BP binding, but these residues are probably core residues in a coiled-coil, implying that they do not directly contribute to binding. In contrast, substitution of either of two relatively conserved Glu residues, predicted to be solvent-exposed, had no effect on C4BP binding, although each of these changes had a major effect on the antigenic properties of the HVR. Together, these findings show that HVRs of M proteins have an extraordinary capacity for sequence divergence and antigenic variability while retaining a specific ligand-binding function.

  6. Modeling the Influence of Diffusion-Controlled Reactions and Residual Termination and Deactivation on the Rate and Control of Bulk ATRP at High Conversions

    Directory of Open Access Journals (Sweden)

    Ali Mohammad Rabea

    2015-04-01

    Full Text Available In high-conversion atom transfer radical polymerization (ATRP, all the reactions, such as radical termination, radical deactivation, dormant chain activation, monomer propagation, etc. could become diffusion controlled sooner or later, depending on relative diffusivities of the involved reacting species. These diffusion-controlled reactions directly affect the rate of polymerization and the control of polymer molecular weight. A model is developed to investigate the influence of diffusion-controlled reactions on the high conversion ATRP kinetics. Model simulation reveals that diffusion-controlled termination slightly increases the rate, but it is the diffusion-controlled deactivation that causes auto-acceleration in the rate (“gel effect” and loss of control. At high conversions, radical chains are “trapped” because of high molecular weight. However, radical centers can still migrate through (1 radical deactivation–activation cycles and (2 monomer propagation, which introduce “residual termination” reactions. It is found that the “residual termination” does not have much influence on the polymerization kinetics. The migration of radical centers through propagation can however facilitate catalytic deactivation of radicals, which improves the control of polymer molecular weight to some extent. Dormant chain activation and monomer propagation also become diffusion controlled and finally stop the polymerization when the system approaches its glass state.

  7. A Resource Conservation Unit.

    Science.gov (United States)

    Porter, Philip D.

    1979-01-01

    Describes a variety of learning activities for teaching elementary and junior high students about air, water, and energy conservation techniques. Suggests community resources, social studies objectives, language skills, and 20 activities. (CK)

  8. Structures of Preferred Human IgV Genes-Based Protective Antibodies Identify How Conserved Residues Contact Diverse Antigens and Assign Source of Specificity to CDR3 Loop Variation.

    Science.gov (United States)

    Bryson, Steve; Thomson, Christy A; Risnes, Louise F; Dasgupta, Somnath; Smith, Kenneth; Schrader, John W; Pai, Emil F

    2016-06-01

    The human Ab response to certain pathogens is oligoclonal, with preferred IgV genes being used more frequently than others. A pair of such preferred genes, IGVK3-11 and IGVH3-30, contributes to the generation of protective Abs directed against the 23F serotype of the pneumonococcal capsular polysaccharide of Streptococcus pneumoniae and against the AD-2S1 peptide of the gB membrane protein of human CMV. Structural analyses of Fab fragments of mAbs 023.102 and pn132p2C05 in complex with portions of the 23F polysaccharide revealed five germline-encoded residues in contact with the key component, l-rhamnose. In the case of the AD-2S1 peptide, the KE5 Fab fragment complex identified nine germline-encoded contact residues. Two of these germline-encoded residues, Arg91L and Trp94L, contact both the l-rhamnose and the AD-2S1 peptide. Comparison of the respective paratopes that bind to carbohydrate and protein reveals that stochastic diversity in both CDR3 loops alone almost exclusively accounts for their divergent specificity. Combined evolutionary pressure by human CMV and the 23F serotype of S. pneumoniae acted on the IGVK3-11 and IGVH3-30 genes as demonstrated by the multiple germline-encoded amino acids that contact both l-rhamnose and AD-2S1 peptide. Copyright © 2016 by The American Association of Immunologists, Inc.

  9. Model My Watershed: A high-performance cloud application for public engagement, watershed modeling and conservation decision support

    Science.gov (United States)

    Aufdenkampe, A. K.; Tarboton, D. G.; Horsburgh, J. S.; Mayorga, E.; McFarland, M.; Robbins, A.; Haag, S.; Shokoufandeh, A.; Evans, B. M.; Arscott, D. B.

    2017-12-01

    The Model My Watershed Web app (https://app.wikiwatershed.org/) and the BiG-CZ Data Portal (http://portal.bigcz.org/) and are web applications that share a common codebase and a common goal to deliver high-performance discovery, visualization and analysis of geospatial data in an intuitive user interface in web browser. Model My Watershed (MMW) was designed as a decision support system for watershed conservation implementation. BiG CZ Data Portal was designed to provide context and background data for research sites. Users begin by creating an Area of Interest, via an automated watershed delineation tool, a free draw tool, selection of a predefined area such as a county or USGS Hydrological Unit (HUC), or uploading a custom polygon. Both Web apps visualize and provide summary statistics of land use, soil groups, streams, climate and other geospatial information. MMW then allows users to run a watershed model to simulate different scenarios of human impacts on stormwater runoff and water-quality. BiG CZ Data Portal allows users to search for scientific and monitoring data within the Area of Interest, which also serves as a prototype for the upcoming Monitor My Watershed web app. Both systems integrate with CUAHSI cyberinfrastructure, including visualizing observational data from CUAHSI Water Data Center and storing user data via CUAHSI HydroShare. Both systems also integrate with the new EnviroDIY Water Quality Data Portal (http://data.envirodiy.org/), a system for crowd-sourcing environmental monitoring data using open-source sensor stations (http://envirodiy.org/mayfly/) and based on the Observations Data Model v2.

  10. Favorable Local Control From Consolidative Radiation Therapy in High-Risk Neuroblastoma Despite Gross Residual Disease, Positive Margins, or Nodal Involvement

    Energy Technology Data Exchange (ETDEWEB)

    Ferris, Matthew J., E-mail: mjferri@emory.edu [Department of Radiation Oncology, Emory University, Atlanta, Georgia (United States); Winship Cancer Institute, Emory University, Atlanta, Georgia (United States); Danish, Hasan [Department of Radiation Oncology, Emory University, Atlanta, Georgia (United States); Winship Cancer Institute, Emory University, Atlanta, Georgia (United States); Switchenko, Jeffrey M. [Winship Cancer Institute, Emory University, Atlanta, Georgia (United States); Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia (United States); Deng, Claudia [Department of Radiation Oncology, Emory University, Atlanta, Georgia (United States); Winship Cancer Institute, Emory University, Atlanta, Georgia (United States); George, Bradley A.; Goldsmith, Kelly C.; Wasilewski, Karen J.; Cash, W. Thomas [Aflac Cancer and Blood Disorders Center, Children' s Healthcare of Atlanta, Atlanta, Georgia (United States); Khan, Mohammad K.; Eaton, Bree R.; Esiashvili, Natia [Department of Radiation Oncology, Emory University, Atlanta, Georgia (United States); Winship Cancer Institute, Emory University, Atlanta, Georgia (United States)

    2017-03-15

    Purpose: To report the influence of radiation therapy (RT) dose and surgical pathology variables on disease control and overall survival (OS) in patients treated for high-risk neuroblastoma at a single institution. Methods and Materials: We conducted a retrospective study of 67 high-risk neuroblastoma patients who received RT as part of definitive management from January 2003 until May 2014. Results: At a median follow-up of 4.5 years, 26 patients (38.8%) failed distantly; 4 of these patients also failed locally. One patient progressed locally without distant failure. Local control was 92.5%, and total disease control was 59.5%. No benefit was demonstrated for RT doses over 21.6 Gy with respect to local relapse–free survival (P=.55), disease-free survival (P=.22), or OS (P=.72). With respect to local relapse–free survival, disease-free survival, and OS, no disadvantage was seen for positive lymph nodes on surgical pathology, positive surgical margins, or gross residual disease. Of the patients with gross residual disease, 75% (6 of 8) went on to have no evidence of disease at time of last follow-up, and the 2 patients who failed did so distantly. Conclusions: Patients with high-risk neuroblastoma in this series maintained excellent local control, with no benefit demonstrated for radiation doses over 21.6 Gy, and no disadvantage demonstrated for gross residual disease after surgery, positive surgical margins, or pathologic lymph node positivity. Though the limitations of a retrospective review for an uncommon disease must be kept in mind, with small numbers in some of the subgroups, it seems that dose escalation should be considered only in exceptional circumstances.

  11. The maize INDETERMINATE1 flowering time regulator defines a highly conserved zinc finger protein family in higher plants

    Directory of Open Access Journals (Sweden)

    Colasanti Joseph

    2006-06-01

    Full Text Available Abstract Background The maize INDETERMINATE1 gene, ID1, is a key regulator of the transition to flowering and the founding member of a transcription factor gene family that encodes a protein with a distinct arrangement of zinc finger motifs. The zinc fingers and surrounding sequence make up the signature ID domain (IDD, which appears to be found in all higher plant genomes. The presence of zinc finger domains and previous biochemical studies showing that ID1 binds to DNA suggests that members of this gene family are involved in transcriptional regulation. Results Comparison of IDD genes identified in Arabidopsis and rice genomes, and all IDD genes discovered in maize EST and genomic databases, suggest that ID1 is a unique member of this gene family. High levels of sequence similarity amongst all IDD genes from maize, rice and Arabidopsis suggest that they are derived from a common ancestor. Several unique features of ID1 suggest that it is a divergent member of the maize IDD family. Although no clear ID1 ortholog was identified in the Arabidopsis genome, highly similar genes that encode proteins with identity extending beyond the ID domain were isolated from rice and sorghum. Phylogenetic comparisons show that these putative orthologs, along with maize ID1, form a group separate from other IDD genes. In contrast to ID1 mRNA, which is detected exclusively in immature leaves, several maize IDD genes showed a broad range of expression in various tissues. Further, Western analysis with an antibody that cross-reacts with ID1 protein and potential orthologs from rice and sorghum shows that all three proteins are detected in immature leaves only. Conclusion Comparative genomic analysis shows that the IDD zinc finger family is highly conserved among both monocots and dicots. The leaf-specific ID1 expression pattern distinguishes it from other maize IDD genes examined. A similar leaf-specific localization pattern was observed for the putative ID1 protein

  12. Determination of hexachlorocyclohexane pesticide residues in wool fat by a combined high-performance liquid chromatographic-gas-liquid chromatographic method

    International Nuclear Information System (INIS)

    Ali, S.L.

    1978-01-01

    Beta- and gamma-hexachlorocyclohexane residues were determined in twelve wool fat samples by using a combined high-performance liquid chromatographic (HPLC)-gas-liquid chromatographic (GLC) method. After extraction and chromatographic clean-up on a silca-gel column, the sample was further purified by HPLC on a reversed-phase C-18 column with methanol as the mobile phase. The final determination was effected by GLC with a 1-mCi nickel-63 electron-capture detector. The analytical method was checked by addition of carbon-14-labelled lindane and measurement of the radioactivity in a liquid scintillation counter. (Auth.)

  13. RNA-Seq transcriptomics and pathway analyses reveal potential regulatory genes and molecular mechanisms in high- and low-residual feed intake in Nordic dairy cattle

    DEFF Research Database (Denmark)

    Salleh, M. S.; Mazzoni, G.; Höglund, J. K.

    2017-01-01

    -throughput RNA sequencing data of liver biopsies from 19 dairy cows were used to identify differentially expressed genes (DEGs) between high- and low-FE groups of cows (based on Residual Feed Intake or RFI). Subsequently, a profile of the pathways connecting the DEGs to FE was generated, and a list of candidate...... genes and biomarkers was derived for their potential inclusion in breeding programmes to improve FE. The bovine RNA-Seq gene expression data from the liver was analysed to identify DEGs and, subsequently, identify the molecular mechanisms, pathways and possible candidate biomarkers of feed efficiency....... On average, 57 million reads (short reads or short mRNA sequences ...

  14. High Residual Collagen-Induced Platelet Reactivity Predicts Development of Restenosis in the Superficial Femoral Artery After Percutaneous Transluminal Angioplasty in Claudicant Patients

    Energy Technology Data Exchange (ETDEWEB)

    Gary, Thomas, E-mail: thomas.gary@medunigraz.at [Medical University of Graz, Division of Angiology, Department of Internal Medicine (Austria); Prüller, Florian, E-mail: florian.prueller@klinikum-graz.at; Raggam, Reinhard, E-mail: reinhard.raggam@klinikum-graz.at [Medical University of Graz, Clinical Institute of Medical and Chemical Laboratory Diagnostics (Austria); Mahla, Elisabeth, E-mail: elisabeth.mahla@medunigraz.at [Medical University of Graz, Department of Anesthesiology and Intensive Care Medicine (Austria); Eller, Philipp, E-mail: philipp.eller@medunigraz.at; Hafner, Franz, E-mail: franz.hafner@klinikum-graz.at; Brodmann, Marianne, E-mail: marianne.brodmann@medunigraz.at [Medical University of Graz, Division of Angiology, Department of Internal Medicine (Austria)

    2016-02-15

    PurposeAlthough platelet reactivity is routinely inhibited with aspirin after percutaneous angioplasty (PTA) in peripheral arteries, the restenosis rate in the superficial femoral artery (SFA) is high. Interaction of activated platelets and the endothelium in the region of intervention could be one reason for this as collagen in the subendothelium activates platelets.Materials and MethodsA prospective study evaluating on-site platelet reactivity during PTA and its influence on the development of restenosis with a total of 30 patients scheduled for PTA of the SFA. Arterial blood was taken from the PTA site after SFA; platelet function was evaluated with light transmission aggregometry. After 3, 6, 12, and 24 months, duplex sonography was performed and the restenosis rate evaluated.ResultsEight out of 30 patients developed a hemodynamically relevant restenosis (>50 % lumen narrowing) in the PTA region during the 24-month follow-up period. High residual collagen-induced platelet reactivity defined as AUC >30 was a significant predictor for the development of restenosis [adjusted odds ratio 11.8 (9.4, 14.2); P = .04].ConclusionsHigh residual collagen-induced platelet reactivity at the interventional site predicts development of restenosis after PTA of the SFA. Platelet function testing may be useful for identifying patients at risk.

  15. Application of ultra-high pressure liquid chromatography linear ion-trap orbitrap to qualitative and quantitative assessment of pesticide residues.

    Science.gov (United States)

    Farré, M; Picó, Y; Barceló, D

    2014-02-07

    The analysis of pesticides residues using a last generation high resolution and high mass accuracy hybrid linear ion trap-Orbitrap mass spectrometer (LTQ-Orbitrap-MS) was explored. Pesticides were extracted from fruits, fish, bees and sediments by QuEChERS and from water by solid-phase with Oasis HLB cartridges. Ultra-high pressure liquid chromatography (UHPLC)-LTQ-Orbitrap mass spectrometer acquired full scan MS data for quantification, and data dependent (dd) MS(2) and MS(3) product ion spectra for identification and/or confirmation. The regression coefficients (r(2)) for the calibration curves (two order of magnitude up to the lowest calibration level) in the study were ≥0.99. The LODs for 54 validated compounds were ≤2ngmL(-1) (analytical standards). The relative standard deviation (RSD), which was used to estimate precision, was always lower than 22%. The recovery of extraction and matrix effects ranged from 58 to 120% and from -92 to 52%, respectively. Mass accuracy was always ≤4ppm, corresponding to a maximum mass error of 1.6millimass units (mmu). This procedure was then successfully applied to pesticide residues in a set of the above-mentioned food and environmental samples. In addition to target analytes, this method enables the simultaneous detection/identification of non-target pesticides, pharmaceuticals, drugs of abuse, mycotoxins, and their metabolites. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. Detoxification of Olive Mill Wastewater and Bioconversion of Olive Crop Residues into High-Value-Added Biomass by the Choice Edible Mushroom Hericium erinaceus.

    Science.gov (United States)

    Koutrotsios, Georgios; Larou, Evangelia; Mountzouris, Konstantinos C; Zervakis, Georgios I

    2016-09-01

    Environmentally acceptable disposal of olive cultivation residues (e.g., olive prunings; olive pruning residues (OLPR)) and olive mill wastes is of paramount importance since they are generated in huge quantities within a short time. Moreover, olive mill wastewater (OMW) or sludge-like effluents ("alperujo"; two-phase olive mill waste (TPOMW)) are highly biotoxic. Hericium erinaceus is a white-rot fungus which produces choice edible mushrooms on substrates rich in lignocellulosics, and its suitability for the treatment of olive by-products was examined for the first time. Fungal growth resulted in a notable reduction of OMW's pollution parameters (i.e., 65 % decolorization, 47 % total phenolic reduction, and 52 % phytotoxicity decrease) and correlated with laccase and manganese peroxidase activities. Solid-state fermentation of various mixtures of OLPR, TPOMW, and beech sawdust (control) by H. erinaceus qualified OLPR in subsequent cultivation experiments, where it exhibited high mushroom yields and biological efficiency (31 %). Analyses of proximate composition and bioactive compound content revealed that mushrooms deriving from OLPR substrates showed significantly higher crude fat, total glucan, β-glucan, total phenolics, and ferric-reducing antioxidant potential values than the control. H. erinaceus demonstrated the potential to detoxify OMW and bioconvert OLPR into high-quality biomass, and hence, this fungus could be successfully exploited for the treatment of such by-products.

  17. FY 2000 report on the basic survey to promote the joint implementation. Potential survey of the greenhouse effect gas reduction by high-efficient utilization of the oil residue in Bataan Refinery in the Philippines; 2000 nendo kyodo jisshi nado suishin kiso chosa hokokusho. Philippines koku Bataan seiyusho ni okeru sekiyu zansa kokoritsu riyo ni yoru onshitsu koka gas sakugen kanosei chosa

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-03-01

    For the purpose of reducing the CO2 emitted from electricity/vapor supply facilities of Bataan Refinery in the Philippines, study was conducted of optimum energy supply facilities considering the effective use of the oil residue and future reinforcement of the refinery. Concerning the high-pressure/high-temperature condensing extraction boiler/turbine cogeneration, gas turbine cogeneration and low speed diesel engine cogeneration, comparative study was carried out in terms of thermal efficiency, reliability/preservation, environmental acceptability, effectiveness of measures for the future excessive oil residue, etc. As a result, the study was concluded as follows: the electric power consumption will markedly increase in the future; however, in the light of the situation of the refinery where the vapor demand will not increase, it is the most suitable to use low speed diesel engine cogeneration facilities as on-site power generation facilities which can burn the excessively increasing oil residue as direct fuel. The CO2 reduction effect estimated from the project on the present scale was 132,880 t-CO2/y, and the energy conservation effect estimated was 50,861 toe/y. (NEDO)

  18. Optimization of a method by liquid chromatography of high resolution to determine residues of ethilenthiourea in samples of tomato

    International Nuclear Information System (INIS)

    Mora, D.; Rodriguez, O.M.

    2002-01-01

    A method was optimized to determine the present residues of ethilenthiourea in samples of tomatoes. The method consisted of three stages: a extraction of ultrasonic bath with methanol; a cleaning of the extract through a glass column of 11 mm of diameter stuffed with 2,5 g of neutral aluminium's mixture and activated coal (97,5:2,5) and 2,5 g of pure-neutral aluminium, it is dissolved with 250 ml of methanol. The third stage was of quantification by HPLC in a C 18 ' column with a methanol and water mixture (90:10) like a mobile phase to an flow of 2,0 ml/min. and with UV detection to 232 nm. The retention's time under theses conditions was of 2,15 minutes. The merit's parameters of the method were determined, proving and lineal sphere between 1,0 and 28,0 (g/ml of ETU; some quantification and detection limits have been calculated by the method of Hubaux and Vos (22) of 0,153 and 0,306 mg/ml respectively and a recuperation of 84%. (Author) [es

  19. Ex Situ gene conservation in high elevation white pine species in the United States-a beginning

    Science.gov (United States)

    Richard A. Sniezko; Anna Schoettle; Joan Dunlap; Detlev Vogler; David Conklin; Andrew Bower; Chris Jensen; Rob Mangold; Doug Daoust; Gary Man

    2011-01-01

    The eight white pine species native to the western United States face an array of biotic and abiotic challenges that impact the viability of populations or the species themselves. Well-established programs are already in place to conserve and restore Pinus monticola Dougl. ex D. Don and P. lambertiana Dougl. throughout significant portions of their geographic ranges....

  20. A Highly Conserved GEQYQQLR Epitope Has Been Identified in the Nucleoprotein of Ebola Virus by Using an In Silico Approach

    Directory of Open Access Journals (Sweden)

    Mohammad Tuhin Ali

    2015-01-01

    Full Text Available Ebola virus (EBOV is a deadly virus that has caused several fatal outbreaks. Recently it caused another outbreak and resulted in thousands afflicted cases. Effective and approved vaccine or therapeutic treatment against this virus is still absent. In this study, we aimed to predict B-cell epitopes from several EBOV encoded proteins which may aid in developing new antibody-based therapeutics or viral antigen detection method against this virus. Multiple sequence alignment (MSA was performed for the identification of conserved region among glycoprotein (GP, nucleoprotein (NP, and viral structural proteins (VP40, VP35, and VP24 of EBOV. Next, different consensus immunogenic and conserved sites were predicted from the conserved region(s using various computational tools which are available in Immune Epitope Database (IEDB. Among GP, NP, VP40, VP35, and VP30 protein, only NP gave a 100% conserved GEQYQQLR B-cell epitope that fulfills the ideal features of an effective B-cell epitope and could lead a way in the milieu of Ebola treatment. However, successful in vivo and in vitro studies are prerequisite to determine the actual potency of our predicted epitope and establishing it as a preventing medication against all the fatal strains of EBOV.

  1. "Toward High School Biology": Helping Middle School Students Understand Chemical Reactions and Conservation of Mass in Nonliving and Living Systems

    Science.gov (United States)

    Herrmann-Abell, Cari F.; Koppal, Mary; Roseman, Jo Ellen

    2016-01-01

    Modern biology has become increasingly molecular in nature, requiring students to understand basic chemical concepts. Studies show, however, that many students fail to grasp ideas about atom rearrangement and conservation during chemical reactions or the application of these ideas to biological systems. To help provide students with a better…

  2. Control of residual carbon concentration in GaN high electron mobility transistor and realization of high-resistance GaN grown by metal-organic chemical vapor deposition

    Energy Technology Data Exchange (ETDEWEB)

    He, X.G. [State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083 (China); Zhao, D.G., E-mail: dgzhao@red.semi.ac.cn [State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083 (China); Jiang, D.S.; Liu, Z.S.; Chen, P.; Le, L.C.; Yang, J.; Li, X.J. [State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, P.O. Box 912, Beijing 100083 (China); Zhang, S.M.; Zhu, J.J.; Wang, H.; Yang, H. [Suzhou Institute of Nano-tech and Nano-bionics, Chinese Academy of Sciences, Suzhou 215125 (China)

    2014-08-01

    GaN films were grown by metal-organic chemical vapor deposition (MOCVD) under various growth conditions. The influences of MOCVD growth parameters, i.e., growth pressure, ammonia (NH{sub 3}) flux, growth temperature, trimethyl-gallium flux and H{sub 2} flux, on residual carbon concentration ([C]) were systematically investigated. Secondary ion mass spectroscopy measurements show that [C] can be effectively modulated by growth conditions. Especially, it can increase by reducing growth pressure up to two orders of magnitude. High-resistance (HR) GaN epilayer with a resistivity over 1.0 × 10{sup 9} Ω·cm is achieved by reducing growth pressure. The mechanism of the formation of HR GaN epilayer is discussed. An Al{sub x}Ga{sub 1−x}N/GaN high electron mobility transistor structure with a HR GaN buffer layer and an additional low-carbon GaN channel layer is presented, exhibiting a high two dimensional electron gas mobility of 1815 cm{sup 2}/Vs. - Highlights: • Influence of MOCVD parameters on residual carbon concentration in GaN is studied. • GaN layer with a resistivity over 1 × 10{sup 9} Ω·cm is achieved by reducing growth pressure. • High electron mobility transistor (HEMT) structures were prepared. • Control of residual carbon content results in HEMT with high 2-D electron gas mobility.

  3. Mild chemical pretreatments are sufficient for complete saccharification of steam-exploded residues and high ethanol production in desirable wheat accessions.

    Science.gov (United States)

    Zahoor; Tu, Yuanyuan; Wang, Lingqiang; Xia, Tao; Sun, Dan; Zhou, Shiguang; Wang, Yanting; Li, Ying; Zhang, Heping; Zhang, Tong; Madadi, Meysam; Peng, Liangcai

    2017-11-01

    In this study, a combined pretreatment was performed in four wheat accessions using steam explosion followed with different concentrations of H 2 SO 4 or NaOH, leading to increased hexoses yields by 3-6 folds from enzymatic hydrolysis. Further co-supplied with 1% Tween-80, Talq90 and Talq16 accessions exhibited an almost complete enzymatic saccharification of steam-exploded (SE) residues after 0.5% H 2 SO 4 or 1% NaOH pretreatment, with the highest bioethanol yields at 18.5%-19.4%, compared with previous reports about wheat bioethanol yields at 11%-17% obtained under relatively strong pretreatment conditions. Furthermore, chemical analysis indicated that much enhanced saccharification in Talq90 and Talq16 may be partially due to their relatively low cellulose CrI and DP values and high hemicellulose Ara and H-monomer levels in raw materials and SE residues. Hence, this study has not only demonstrated a mild pretreatment technology for a complete saccharification, but it has also obtained the high ethanol production in desirable wheat accessions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. A complementary role of multiparameter flow cytometry and high-throughput sequencing for minimal residual disease detection in chronic lymphocytic leukemia: an European Research Initiative on CLL study.

    LENUS (Irish Health Repository)

    Rawstron, A C

    2016-04-01

    In chronic lymphocytic leukemia (CLL) the level of minimal residual disease (MRD) after therapy is an independent predictor of outcome. Given the increasing number of new agents being explored for CLL therapy, using MRD as a surrogate could greatly reduce the time necessary to assess their efficacy. In this European Research Initiative on CLL (ERIC) project we have identified and validated a flow-cytometric approach to reliably quantitate CLL cells to the level of 0.0010% (10(-5)). The assay comprises a core panel of six markers (i.e. CD19, CD20, CD5, CD43, CD79b and CD81) with a component specification independent of instrument and reagents, which can be locally re-validated using normal peripheral blood. This method is directly comparable to previous ERIC-designed assays and also provides a backbone for investigation of new markers. A parallel analysis of high-throughput sequencing using the ClonoSEQ assay showed good concordance with flow cytometry results at the 0.010% (10(-4)) level, the MRD threshold defined in the 2008 International Workshop on CLL guidelines, but it also provides good linearity to a detection limit of 1 in a million (10(-6)). The combination of both technologies would permit a highly sensitive approach to MRD detection while providing a reproducible and broadly accessible method to quantify residual disease and optimize treatment in CLL.

  5. In-coupled syringe assisted octanol-water partition microextraction coupled with high-performance liquid chromatography for simultaneous determination of neonicotinoid insecticide residues in honey.

    Science.gov (United States)

    Vichapong, Jitlada; Burakham, Rodjana; Srijaranai, Supalax

    2015-07-01

    A simple and fast method namely in-coupled syringe assisted octanol-water partition microextraction combined with high performance liquid chromatography (HPLC) has been developed for the extraction, preconcentration and determination of neonicotinoid insecticide residues (e.g. imidacloprid, acetamiprid, clothianidin, thiacloprid, thiamethoxam, dinotefuran, and nitenpyram) in honey. The experimental parameters affected the extraction efficiency, including kind and concentration of salt, kind of disperser solvent and its volume, kind of extraction solvent and its volume, shooting times and extraction time were investigated. The extraction process was carried out by rapid shooting of two syringes. Therefore, rapid dispersion and mass transfer processes was created between phases, and thus affects the extraction efficiency of the proposed method. The optimum extraction conditions were 10.00 mL of aqueous sample, 10% (w/v) Na2SO4, 1-octanol (100µL) as an extraction solvent, shooting 4 times and extraction time 2min. No disperser solvent and centrifugation step was necessary. Linearity was obtained within the range of 0.1-3000 ngmL(-1), with the correlation coefficients greater than 0.99. The high enrichment factor of the target analytes was 100 fold and low limit of detection (0.25-0.50 ngmL(-1)) could be obtained. This proposed method has been successfully applied in the analysis of neonicotinoid residues in honey, and good recoveries in the range of 96.93-107.70% were obtained. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Inhibitory control and visuo-spatial reversibility in Piaget’s seminal number conservation task: A high-density ERP study.

    Directory of Open Access Journals (Sweden)

    Gregoire eBorst

    2013-12-01

    Full Text Available The present high-density ERP study on 13 adults aimed to determine whether number conservation relies on the ability to inhibit the overlearned length-equals-number strategy and then imagine the shortening of the row that was lengthened. Participants performed the number-conservation task and, after the EEG session, the mental imagery task. In the number-conservation task, first two rows with the same number of tokens and the same length were presented on a computer screen (COV condition and then, the tokens in one of the two rows were spread apart (INT condition. Participants were instructed to determine whether the two rows had an identical number of tokens. In the mental imagery task, two rows with different lengths but the same number of tokens were presented and participants were instructed to imagine the tokens in the longer row aligning with the tokens in the shorter row. In the number-conservation task, we found that the amplitudes of the centro-parietal N2 and fronto-central P3 were higher in the INT than in the COV conditions. In addition, the differences in response times between the two conditions were correlated with the differences in the amplitudes of the fronto-central P3. In light of previous results reported on the number-conservation task in adults, the present results suggest that inhibition might be necessary to succeed the number-conservation task in adults even when the transformation of the length of one of the row is displayed. Finally, we also reported correlations between the speed at which participants could imagine the shortening of one of the row in the mental imagery task, the speed at which participants could determine that the two rows had the same number of tokens after the tokens in one of the row were spread apart and the latency of the late positive parietal component in the number-conservation task. Therefore, performing the number-conservation task might involve mental transformation processes in adults.

  7. A zebrafish screen for craniofacial mutants identifies wdr68 as a highly conserved gene required for endothelin-1 expression

    Directory of Open Access Journals (Sweden)

    Amsterdam Adam

    2006-06-01

    identification of approximately 25% of the essential genes required for craniofacial development. The identification of zebrafish models for two human disease syndromes indicates that homologs to the other genes are likely to also be relevant for human craniofacial development. The initial characterization of wdr68 suggests an important role in craniofacial development for the highly conserved Wdr68-Dyrk1 protein complexes.

  8. Functional and genetic evidence that nucleoside transport is highly conserved in Leishmania species: Implications for pyrimidine-based chemotherapy.

    Science.gov (United States)

    Alzahrani, Khalid J H; Ali, Juma A M; Eze, Anthonius A; Looi, Wan Limm; Tagoe, Daniel N A; Creek, Darren J; Barrett, Michael P; de Koning, Harry P

    2017-08-01

    Leishmania pyrimidine salvage is replete with opportunities for therapeutic intervention with enzyme inhibitors or antimetabolites. Their uptake into cells depends upon specific transporters; therefore it is essential to establish whether various Leishmania species possess similar pyrimidine transporters capable of drug uptake. Here, we report a comprehensive characterization of pyrimidine transport in L. major and L. mexicana. In both species, two transporters for uridine/adenosine were detected, one of which also transported uracil and the antimetabolites 5-fluoruracil (5-FU) and 5F,2'deoxyuridine (5F,2'dUrd), and was designated uridine-uracil transporter 1 (UUT1); the other transporter mediated uptake of adenosine, uridine, 5F,2'dUrd and thymidine and was designated Nucleoside Transporter 1 (NT1). To verify the reported L. donovani model of two NT1-like genes encoding uridine/adenosine transporters, and an NT2 gene encoding an inosine transporter, we cloned the corresponding L. major and L. mexicana genes, expressing each in T. brucei. Consistent with the L. donovani reports, the NT1-like genes of either species mediated the adenosine-sensitive uptake of [ 3 H]-uridine but not of [ 3 H]-inosine. Conversely, the NT2-like genes mediated uptake of [ 3 H]-inosine but not [ 3 H]-uridine. Among pyrimidine antimetabolites tested, 5-FU and 5F,2'dUrd were the most effective antileishmanials; resistance to both analogs was induced in L. major and L. mexicana. In each case it was found that the resistant cells had lost the transport capacity for the inducing drug. Metabolomics analysis found that the mechanism of action of 5-FU and 5F-2'dUrd was similar in both Leishmania species, with major changes in deoxynucleotide metabolism. We conclude that the pyrimidine salvage system is highly conserved in Leishmania species - essential information for the development of pyrimidine-based chemotherapy. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights

  9. Functional and genetic evidence that nucleoside transport is highly conserved in Leishmania species: Implications for pyrimidine-based chemotherapy

    Directory of Open Access Journals (Sweden)

    Khalid J.H. Alzahrani

    2017-08-01

    Full Text Available Leishmania pyrimidine salvage is replete with opportunities for therapeutic intervention with enzyme inhibitors or antimetabolites. Their uptake into cells depends upon specific transporters; therefore it is essential to establish whether various Leishmania species possess similar pyrimidine transporters capable of drug uptake. Here, we report a comprehensive characterization of pyrimidine transport in L. major and L. mexicana. In both species, two transporters for uridine/adenosine were detected, one of which also transported uracil and the antimetabolites 5-fluoruracil (5-FU and 5F,2′deoxyuridine (5F,2′dUrd, and was designated uridine-uracil transporter 1 (UUT1; the other transporter mediated uptake of adenosine, uridine, 5F,2′dUrd and thymidine and was designated Nucleoside Transporter 1 (NT1. To verify the reported L. donovani model of two NT1-like genes encoding uridine/adenosine transporters, and an NT2 gene encoding an inosine transporter, we cloned the corresponding L. major and L. mexicana genes, expressing each in T. brucei. Consistent with the L. donovani reports, the NT1-like genes of either species mediated the adenosine-sensitive uptake of [3H]-uridine but not of [3H]-inosine. Conversely, the NT2-like genes mediated uptake of [3H]-inosine but not [3H]-uridine. Among pyrimidine antimetabolites tested, 5-FU and 5F,2′dUrd were the most effective antileishmanials; resistance to both analogs was induced in L. major and L. mexicana. In each case it was found that the resistant cells had lost the transport capacity for the inducing drug. Metabolomics analysis found that the mechanism of action of 5-FU and 5F-2′dUrd was similar in both Leishmania species, with major changes in deoxynucleotide metabolism. We conclude that the pyrimidine salvage system is highly conserved in Leishmania species - essential information for the development of pyrimidine-based chemotherapy. Keywords: Leishmania, Pyrimidine metabolism, Uracil

  10. Energy partitioning and thyroid hormone levels during Salmonella enteritidis infections in pullets with high or low residual feed intake.

    Science.gov (United States)

    Van Eerden, E; Van Den Brand, H; Heetkamp, M J W; Decuypere, E; Kemp, B

    2006-10-01

    This experiment was conducted to investigate whether feed efficiency, as measured by residual feed intake as a phenotypic trait, affects energy partitioning in pullets that have received Salmonella inoculation as an immune challenge. In each of 8 trials, energy partitioning was measured during 5 wk in 15-wk-old efficient (R-) and nonefficient (R+) pullets, which were housed per efficiency group in 2 identical climate respiration chambers. After 1 wk of adaptation, the pullets in 4 trials were orally inoculated with 10(8) cfu of Salmonella enteritidis; pullets in the remaining trials were not inoculated and served as controls. Heat production was calculated from continuous recordings of O(2) consumption and CO(2) production. Energy and N partitioning were recorded on a weekly basis. Blood samples for analyses on thyroid hormones were taken at 16, 17, and 19 wk of age. There were no interactions between efficiency type and Salmonella treatment or Salmonella treatment effects in energy partitioning, except for a short-term increase in heat production in inoculated pullets. Nonefficient pullets had higher gross energy and ME intake, higher estimated ME for maintenance, lower ME:gross energy ratio, and higher total heat production and nonactivity-related heat production compared with R- pullets. Triiodothyronine levels in R+ pullets were higher at 16 and 17 wk but were lower at 19 wk of age compared with R- pullets. Thyroxine levels were higher in R- at 16 wk and showed interactions between efficiency type and Salmonella treatment at 17 and 19 wk of age. Body weights and spleen weights did not differ between efficiency groups. Nonefficient pullets had higher heart, liver, and ovary weights and more large yellow follicles than R- pullets. There were no Salmonella effects on body and organ weights. We conclude that R+ pullets have a faster running energy metabolism and that they put more resources into organ development than R- pullets. Inoculation with Salmonella has a

  11. Protein structure based prediction of catalytic residues.

    Science.gov (United States)

    Fajardo, J Eduardo; Fiser, Andras

    2013-02-22

    Worldwide structural genomics projects continue to release new protein structures at an unprecedented pace, so far nearly 6000, but only about 60% of these proteins have any sort of functional annotation. We explored a range of features that can be used for the prediction of functional residues given a known three-dimensional structure. These features include various centrality measures of nodes in graphs of interacting residues: closeness, betweenness and page-rank centrality. We also analyzed the distance of functional amino acids to the general center of mass (GCM) of the structure, relative solvent accessibility (RSA), and the use of relative entropy as a measure of sequence conservation. From the selected features, neural networks were trained to identify catalytic residues. We found that using distance to the GCM together with amino acid type provide a good discriminant function, when combined independently with sequence conservation. Using an independent test set of 29 annotated protein structures, the method returned 411 of the initial 9262 residues as the most likely to be involved in function. The output 411 residues contain 70 of the annotated 111 catalytic residues. This represents an approximately 14-fold enrichment of catalytic residues on the entire input set (corresponding to a sensitivity of 63% and a precision of 17%), a performance competitive with that of other state-of-the-art methods. We found that several of the graph based measures utilize the same underlying feature of protein structures, which can be simply and more effectively captured with the distance to GCM definition. This also has the added the advantage of simplicity and easy implementation. Meanwhile sequence conservation remains by far the most influential feature in identifying functional residues. We also found that due the rapid changes in size and composition of sequence databases, conservation calculations must be recalibrated for specific reference databases.

  12. Conservation endocrinology

    Science.gov (United States)

    McCormick, Stephen; Romero, L. Michael

    2017-01-01

    Endocrinologists can make significant contributions to conservation biology by helping to understand the mechanisms by which organisms cope with changing environments. Field endocrine techniques have advanced rapidly in recent years and can provide substantial information on the growth, stress, and reproductive status of individual animals, thereby providing insight into current and future responses of populations to changes in the environment. Environmental stressors and reproductive status can be detected nonlethally by measuring a number of endocrine-related endpoints, including steroids in plasma, living and nonliving tissue, urine, and feces. Information on the environmental or endocrine requirements of individual species for normal growth, development, and reproduction will provide critical information for species and ecosystem conservation. For many taxa, basic information on endocrinology is lacking, and advances in conservation endocrinology will require approaches that are both “basic” and “applied” and include integration of laboratory and field approaches.

  13. Effect of the heating rate on residual thermo-hydro-mechanical properties of a high-strength concrete in the context of nuclear waste storage

    International Nuclear Information System (INIS)

    Galle, C.; Pin, M.; Ranc, G.; Rodrigues, S.

    2003-01-01

    Concrete is likely to be used in massive structures for nuclear waste long-term storage facilities in France. In the framework of vitrified waste and spent fuel management, these structures could be submitted to high temperatures. In standard conditions, ambient temperature should not exceed 60 degC but in case of failure of a cooling system, concretes could be temporarily exposed to temperatures up to 250 degC. Depending on the temperature rise kinetics, concretes could be damaged to a greater or lesser extent. In this context, an experimental study on the effect of heating rate on concrete thermo-hydro-mechanical properties exposed to high temperatures (110 - 250 degC) was carried out at the French Atomic Energy Commission (CEA). Data analysis and interpretation provided enough arguments to conclude that, at local scale, the impact of heating rate on residual properties was real though relatively limited. (author)

  14. Multidisciplinary approach for the esophageal carcinoma with intent to conserve the esophagus centering on high-dose radiotherapy and concurrent chemotherapy

    International Nuclear Information System (INIS)

    Murakami, Masao; Kuroda, Yasumasa; Okamoto, Yoshiaki

    1997-01-01

    Forty-seven patients with operable squamous cell carcinoma of the thoracic esophagus were treated by initial concurrent chemoradiotherapy (CDDP-5 FU-44 Gy) followed by definitive high-dose of radiotherapy (CRT group: 35 patients) or surgery (CRT-S group: 12 patients). Clinical CR rate showed 86% in CRT group; and pathological CR rate 18% in CRT-S group. The overall median survival was 45 months, survival at 1, 3, 5 years being 96%, 52%, 48%, respectively. No treatment-related mortality was observed. The rate of the 'esophagus conservation' was 66%. Our results demonstrated that the multidisciplinary approach with intent to conserve the esophagus centering on high-dose radiotherapy and concurrent chemotherapy provides a significant improvement of both survival and quality of life in patients with operable esophageal carcinoma. (author)

  15. Forensic analysis of high explosives residues in post-blast water samples employing solid phase extraction for analyte pro-concentration

    International Nuclear Information System (INIS)

    Umi Kalsom Ahmad; Rajendran, Sumathy; Ling, Lee Woan

    2008-01-01

    Nitro aromatic, nitramine and nitrate ester compounds are a major group of high order explosive or better known as military explosives. Octahydro-1,3,5,7-tetrazocine (HMX), 1,3,5-hexahydro-1,3,5-trinitro triazine (RDX), 2,4,6-trinitro-toluene (TNT), pentaerythritol tetranitrate (PETN) and 2,4-dinitrotoluene (2,4-DNT) are secondary high explosives classified as most commonly used explosives components. There is an increasing demand for pre-concentration of these compounds in water samples as the sensitivity achieved by instrumental analytical methods for these high explosives residues are the main drawback in the application at trace levels for forensic analysis. Hence, a simple cartridge solid phase extraction (SPE) procedure was optimized as the off-line extraction and pre-concentration method to enhance the detection limit of high explosive residues using micellar electrokinetic chromatography (MEKC) and gas chromatography with electron-capture detection (GC-ECD) methods. The SPE cartridges utilized LiChrolut EN as the SPE adsorbent. By emplying pre-concentration using SPE, the detection limits of the target analytes in water sample were lowered by more than 1000 times with good percentage recovery (>87%) for MEKC method and lowered by 120 times with more than 2 % percentage recovery for GC-ECD methods. In order to test the feasibility of the developed method to real cases, post-blast water samples were analyzed. The post-blast water samples which were collected from Baling Bom training range, Ulu Kinta, Perak contained RDX and PETN in the range of 0.05 - 0.17 ppm and 0.0124 - 0.0390 ppm respectively. (author)

  16. Highly transparent poly(2-ethyl-2-oxazoline)-TiO2 nanocomposite coatings for the conservation of matte painted artworks

    OpenAIRE

    Colombo, A.; Gherardi, Francesca; Goidanich, S.; Delaney, J. K.; de la Rie, E. R.; Ubaldi, M. C.; Toniolo, L.; Simonutti, R.

    2015-01-01

    A nanocomposite coating based on TiO2 nanoparticles and poly(2-ethyl-2-oxazoline) is used as consolidant of matte painted surfaces (temperas, watercolors, modern paintings). The aim of this work is to provide advances in the conservation of these works of art, while preserving their optical appearance, in terms of colour and gloss. Fiber Optic Reflectance Spectroscopy (FORS) measurements of a painting-model (an acrylic black monochrome) treated with the nanocomposite coatings revealed that it...

  17. DNA analysis indicates that Asian elephants are native to Borneo and are therefore a high priority for conservation.

    Directory of Open Access Journals (Sweden)

    Prithiviraj Fernando

    2003-10-01

    Full Text Available The origin of Borneo's elephants is controversial. Two competing hypotheses argue that they are either indigenous, tracing back to the Pleistocene, or were introduced, descending from elephants imported in the 16th-18th centuries. Taxonomically, they have either been classified as a unique subspecies or placed under the Indian or Sumatran subspecies. If shown to be a unique indigenous population, this would extend the natural species range of the Asian elephant by 1300 km, and therefore Borneo elephants would have much greater conservation importance than if they were a feral population. We compared DNA of Borneo elephants to that of elephants from across the range of the Asian elephant, using a fragment of mitochondrial DNA, including part of the hypervariable d-loop, and five autosomal microsatellite loci. We find that Borneo's elephants are genetically distinct, with molecular divergence indicative of a Pleistocene colonisation of Borneo and subsequent isolation. We reject the hypothesis that Borneo's elephants were introduced. The genetic divergence of Borneo elephants warrants their recognition as a separate evolutionary significant unit. Thus, interbreeding Borneo elephants with those from other populations would be contraindicated in ex situ conservation, and their genetic distinctiveness makes them one of the highest priority populations for Asian elephant conservation.

  18. Quantum oscillation signatures of spin-orbit interactions controlling the residual nodal bilayer-splitting in underdoped high-Tc cuprates

    Science.gov (United States)

    Harrison, Neil; Shekhter, Arkady

    2015-03-01

    We investigate the origin of the small residual nodal bilayer-splitting in the underdoped high-Tc superconductor YBa2Cu3O6+x using the results of recently published angle-resolved quantum oscillation data [Sebastian et al., Nature 511, 61 (2014)]. A crucial clue to the origin of the residual bilayer-splitting is found to be provided by the anomalously small Zeeman-splitting of some of the observed cyclotron orbits. We show that such an anomalously Zeeman-splitting (or small effective g-factor) for a subset of orbits can be explained by spin-orbit interactions, which become significant in the nodal regions as a result of the vanishing bilayer coupling. The primary effect of spin-orbit interactions is to cause quasiparticles traversing the nodal region of the Brillouin zone to undergo a spin flip. We suggest that the Rashba-like spin-orbit interactions, naturally present in bilayer systems, have the right symmetry and magnitude to give rise to a network of coupled orbits consistent with experimental observations in underdoped YBa2Cu3O6+x. This work is supported by the DOEm BES proposal LANLF100, while the magnet lab is supported by the NSF and Florida State.

  19. Determination of anthelmintic drug residues in milk using ultra high performance liquid chromatography-tandem mass spectrometry with rapid polarity switching.

    Science.gov (United States)

    Whelan, Michelle; Kinsella, Brian; Furey, Ambrose; Moloney, Mary; Cantwell, Helen; Lehotay, Steven J; Danaher, Martin

    2010-07-02

    A new UHPLC-MS/MS (ultra high performance liquid chromatography coupled to tandem mass spectrometry) method was developed and validated to detect 38 anthelmintic drug residues, consisting of benzimidazoles, avermectins and flukicides. A modified QuEChERS-type extraction method was developed with an added concentration step to detect most of the analytes at keeper to ensure analytes remain in solution. Using rapid polarity switching in electrospray ionisation, a single injection was capable of detecting both positively and negatively charged ions in a 13 min run time. The method was validated at two levels: the unapproved use level and at the maximum residue level (MRL) according to Commission Decision (CD) 2002/657/EC criteria. The decision limit (CCalpha) of the method was in the range of 0.14-1.9 and 11-123 microg kg(-1) for drugs validated at unapproved and MRL levels, respectively. The performance of the method was successfully verified for benzimidazoles and levamisole by participating in a proficiency study.

  20. Fabric phase sorptive extraction of selected penicillin antibiotic residues from intact milk followed by high performance liquid chromatography with diode array detection.

    Science.gov (United States)

    Samanidou, Victoria; Michaelidou, Katia; Kabir, Abuzar; Furton, Kenneth G

    2017-06-01

    Fabric phase sorptive extraction (FPSE), a novel sorbent-based microextraction method, was evaluated as a simple and rapid strategy for the extraction of four penicillin antibiotic residues (benzylpenicillin, cloxacillin, dicloxacillin and oxacillin) from cows' milk, without prior protein precipitation. Time-consuming solvent evaporation and reconstitution steps were eliminated successfully from the sample preparation workflow. FPSE utilizes a flexible fabric substrate, chemically coated with sol-gel derived, highly efficient, organic-inorganic hybrid sorbent as the extraction medium. Herein short-chain poly(ethylene glycol) provided optimum extraction sensitivity for the selected penicillins, which were analysed using an RP-HPLC method, validated according to the European Decision 657/2002/EC. The limit of quantitation was 10μg/kg for benzylpenicillin, 20μg/kg for cloxacillin, 25μg/kg dicloxacillin and 30μg/kg oxacillin. These are a similar order of magnitude with those reported in the literature and (with the exception of benzylpenicillin) are less than the maximum residue limits (MRL) set by European legislation. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Quantitative Multiclass Pesticide Residue Analysis in Apple, Pear, and Grape by Modified QuEChERS and Liquid Chromatography Coupled to High-Resolution Mass Spectrometry.

    Science.gov (United States)

    Munaretto, Juliana S; Viera, Mariela de S; Martins, Manoel L; Adaime, Martha B; Zanella, Renato

    2016-11-01

    Most of the analytical methods currently applied in food control laboratories are focused on the determination of target compounds using LC coupled to tandem MS, which is an effective technique, but low-resolution MS is limited. Thus, a method for determination of pesticide multiresidues in fruits (pear, apple, and grape) using a modified quick, easy, cheap, effective, rugged, and safe method and LC coupled to quadrupole time-of-flight (Q-TOF) MS was developed and validated. The proposed method showed good linearity (r2 > 0.99) from 1 to 100 μg/L. Recoveries for blank samples spiked at 0.01, 0.04, and 0.10 mg/kg were between 66 and 122%, with RSDs apple, pear, and grape matrixes were 0.01 mg/kg for 112, 120, and 118 compounds, and 0.04 mg/kg for 22, 12, and 17 compounds, and average mass accuracy error was 3.2 ppm. LC with Q-TOF MS detection using protonated molecular ion and/or adducts and mass accuracy provided reliability for the method. The proposed method is effective for pesticide residue determination in apple, pear, and grape samples, proving that high-resolution MS using full scan mode can be a powerful and reliable technique for quantification purposes, being adequate for application in the surveillance of maximum residue limits set by different legislations.

  2. Facile and Low-Cost Preparation of Nb/Al Oxide Catalyst with High Performance for the Conversion of Kiwifruit Waste Residue to Levulinic Acid

    Directory of Open Access Journals (Sweden)

    Rui Wang

    2015-09-01

    Full Text Available The kiwifruit industry is booming worldwide. As a result, a great deal of kiwifruit waste residue (KWR containing monosaccharides is produced and discarded. This material shows great potential for the production of platform chemicals. In this study, a series of Nb/Al oxide catalysts were synthesized via a facile and low-cost coprecipitation method, and their structures were characterized using: thermal gravimetric analysis (TGA, XRD, FESEM, TEM, X-ray photoelectron spectroscopy (XPS, NH3-TPD, N2 adsorption-desorption, and FTIR-Pyridine adsorption. Experimental results of sugar-to-levulinic acid (LA conversion revealed that the 20%Nb/Al oxide catalyst provided the highest catalytic performance and durability in terms of LA yield from fructose (74.2% at 463 K after 10 min and from glucose (47.5% at 473 K after 15 min. Notably, the 20% Nb/Al oxide catalyst with a 10% dosage is capable of converting kiwifruit waste residue to LA at 473 K after 10 min. In conclusion, the enhanced catalytic performance was obtained due to the high acidity, and large surface areaof Nb/Al oxide catalyst.

  3. The selective conservative management of small traumatic pneumothoraces following stab injuries is safe: experience from a high-volume trauma service in South Africa.

    Science.gov (United States)

    Kong, V Y; Oosthuizen, G V; Clarke, D L

    2015-02-01

    The selective conservative management of small pneumothoraces (PTXs) following stab injuries is controversial. We reviewed a cohort of patients managed conservatively in a high volume trauma service in South Africa. A retrospective review over a 2-year period identified 125 asymptomatic patients with small PTXs measuring chest radiograph who were managed conservatively. Of the 125 patients included in the study, 92% were male (115/125), and the median age for all patients was 21 years (19-24). Ninety-seven per cent (121/125) of the weapons involved were knives, and 3% (4/125) were screwdrivers. Sixty-one per cent of all injuries were on the left side. Eighty-two per cent (102/125) sustained a single stab, and 18% (23/125) had multiple stabs. Thirty-nine per cent (49/125) had a PTX <0.5 cm (Group A), 26% (32/125) were ≥ 0.5 to <1 cm (Group B), 19% (24/125) were ≥ 1 to <1.5 cm (Group C) and 15% (20/125) were ≥ 1.5 to <2 cm (Group D). Three per cent of all patients (4/125) eventually required ICDs (one in Group C, three in Group D). All four patients had ICDs in situ for 24 h. The remaining 97% (121/125) were all managed successfully by active clinical observation alone. There were no subsequent readmissions, morbidity or mortality as a direct result of our conservative approach. The selective conservative management of asymptomatic small PTXs from stab injuries is safe if undertaken in the appropriate setting.

  4. [Conservation Units.

    Science.gov (United States)

    Texas Education Agency, Austin.

    Each of the six instructional units deals with one aspect of conservation: forests, water, rangeland, minerals (petroleum), and soil. The area of the elementary school curriculum with which each correlates is indicated. Lists of general and specific objectives are followed by suggested teaching procedures, including ideas for introducing the…

  5. Creative conservation

    NARCIS (Netherlands)

    Bentham, Roelof J.

    1968-01-01

    The increasing exploitation of our natural resources, the unlimited occupation of ever more new areas, and the intensification of land-use, make it necessary for us to expand the concept of conservation. But we also need to reconsider that concept itself. For the changing conditions in the

  6. Reshaping conservation

    DEFF Research Database (Denmark)

    Funder, Mikkel; Danielsen, Finn; Ngaga, Yonika

    2013-01-01

    members strengthen the monitoring practices to their advantage, and to some extent move them beyond the reach of government agencies and conservation and development practitioners. This has led to outcomes that are of greater social and strategic value to communities than the original 'planned' benefits...

  7. Novel cross-strand three-purine stack of the highly conserved 5'-GA/AAG-5' internal loop at the 3'-end termini of Parvovirus Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Chou, S.-H.; Chin, K.-H. [National Chung-Hsing University, Institute of Biochemistry (China)

    2001-12-15

    We have used two-dimensional nuclear magnetic resonance (2D-NMR), distance geometry (DG) and molecular dynamics / energy minimization (MD/EM) methods to study a 2x3 asymmetric internal loop structure of the highly conserved '5'-(GA)/(AAG)-5' bubble' present at the 3'-end hairpin of the single-stranded DNA genome of parvoviruses. This motif contains an unpaired adenosine stacked between two bracketed sheared G{center_dot}A pairs. However, the phenomenal cross-strand G-G and A-A stacking in the tandem sheared G{center_dot}A pairs has undergone considerable change. A novel three-purine stacking pattern is observed instead; the inserted A18 base is completely un-stacked from its neighboring G17 and A19 bases, but well stacked with the cross-strand A4 and G3 bases to form a novel A4/A18/G3 stack that is different from the double G/G, A/A or quadruple G/G/G/G stack present in the 5'-(GA)/(AG)-5' or 5'-(GGA)/(AGG)-5' motifs. Unlike the bulged purine residue that usually causes about 20 degree kink in the helical axis of the parent helix when bracketed by canonical G{center_dot}C or A{center_dot}T base pairs, no significant kink is observed in the present helix containing a bulged-adenine that is bracketed by sheared G {center_dot}A pairs. The phosphodiesters connecting G3-A4 and G17-A18 residues adopt unusual {zeta} torsional angles close to the trans domain, yet that connecting A18-A19 residues resumes the normal {zeta}(g{sup -}) value. The well structured '5'-(GAA)/(AG)-5'' internal loop in the parvovirus genomes explains its resistance to single-strand specific endonuclease susceptibility.

  8. Integrating conservation costs into sea level rise adaptive conservation prioritization

    Directory of Open Access Journals (Sweden)

    Mingjian Zhu

    2015-07-01

    Full Text Available Biodiversity conservation requires strategic investment as resources for conservation are often limited. As sea level rises, it is important and necessary to consider both sea level rise and costs in conservation decision making. In this study, we consider costs of conservation in an integrated modeling process that incorporates a geomorphological model (SLAMM, species habitat models, and conservation prioritization (Zonation to identify conservation priorities in the face of landscape dynamics due to sea level rise in the Matanzas River basin of northeast Florida. Compared to conservation priorities that do not consider land costs in the analysis process, conservation priorities that consider costs in the planning process change significantly. The comparison demonstrates that some areas with high conservation values might be identified as lower priorities when integrating economic costs in the planning process and some areas with low conservation values might be identified as high priorities when considering costs in the planning process. This research could help coastal resources managers make informed decisions about where and how to allocate conservation resources more wisely to facilitate biodiversity adaptation to sea level rise.

  9. A Single Residue in Ebola Virus Receptor NPC1 Influences Cellular Host Range in Reptiles

    Science.gov (United States)

    2016-09-07

    VH-2) is resistant to infection in an NPC1-36   dependent manner . We found that VH-2 cells are resistant to EBOV infection because the Rus-37...infection in a host species-dependent manner (24). Here, we demonstrate that an adjacent 89   residue, 503, highly conserved in the domain C of NPC1...Tyr sequence 194   change at residue 503 might influence EBOV GPCL–NPC1 binding in a bidirectional manner . 195   Accordingly, we expressed and

  10. RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database.

    Science.gov (United States)

    Miao, Zhichao; Westhof, Eric

    2016-07-08

    RBscore&NBench combines a web server, RBscore and a database, NBench. RBscore predicts RNA-/DNA-binding residues in proteins and visualizes the prediction scores and features on protein structures. The scoring scheme of RBscore directly links feature values to nucleic acid binding probabilities and illustrates the nucleic acid binding energy funnel on the protein surface. To avoid dataset, binding site definition and assessment metric biases, we compared RBscore with 18 web servers and 3 stand-alone programs on 41 datasets, which demonstrated the high and stable accuracy of RBscore. A comprehensive comparison led us to develop a benchmark database named NBench. The web server is available on: http://ahsoka.u-strasbg.fr/rbscorenbench/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. Exploration of a mechanism for the production of highly unsaturated fatty acids in Scenedesmus sp. at low temperature grown on oil crop residue based medium.

    Science.gov (United States)

    Lu, Qian; Li, Jun; Wang, Jinghan; Li, Kun; Li, Jingjing; Han, Pei; Chen, Paul; Zhou, Wenguang

    2017-11-01

    The ability of algae to produce lipids comprising of unsaturated fatty acids varies with strains and culture conditions. This study investigates the effect of temperature on the production of unsaturated fatty acids in Scenedesmus sp. grown on oil crop residue based medium. At low temperature (10°C), synthesis of lipids compromising of high contents of unsaturated fatty acids took place primarily in the early stage while protein accumulation mainly occurred in the late stage. This stepwise lipid-protein synthesis process was found to be associated with the contents of acetyl-CoA and α-KG in the algal cells. A mechanism was proposed and tested through simulation experiments which quantified the carbon flux allocation in algal cells at different cultivation stages. It is concluded that low culture temperature such as 10°C is suitable for the production of lipids comprising of unsaturated fatty acids. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Cytoplasmic protein binding to highly conserved sequences in the 3' untranslated region of mouse protamine 2 mRNA, a translationally regulated transcript of male germ cells

    International Nuclear Information System (INIS)

    Kwon, Y.K.; Hecht, N.B.

    1991-01-01

    The expression of the protamines, the predominant nuclear proteins of mammalian spermatozoa, is regulated translationally during male germ-cell development. The 3' untranslated region (UTR) of protamine 1 mRNA has been reported to control its time of translation. To understand the mechanisms controlling translation of the protamine mRNAs, we have sought to identify cis elements of the 3' UTR of protamine 2 mRNA that are recognized by cytoplasmic factors. From gel retardation assays, two sequence elements are shown to form specific RNA-protein complexes. Protein binding sites of the two complexes were determined by RNase T1 mapping, by blocking the putative binding sites with antisense oligonucleotides, and by competition assays. The sequences of these elements, located between nucleotides + 537 and + 572 in protamine 2 mRNA, are highly conserved among postmeiotic translationally regulated nuclear proteins of the mammalian testis. Two closely linked protein binding sites were detected. UV-crosslinking studies revealed that a protein of about 18 kDa binds to one of the conserved sequences. These data demonstrate specific protein binding to a highly conserved 3' UTR of translationally regulated testicular mRNA

  13. The Highly Conserved COPII Coat Complex Sorts Cargo from the Endoplasmic Reticulum and Targets It to the Golgi

    OpenAIRE

    Lord, Christopher; Ferro-Novick, Susan; Miller, Elizabeth A.

    2013-01-01

    Protein egress from the endoplasmic reticulum (ER) is driven by a conserved cytoplasmic coat complex called the COPII coat. The COPII coat complex contains an inner shell (Sec23/Sec24) that sorts cargo into ER-derived vesicles and an outer cage (Sec13/Sec31) that leads to coat polymerization. Once released from the ER, vesicles must tether to and fuse with the target membrane to deliver their protein and lipid contents. This delivery step also depends on the COPII coat, with coat proteins bin...

  14. Residual stress by repair welds

    International Nuclear Information System (INIS)

    Mochizuki, Masahito; Toyoda, Masao

    2003-01-01

    Residual stress by repair welds is computed using the thermal elastic-plastic analysis with phase-transformation effect. Coupling phenomena of temperature, microstructure, and stress-strain fields are simulated in the finite-element analysis. Weld bond of a plate butt-welded joint is gouged and then deposited by weld metal in repair process. Heat source is synchronously moved with the deposition of the finite-element as the weld deposition. Microstructure is considered by using CCT diagram and the transformation behavior in the repair weld is also simulated. The effects of initial stress, heat input, and weld length on residual stress distribution are studied from the organic results of numerical analysis. Initial residual stress before repair weld has no influence on the residual stress after repair treatment near weld metal, because the initial stress near weld metal releases due to high temperature of repair weld and then stress by repair weld regenerates. Heat input has an effect for residual stress distribution, for not its magnitude but distribution zone. Weld length should be considered reducing the magnitude of residual stress in the edge of weld bead; short bead induces high tensile residual stress. (author)

  15. Biochar from sugarcane filtercake reduces soil CO2 emissions relative to raw residue and improves water retention and nutrient availability in a highly-weathered tropical soil.

    Science.gov (United States)

    Eykelbosh, Angela Joy; Johnson, Mark S; Santos de Queiroz, Edmar; Dalmagro, Higo José; Guimarães Couto, Eduardo

    2014-01-01

    In Brazil, the degradation of nutrient-poor Ferralsols limits productivity and drives agricultural expansion into pristine areas. However, returning agricultural residues to the soil in a stabilized form may offer opportunities for maintaining or improving soil quality, even under conditions that typically promote carbon loss. We examined the use of biochar made from filtercake (a byproduct of sugarcane processing) on the physicochemical properties of a cultivated tropical soil. Filtercake was pyrolyzed at 575°C for 3 h yielding a biochar with increased surface area and porosity compared to the raw filtercake. Filtercake biochar was primarily composed of aromatic carbon, with some residual cellulose and hemicellulose. In a three-week laboratory incubation, CO2 effluxes from a highly weathered Ferralsol soil amended with 5% biochar (dry weight, d.w.) were roughly four-fold higher than the soil-only control, but 23-fold lower than CO2 effluxes from soil amended with 5% (d.w.) raw filtercake. We also applied vinasse, a carbon-rich liquid waste from bioethanol production typically utilized as a fertilizer on sugarcane soils, to filtercake- and biochar-amended soils. Total CO2 efflux from the biochar-amended soil in response to vinasse application was only 5% of the efflux when vinasse was applied to soil amended with raw filtercake. Furthermore, mixtures of 5 or 10% biochar (d.w.) in this highly weathered tropical soil significantly increased water retention within the plant-available range and also improved nutrient availability. Accordingly, application of sugarcane filtercake as biochar, with or without vinasse application, may better satisfy soil management objectives than filtercake applied to soils in its raw form, and may help to build soil carbon stocks in sugarcane-cultivating regions.

  16. Biochar from Sugarcane Filtercake Reduces Soil CO2 Emissions Relative to Raw Residue and Improves Water Retention and Nutrient Availability in a Highly-Weathered Tropical Soil

    Science.gov (United States)

    Eykelbosh, Angela Joy; Johnson, Mark S.; Santos de Queiroz, Edmar; Dalmagro, Higo José; Guimarães Couto, Eduardo

    2014-01-01

    In Brazil, the degradation of nutrient-poor Ferralsols limits productivity and drives agricultural expansion into pristine areas. However, returning agricultural residues to the soil in a stabilized form may offer opportunities for maintaining or improving soil quality, even under conditions that typically promote carbon loss. We examined the use of biochar made from filtercake (a byproduct of sugarcane processing) on the physicochemical properties of a cultivated tropical soil. Filtercake was pyrolyzed at 575°C for 3 h yielding a biochar with increased surface area and porosity compared to the raw filtercake. Filtercake biochar was primarily composed of aromatic carbon, with some residual cellulose and hemicellulose. In a three-week laboratory incubation, CO2 effluxes from a highly weathered Ferralsol soil amended with 5% biochar (dry weight, d.w.) were roughly four-fold higher than the soil-only control, but 23-fold lower than CO2 effluxes from soil amended with 5% (d.w.) raw filtercake. We also applied vinasse, a carbon-rich liquid waste from bioethanol production typically utilized as a fertilizer on sugarcane soils, to filtercake- and biochar-amended soils. Total CO2 efflux from the biochar-amended soil in response to vinasse application was only 5% of the efflux when vinasse was applied to soil amended with raw filtercake. Furthermore, mixtures of 5 or 10% biochar (d.w.) in this highly weathered tropical soil significantly increased water retention within the plant-available range and also improved nutrient availability. Accordingly, application of sugarcane filtercake as biochar, with or without vinasse application, may better satisfy soil management objectives than filtercake applied to soils in its raw form, and may help to build soil carbon stocks in sugarcane-cultivating regions. PMID:24897522

  17. Biochar from sugarcane filtercake reduces soil CO2 emissions relative to raw residue and improves water retention and nutrient availability in a highly-weathered tropical soil.

    Directory of Open Access Journals (Sweden)

    Angela Joy Eykelbosh

    Full Text Available In Brazil, the degradation of nutrient-poor Ferralsols limits productivity and drives agricultural expansion into pristine areas. However, returning agricultural residues to the soil in a stabilized form may offer opportunities for maintaining or improving soil quality, even under conditions that typically promote carbon loss. We examined the use of biochar made from filtercake (a byproduct of sugarcane processing on the physicochemical properties of a cultivated tropical soil. Filtercake was pyrolyzed at 575°C for 3 h yielding a biochar with increased surface area and porosity compared to the raw filtercake. Filtercake biochar was primarily composed of aromatic carbon, with some residual cellulose and hemicellulose. In a three-week laboratory incubation, CO2 effluxes from a highly weathered Ferralsol soil amended with 5% biochar (dry weight, d.w. were roughly four-fold higher than the soil-only control, but 23-fold lower than CO2 effluxes from soil amended with 5% (d.w. raw filtercake. We also applied vinasse, a carbon-rich liquid waste from bioethanol production typically utilized as a fertilizer on sugarcane soils, to filtercake- and biochar-amended soils. Total CO2 efflux from the biochar-amended soil in response to vinasse application was only 5% of the efflux when vinasse was applied to soil amended with raw filtercake. Furthermore, mixtures of 5 or 10% biochar (d.w. in this highly weathered tropical soil significantly increased water retention within the plant-available range and also improved nutrient availability. Accordingly, application of sugarcane filtercake as biochar, with or without vinasse application, may better satisfy soil management objectives than filtercake applied to soils in its raw form, and may help to build soil carbon stocks in sugarcane-cultivating regions.

  18. Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model

    Directory of Open Access Journals (Sweden)

    Tekpinar Mustafa

    2009-07-01

    Full Text Available Abstract Backgrounds It is increasingly recognized that protein functions often require intricate conformational dynamics, which involves a network of key amino acid residues that couple spatially separated functional sites. Tremendous efforts have been made to identify these key residues by experimental and computational means. Results We have performed a large-scale evaluation of the predictions of dynamically important residues by a variety of computational protocols including three based on the perturbation and correlation analysis of a coarse-grained elastic model. This study is performed for two lists of test cases with >500 pairs of protein structures. The dynamically important residues predicted by the perturbation and correlation analysis are found to be strongly or moderately conserved in >67% of test cases. They form a sparse network of residues which are clustered both in 3D space and along protein sequence. Their overall conservation is attributed to their dynamic role rather than ligand binding or high network connectivity. Conclusion By modeling how the protein structural fluctuations respond to residue-position-specific perturbations, our highly efficient perturbation and correlation analysis can be used to dissect the functional conformational changes in various proteins with a residue level of detail. The predictions of dynamically important residues serve as promising targets for mutational and functional studies.

  19. Conservation of Charge and Conservation of Current

    OpenAIRE

    Eisenberg, Bob

    2016-01-01

    Conservation of current and conservation of charge are nearly the same thing: when enough is known about charge movement, conservation of current can be derived from conservation of charge, in ideal dielectrics, for example. Conservation of current is enforced implicitly in ideal dielectrics by theories that conserve charge. But charge movement in real materials like semiconductors or ionic solutions is never ideal. We present an apparently universal derivation of conservation of current and ...

  20. High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute

    Directory of Open Access Journals (Sweden)

    Md. Tariqul Islam

    2015-01-01

    Full Text Available MicroRNAs play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. A group of plant microRNAs are evolutionarily conserved; however, others are expressed in a species-specific manner. Jute is an agroeconomically important fibre crop; nonetheless, no practical information is available for microRNAs in jute to date. In this study, Illumina sequencing revealed a total of 227 known microRNAs and 17 potential novel microRNA candidates in jute, of which 164 belong to 23 conserved families and the remaining 63 belong to 58 nonconserved families. Among a total of 81 identified microRNA families, 116 potential target genes were predicted for 39 families and 11 targets were predicted for 4 among the 17 identified novel microRNAs. For understanding better the functions of microRNAs, target genes were analyzed by Gene Ontology and their pathways illustrated by KEGG pathway analyses. The presence of microRNAs identified in jute was validated by stem-loop RT-PCR followed by end point PCR and qPCR for randomly selected 20 known and novel microRNAs. This study exhaustively identifies microRNAs and their target genes in jute which will ultimately pave the way for understanding their role in this crop and other crops.

  1. Relatively High Complication and Revision Rates of the Mayo® Metaphysical Conservative Femoral Stem in Young Patients.

    Science.gov (United States)

    Rutenberg, Tal Frenkel; Warshevski, Yaniv; Gold, Aviram; Shasha, Nadav; Snir, Nimrod; Chechik, Ofir; Dolkart, Oleg; Eilig, Dynai; Herman, Amir; Rath, Ehud; Kramer, Moti; Drexler, Michael

    2018-05-08

    The Mayo metaphysical conservative femoral stem (Zimmer, Warsaw, Indiana) is a wedge-shaped implant designed to transfer loads proximally, reduce femoral destruction, and enable the preservation of bone stock in the proximal femur. Thus, it is a potentially preferred prosthesis for active, non-elderly patients who may require additional future surgeries. This retrospective case study analyzed the outcomes of consecutive patients who underwent total hip replacements with this stem between May 2001 and February 2013. All patients underwent clinical assessment, radiological evaluation for the presence and development of radiolucent lines, and functional assessment (numerical analog scale, Harris hip score, and Short Form-12 questionnaire). Ninety-five hips (79 patients) were available for analysis. The patients' mean age was 43 years (range, 18-64 years), and the mean follow-up was 97 months (range, 26.9-166 months). The postoperative clinical assessments and functional assessments revealed significant improvements. Sixteen patients (20.3%) had 18 orthopedic complications, the most common of which were an intraoperative femoral fracture and implant dislocation requiring revision surgeries in 10 hips (10.5%). Radiological analysis revealed evidence of femoral remodeling in 64 (67.4%) implants, spot welds (neocortex) in 35 (36.8%), and osteolysis in 3 (3.2%). These results suggest that the conservative hip femoral implant has an unacceptable complication rate for non-elderly patients. [Orthopedics. 201x; xx(x):xx-xx.]. Copyright 2018, SLACK Incorporated.

  2. Genome Analysis of Conserved Dehydrin Motifs in Vascular Plants

    Directory of Open Access Journals (Sweden)

    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.

  3. Significant relaxation of residual negative carrier in polar Alq3 film directly detected by high-sensitivity photoemission

    Science.gov (United States)

    Kinjo, Hiroumi; Lim, Hyunsoo; Sato, Tomoya; Noguchi, Yutaka; Nakayama, Yasuo; Ishii, Hisao

    2016-02-01

    Tris(8-hydroxyquinoline)aluminum (Alq3) has been widely applied as a good electron-injecting layer (EIL) in organic light-emitting diodes. High-sensitivity photoemission measurement revealed a clear photoemission by visible light, although its ionization energy is 5.7 eV. This unusual photoemission is ascribed to Alq3 anions captured by positive polarization charges. The observed electron detachment energy of the anion was about 1 eV larger than the electron affinity reported by inverse photoemission. This difference suggests that the injected electron in the Alq3 layer is energetically relaxed, leading to the reduction in injection barrier. This nature is one of the reasons why Alq3 worked well as the EIL.

  4. Thermodynamic study of residual heat from a high temperature nuclear reactor to analyze its viability in cogeneration processes

    International Nuclear Information System (INIS)

    Santillan R, A.; Valle H, J.; Escalante, J. A.

    2015-09-01

    In this paper the thermodynamic study of a nuclear power plant of high temperature at gas turbine (GTHTR300) is presented for estimating the exploitable waste heat in a process of desalination of seawater. One of the most studied and viable sustainable energy for the production of electricity, without the emission of greenhouse gases, is the nuclear energy. The fourth generation nuclear power plants have greater advantages than those currently installed plants; these advantages have to do with security, increased efficiencies and feasibility to be coupled to electrical cogeneration processes. In this paper the thermodynamic study of a nuclear power plant type GTHTR300 is realized, which is selected by greater efficiencies and have optimal conditions for use in electrical cogeneration processes due to high operating temperatures, which are between 700 and 950 degrees Celsius. The aim of the study is to determine the heat losses and the work done at each stage of the system, determining where they are the greatest losses and analyzing in that processes can be taken advantage. Based on the study was appointed that most of the energy losses are in form of heat in the coolers and usually this is emitted into the atmosphere without being used. From the results a process of desalination of seawater as electrical cogeneration process is proposed. This paper contains a brief description of the operation of the nuclear power plant, focusing on operation conditions and thermodynamic characteristics for the implementation of electrical cogeneration process, a thermodynamic analysis based on mass and energy balance was developed. The results allow quantifying the losses of thermal energy and determining the optimal section for coupling of the reactor with the desalination process, seeking to have a great overall efficiency. (Author)

  5. Diesel conservation: GSRTC'S experience

    Energy Technology Data Exchange (ETDEWEB)

    Ramesh Kumar, I V

    1980-01-01

    The Gujarat State Road Transport Corporation (GSRTC) in India has a fleet of about 6000 buses. The increasing cost of fuel and lubricants added to uncertainty in supplies, has necessitated the need for conserving High Speed Diesel Oil (HSD). GSRTC had achieved an overall average Kilometre Per Litre (kmpl) of 4.44 in the year 1976-1977 due to a variety of measures. In the year 1978-1979 the average kmpl was 4.52 and it is expected to be 4.60 for 1979-1980. The case study outlined describes the measures taken by GSRTC in conserving high speed diesel oil by various methods.

  6. Mineral Phases and Release Behaviors of As in the Process of Sintering Residues Containing As at High Temperature

    Directory of Open Access Journals (Sweden)

    Xingrun Wang

    2014-01-01

    Full Text Available To investigate the effect of sintering temperature and sintering time on arsenic volatility and arsenic leaching in the sinter, we carried out experimental works and studied the structural changes of mineral phases and microstructure observation of the sinter at different sintering temperatures. Raw materials were shaped under the pressure of 10 MPa and sintered at 1000~1350°C for 45 min with air flow rate of 2000 mL/min. The results showed that different sintering temperatures and different sintering times had little impact on the volatilization of arsenic, and the arsenic fixed rate remained above 90%; however, both factors greatly influenced the leaching concentration of arsenic. Considering the product’s environmental safety, the best sintering temperature was 1200°C and the best sintering time was 45 min. When sintering temperature was lower than 1000°C, FeAsS was oxidized into calcium, aluminum, and iron arsenide, mainly Ca3(AsO42 and AlAsO4, and the arsenic leaching was high. When it increased to 1200°C, arsenic was surrounded by a glass matrix and became chemically bonded inside the matrix, which lead to significantly lower arsenic leaching.

  7. Characterisation and management of concrete grinding residuals.

    Science.gov (United States)

    Kluge, Matt; Gupta, Nautasha; Watts, Ben; Chadik, Paul A; Ferraro, Christopher; Townsend, Timothy G

    2018-02-01

    Concrete grinding residue is the waste product resulting from the grinding, cutting, and resurfacing of concrete pavement. Potential beneficial applications for concrete grinding residue include use as a soil amendment and as a construction material, including as an additive to Portland cement concrete. Concrete grinding residue exhibits a high pH, and though not hazardous, it is sufficiently elevated that precautions need to be taken around aquatic ecosystems. Best management practices and state regulations focus on reducing the impact on such aquatic environment. Heavy metals are present in concrete grinding residue, but concentrations are of the same magnitude as typically recycled concrete residuals. The chemical composition of concrete grinding residue makes it a useful product for some soil amendment purposes at appropriate land application rates. The presence of unreacted concrete in concrete grinding residue was examined for potential use as partial replacement of cement in new concrete. Testing of Florida concrete grinding residue revealed no dramatic reactivity or improvement in mortar strength.

  8. Comparative interactomics: analysis of arabidopsis 14-3-3 complexes reveals highly conserved 14-3-3 interactions between humans and plants.

    Science.gov (United States)

    Paul, Anna-Lisa; Liu, Li; McClung, Scott; Laughner, Beth; Chen, Sixue; Ferl, Robert J

    2009-04-01

    As a first step in the broad characterization of plant 14-3-3 multiprotein complexes in vivo, stringent and specific antibody affinity purification was used to capture 14-3-3s together with their interacting proteins from extracts of Arabidopsis cell suspension cultures. Approximately 120 proteins were identified as potential in vivo 14-3-3 interacting proteins by mass spectrometry of the recovered complexes. Comparison of the proteins in this data set with the 14-3-3 interacting proteins from a similar study in human embryonic kidney cell cultures revealed eight interacting proteins that likely represent reasonably abundant, fundamental 14-3-3 interaction complexes that are highly conserved across all eukaryotes. The Arabidopsis 14-3-3 interaction data set was also compared to a yeast in vivo 14-3-3 interaction data set. Four 14-3-3 interacting proteins are conserved in yeast, humans, and Arabidopsis. Comparisons of the data sets based on biochemical function revealed many additional similarities in the human and Arabidopsis data sets that represent conserved functional interactions, while also leaving many proteins uniquely identified in either Arabidopsis or human cells. In particular, the Arabidopsis interaction data set is enriched for proteins involved in metabolism.

  9. Highly sensitive in vitro methods for detection of residual undifferentiated cells in retinal pigment epithelial cells derived from human iPS cells.

    Directory of Open Access Journals (Sweden)

    Takuya Kuroda

    Full Text Available Human induced pluripotent stem cells (hiPSCs possess the capabilities of self-renewal and differentiation into multiple cell types, and they are free of the ethical problems associated with human embryonic stem cells (hESCs. These characteristics make hiPSCs a promising choice for future regenerative medicine research. There are significant obstacles, however, preventing the clinical use of hiPSCs. One of the most obvious safety issues is the presence of residual undifferentiated cells that have tumorigenic potential. To locate residual undifferentiated cells, in vivo teratoma formation assays have been performed with immunodeficient animals, which is both costly and time-consuming. Here, we examined three in vitro assay methods to detect undifferentiated cells (designated an in vitro tumorigenicity assay: soft agar colony formation assay, flow cytometry assay and quantitative real-time polymerase chain reaction assay (qRT-PCR. Although the soft agar colony formation assay was unable to detect hiPSCs even in the presence of a ROCK inhibitor that permits survival of dissociated hiPSCs/hESCs, the flow cytometry assay using anti-TRA-1-60 antibody detected 0.1% undifferentiated hiPSCs that were spiked in primary retinal pigment epithelial (RPE cells. Moreover, qRT-PCR with a specific probe and primers was found to detect a trace amount of Lin28 mRNA, which is equivalent to that present in a mixture of a single hiPSC and 5.0×10⁴ RPE cells. Our findings provide highly sensitive and quantitative in vitro assays essential for facilitating safety profiling of hiPSC-derived products for future regenerative medicine research.

  10. Determination of niclosamide residues in rainbow trout (Oncorhynchus mykiss) and channel catfish (Ictalurus punctatus) fillet tissue by high-performance liquid chromatography

    Science.gov (United States)

    Schreier, Theresa M.; Dawson, V.K.; Cho, Yirang; Spanjers, N.J.; Boogaard, M.A.

    2000-01-01

    Bayluscide [the ethanolamine salt of niclosamide (NIC)] is a registered piscicide used in combination with 3-(trifluoromethyl)-4-nitrophenol (TFM) to control sea lamprey populations in streams tributary to the Great Lakes. A high-performance liquid chromatography (HPLC) method was developed for the determination of NIC residues in muscle fillet tissues of fish exposed to NIC and TFM during sea lamprey control treatments. NIC was extracted from fortified channel catfish and rainbow trout fillet tissue with a series of acetone extractions and cleaned up on C-18 solid-phase extraction cartridges. NIC concentrations were determined by HPLC with detection at 360 and 335 nm for rainbow trout and catfish, respectively. Recovery of NIC from rainbow trout (n = 7) fortified at 0.04 mu g/g was 77 +/- 6.5% and from channel catfish (n = 7) fortified at 0.02 mu g/g was 113 +/- 11%. NIC detection limit was 0.0107 mu g/g for rainbow trout and 0.0063 mu g/g for catfish. Percent recovery of incurred radioactive residues by this method from catfish exposed to [C-14]NIC was 89.3 +/- 4.1%. Percent recoveries of NIC from fortified storage stability tissue samples for rainbow trout (n = 3) analyzed at 5 and 7.5 month periods were 78 +/- 5.1 and 68 +/- 2.4%, respectively. Percent recoveries of NIC from fortified storage stability tissue samples for channel catfish (n = 3) analyzed at 5 and 7.5 month periods were 88 +/- 13 and 76 +/- 21%, respectively.

  11. Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms.

    Directory of Open Access Journals (Sweden)

    Deanne W Sammond

    Full Text Available Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research. Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. Thus the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions.

  12. Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms.

    Science.gov (United States)

    Sammond, Deanne W; Kastelowitz, Noah; Himmel, Michael E; Yin, Hang; Crowley, Michael F; Bomble, Yannick J

    2016-01-01

    Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research. Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. Thus the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions.

  13. Convergence of a residual based artificial viscosity finite element method

    KAUST Repository

    Nazarov, Murtazo

    2013-02-01

    We present a residual based artificial viscosity finite element method to solve conservation laws. The Galerkin approximation is stabilized by only residual based artificial viscosity, without any least-squares, SUPG, or streamline diffusion terms. We prove convergence of the method, applied to a scalar conservation law in two space dimensions, toward an unique entropy solution for implicit time stepping schemes. © 2012 Elsevier B.V. All rights reserved.

  14. Monitoring minimal residual disease in children with high-risk relapses of acute lymphoblastic leukemia: prognostic relevance of early and late assessment.

    Science.gov (United States)

    Eckert, C; Hagedorn, N; Sramkova, L; Mann, G; Panzer-Grümayer, R; Peters, C; Bourquin, J-P; Klingebiel, T; Borkhardt, A; Cario, G; Alten, J; Escherich, G; Astrahantseff, K; Seeger, K; Henze, G; von Stackelberg, A

    2015-08-01

    The prognosis for children with high-risk relapsed acute lymphoblastic leukemia (ALL) is poor. Here, we assessed the prognostic importance of response during induction and consolidation treatment prior to hematopoietic stem cell transplantation (HSCT) aiming to evaluate the best time to assess minimal residual disease (MRD) for intervention strategies and in future trials in high-risk ALL relapse patients. Included patients (n=125) were treated uniformly according to the ALL-REZ BFM (Berlin-Frankfurt-Münster) 2002 relapse trial (median follow-up time=4.8 years). Patients with MRD ⩾10(-3) after induction treatment (76/119, 64%) or immediately preceding HSCT (19/71, 27%) had a significantly worse probability of disease-free survival 10 years after relapse treatment begin, with 26% (±6%) or 23% (±7%), respectively, compared with 58% (±8%) or 48% (±7%) for patients with MRD treatment reduced MRD to treatment can be used to quantify the activity of different induction treatment strategies in phase II trials. MRD persistence at ⩾10(-3) before HSCT reflects a disease highly resistant to conventional intensive chemotherapy and requiring prospective controlled investigation of new treatment strategies and drugs.

  15. Investigation of the influence on residual stresses of porosity in high temperature ZrO2 coatings on Ag tape for magnet technologies

    International Nuclear Information System (INIS)

    Arman, Yusuf; Aktas, Mehmet; Celik, Erdal; Mutlu, Ibrahim H.; Sayman, Onur

    2007-01-01

    The present paper reports on the effect on residual stresses of porosity in high temperature ZrO 2 coatings on Ag tape for magnet technologies. ZrO 2 coatings were fabricated on Ag tape substrate using a reel-to-reel sol-gel system. The microstructural evolution of high temperature ZrO 2 coatings was investigated by a scanning electron microscope (SEM). SEM observations revealed that ZrO 2 coatings with crack had some porosity and mosaic structure. Stress analysis was carried out on ZrO 2 coatings with porosity on Ag tape substrates under cryogenic conditions by using classical lamination theory (CLT) for elastic solution and finite element method (FEM) for elasto-plastic solution in the temperature range of 0 o C to -223 o C in liquid helium media. Because of the static equilibrium, tensile force is applied to the Ag substrate, by ZrO 2 coating. The stress component (σ x ) values change rapidly at coating-substrate interface owing to the different moduli of elasticity and thermal expansion coefficient. In spite of the thickness of Ag substrate, the stress components vary from tensile to compressive. In addition, along the thickness of ZrO 2 coating and Ag substrate system, the stress distribution changes linearly. FEM results demonstrate that the failure does not occur in ZrO 2 coating for all porosities due to its high yield strength

  16. What is a conservation actor?

    Directory of Open Access Journals (Sweden)

    Paul Jepson

    2011-01-01

    Full Text Available As a crisis-oriented discipline, conservation biology needs actions to understand the state of nature and thwart declines in biodiversity. Actors-traditionally individuals, institutions, and collectives-have been central to delivering such goals in practice. However, the definition of actors within the discipline has been narrow and their role in influencing conservation outcomes inadequately conceptualised. In this paper, we examine the question ′What is a conservation actor?′ Who or what creates the capacity to influence conservation values and actions? Drawing from theoretical developments in Actor-Network Theory and collective governance, we argue that the concept of an actor in conservation biology should be broadened to include non-humans, such as species and devices, because they have the agency and ability to influence project goals and outcomes. We illustrate this through four examples: the Asian elephant, International Union for Conservation of Nature red lists, the High Conservation Value approach, and an Integrated Conservation and Development Project. We argue that a broader conceptualisation of actors in conservation biology will produce new forms of understanding that could open up new areas of conservation research, enhance practice and draw attention to spheres of conservation activity that might require stronger oversight and governance.

  17. Spectrum Fatigue Lifetime and Residual Strength for Fiberglass Laminates; TOPICAL

    International Nuclear Information System (INIS)

    WAHL, NEIL K.; MANDELL, JOHN F.; SAMBORSKY, DANIEL D.

    2002-01-01

    This report addresses the effects of spectrum loading on lifetime and residual strength of a typical fiberglass laminate configuration used in wind turbine blade construction. Over 1100 tests have been run on laboratory specimens under a variety of load sequences. Repeated block loading at two or more load levels, either tensile-tensile, compressive-compressive, or reversing, as well as more random standard spectra have been studied. Data have been obtained for residual strength at various stages of the lifetime. Several lifetime prediction theories have been applied to the results. The repeated block loading data show lifetimes that are usually shorter than predicted by the most widely used linear damage accumulation theory, Miner's sum. Actual lifetimes are in the range of 10 to 20 percent of predicted lifetime in many cases. Linear and nonlinear residual strength models tend to fit the data better than Miner's sum, with the nonlinear providing a better fit of the two. Direct tests of residual strength at various fractions of the lifetime are consistent with the residual strength models. Load sequencing effects are found to be insignificant. The more a spectrum deviates from constant amplitude, the more sensitive predictions are to the damage law used. The nonlinear model provided improved correlation with test data for a modified standard wind turbine spectrum. When a single, relatively high load cycle was removed, all models provided similar, though somewhat non-conservative correlation with the experimental results. Predictions for the full spectrum, including tensile and compressive loads were slightly non-conservative relative to the experimental data, and accurately captured the trend with varying maximum load. The nonlinear residual strength based prediction with a power law S-N curve extrapolation provided the best fit to the data in most cases. The selection of the constant amplitude fatigue regression model becomes important at the lower stress, higher

  18. Determination of 5 '-leader sequences from radically disparate strains of porcine reproductive and respiratory syndrome virus reveals the presence of highly conserved sequence motifs

    DEFF Research Database (Denmark)

    Oleksiewicz, M.B.; Bøtner, Anette; Nielsen, Jens

    1999-01-01

    We determined the untranslated 5'-leader sequence for three different isolates of porcine reproductive and respiratory syndrome virus (PRRSV): pathogenic European- and American-types, as well as an American-type vaccine strain. 5'-leader from European- and American-type PRRSV differed in length...... (220 and 190 nt, respectively), and exhibited only approximately 50% nucleotide homology. Nevertheless, highly conserved areas were identified in the leader of all 3 PRRSV isolates, which constitute candidate motifs for binding of protein(s) involved in viral replication. These comparative data provide...

  19. UK114, a YjgF/Yer057p/UK114 family protein highly conserved from bacteria to mammals, is localized in rat liver peroxisomes

    International Nuclear Information System (INIS)

    Antonenkov, Vasily D.; Ohlmeier, Steffen; Sormunen, Raija T.; Hiltunen, J. Kalervo

    2007-01-01

    Mammalian UK114 belongs to a highly conserved family of proteins with unknown functions. Although it is believed that UK114 is a cytosolic or mitochondrial protein there is no detailed study of its intracellular localization. Using analytical subcellular fractionation, electron microscopic colloidal gold technique, and two-dimensional gel electrophoresis of peroxisomal matrix proteins combined with mass spectrometric analysis we show here that a large portion of UK114 is present in rat liver peroxisomes. The peroxisomal UK114 is a soluble matrix protein and it is not inducible by the peroxisomal proliferator clofibrate. The data predict involvement of UK114 in peroxisomal metabolism

  20. Conserved water-mediated hydrogen bond network between TM-I, -II, -VI, and -VII in 7TM receptor activation

    DEFF Research Database (Denmark)

    Nygaard, Rie; Hansen, Louise Valentin; Mokrosinski, Jacek

    2010-01-01

    Five highly conserved polar residues connected by a number of structural water molecules together with two rotamer micro-switches, TrpVI:13 and TyrVII:20, constitute an extended hydrogen bond network between the intracellular segments of TM-I, -II, -VI, and -VII of 7TM receptors. Molecular dynamics...... to apparently function as a catching trap for water molecules. Mutational analysis of the beta2-adrenergic receptor demonstrated that the highly conserved polar residues of the hydrogen bond network were all important for receptor signaling but served different functions, some dampening constitutive activity...... (AsnI:18, AspII:10, and AsnVII:13), whereas others (AsnVII:12 and AsnVII:16) located one helical turn apart and sharing a water molecule were shown to be essential for agonist-induced signaling. It is concluded that the conserved water hydrogen bond network of 7TM receptors constitutes an extended...